HOM ID "HOM name" entity "entity name" qualifier taxon ID "taxon name" CIO ID "CIO name" ECO ID "ECO name" reference "reference title" "supporting text" assigned by curator date HOM:0000007 "historical homology" CL:0000000 "cell" 2759 "Eukaryota" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" DOI:10.1073/pnas.032658599 "Hartman H, Fedorov A, The origin of the eukaryotic cell: A genomic investigation. PNAS (2002)" "We have collected a set of 347 proteins that are found in eukaryotic cells but have no significant homology to proteins in Archaea and Bacteria. We call these proteins eukaryotic signature proteins (ESPs). The dominant hypothesis for the formation of the eukaryotic cell is that it is a fusion of an archaeon with a bacterium. If this hypothesis is accepted then the three cellular domains, Eukarya, Archaea, and Bacteria, would collapse into two cellular domains. We have used the existence of this set of ESPs to test this hypothesis. The evidence of the ESPs implicates a third cell (chronocyte) in the formation of the eukaryotic cell. [...] The eukaryotic cell is not a simple fusion of an archaeon and bacterium. This statement is borne out by the existence of 347 ESPs. [...] We agree with Horiike et al. that the nucleus is an endosymbiont with inputs from Bacteria and Archaea. We disagree that the host cell came from the Bacteria. The host cell or chronocyte was not a prokaryotic cell but one that had a cytoskeleton composed of actin and tubulin and an extensive membrane system." bgee ANN 2013-06-21 HOM:0000007 "historical homology" CL:0000015 "male germ cell" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1002/bies.950161213 "Denis H, A parallel between development and evolution: Germ cell recruitment by the gonads. BioEssays (1994)" "The basic assumption is that primitive Metazoa already had germ cells, but no gonads to harbour them." bgee ANN 2013-08-29 HOM:0000007 "historical homology" CL:0000015 "male germ cell" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.249" "Gametes must have been present already in the metazoan ancestor, because they are present in every metazoan taxon." bgee ANN 2013-08-29 HOM:0000007 "historical homology" CL:0000021 "female germ cell" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1002/bies.950161213 "Denis H, A parallel between development and evolution: Germ cell recruitment by the gonads. BioEssays (1994)" "The basic assumption is that primitive Metazoa already had germ cells, but no gonads to harbour them." bgee ANN 2013-08-29 HOM:0000007 "historical homology" CL:0000021 "female germ cell" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.249" "Gametes must have been present already in the metazoan ancestor, because they are present in every metazoan taxon." bgee ANN 2013-08-29 HOM:0000007 "historical homology" CL:0000037 "hematopoietic stem cell" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1111/j.1600-065X.1998.tb01264.x "Hansen JD, Zapata AG, Lymphocyte development in fish and amphibians. Immunological Reviews (1998)" "In all gnathostomes there appear to be two main embryonic locations derived from the early mesoderm, both intra- and extraembryonic, which contribute to primitive and definitive hematopoiesis based upon their differential expression of SCL, Gata-1, Gata-2 and myeloblastosis oncogene (c-myb)." bgee ANN 2015-03-30 HOM:0000007 "historical homology" CL:0000037 "hematopoietic stem cell" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1111/j.1600-065X.1998.tb01264.x "Hansen JD, Zapata AG, Lymphocyte development in fish and amphibians. Immunological Reviews (1998)" "In all gnathostomes there appear to be two main embryonic locations derived from the early mesoderm, both intra- and extraembryonic, which contribute to primitive and definitive hematopoiesis based upon their differential expression of SCL, Gata-1, Gata-2 and myeloblastosis oncogene (c-myb)." bgee ANN 2015-03-30 HOM:0000007 "historical homology" CL:0000037 "hematopoietic stem cell" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1146/annurev.cellbio.22.010605.093317 "Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006)" "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrate phyla. (...)a brief survey of the different types of blood cell lineages among metazoa. There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast." bgee ANN 2015-03-30 HOM:0000007 "historical homology" CL:0000037 "hematopoietic stem cell" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1146/annurev.cellbio.22.010605.093317 "Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006)" "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrate phyla. (...)a brief survey of the different types of blood cell lineages among metazoa. There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast." bgee ANN 2015-03-30 HOM:0000007 "historical homology" CL:0000056 "myoblast" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75" "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa." bgee ANN 2013-09-23 HOM:0000007 "historical homology" CL:0000057 "fibroblast" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.177" "Fibroblast is the distinctive cell of the fibrous connective tissue, the most common connective tissue in vertebrates. [curator]" bgee ANN 2013-07-17 HOM:0000007 "historical homology" CL:0000057 "fibroblast" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:20174584 "Ingerslev HC, Ossum CG, Lindenstrom T, Nielsen ME, Fibroblasts express immune relevant genes and are important sentinel cells during tissue damage in rainbow trout (Oncorhynchus mykiss). PLoS One (2010)" "this study provides new and important information about the role of fibroblasts in lower vertebrates in relation to inflammation, tissue damage and immune competence. (...) evolutionary fibroblasts are primitive cells, which have maintained the ability to express genes of immune functions, when stimulated." bgee ANN 2013-07-17 HOM:0000007 "historical homology" CL:0000064 "ciliated cell" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/S0070-2153(08)00806-5 "Basu B, Brueckner M, Cilia multifunctional organelles at the center of vertebrate left-right asymetry. Current topics in developmental biology (2008)" "Cilia establish the vertebrate left-right (LR) axis and are integral to the development and function of the kidney, liver, and brain. Left-right asymmetry is established in the ciliated ventral node cells of the mouse. The chiral structure of the cilium provides a reference asymmetry to impose handed LR asymmetric development on the bilaterally symmetric vertebrate embryo. A ciliary mechanism of LR development is evolutionarily conserved, as ciliated organs essential to LR axis formation, called LR organizers, are found in other vertebrates, including rabbit, fish, and Xenopus." bgee ANN 2013-07-03 HOM:0000007 "historical homology" CL:0000064 "ciliated cell" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1016/S0070-2153(08)00806-5 "Basu B, Brueckner M, Cilia multifunctional organelles at the center of vertebrate left-right asymetry. Current topics in developmental biology (2008)" "Cilia establish the vertebrate left-right (LR) axis and are integral to the development and function of the kidney, liver, and brain. Left-right asymmetry is established in the ciliated ventral node cells of the mouse. The chiral structure of the cilium provides a reference asymmetry to impose handed LR asymmetric development on the bilaterally symmetric vertebrate embryo. A ciliary mechanism of LR development is evolutionarily conserved, as ciliated organs essential to LR axis formation, called LR organizers, are found in other vertebrates, including rabbit, fish, and Xenopus." bgee ANN 2013-07-03 HOM:0000007 "historical homology" CL:0000066 "epithelial cell" 33208 "Metazoa" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" ISBN:978-0030259821 "Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59" "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals." bgee ANN 2013-08-23 HOM:0000007 "historical homology" CL:0000082 "epithelial cell of lung" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0002048|UBERON:0006860, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" CL:0000083 "epithelial cell of pancreas" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0001264, negated: false, taxon ID: 89593" bgee HOM:0000007 "historical homology" CL:0000084 "T cell" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:21046016 "Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010)" "The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes." bgee ANN 2013-07-01 HOM:0000007 "historical homology" CL:0000092 "osteoclast" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:27620531 "Mueller CG, Voisin B, Of skin and bone: did Langerhans cells and osteoclasts evolve from a common ancestor? J Anat (2016)" "Whereas the function of osteoclasts in bone degradation has been established since the first vertebrates, Langerhans cells may have undergone a stepwise adaptation from aquatic to terrestrial life." bgee ANN 2018-03-27 HOM:0000007 "historical homology" CL:0000092|CL:0000453 "osteoclast|Langerhans cell" 7742 "Vertebrata" CIO:0000005 "low confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:27620531 "Mueller CG, Voisin B, Of skin and bone: did Langerhans cells and osteoclasts evolve from a common ancestor? J Anat (2016)" "Of skin and bone: did Langerhans cells and osteoclasts evolve from a common ancestor? Skin Langerhans cells are antigen-presenting cells of the interfollicular epidermis and the upper part of the hair follicle, whereas osteoclasts are specialized bone-resorbing macrophages. Although at first view these two cell types appear to have little in common, a closer analysis reveals shared features, and when taking into account their surrounding environment, a hypothesis can be developed that Langerhans cells and osteoclasts have evolved from a common ancestral cell type. In this mini-review, we have compared the ontogenetic features of Langerhans cells and osteoclasts from a genetic and a functional point of view, an issue that so far has been overlooked...Taken together, the features shared by LCs and OCLs raise the possibility that an ancestral cell regulating exoskeleton/skin hemostasis of early vertebrates gave rise to skin-specialized LCs and bone-specialized OCLs of higher vertebrates. Beyond its general interest in biology, investigations into this proposed model may provide unexpected answers for medically relevant issues such as osteoimmunology, autoimmunity and cancer." bgee ANN 2016-09-20 HOM:0000007 "historical homology" CL:0000092|CL:0000453 "osteoclast|Langerhans cell" 7742 "Vertebrata" CIO:0000005 "low confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:27620531 "Mueller CG, Voisin B, Of skin and bone: did Langerhans cells and osteoclasts evolve from a common ancestor? J Anat (2016)" "Of skin and bone: did Langerhans cells and osteoclasts evolve from a common ancestor? Skin Langerhans cells are antigen-presenting cells of the interfollicular epidermis and the upper part of the hair follicle, whereas osteoclasts are specialized bone-resorbing macrophages. Although at first view these two cell types appear to have little in common, a closer analysis reveals shared features, and when taking into account their surrounding environment, a hypothesis can be developed that Langerhans cells and osteoclasts have evolved from a common ancestral cell type. In this mini-review, we have compared the ontogenetic features of Langerhans cells and osteoclasts from a genetic and a functional point of view, an issue that so far has been overlooked...Taken together, the features shared by LCs and OCLs raise the possibility that an ancestral cell regulating exoskeleton/skin hemostasis of early vertebrates gave rise to skin-specialized LCs and bone-specialized OCLs of higher vertebrates. Beyond its general interest in biology, investigations into this proposed model may provide unexpected answers for medically relevant issues such as osteoimmunology, autoimmunity and cancer." bgee ANN 2016-09-20 HOM:0000007 "historical homology" CL:0000100 "motor neuron" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1038/nrg2416 "Arendt D, The evolution of cell types in animals: emerging principles from molecular studies. Nature Reviews Genetics (2008)" "Pioneering studies revealed the homology of somatic motor neurons between vertebrates, insects (Drosophila spp.) and nematodes (Caenorhabditis spp.)." bgee ANN 2013-06-10 HOM:0000007 "historical homology" CL:0000107 "autonomic neuron" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000540, negated: false, taxon ID: 6072 - entity: UBERON:0002410, negated: false, taxon ID: 89593" bgee HOM:0000007 "historical homology" CL:0000148 "melanocyte" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.210" "The skin of all vertebrates, except albinos, contains pigments of various types within cells collectively known as chromatophores. Chromatophores are of neural crest origin. They lie in the upper part of the dermis in fishes, amphibians, and reptiles, but they penetrate or are located in the epidermis in birds and mammals. When the pigment is a dark melanin, the cells are called melanophores." bgee ANN 2013-07-17 HOM:0000007 "historical homology" CL:0000148 "melanocyte" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.210" "The skin of all vertebrates, except albinos, contains pigments of various types within cells collectively known as chromatophores. Chromatophores are of neural crest origin. They lie in the upper part of the dermis in fishes, amphibians, and reptiles, but they penetrate or are located in the epidermis in birds and mammals. When the pigment is a dark melanin, the cells are called melanophores." bgee ANN 2013-07-17 HOM:0000007 "historical homology" CL:0000178 "Leydig cell" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:17026980 "Sekido R, Lovell-Badge R, Mechanisms of gonadal morphogenesis are not conserved between chick and mouse. Dev Biol (2007)" "Despite the fact that different determinants trigger testis formation amongst vertebrates, the adult testis is very similar in morphology, cellular organisation and physiology. (...) Leydig cells are the steroidogenic cells present in the interstitium between the cords along with blood vessels and other miscellaneous connective tissue cells. (...) it has been reported, using a similar DiI labelling and technique, that Sertoli cells originate from the coelomic epithelium in the turtle (Yao et al., 2004). From these data, it seemed likely that there would be a conserved cellular origin for Sertoli cells during vertebrate evolution. (...) Male-specific cell migration from the mesonephros has also recently demonstrated to occur when chicken gonads are co-cultured with quail mesonephros at stage 29 (as described by Hamburger and Hamilton, 1951), corresponding to just after 6 days of incubation (day 6). In this experiment, the quail mesonephric cells contribute to interstitial cells in the male chicken gonads although the identity of these cells remains unknown (Smith et al., 2005). The origin of Leydig cells has therefore remained uncertain in both mouse or chick." bgee ANN 2013-08-30 HOM:0000007 "historical homology" CL:0000216 "Sertoli cell" 7711 "Chordata" CIO:0000005 "low confidence from single evidence" ECO:0000067 "developmental similarity evidence" http://f50006a.eos-intl.net/ELIBSQL12_F50006A_Documents/93grier.pdf "Grier HJ, Comparative organization of Sertoli cells including the Sertoli cell barrier. The Sertoli Cell (1993)" "In this chapter, Sertoli cells, as they form part of the germinal epithelia in all chordate taxa, are described. The germinal epithelium and germinal compartments in the chordate testis have been defined, and a nomenclature based upon phylogeny and literal definitions of terminology is proposed...It is proposed that both the phagocytic properties of Sertoli cells and the evolution of a Sertoli cell barrier argue for homology of Sertoli cells between all chordates." bgee ANN 2015-02-03 HOM:0000007 "historical homology" CL:0000216 "Sertoli cell" NOT 7711 "Chordata" CIO:0000005 "low confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:17026980 "Sekido R, Lovell-Badge R, Mechanisms of gonadal morphogenesis are not conserved between chick and mouse. Dev Biol (2007)" "(...) nephrogenous mesenchyme contributes to both Sertoli cells and steroidogenic cells. This is the first demonstration via lineage analysis that steroidogenic cells originate from nephrogenous mesenchyme, but the revelation that Sertoli cells have different origins between chick and mouse suggests that, during evolution, mechanisms of gonad morphogenesis may diverge alongside those of sex determination." bgee ANN 2015-03-23 HOM:0000007 "historical homology" CL:0000216 "Sertoli cell" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0125449045 "Pang PKT, Vertebrate Endocrinology: Fundamentals and Biomedical Implications. Reproduction (1991) p.312" "In all vertebrates and many invertebrates, developing germ cell clones are intimately associated with Sertoli cells (Roosen-Runge, 1977). This somatic cell type was first observed in teased preparations of human testis (Sertoli, 1865) and, although it has been argued that the term should be reserved for fully differentiated Sertoli cells of the mammalian type, this view seems unduly narrow in view of the bulk of evidence supporting cross-species homologies. The term is applied here to the somatic cell of the germinal compartment, regardless of species or stage of development. Sertoli cells share a common origin with cells destined to form the collecting duct system of the testis and begin their association with germ cells early in spermatogenesis, even before definitive clone formation. However, the symbiotic relationship between germ cells and Sertoli cells shows a trend toward increased intimacy and complexity as germ cells mature in a given species and when representatives of different classes are compared through vertebrate phylogeny." bgee ANN 2015-02-03 HOM:0000007 "historical homology" CL:0000216 "Sertoli cell" NOT 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:17026980 "Sekido R, Lovell-Badge R, Mechanisms of gonadal morphogenesis are not conserved between chick and mouse. Dev Biol (2007)" "(...) nephrogenous mesenchyme contributes to both Sertoli cells and steroidogenic cells. This is the first demonstration via lineage analysis that steroidogenic cells originate from nephrogenous mesenchyme, but the revelation that Sertoli cells have different origins between chick and mouse suggests that, during evolution, mechanisms of gonad morphogenesis may diverge alongside those of sex determination." bgee ANN 2015-03-23 HOM:0000007 "historical homology" CL:0000216 "Sertoli cell" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1002/jemt.1070320602 "Pudney J, Spermatogenesis in nonmammalian vertebrates. Microscopy Research and Technique (2010)" "Spermatogenesis appears to be a fairly conserved process throughout the vertebrate series. (...) There is, however, variation amongst the vertebrates in how germ cell development and maturation is accomplished. This difference can be broadly divided into two distinct patterns, one present in anamniotes (fish, amphibia) and the other in amniotes (reptiles, birds, mammals). For anamniotes, spermatogenesis occurs in spermatocysts (cysts) which for most species develop within seminiferous lobules. Cysts are produced when a Sertoli cell becomes associated with a primary spermatogonium. Mitotic divisions of the primary spermatogonium produce a cohort of secondary spermatogonia that are enclosed by the Sertoli cell which forms the wall of the cyst. With spermatogenic progression a clone of isogeneic spermatozoa is produced which are released, by rupture of the cyst, into the lumen of the seminiferous lobule. Following spermiation, the Sertoli cell degenerates. For anamniotes, therefore, there is no permanent germinal epithelium since spermatocysts have to be replaced during successive breeding seasons. By contrast, spermatogenesis in amniotes does not occur in cysts but in seminiferous tubules that possess a permanent population of Sertoli cells and spermatogonia which act as a germ cell reservoir for succeeding bouts of spermatogenic activity. There is, in general, a greater variation in the organization of the testis and pattern of spermatogenesis in the anamniotes compared to amniotes." bgee ANN 2015-02-03 HOM:0000007 "historical homology" CL:0000216 "Sertoli cell" NOT 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:17026980 "Sekido R, Lovell-Badge R, Mechanisms of gonadal morphogenesis are not conserved between chick and mouse. Dev Biol (2007)" "(...) nephrogenous mesenchyme contributes to both Sertoli cells and steroidogenic cells. This is the first demonstration via lineage analysis that steroidogenic cells originate from nephrogenous mesenchyme, but the revelation that Sertoli cells have different origins between chick and mouse suggests that, during evolution, mechanisms of gonad morphogenesis may diverge alongside those of sex determination." bgee ANN 2013-08-30 HOM:0000007 "historical homology" CL:0000236 "B cell" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:21046016 "Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010)" "The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes." bgee ANN 2013-07-01 HOM:0000007 "historical homology" CL:0000247 "Rohon-Beard neuron" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1038/nrn2703 "Holland LZ, Chordate roots of the vertebrate nervous system: expanding the molecular toolkit. Nature Reviews Neuroscience (2009)" "Unequivocal homologues of the neural crest and placodes, other than the olfactory and adenohypophyseal placodes, are lacking in amphioxus, although intramedullary sensory cells in the dorsal portion of the amphioxus CNS are thought to be homologous to Rohon-Beard sensory neurons (Large, mechanosensory neurons in the dorsal portion of the spinal cord of larval anamniote vertebrates. They typically degenerate later in development) ." bgee ANN 2013-06-10 HOM:0000007 "historical homology" CL:0000255 "eukaryotic cell" 2759 "Eukaryota" CIO:0000003 "high confidence from single evidence" ECO:0000033 "traceable author statement" DOI:10.1073/pnas.032658599 "Hartman H, Fedorov A, The origin of the eukaryotic cell: A genomic investigation. PNAS (2002)" "We have collected a set of 347 proteins that are found in eukaryotic cells but have no significant homology to proteins in Archaea and Bacteria. We call these proteins eukaryotic signature proteins (ESPs). The dominant hypothesis for the formation of the eukaryotic cell is that it is a fusion of an archaeon with a bacterium. If this hypothesis is accepted then the three cellular domains, Eukarya, Archaea, and Bacteria, would collapse into two cellular domains. We have used the existence of this set of ESPs to test this hypothesis. The evidence of the ESPs implicates a third cell (chronocyte) in the formation of the eukaryotic cell. [...] The eukaryotic cell is not a simple fusion of an archaeon and bacterium. This statement is borne out by the existence of 347 ESPs. [...] We agree with Horiike et al. that the nucleus is an endosymbiont with inputs from Bacteria and Archaea. We disagree that the host cell came from the Bacteria. The host cell or chronocyte was not a prokaryotic cell but one that had a cytoskeleton composed of actin and tubulin and an extensive membrane system." bgee ANN 2013-11-29 HOM:0000007 "historical homology" CL:0000300 "gamete" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.249" "Gametes must have been present already in the metazoan ancestor, because they are present in every metazoan taxon." bgee ANN 2013-08-29 HOM:0000007 "historical homology" CL:0000307 "tracheal epithelial cell" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0003126, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" CL:0000342 "pigment cell (sensu Vertebrata)" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.210" "The skin of all vertebrates, except albinos, contains pigments of various types within cells collectively known as chromatophores. Chromatophores are of neural crest origin. They lie in the upper part of the dermis in fishes, amphibians, and reptiles, but they penetrate or are located in the epidermis in birds and mammals. When the pigment is a dark melanin, the cells are called melanophores." bgee ANN 2013-07-17 HOM:0000007 "historical homology" CL:0000342 "pigment cell (sensu Vertebrata)" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.210" "The skin of all vertebrates, except albinos, contains pigments of various types within cells collectively known as chromatophores. Chromatophores are of neural crest origin. They lie in the upper part of the dermis in fishes, amphibians, and reptiles, but they penetrate or are located in the epidermis in birds and mammals. When the pigment is a dark melanin, the cells are called melanophores." bgee ANN 2013-07-17 HOM:0000007 "historical homology" CL:0000353 "blastoderm cell" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/j.ydbio.2009.05.543 "Takeuchi M, Takahashi M, Okabe M, Aizawa S, Germ layer patterning in bichir and lamprey; an insight into its evolution in vertebrates. Developmental Biology (2009) Figure 1" "Amphibian holoblastic cleavage in which all blastomeres contribute to any one of the three primary germ layers has been widely thought to be a developmental pattern in the stem lineage of vertebrates, and meroblastic cleavage to have evolved independently in each vertebrate lineage. (...) The study raises the viewpoint that the lamprey/bichir type holoblastic development would have been ancestral to extant vertebrates and retained in their stem lineage; amphibian-type holoblastic development would have been acquired secondarily, accompanied by the exploitation of new molecular machinery such as maternal VegT" bgee ANN 2013-07-11 HOM:0000007 "historical homology" CL:0000362 "epidermal cell" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72" "(...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell." bgee ANN 2013-07-17 HOM:0000007 "historical homology" CL:0000365 "animal zygote" 33208 "Metazoa" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030259821 "Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107" "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote." bgee ANN 2013-07-11 HOM:0000007 "historical homology" CL:0000408 "male gamete" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.249" "Gametes must have been present already in the metazoan ancestor, because they are present in every metazoan taxon." bgee ANN 2013-08-29 HOM:0000007 "historical homology" CL:0000453 "Langerhans cell" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:2148747 "Carrillo-Farga J, Castell A, Perez A, Rondan A, Langerhans-like cells in amphibian epidermis. J Anat (1990)" "Langerhans cells have been described in epidermis and other stratified epithelia of mammals. In other vertebrates equivalent cells have not been found. Amphibians show skin graft rejection, so it is possible that these animals have epidermal cells homologous to Langerhans cells. In this work we demonstrate the existence of ATPase-positive dendritic cells in frog epidermis that are similar ultrastructurally to mammalian Langerhans cells, except for the absence of Birbeck granules." bgee ANN 2018-03-27 HOM:0000007 "historical homology" CL:0000453 "Langerhans cell" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:20733076 "Lugo-Villarino G, Balla KM, Stachura DL, Banuelos K, Werneck MB, Traver D, Identification of dendritic antigen-presenting cells in the zebrafish. Proc Natl Acad Sci U S A (2010)" "In seeking to describe antigen-presenting cells in zebrafish, we have identified and characterized DCs in this animal model. Our findings suggest that DCs were present in the ancestor common to teleosts and mammals, and that this key link between the innate and adaptive immune systems has been in place for over 450 million years...Here we present the identification and characterization of a zebrafish APC subset strongly resembling mammalian DCs. Rare DCs are present in various adult tissues, and can be enriched by their affinity for the lectin peanut agglutinin (PNA). We show that PNA(hi) myeloid cells possess the classical morphological features of mammalian DCs as revealed by histochemical and ultrastructural analyses, phagocytose-labeled bacterial preparations in vivo, and exhibit expression of genes associated with DC function and antigen presentation, including il12, MHC class II invariant chain iclp1, and csf1r." bgee ANN 2018-03-27 HOM:0000007 "historical homology" CL:0000453 "Langerhans cell" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:20733076 "Lugo-Villarino G, Balla KM, Stachura DL, Banuelos K, Werneck MB, Traver D, Identification of dendritic antigen-presenting cells in the zebrafish. Proc Natl Acad Sci U S A (2010)" "In seeking to describe antigen-presenting cells in zebrafish, we have identified and characterized DCs in this animal model. Our findings suggest that DCs were present in the ancestor common to teleosts and mammals, and that this key link between the innate and adaptive immune systems has been in place for over 450 million years...Here we present the identification and characterization of a zebrafish APC subset strongly resembling mammalian DCs. Rare DCs are present in various adult tissues, and can be enriched by their affinity for the lectin peanut agglutinin (PNA). We show that PNA(hi) myeloid cells possess the classical morphological features of mammalian DCs as revealed by histochemical and ultrastructural analyses, phagocytose-labeled bacterial preparations in vivo, and exhibit expression of genes associated with DC function and antigen presentation, including il12, MHC class II invariant chain iclp1, and csf1r." bgee ANN 2018-03-27 HOM:0000007 "historical homology" CL:0000453 "Langerhans cell" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:20733076 "Lugo-Villarino G, Balla KM, Stachura DL, Banuelos K, Werneck MB, Traver D, Identification of dendritic antigen-presenting cells in the zebrafish. Proc Natl Acad Sci U S A (2010)" "In seeking to describe antigen-presenting cells in zebrafish, we have identified and characterized DCs in this animal model. Our findings suggest that DCs were present in the ancestor common to teleosts and mammals, and that this key link between the innate and adaptive immune systems has been in place for over 450 million years...Here we present the identification and characterization of a zebrafish APC subset strongly resembling mammalian DCs. Rare DCs are present in various adult tissues, and can be enriched by their affinity for the lectin peanut agglutinin (PNA). We show that PNA(hi) myeloid cells possess the classical morphological features of mammalian DCs as revealed by histochemical and ultrastructural analyses, phagocytose-labeled bacterial preparations in vivo, and exhibit expression of genes associated with DC function and antigen presentation, including il12, MHC class II invariant chain iclp1, and csf1r." bgee ANN 2018-03-27 HOM:0000007 "historical homology" CL:0000540 "neuron" 6072 "Eumetazoa" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.96" "As any textbook tells, the 'first' nerves recognizable at a cellular level are found in cnidarians. This means that nerve cells evolved in the eumetazoan ancestor." bgee ANN 2013-06-10 HOM:0000007 "historical homology" CL:0000542 "lymphocyte" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1146/annurev.immunol.24.021605.090542 "Pancer Z, Cooper MD, The evolution of adaptive immunity. Annual Review of Immunology (2006)" "A new type of circulatory cell with the potential for self-renewal and clonal expansion appeared near the beginning of vertebrate radiation in the form of the long-lived lymphocyte. (...) Exactly when during evolution the lymphocytes appeared as a specialized type of immunocompetent cells is unknown, but cells comparable to the lymphocytes in jawed vertebrates have never been characterized in invertebrates. On the other hand, increasing evidence for bona fide lymphocytes in lamprey and hagfish suggests that lymphocytes must have evolved in the common ancestor of the vertebrates." bgee ANN 2013-06-28 HOM:0000007 "historical homology" CL:0000586 "germ cell" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.249" "Gametes must have been present already in the metazoan ancestor, because they are present in every metazoan taxon." bgee ANN 2013-08-29 HOM:0000007 "historical homology" CL:0000586 "germ cell" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1002/bies.950161213 "Denis H, A parallel between development and evolution: Germ cell recruitment by the gonads. BioEssays (1994)" "The basic assumption is that primitive Metazoa already had germ cells, but no gonads to harbour them." bgee ANN 2013-08-29 HOM:0000007 "historical homology" CL:0000623 "natural killer cell" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1146/annurev.immunol.24.021605.090542 "Pancer Z, Cooper MD, The evolution of adaptive immunity. Annual Review of Immunology (2006)" "A new type of circulatory cell with the potential for self-renewal and clonal expansion appeared near the beginning of vertebrate radiation in the form of the long-lived lymphocyte. (...) Exactly when during evolution the lymphocytes appeared as a specialized type of immunocompetent cells is unknown, but cells comparable to the lymphocytes in jawed vertebrates have never been characterized in invertebrates. On the other hand, increasing evidence for bona fide lymphocytes in lamprey and hagfish suggests that lymphocytes must have evolved in the common ancestor of the vertebrates." bgee ANN 2013-06-28 HOM:0000007 "historical homology" CL:0000653 "glomerular visceral epithelial cell" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1038/nature07526 "Weavers H, Prieto-Sanchez S, Grawe F, Garcia-Lopez A, Artero R, Wilsch-Brauninger M, Ruiz-Gomez M, Skaer H, Denholm B, The insect nephrocyte is a podocyte-like cell with filtration slit diaphragm. Nature (2009)" "Here we show that the insect nephrocyte has remarkable anatomical, molecular and functional similarity to the glomerular podocyte, a cell in the vertebrate kidney that forms the main size-selective barrier as blood is ultrafiltered to make urine. In particular, both cell types possess a specialized filtration diaphragm, known as the slit diaphragm in podocytes or the nephrocyte diaphragm in nephrocytes. We find that fly (Drosophila melanogaster) orthologues of the major constituents of the slit diaphragm, including nephrin, NEPH1 (also known as KIRREL), CD2AP, ZO-1 (TJP1) and podocin, are expressed in the nephrocyte and form a complex of interacting proteins that closely mirrors the vertebrate slit diaphragm complex. Furthermore, we find that the nephrocyte diaphragm is completely lost in flies lacking the orthologues of nephrin or NEPH1 - a phenotype resembling loss of the slit diaphragm in the absence of either nephrin (as in human congenital nephrotic syndrome of the Finnish type, NPHS1) or NEPH1. These changes markedly impair filtration function in the nephrocyte. The similarities we describe between invertebrate nephrocytes and vertebrate podocytes provide evidence suggesting that the two cell types are evolutionarily related, and establish the nephrocyte as a simple model in which to study podocyte biology and podocyte-associated diseases." bgee ANN 2015-03-31 HOM:0000007 "historical homology" CL:0000653 "glomerular visceral epithelial cell" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1038/nature07526 "Weavers H, Prieto-Sanchez S, Grawe F, Garcia-Lopez A, Artero R, Wilsch-Brauninger M, Ruiz-Gomez M, Skaer H, Denholm B, The insect nephrocyte is a podocyte-like cell with filtration slit diaphragm. Nature (2009)" "Here we show that the insect nephrocyte has remarkable anatomical, molecular and functional similarity to the glomerular podocyte, a cell in the vertebrate kidney that forms the main size-selective barrier as blood is ultrafiltered to make urine. In particular, both cell types possess a specialized filtration diaphragm, known as the slit diaphragm in podocytes or the nephrocyte diaphragm in nephrocytes. We find that fly (Drosophila melanogaster) orthologues of the major constituents of the slit diaphragm, including nephrin, NEPH1 (also known as KIRREL), CD2AP, ZO-1 (TJP1) and podocin, are expressed in the nephrocyte and form a complex of interacting proteins that closely mirrors the vertebrate slit diaphragm complex. Furthermore, we find that the nephrocyte diaphragm is completely lost in flies lacking the orthologues of nephrin or NEPH1 - a phenotype resembling loss of the slit diaphragm in the absence of either nephrin (as in human congenital nephrotic syndrome of the Finnish type, NPHS1) or NEPH1. These changes markedly impair filtration function in the nephrocyte. The similarities we describe between invertebrate nephrocytes and vertebrate podocytes provide evidence suggesting that the two cell types are evolutionarily related, and establish the nephrocyte as a simple model in which to study podocyte biology and podocyte-associated diseases." bgee ANN 2015-03-31 HOM:0000007 "historical homology" CL:0000653|CL:0002520 "glomerular visceral epithelial cell|nephrocyte" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1038/nature07526 "Weavers H, Prieto-Sanchez S, Grawe F, Garcia-Lopez A, Artero R, Wilsch-Brauninger M, Ruiz-Gomez M, Skaer H, Denholm B, The insect nephrocyte is a podocyte-like cell with filtration slit diaphragm. Nature (2009)" "Here we show that the insect nephrocyte has remarkable anatomical, molecular and functional similarity to the glomerular podocyte, a cell in the vertebrate kidney that forms the main size-selective barrier as blood is ultrafiltered to make urine. In particular, both cell types possess a specialized filtration diaphragm, known as the slit diaphragm in podocytes or the nephrocyte diaphragm in nephrocytes. We find that fly (Drosophila melanogaster) orthologues of the major constituents of the slit diaphragm, including nephrin, NEPH1 (also known as KIRREL), CD2AP, ZO-1 (TJP1) and podocin, are expressed in the nephrocyte and form a complex of interacting proteins that closely mirrors the vertebrate slit diaphragm complex. Furthermore, we find that the nephrocyte diaphragm is completely lost in flies lacking the orthologues of nephrin or NEPH1 - a phenotype resembling loss of the slit diaphragm in the absence of either nephrin (as in human congenital nephrotic syndrome of the Finnish type, NPHS1) or NEPH1. These changes markedly impair filtration function in the nephrocyte. The similarities we describe between invertebrate nephrocytes and vertebrate podocytes provide evidence suggesting that the two cell types are evolutionarily related, and establish the nephrocyte as a simple model in which to study podocyte biology and podocyte-associated diseases." bgee ANN 2013-08-28 HOM:0000007 "historical homology" CL:0000653|CL:0002520 "glomerular visceral epithelial cell|nephrocyte" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1038/nature07526 "Weavers H, Prieto-Sanchez S, Grawe F, Garcia-Lopez A, Artero R, Wilsch-Brauninger M, Ruiz-Gomez M, Skaer H, Denholm B, The insect nephrocyte is a podocyte-like cell with filtration slit diaphragm. Nature (2009)" "Here we show that the insect nephrocyte has remarkable anatomical, molecular and functional similarity to the glomerular podocyte, a cell in the vertebrate kidney that forms the main size-selective barrier as blood is ultrafiltered to make urine. In particular, both cell types possess a specialized filtration diaphragm, known as the slit diaphragm in podocytes or the nephrocyte diaphragm in nephrocytes. We find that fly (Drosophila melanogaster) orthologues of the major constituents of the slit diaphragm, including nephrin, NEPH1 (also known as KIRREL), CD2AP, ZO-1 (TJP1) and podocin, are expressed in the nephrocyte and form a complex of interacting proteins that closely mirrors the vertebrate slit diaphragm complex. Furthermore, we find that the nephrocyte diaphragm is completely lost in flies lacking the orthologues of nephrin or NEPH1 - a phenotype resembling loss of the slit diaphragm in the absence of either nephrin (as in human congenital nephrotic syndrome of the Finnish type, NPHS1) or NEPH1. These changes markedly impair filtration function in the nephrocyte. The similarities we describe between invertebrate nephrocytes and vertebrate podocytes provide evidence suggesting that the two cell types are evolutionarily related, and establish the nephrocyte as a simple model in which to study podocyte biology and podocyte-associated diseases." bgee ANN 2013-08-28 HOM:0000007 "historical homology" CL:0000670 "primordial germ cell" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.260, Table 13.3" "[Craniota] Primordial germ cells originate as mesodermal cells early in development and migrate to the gonad anlagen." bgee ANN 2013-08-29 HOM:0000007 "historical homology" CL:0000670 "primordial germ cell" NOT 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.249" "In their review, Extavour and Akam (2003) suggested that PGCs [primordial germ cells] can be regarded as homologous across all metazoans. The similar function of these cells, as well as similar structural and molecular characteristics, support this assumption. However, homology implies common origin also, and this is not the case in PGCs." bgee ANN 2013-08-29 HOM:0000007 "historical homology" CL:0000675 "female gamete" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.249" "Gametes must have been present already in the metazoan ancestor, because they are present in every metazoan taxon." bgee ANN 2013-08-29 HOM:0000007 "historical homology" CL:0000740 "retinal ganglion cell" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1038/nature07891 "Shubin N, Tabin C, Caroll S, Deep homology and the origins of evolutionary novelty. Nature (2009)" "The photoreceptors of different taxa are of two main types, rhabdomeric and ciliary (Fig. 1b), which have distinct phototransduction signalling cascades. (...) It is clear that these photoreceptors were not separate inventions in each respective lineage. In polychaete annelids, both photoreceptor types are found, with the ciliary-type opsin (c-opsin) expressed in the brain and rhabdomeric opsin (r-opsin) expressed in the eyes of the same animal. The best explanation for the phylogenetic distribution of photoreceptor types is that both cell types coexisted in the common bilaterian ancestor of vertebrates and invertebrates, and each lineage then used different cell types for light detection in their visual systems. Both types of photoreceptor seem to have been incorporated into the evolving vertebrate eye, with the rhabdomeric photoreceptor cells being transformed into ganglion cells and having a key role in image processing." bgee ANN 2015-04-14 HOM:0000007 "historical homology" CL:0000740|FBbt:00007251 "retinal ganglion cell|rhabdomeric photoreceptor cell (Drosophila)" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1038/nature07891 "Shubin N, Tabin C, Caroll S, Deep homology and the origins of evolutionary novelty. Nature (2009)" "The photoreceptors of different taxa are of two main types, rhabdomeric and ciliary (Fig. 1b), which have distinct phototransduction signalling cascades. (...) It is clear that these photoreceptors were not separate inventions in each respective lineage. In polychaete annelids, both photoreceptor types are found, with the ciliary-type opsin (c-opsin) expressed in the brain and rhabdomeric opsin (r-opsin) expressed in the eyes of the same animal. The best explanation for the phylogenetic distribution of photoreceptor types is that both cell types coexisted in the common bilaterian ancestor of vertebrates and invertebrates, and each lineage then used different cell types for light detection in their visual systems. Both types of photoreceptor seem to have been incorporated into the evolving vertebrate eye, with the rhabdomeric photoreceptor cells being transformed into ganglion cells and having a key role in image processing." bgee ANN 2013-06-21 HOM:0000007 "historical homology" CL:0002091 "primary polar body" 33208 "Metazoa" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.6" "There are a number of characters that occur only among metazoans and therefore evolved in their common ancestor. Such characters are : (...) an oogenesis during which one oocyte and three polar bodies are formed." bgee ANN 2013-08-30 HOM:0000007 "historical homology" CL:0002093 "secondary polar body" 33208 "Metazoa" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.6" "There are a number of characters that occur only among metazoans and therefore evolved in their common ancestor. Such characters are : (...) an oogenesis during which one oocyte and three polar bodies are formed." bgee ANN 2013-08-30 HOM:0000007 "historical homology" CL:0002178 "epithelial cell of stomach" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0000945, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" CL:0002238 "male gonocyte" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.249" "In their review, Extavour and Akam (2003) suggested that PGCs [primordial germ cells] can be regarded as homologous across all metazoans. The similar function of these cells, as well as similar structural and molecular characteristics, support this assumption. However, homology implies common origin also, and this is not the case in PGCs." bgee ANN 2013-08-29 HOM:0000007 "historical homology" CL:0002238 "male gonocyte" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.260, Table 13.3" "[Craniota] Primordial germ cells originate as mesodermal cells early in development and migrate to the gonad anlagen." bgee ANN 2013-09-05 HOM:0000007 "historical homology" CL:0002239 "ooblast" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.249" "In their review, Extavour and Akam (2003) suggested that PGCs [primordial germ cells] can be regarded as homologous across all metazoans. The similar function of these cells, as well as similar structural and molecular characteristics, support this assumption. However, homology implies common origin also, and this is not the case in PGCs." bgee ANN 2013-08-29 HOM:0000007 "historical homology" CL:0002239 "ooblast" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.260, Table 13.3" "[Craniota] Primordial germ cells originate as mesodermal cells early in development and migrate to the gonad anlagen." bgee ANN 2013-08-29 HOM:0000007 "historical homology" CL:0002240 "marrow fibroblast" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0002371, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" CL:0002246 "peripheral blood stem cell" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000037, negated: false, taxon ID: 7776 - entity: UBERON:0000178, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" CL:0002246 "peripheral blood stem cell" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000037, negated: false, taxon ID: 33208 - entity: UBERON:0000178, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" CL:0002251 "epithelial cell of alimentary canal" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0001555, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CL:0002251 "epithelial cell of alimentary canal" NOT 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0001555, negated: true, taxon ID: 33213" bgee HOM:0000007 "historical homology" CL:0002252 "epithelial cell of esophagus" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0001043, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CL:0002252 "epithelial cell of esophagus" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0001043, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" CL:0002319 "neural cell" 6072 "Eumetazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000000, negated: false, taxon ID: 2759 - entity: UBERON:0001016, negated: false, taxon ID: 6072" bgee HOM:0000007 "historical homology" CL:0002327 "mammary gland epithelial cell" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0001911, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" CL:0002328 "bronchial epithelial cell" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0002185, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" CL:0002332 "ciliated cell of the bronchus" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000064, negated: false, taxon ID: 7742 - entity: UBERON:0002185, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" CL:0002352 "gestational hematopoietic stem cell" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000037, negated: false, taxon ID: 7776 - entity: UBERON:0000922, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" CL:0002352 "gestational hematopoietic stem cell" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000037, negated: false, taxon ID: 33208 - entity: UBERON:0000922, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" CL:0002359 "placental hematopoietic stem cell" 9347 "Eutheria" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000037, negated: false, taxon ID: 7776 - entity: UBERON:0001987, negated: false, taxon ID: 9347" bgee HOM:0000007 "historical homology" CL:0002359 "placental hematopoietic stem cell" 32525 "Theria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000037, negated: false, taxon ID: 7776 - entity: UBERON:0001987, negated: false, taxon ID: 32525" bgee HOM:0000007 "historical homology" CL:0002482 "dermal melanocyte" 7742 "Vertebrata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000148, negated: false, taxon ID: 7742 - entity: UBERON:0002067, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" CL:0002482 "dermal melanocyte" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000148, negated: false, taxon ID: 7742 - entity: UBERON:0002067, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" CL:0002483 "hair follicle melanocyte" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000148, negated: false, taxon ID: 7742 - entity: UBERON:0002073, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" CL:0002484 "epithelial melanocyte" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000148, negated: false, taxon ID: 7742 - entity: UBERON:0000483, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" CL:0002485 "retinal melanocyte" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000148, negated: false, taxon ID: 7742 - entity: UBERON:0000966, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CL:0002518 "kidney epithelial cell" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0002113, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CL:0002520 "nephrocyte" 6960 "Hexapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1038/nature07526 "Weavers H, Prieto-Sanchez S, Grawe F, Garcia-Lopez A, Artero R, Wilsch-Brauninger M, Ruiz-Gomez M, Skaer H, Denholm B, The insect nephrocyte is a podocyte-like cell with filtration slit diaphragm. Nature (2009)" "Here we show that the insect nephrocyte has remarkable anatomical, molecular and functional similarity to the glomerular podocyte, a cell in the vertebrate kidney that forms the main size-selective barrier as blood is ultrafiltered to make urine. In particular, both cell types possess a specialized filtration diaphragm, known as the slit diaphragm in podocytes or the nephrocyte diaphragm in nephrocytes. We find that fly (Drosophila melanogaster) orthologues of the major constituents of the slit diaphragm, including nephrin, NEPH1 (also known as KIRREL), CD2AP, ZO-1 (TJP1) and podocin, are expressed in the nephrocyte and form a complex of interacting proteins that closely mirrors the vertebrate slit diaphragm complex. Furthermore, we find that the nephrocyte diaphragm is completely lost in flies lacking the orthologues of nephrin or NEPH1 - a phenotype resembling loss of the slit diaphragm in the absence of either nephrin (as in human congenital nephrotic syndrome of the Finnish type, NPHS1) or NEPH1. These changes markedly impair filtration function in the nephrocyte. The similarities we describe between invertebrate nephrocytes and vertebrate podocytes provide evidence suggesting that the two cell types are evolutionarily related, and establish the nephrocyte as a simple model in which to study podocyte biology and podocyte-associated diseases." bgee ANN 2015-03-31 HOM:0000007 "historical homology" CL:0002520 "nephrocyte" 6960 "Hexapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1038/nature07526 "Weavers H, Prieto-Sanchez S, Grawe F, Garcia-Lopez A, Artero R, Wilsch-Brauninger M, Ruiz-Gomez M, Skaer H, Denholm B, The insect nephrocyte is a podocyte-like cell with filtration slit diaphragm. Nature (2009)" "Here we show that the insect nephrocyte has remarkable anatomical, molecular and functional similarity to the glomerular podocyte, a cell in the vertebrate kidney that forms the main size-selective barrier as blood is ultrafiltered to make urine. In particular, both cell types possess a specialized filtration diaphragm, known as the slit diaphragm in podocytes or the nephrocyte diaphragm in nephrocytes. We find that fly (Drosophila melanogaster) orthologues of the major constituents of the slit diaphragm, including nephrin, NEPH1 (also known as KIRREL), CD2AP, ZO-1 (TJP1) and podocin, are expressed in the nephrocyte and form a complex of interacting proteins that closely mirrors the vertebrate slit diaphragm complex. Furthermore, we find that the nephrocyte diaphragm is completely lost in flies lacking the orthologues of nephrin or NEPH1 - a phenotype resembling loss of the slit diaphragm in the absence of either nephrin (as in human congenital nephrotic syndrome of the Finnish type, NPHS1) or NEPH1. These changes markedly impair filtration function in the nephrocyte. The similarities we describe between invertebrate nephrocytes and vertebrate podocytes provide evidence suggesting that the two cell types are evolutionarily related, and establish the nephrocyte as a simple model in which to study podocyte biology and podocyte-associated diseases." bgee ANN 2015-03-31 HOM:0000007 "historical homology" CL:0002523 "mesonephric glomerular visceral epithelial cell" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000653, negated: false, taxon ID: 7742 - entity: UBERON:0000080, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CL:0002525 "metanephric glomerular visceral epithelial cell" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000653, negated: false, taxon ID: 7742 - entity: UBERON:0000081, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" CL:0002535 "epithelial cell of cervix" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0000002, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" CL:0002536 "epithelial cell of amnion" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0000305, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" CL:0002548 "fibroblast of cardiac tissue" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0000948, negated: false, taxon ID: 7742 - entity: UBERON:0000948|UBERON:0002376, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CL:0002548 "fibroblast of cardiac tissue" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0000948, negated: false, taxon ID: 8782" bgee HOM:0000007 "historical homology" CL:0002548 "fibroblast of cardiac tissue" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0000948, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" CL:0002549 "fibroblast of choroid plexus" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0001886, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" CL:0002552 "fibroblast of gingiva" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0001828, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" CL:0002553 "fibroblast of lung" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0002048|UBERON:0006860, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" CL:0002554 "fibroblast of lymphatic vessel" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0001473, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" CL:0002555 "fibroblast of mammary gland" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0001911, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" CL:0002556 "fibroblast of periodontium" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0001758, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" CL:0002557 "fibroblast of pulmonary artery" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0002012, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" CL:0002557 "fibroblast of pulmonary artery" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0002012, negated: false, taxon ID: 117571" bgee HOM:0000007 "historical homology" CL:0002563 "intestinal epithelial cell" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0000160, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CL:0002577 "placental epithelial cell" 9347 "Eutheria" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0001987, negated: false, taxon ID: 9347" bgee HOM:0000007 "historical homology" CL:0002577 "placental epithelial cell" 32525 "Theria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0001987, negated: false, taxon ID: 32525" bgee HOM:0000007 "historical homology" CL:0002586 "retinal pigment epithelial cell" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0001782, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CL:0002620 "skin fibroblast" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CL:0002625 "seminiferous tubule epithelial cell" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0001343, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" CL:0010002 "epithelial cell of umbilical artery" 9347 "Eutheria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0001310, negated: false, taxon ID: 9347" bgee HOM:0000007 "historical homology" CL:0010003 "epithelial cell of alveolus of lung" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0002299, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" CL:0010012 "cerebral cortex neuron" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000540, negated: false, taxon ID: 6072 - entity: UBERON:0000956, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" CL:0010022 "cardiac neuron" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000540, negated: false, taxon ID: 6072 - entity: UBERON:0000948, negated: false, taxon ID: 7742 - entity: UBERON:0000948|UBERON:0002376, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CL:0010022 "cardiac neuron" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000540, negated: false, taxon ID: 6072 - entity: UBERON:0000948, negated: false, taxon ID: 8782" bgee HOM:0000007 "historical homology" CL:0010022 "cardiac neuron" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000540, negated: false, taxon ID: 6072 - entity: UBERON:0000948, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" CL:0011108 "colon epithelial cell" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0001155, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CL:0011113 "spiral ganglion neuron" 89593 "Craniata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000540, negated: false, taxon ID: 6072 - entity: UBERON:0000395, negated: false, taxon ID: 89593" bgee HOM:0000007 "historical homology" CL:1000271 "lung ciliated cell" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000064, negated: false, taxon ID: 7742 - entity: UBERON:0002048|UBERON:0006860, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" CL:1000296 "epithelial cell of urethra" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0000057, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" CL:1000405 "epithelial cell of appendix" 38609 "Diprotodontia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0001154, negated: false, taxon ID: 38609" bgee HOM:0000007 "historical homology" CL:1000405 "epithelial cell of appendix" NOT 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0001154, negated: true, taxon ID: 40674" bgee HOM:0000007 "historical homology" CL:1000405 "epithelial cell of appendix" 314146 "Euarchontoglires" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0001154, negated: false, taxon ID: 314146" bgee HOM:0000007 "historical homology" CL:1000415 "epithelial cell of gall bladder" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0002110, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CL:1000448 "epithelial cell of sweat gland" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0001820, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" CL:1000449 "epithelial cell of nephron" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0001285, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CL:1000458 "melanocyte of skin" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000148, negated: false, taxon ID: 7742 - entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CL:1000606 "kidney nerve cell" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000540, negated: false, taxon ID: 6072 - entity: UBERON:0002113, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CL:1001433 "epithelial cell of exocrine pancreas" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0000017, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" CL:1001573 "nasopharyngeal epithelial cell" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0001728, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" CL:1001582 "lateral ventricle neuron" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000540, negated: false, taxon ID: 6072 - entity: UBERON:0002285, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CL:1001609 "muscle fibroblast" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0001630, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" CL:1001611 "cerebellar neuron" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000540, negated: false, taxon ID: 6072 - entity: UBERON:0002037, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" CL:2000000 "epidermal melanocyte" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000148, negated: false, taxon ID: 7742 - entity: UBERON:0001003, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" CL:2000017 "fibroblast of peridontal ligament" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0008266, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" CL:2000029 "central nervous system neuron" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000540, negated: false, taxon ID: 6072 - entity: UBERON:0001017, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" CL:2000032 "peripheral nervous system neuron" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000540, negated: false, taxon ID: 6072 - entity: UBERON:0000010, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" CL:2000042 "embryonic fibroblast" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0000922, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" CL:2000045 "foreskin melanocyte" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000148, negated: false, taxon ID: 7742 - entity: UBERON:0001332, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" CL:2000047 "brainstem motor neuron" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000100, negated: false, taxon ID: 33213 - entity: UBERON:0002298, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" CL:2000051 "splenic fibroblast" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0002106, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" CL:2000063 "ovarian fibroblast" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0000992, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CL:2000064 "ovarian surface epithelial cell" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0000992, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CL:2000064 "ovarian surface epithelial cell" NOT 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0000992, negated: true, taxon ID: 33208" bgee HOM:0000007 "historical homology" CL:2000064 "ovarian surface epithelial cell" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000066, negated: false, taxon ID: 33208 - entity: UBERON:0000992, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" CL:2000066 "cardiac ventricle fibroblast" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0002082, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CL:2000067 "cardiac atrium fibroblast" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0002081, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CL:2000068 "pericardium fibroblast" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0002407, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" CL:2000069 "gallbladder fibroblast" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0002110, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CL:2000070 "optic choroid fibroblast" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: CL:0000057, negated: false, taxon ID: 7742 - entity: UBERON:0001776, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" CTENO:0000033 "anal pore" 10197 "Ctenophora" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:27568594 "Presnell JS, Vandepas LE, Warren KJ, Swalla BJ, Amemiya CT, Browne WE, The Presence of a Functionally Tripartite Through-Gut in Ctenophora Has Implications for Metazoan Character Trait Evolution. Curr Biol (2016)" "descriptions of the ctenophore digestive system dating to Agassiz [16] that identify two openings of the digestive system opposite of the mouth-called ""excretory pores"" by Chun [17], referred to as an ""anus"" by Main [18], and coined ""anal pores"" by Hyman [19]" bgee ANN 2018-03-26 HOM:0000007 "historical homology" CTENO:0000033|UBERON:0001245 "anal pore|anus" 6072 "Eumetazoa" CIO:0000005 "low confidence from single evidence" ECO:0000033 "traceable author statement" http://www.sciencemag.org/news/2016/03/why-watching-comb-jellies-poop-has-stunned-evolutionary-biologists "Why watching comb jellies poop has stunned evolutionary biologists (2016)" "On 15 March (2016), at the Ctenopolooza meeting in St. Augustine, Florida, evolutionary biologist William Browne of the University of Miami in Florida debuted films of comb jellies pooping - and it wasn’t through their mouths (...) Browne’s videos elicited gasps from the audience because comb jellies, whose lineage evolved long before other animals with through-guts, had been thought to eat and excrete through a single hole leading to a saclike gut (...) According to recent DNA analyses, comb jellies evolved earlier than other animals considered to have one hole, including sea anemones, jellyfish, and possibly sea sponges. (Some studies suggest sponges arose first.) Consequently, Browne’s as-yet unpublished findings disrupt the stepwise progression of digestive anatomy from one to two holes early in animal evolution. One possibility is that the comb jellies evolved through-guts and anuslike pores on their own, independent of all other animals, over hundreds of millions of years. Alternatively, a through-gut and exit hole may have evolved once in an ancient animal ancestor, and subsequently became lost in anemones, jellyfish, and sponges." bgee ANN 2016-04-25 HOM:0000007 "historical homology" FBbt:00003632 "adult central complex (Drosophila)" 6656 "Arthropoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:24296550 "Strausfeld NJ, Hirth F, Homology versus Convergence in Resolving Transphyletic Correspondences of Brain Organization. Brain Behav Evol (2013)" "Based on a multitude of similarities, together with the principle of parsimony, these approaches identify homologous ground patterns of the arthropod central complex and vertebrate basal ganglia." bgee ANN 2015-04-14 HOM:0000007 "historical homology" FBbt:00003632|UBERON:0010011 "adult central complex (Drosophila)|collection of basal ganglia" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:24296550 "Strausfeld NJ, Hirth F, Homology versus Convergence in Resolving Transphyletic Correspondences of Brain Organization. Brain Behav Evol (2013)" "The use of a multitude of comparative criteria, including developmental genetics, phylogenomics and neural circuit architecture, has recently resolved a highly conserved structural and functional ground pattern organization in the arthropod central complex and vertebrate basal ganglia. (...) Simpson's signature approach to resolving homology [Simpson, 1961], together with comparative developmental genetics and phylogenomics, provides the strategies and logic used for comparing ground patterns of organization across different taxa. Based on a multitude of similarities, together with the principle of parsimony, these approaches identify homologous ground patterns of the arthropod central complex and vertebrate basal ganglia. They also suggest that 'brainlessness' is an evolved adaptation to an ecology undemanding of an errant life that dictates circuits for context-dependent sensory integration, memories, action selection and directed behavior; in a word, the brain that the protostome-deuterostome ancestor is likely to have possessed." bgee ANN 2014-01-13 HOM:0000007 "historical homology" FBbt:00003632|UBERON:0010011 "adult central complex (Drosophila)|collection of basal ganglia" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:24296550 "Strausfeld NJ, Hirth F, Homology versus Convergence in Resolving Transphyletic Correspondences of Brain Organization. Brain Behav Evol (2013)" "The use of a multitude of comparative criteria, including developmental genetics, phylogenomics and neural circuit architecture, has recently resolved a highly conserved structural and functional ground pattern organization in the arthropod central complex and vertebrate basal ganglia. (...) Simpson's signature approach to resolving homology [Simpson, 1961], together with comparative developmental genetics and phylogenomics, provides the strategies and logic used for comparing ground patterns of organization across different taxa. Based on a multitude of similarities, together with the principle of parsimony, these approaches identify homologous ground patterns of the arthropod central complex and vertebrate basal ganglia. They also suggest that 'brainlessness' is an evolved adaptation to an ecology undemanding of an errant life that dictates circuits for context-dependent sensory integration, memories, action selection and directed behavior; in a word, the brain that the protostome-deuterostome ancestor is likely to have possessed." bgee ANN 2014-01-13 HOM:0000007 "historical homology" FBbt:00003632|UBERON:0010011 "adult central complex (Drosophila)|collection of basal ganglia" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:24296550 "Strausfeld NJ, Hirth F, Homology versus Convergence in Resolving Transphyletic Correspondences of Brain Organization. Brain Behav Evol (2013)" "The use of a multitude of comparative criteria, including developmental genetics, phylogenomics and neural circuit architecture, has recently resolved a highly conserved structural and functional ground pattern organization in the arthropod central complex and vertebrate basal ganglia. (...) Simpson's signature approach to resolving homology [Simpson, 1961], together with comparative developmental genetics and phylogenomics, provides the strategies and logic used for comparing ground patterns of organization across different taxa. Based on a multitude of similarities, together with the principle of parsimony, these approaches identify homologous ground patterns of the arthropod central complex and vertebrate basal ganglia. They also suggest that 'brainlessness' is an evolved adaptation to an ecology undemanding of an errant life that dictates circuits for context-dependent sensory integration, memories, action selection and directed behavior; in a word, the brain that the protostome-deuterostome ancestor is likely to have possessed." bgee ANN 2014-01-13 HOM:0000007 "historical homology" FBbt:00007251 "rhabdomeric photoreceptor cell (Drosophila)" 6656 "Arthropoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1038/nature07891 "Shubin N, Tabin C, Caroll S, Deep homology and the origins of evolutionary novelty. Nature (2009)" "The photoreceptors of different taxa are of two main types, rhabdomeric and ciliary (Fig. 1b), which have distinct phototransduction signalling cascades. (...) It is clear that these photoreceptors were not separate inventions in each respective lineage. In polychaete annelids, both photoreceptor types are found, with the ciliary-type opsin (c-opsin) expressed in the brain and rhabdomeric opsin (r-opsin) expressed in the eyes of the same animal. The best explanation for the phylogenetic distribution of photoreceptor types is that both cell types coexisted in the common bilaterian ancestor of vertebrates and invertebrates, and each lineage then used different cell types for light detection in their visual systems. Both types of photoreceptor seem to have been incorporated into the evolving vertebrate eye, with the rhabdomeric photoreceptor cells being transformed into ganglion cells and having a key role in image processing." bgee ANN 2015-04-14 HOM:0000007 "historical homology" PORO:0000018 "osculum" 6040 "Porifera" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:24844197 "Leininger S, Adamski M, Bergum B, Guder C, Liu J, Laplante M, Brate J, Hoffmann F, Fortunato S, Jordal S, Rapp HT, Adamska M, Developmental gene expression provides clues to relationships between sponge and eumetazoan body plans. Nat Commun (2014)" "Thus, while sponges contain only a limited number of direct orthologues of genes involved in body plan patterning in the eumetazoans, all of them are expressed in patterns supporting Haeckel's view that body plans of sponges and cnidarians are homologous: choanoderm corresponds to the gastrodermis and osculum to the mouth of the polyp." bgee ANN 2015-03-10 HOM:0000007 "historical homology" PORO:0000018|UBERON:0000165 "osculum|mouth" 33208 "Metazoa" CIO:0000005 "low confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:24844197 "Leininger S, Adamski M, Bergum B, Guder C, Liu J, Laplante M, Brate J, Hoffmann F, Fortunato S, Jordal S, Rapp HT, Adamska M, Developmental gene expression provides clues to relationships between sponge and eumetazoan body plans. Nat Commun (2014)" "Thus, while sponges contain only a limited number of direct orthologues of genes involved in body plan patterning in the eumetazoans, all of them are expressed in patterns supporting Haeckel's view that body plans of sponges and cnidarians are homologous: choanoderm corresponds to the gastrodermis and osculum to the mouth of the polyp. Clearly, the described expression patterns of the developmental regulatory genes, while highly suggestive, do not prove homology of the body plans. Rather, they provide the necessary first step and a framework for studies aimed at determining the regulatory networks governing development of sponges. Once established, these networks can be further compared with developmental regulatory networks in other animals and provide insights into the molecular mechanisms underlying diversification of animal body plans" bgee ANN 2015-03-10 HOM:0000007 "historical homology" PORO:0000200 "choanoderm" 6040 "Porifera" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:24844197 "Leininger S, Adamski M, Bergum B, Guder C, Liu J, Laplante M, Brate J, Hoffmann F, Fortunato S, Jordal S, Rapp HT, Adamska M, Developmental gene expression provides clues to relationships between sponge and eumetazoan body plans. Nat Commun (2014)" "Genes involved in formation of the eumetazoan endomesoderm, such as beta-catenin, Brachyury and Gata, as well as germline markers Vasa and Pl10, are expressed during formation and maintenance of choanoderm, the feeding epithelium of sponges." bgee ANN 2015-04-14 HOM:0000007 "historical homology" PORO:0000200|UBERON:0003929 "choanoderm|digestive tract epithelium" 33208 "Metazoa" CIO:0000005 "low confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:24844197 "Leininger S, Adamski M, Bergum B, Guder C, Liu J, Laplante M, Brate J, Hoffmann F, Fortunato S, Jordal S, Rapp HT, Adamska M, Developmental gene expression provides clues to relationships between sponge and eumetazoan body plans. Nat Commun (2014)" "Thus, while sponges contain only a limited number of direct orthologues of genes involved in body plan patterning in the eumetazoans, all of them are expressed in patterns supporting Haeckel's view that body plans of sponges and cnidarians are homologous: choanoderm corresponds to the gastrodermis and osculum to the mouth of the polyp. Clearly, the described expression patterns of the developmental regulatory genes, while highly suggestive, do not prove homology of the body plans. Rather, they provide the necessary first step and a framework for studies aimed at determining the regulatory networks governing development of sponges. Once established, these networks can be further compared with developmental regulatory networks in other animals and provide insights into the molecular mechanisms underlying diversification of animal body plans" bgee ANN 2015-03-10 HOM:0000007 "historical homology" UBERON:0000002 "uterine cervix" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" DOI:10.1098/rspb.2004.2848 "Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP, Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings of the Royal Society of London, Series B (2004)" "The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0000003 "naris" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1038/nature02843 "Zhu M, Ahlberg PE, The origin of the internal nostril in tetrapodes. Nature (2004)" "The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla." bgee ANN 2013-06-26 HOM:0000007 "historical homology" UBERON:0000006 "islet of Langerhans" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:18056636 "Wang S, Tulina N, Carlin DL, Rulifson EJ, The origin of islet-like cells in Drosophila identifies parallels to the vertebrate endocrine axis. PNAS (2007)" "Here, we identify a single pair of neural stem cells (neuroblasts) as progenitors of the brain insulin-producing neurosecretory cells of Drosophila, which are homologous to islet beta cells. Likewise, we identify a second pair of neuroblasts as progenitors of the neurosecretory Corpora cardiaca cells, which are homologous to the glucagon-secreting islet alpha cells. (...) ontogenic-molecular concordance suggests that a rudimentary brain endocrine axis was present in the common ancestor of humans and flies, where it orchestrated the islet-like endocrine functions of insulin and glucagon biology." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0000007 "pituitary gland" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510" "A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates. The neural gland of ascidians and Hatschek's pit of amphioxus may be partly homologous to the hypophysis." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0000010 "peripheral nervous system" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1007/978-0-387-46954-6_6 "Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006)" "(...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS [peripheral nervous system], and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives." bgee ANN 2013-06-10 HOM:0000007 "historical homology" UBERON:0000013 "sympathetic nervous system" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471210054 "Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.461-463" "The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage." bgee ANN 2013-06-10 HOM:0000007 "historical homology" UBERON:0000013 "sympathetic nervous system" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471210054 "Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.461-463" "The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage." bgee ANN 2013-06-10 HOM:0000007 "historical homology" UBERON:0000014|UBERON:0002097 "zone of skin|skin of body" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" DOI:10.1111/j.1469-7580.2008.01043.x "Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)" "Whereas direct evidence in the form of lineage tracing of elements such as osteoderms, dermal scales and the lamina calcarea remains wanting, the neural crest hypothesis is clearly consistent with available data. For example, it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina" bgee ANN 2013-07-17 HOM:0000007 "historical homology" UBERON:0000016 "endocrine pancreas" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" DOI:10.1016/j.crvi.2007.03.006 "Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007)" "In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0000017 "exocrine pancreas" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" DOI:10.1016/j.crvi.2007.03.006 "Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007)" "In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0000019 "camera-type eye" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina." bgee AUC 2013-05-22 HOM:0000007 "historical homology" UBERON:0000019 "camera-type eye" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1038/nrn2283 "Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)" "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya." bgee AUC 2013-05-22 HOM:0000007 "historical homology" UBERON:0000019 "camera-type eye" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1038/nrn2283 "Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)" "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya." bgee AUC 2013-05-22 HOM:0000007 "historical homology" UBERON:0000020 "sense organ" 33208 "Metazoa" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.118-123 and Table 7.1" "Sensory structures defined by morphologically recognizable structures (and neglecting the function) are already present in eumetazoan taxa. [curator]" bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0000024 "forelimb wing" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0226313375 "Hall BK, Fins into Limbs: Evolution, Development, and Transformation (2007) p.269" "Because flapping flight originated in both Reptilia (pterosaurs, birds) and Synapsida (bats), the most recent common ancestor of these groups lies at the root of the clade Amniota (e.g., Gauthier et al. 1988b). Following Sumida (1997), we use closely related fossil taxa to reconstruct the forelimb skeleton and pectoral girdle in the hypothetical ancestral amniote. This allow us to characterize wing osteology in each group relative to a common reference point in their evolutionary history." bgee ANN 2018-03-27 HOM:0000007 "historical homology" UBERON:0000024|UBERON:0002102 "forelimb wing|forelimb" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" ISBN:978-0691149776 "Losos JB, The Princeton Guide to Evolution (2014) p.92" "the forelimb of humans, horses, bats, birds, lizards, and frogs are all homologous to each other as vertebrate forelimbs despite enormous dissimilarities in overall form; the homologies reveal themselves in the major bones present and the patterns by which the bones connect to each other and to the rest of the body; specific homologies of the limb bones and their developmental genetic origins are evident across all four-limbed vertebrates and even among bony fishes. Note that although the forelimbs of bats and birds are homologous as vertebrate forelimbs, they are not homologous as wings. The most recent common ancestor of birds and bats had forelimbs that did not form wings, and the structural modifications that make a bird's forelimb a wing are very different from those that make the bat's forelimb a wing. Bird wings and bat wings thus pass similarity testing as vertebrate forelimbs, but they fail similarity testing as wings." bgee ANN 2017-09-12 HOM:0000007 "historical homology" UBERON:0000024|UBERON:0002102 "forelimb wing|forelimb" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0691149776 "Losos JB, The Princeton Guide to Evolution (2014) p.92" "the forelimb of humans, horses, bats, birds, lizards, and frogs are all homologous to each other as vertebrate forelimbs despite enormous dissimilarities in overall form; the homologies reveal themselves in the major bones present and the patterns by which the bones connect to each other and to the rest of the body; specific homologies of the limb bones and their developmental genetic origins are evident across all four-limbed vertebrates and even among bony fishes. Note that although the forelimbs of bats and birds are homologous as vertebrate forelimbs, they are not homologous as wings. The most recent common ancestor of birds and bats had forelimbs that did not form wings, and the structural modifications that make a bird's forelimb a wing are very different from those that make the bat's forelimb a wing. Bird wings and bat wings thus pass similarity testing as vertebrate forelimbs, but they fail similarity testing as wings." bgee ANN 2017-09-12 HOM:0000007 "historical homology" UBERON:0000024|UBERON:0002102 "forelimb wing|forelimb" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" ISBN:978-0226313375 "Hall BK, Fins into Limbs: Evolution, Development, and Transformation (2007) p.269" "Because flapping flight originated in both Reptilia (pterosaurs, birds) and Synapsida (bats), the most recent common ancestor of these groups lies at the root of the clade Amniota (e.g., Gauthier et al. 1988b). Following Sumida (1997), we use closely related fossil taxa to reconstruct the forelimb skeleton and pectoral girdle in the hypothetical ancestral amniote. This allow us to characterize wing osteology in each group relative to a common reference point in their evolutionary history." bgee ANN 2017-09-12 HOM:0000007 "historical homology" UBERON:0000024|UBERON:0002102 "forelimb wing|forelimb" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0226313375 "Hall BK, Fins into Limbs: Evolution, Development, and Transformation (2007) p.269" "Because flapping flight originated in both Reptilia (pterosaurs, birds) and Synapsida (bats), the most recent common ancestor of these groups lies at the root of the clade Amniota (e.g., Gauthier et al. 1988b). Following Sumida (1997), we use closely related fossil taxa to reconstruct the forelimb skeleton and pectoral girdle in the hypothetical ancestral amniote. This allow us to characterize wing osteology in each group relative to a common reference point in their evolutionary history." bgee ANN 2017-09-12 HOM:0000007 "historical homology" UBERON:0000029 "lymph node" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.630" "Lymph nodes that are associated with the lymphatic system have evolved in mammals." bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0000033 "head" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82" "Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head." bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0000033 "head" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:12070079 "Erwin DH, Davidson EH, The last common bilaterian ancestor. Development (2002)" "Many regulatory genes appear to be utilized in at least superficially similar ways in the development of particular body parts in Drosophila and in chordates. These similarities have been widely interpreted as functional homologies, producing the conventional view of the last common protostome-deuterostome ancestor (PDA) as a complex organism that possessed some of the same body parts as modern bilaterians. Here we discuss an alternative view, in which the last common PDA had a less complex body plan than is frequently conceived. (...) Although the heads, hearts, eyes, etc., of insects, vertebrates and other creatures carry out analogous functions, neither their developmental morphogenesis, nor their functional anatomies are actually very similar if considered in any detail. However, in each of the body parts, respectively, the same differentiated cell types are employed across the Bilateria, and it is this fact that underlies their analogous functions: heads all require various types of neurons and their ganglionic associations (...)" bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0000033 "head" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:12070079 "Erwin DH, Davidson EH, The last common bilaterian ancestor. Development (2002)" "Many regulatory genes appear to be utilized in at least superficially similar ways in the development of particular body parts in Drosophila and in chordates. These similarities have been widely interpreted as functional homologies, producing the conventional view of the last common protostome-deuterostome ancestor (PDA) as a complex organism that possessed some of the same body parts as modern bilaterians. Here we discuss an alternative view, in which the last common PDA had a less complex body plan than is frequently conceived. (...) Although the heads, hearts, eyes, etc., of insects, vertebrates and other creatures carry out analogous functions, neither their developmental morphogenesis, nor their functional anatomies are actually very similar if considered in any detail. However, in each of the body parts, respectively, the same differentiated cell types are employed across the Bilateria, and it is this fact that underlies their analogous functions: heads all require various types of neurons and their ganglionic associations (...)" bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0000043 "tendon" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1016/S1095-6433(02)00241-6 "Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002)" "Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0000043|UBERON:2001089 "tendon|myoseptum" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1016/S1095-6433(02)00241-6 "Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002)" "Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0000043|UBERON:2001089 "tendon|myoseptum" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1016/S1095-6433(02)00241-6 "Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002)" "Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0000044 "dorsal root ganglion" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1002/1097-0185(20000615)261:3<111::AID-AR6>3.0.CO;2-F "Butler AB, Chordate evolution and the origin of craniates: An old brain in a new head. AnaT Rec (New Anat) (2000)" "From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system." bgee ANN 2013-06-13 HOM:0000007 "historical homology" UBERON:0000044 "dorsal root ganglion" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1002/1097-0185(20000615)261:3<111::AID-AR6>3.0.CO;2-F "Butler AB, Chordate evolution and the origin of craniates: An old brain in a new head. AnaT Rec (New Anat) (2000)" "From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system." bgee ANN 2013-06-13 HOM:0000007 "historical homology" UBERON:0000045 "ganglion" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23580521 "Strausfeld NJ, Hirth F, Deep homology of arthropod central complex and vertebrate basal ganglia. Science (2013)" "Monophyly of Bilateria, together with the presence of a midline neuropil in both annelids and arthropods, suggests that a central complex-like midline structure already existed in the common bilaterian ancestor before the split to Protostomia and Deuterostomia, which likely possessed a complex, tripartite brain (11, 57). It follows that genealogical correspondence due to common evolutionary origin (58) is the most parsimonious explanation for the observed multitude of similarities between basal ganglia and the central complex, which suggests that homologous circuits mediate comparable behavioral functions across phyla." bgee ANN 2013-06-14 HOM:0000007 "historical homology" UBERON:0000056 "ureter" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543" "The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0000057 "urethra" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/j.ydbio.2008.03.017 "Seifert AW, Harfe BD, Cohn MJ, Cell lineage analysis demonstrates an endodermal origin of the distal urethra and perineum. Developmental Biology (2008)" "In both male and female mammalian embryos, development of the external genitalia begins with the emergence of the paired genital swellings immediately above the cloaca (see Perriton et al. 2002 for a detailed description of normal external genitalia development in mouse). These swellings fuse medially and give rise to the bipotential genital tubercle, which can be masculinized to form the penis or feminized to form the clitoris. As the genital tubercle grows out, the ventral side of the cloacal endoderm forms a bilaminar urethral plate that extends into the genital tubercle, and this structure later cavitates in a proximal to distal direction to form the urethral tube (Hynes and Fraher, 2004a; Perriton et al., 2002)." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0000059 "large intestine" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566" "Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0000065 "respiratory tract" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.592 Figure 18-15" "Respiratory tract of tetrapods has different degree of compartimentalization. [curator]" bgee ANN 2013-09-06 HOM:0000007 "historical homology" UBERON:0000065 "respiratory tract" 436491 "Theropoda" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" PMID:19711481 "Schachner ER, Lyson TR, Dodson P, Evolution of the respiratory system in nonavian theropods: evidence from rib and vertebral morphology. Anat Rec (Hoboken) (2009)" "The avian respiratory tract is composed of two main components: the rigid gas exchanging bronchial lungs and the nonvascularized ventilatory air sacs (...) Analyses of diapophyseal and parapophyseal position and thoracic rib morphology suggest that most nonavian theropods possessed lungs that were deeply incised by the adjacent bicapitate thoracic ribs. This functionally constrains the lungs as rigid nonexpansive organs that were likely ventilated by accessory nonvascularized air sacs. The axial anatomy of this group also reveals that a crocodilian-like hepatic-piston lung would be functionally and biomechanically untenable. Taken together with the evidence that avian-like air sacs were present in basal theropods, these data lead us to conclude that an avian-style pulmonary system was likely a universal theropod trait." bgee ANN 2013-09-06 HOM:0000007 "historical homology" UBERON:0000065 "respiratory tract" 436491 "Theropoda" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:19711481 "Schachner ER, Lyson TR, Dodson P, Evolution of the respiratory system in nonavian theropods: evidence from rib and vertebral morphology. Anat Rec (Hoboken) (2009)" "The avian respiratory tract is composed of two main components: the rigid gas exchanging bronchial lungs and the nonvascularized ventilatory air sacs (...) Analyses of diapophyseal and parapophyseal position and thoracic rib morphology suggest that most nonavian theropods possessed lungs that were deeply incised by the adjacent bicapitate thoracic ribs. This functionally constrains the lungs as rigid nonexpansive organs that were likely ventilated by accessory nonvascularized air sacs. The axial anatomy of this group also reveals that a crocodilian-like hepatic-piston lung would be functionally and biomechanically untenable. Taken together with the evidence that avian-like air sacs were present in basal theropods, these data lead us to conclude that an avian-style pulmonary system was likely a universal theropod trait." bgee ANN 2013-09-06 HOM:0000007 "historical homology" UBERON:0000066 "fully formed stage" 6073 "Cnidaria" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:23957497 "Nielsen C, Life cycle evolution: was the eumetazoan ancestor a holopelagic, planktotrophic gastraea? BMC Evol Biol (2013)" "All the available information is strongly in favor of multiple evolution of non-planktotrophic development, and only the terminal addition theory is in accordance with the Darwinian theory by explaining the evolution through continuous series of adaptational changes. This implies that the ancestor of the eumetazoans was a holopelagic, planktotrophic gastraea, and that the adult stages of cnidarians (sessile) and bilaterians (creeping) were later additions to the life cycle. It further implies that the various larval types are of considerable phylogenetic value." bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0000066 "fully formed stage" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:20083640 "Arenas-Mena C, Indirect development, transdifferentiation and the macroregulatory evolution of metazoans. Philos Trans R Soc Lond B Biol Sci (2010)" "The adult stages of bilaterians are generally considered homologous, at least at a very deep level, but we do not know if the feeding ciliated larvae of indirectly developing protostomes and deuterostomes represent convergent adaptations or derive from a larva already present in the life cycle of the PDA." bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0000066 "fully formed stage" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:23957497 "Nielsen C, Life cycle evolution: was the eumetazoan ancestor a holopelagic, planktotrophic gastraea? BMC Evol Biol (2013)" "All the available information is strongly in favor of multiple evolution of non-planktotrophic development, and only the terminal addition theory is in accordance with the Darwinian theory by explaining the evolution through continuous series of adaptational changes. This implies that the ancestor of the eumetazoans was a holopelagic, planktotrophic gastraea, and that the adult stages of cnidarians (sessile) and bilaterians (creeping) were later additions to the life cycle. It further implies that the various larval types are of considerable phylogenetic value." bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0000068 "embryo stage" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:23799133 "Schep AN, Adryan B, A comparative analysis of transcription factor expression during metazoan embryonic development. PLoS One (2013)" "During metazoan embryonic development, a single cell grows, divides, and differentiates into a complex organism with numerous distinct tissues. While the specifics of embryogenesis differ between animal species, all bilateria share certain features of development" bgee ANN 2013-10-07 HOM:0000007 "historical homology" UBERON:0000068 "embryo stage" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:23799133 "Schep AN, Adryan B, A comparative analysis of transcription factor expression during metazoan embryonic development. PLoS One (2013)" "The pattern of TF expression and TF family utilization throughout development appears to be largely similar in a diverse group of species including two vertebrates (Xenopus tropicalis and Danio rerio) and four invertebrates (Ciona intestinalis, Caenorhabditis elegans, Anopheles gambiae and Drosophila melanogaster)." bgee ANN 2013-10-07 HOM:0000007 "historical homology" UBERON:0000069 "larval stage" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:20083640 "Arenas-Mena C, Indirect development, transdifferentiation and the macroregulatory evolution of metazoans. Philos Trans R Soc Lond B Biol Sci (2010)" "The adult stages of bilaterians are generally considered homologous, at least at a very deep level, but we do not know if the feeding ciliated larvae of indirectly developing protostomes and deuterostomes represent convergent adaptations or derive from a larva already present in the life cycle of the PDA." bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0000079 "male reproductive system" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0792383369 "Lombardi J, Comparative vertebrate reproduction (1998) p.43" "By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0000080 "mesonephros" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639" "As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0000081 "metanephros" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543" "The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0000083 "mesonephric tubule" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639" "As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0000084 "ureteric bud" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639" "The ureteric bud itself forms the collecting tubules and the ureter that drain the adult kidney. This type of kidney, called the metanephros, occurs in all adult amniotes." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0000084 "ureteric bud" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543" "The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0000086 "zona pellucida" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.159" "Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0000086|UBERON:0003125 "zona pellucida|vitelline membrane" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.159" "Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0000087 "inner cell mass" 9347 "Eutheria" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:20079531 "Renfree MB, Review: Marsupials: placental mammals with a difference. Placenta (2010)" "There are many similarities, as well as some differences, between the marsupial embryo and those of eutherian mammals. The most striking difference is the lack of the inner cell mass in the blastocyst which consists solely of a single layer of trophoblast cells." bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0000087 "inner cell mass" 9347 "Eutheria" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:20079531 "Renfree MB, Review: Marsupials: placental mammals with a difference. Placenta (2010)" "There are many similarities, as well as some differences, between the marsupial embryo and those of eutherian mammals. The most striking difference is the lack of the inner cell mass in the blastocyst which consists solely of a single layer of trophoblast cells." bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0000087 "inner cell mass" 9347 "Eutheria" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:23344710 "Frankenberg S, Shaw G, Freyer C, Pask AJ, Renfree MB, Early cell lineage specification in a marsupial: a case for diverse mechanisms among mammals. Development (2013)" "Early cell lineage specification in eutherian mammals results in the formation of a pluripotent inner cell mass (ICM) and trophoblast. By contrast, marsupials have no ICM." bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0000090 "blastocele" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.150" "In the development of many animals, a hollow blastula stage is formed during early embryogenesis. Such a hollow blastula is even regarded as an autapomorphy of Metazoa and is present already in some sponges." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0000090 "blastocele" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.150" "In the development of many animals, a hollow blastula stage is formed during early embryogenesis. Such a hollow blastula is even regarded as an autapomorphy of Metazoa and is present already in some sponges." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0000100 "blastopore" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.139" "The inward movement of cells along the primitive streak has been called ingression, but it is functionally comparable to the involution of cells in amphibian embryos. Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0000100|UBERON:0000931 "blastopore|proctodeum" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:9609826 "Wu LH, Lengyel JA, Role of caudal in hindgut specification and gastrulation suggests homology between Drosophila amnioproctodeal invagination and vertebrate blastopore. Development (1998)" "The fact that the same four genes are expressed at the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) and the amnioproctodeal invagination of Drosophila suggests that these two highly dynamic domains are homologous. (...) While there continues to be uncertainty in our understanding of 'protostome' and 'deuterostome' phyla, the significant conclusion of the data presented here is that there may be a homology between the blastopore of vertebrates and the amnioproctodeal (posterior) invagination of insects." bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0000100|UBERON:0004341 "blastopore|primitive streak" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.139" "The inward movement of cells along the primitive streak has been called ingression, but it is functionally comparable to the involution of cells in amphibian embryos. Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s." bgee ANN 2015-02-23 HOM:0000007 "historical homology" UBERON:0000100|UBERON:0004341 "blastopore|primitive streak" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" PMID:17928866 "Voiculescu O, Bertocchini F, Wolpert L, Keller RE, Stern CD, The amniote primitive streak is defined by epithelial cell intercalation before gastrulation. Nature (2007)" "We propose that the amniote primitive streak evolved from the ancestral blastopore by acquisition of an additional medio-lateral intercalation event, preceding gastrulation and acting independently of mesendoderm formation to position the primitive streak at the midline." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0000100|UBERON:0004341 "blastopore|primitive streak" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:17928866 "Voiculescu O, Bertocchini F, Wolpert L, Keller RE, Stern CD, The amniote primitive streak is defined by epithelial cell intercalation before gastrulation. Nature (2007)" "We propose that the amniote primitive streak evolved from the ancestral blastopore by acquisition of an additional medio-lateral intercalation event, preceding gastrulation and acting independently of mesendoderm formation to position the primitive streak at the midline." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0000102 "lung vasculature" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002048|UBERON:0006860, negated: false, taxon ID: 7776 - entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0000106 "zygote stage" 33208 "Metazoa" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030259821 "Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107" "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote." bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0000107 "cleavage stage" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:23799133 "Schep AN, Adryan B, A comparative analysis of transcription factor expression during metazoan embryonic development. PLoS One (2013)" "During metazoan embryonic development, a single cell grows, divides, and differentiates into a complex organism with numerous distinct tissues. While the specifics of embryogenesis differ between animal species, all bilateria share certain features of development. Repeated cleavage divisions follow egg fertilization and activation. During gastrulation, the three major germ layers are formed, and during organogenesis those germ layers differentiate into the organs of the animal" bgee ANN 2013-10-07 HOM:0000007 "historical homology" UBERON:0000109 "gastrula stage" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:23799133 "Schep AN, Adryan B, A comparative analysis of transcription factor expression during metazoan embryonic development. PLoS One (2013)" "During metazoan embryonic development, a single cell grows, divides, and differentiates into a complex organism with numerous distinct tissues. While the specifics of embryogenesis differ between animal species, all bilateria share certain features of development. Repeated cleavage divisions follow egg fertilization and activation. During gastrulation, the three major germ layers are formed, and during organogenesis those germ layers differentiate into the organs of the animal" bgee ANN 2013-10-07 HOM:0000007 "historical homology" UBERON:0000111 "organogenesis stage" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:23799133 "Schep AN, Adryan B, A comparative analysis of transcription factor expression during metazoan embryonic development. PLoS One (2013)" "During metazoan embryonic development, a single cell grows, divides, and differentiates into a complex organism with numerous distinct tissues. While the specifics of embryogenesis differ between animal species, all bilateria share certain features of development. Repeated cleavage divisions follow egg fertilization and activation. During gastrulation, the three major germ layers are formed, and during organogenesis those germ layers differentiate into the organs of the animal" bgee ANN 2013-10-07 HOM:0000007 "historical homology" UBERON:0000115 "lung epithelium" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002048|UBERON:0006860, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0000151 "pectoral fin" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19324642 "Zhu M, Yu X, Stem sarcopterygians have primitive polybasal fin articulation. Biology letters (2009)" "In the fin-limb transition, the origin of the sarcopterygian paired fins triggered new possibilities of fin articulation and movement, and established the proximal segments (stylopod and zeugopod) of the presumptive tetrapod limb." bgee ANN 2015-04-14 HOM:0000007 "historical homology" UBERON:0000151|UBERON:0001460 "pectoral fin|arm" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:19324642 "Zhu M, Yu X, Stem sarcopterygians have primitive polybasal fin articulation. Biology letters (2009)" "In the fin-limb transition, the origin of the sarcopterygian paired fins triggered new possibilities of fin articulation and movement, and established the proximal segments (stylopod and zeugopod) of the presumptive tetrapod limb." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0000151|UBERON:0002102 "pectoral fin|forelimb" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:17587327 "Mercader N, Early steps of paired fin development in zebrafish compared with tetrapod limb development. Development, growth and differentiation (2007)" "Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively." bgee ANN 2013-07-12 HOM:0000007 "historical homology" UBERON:0000152 "pelvic fin" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:22913749 "Don EK, Currie PD, Cole NJ, The evolutionary history of the development of the pelvic fin/hindlimb. J Anat (2013)" "The hindlimbs of tetrapods are derived from the pelvic fins of ancestral fish. These evolutionary origins can be seen in the examination of shared gene and protein expression patterns during the development of pelvic fins and tetrapod hindlimbs." bgee ANN 2015-04-14 HOM:0000007 "historical homology" UBERON:0000152|UBERON:0000978 "pelvic fin|leg" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:19324642 "Zhu M, Yu X, Stem sarcopterygians have primitive polybasal fin articulation. Biology letters (2009)" "In the fin-limb transition, the origin of the sarcopterygian paired fins triggered new possibilities of fin articulation and movement, and established the proximal segments (stylopod and zeugopod) of the presumptive tetrapod limb." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0000152|UBERON:0002103 "pelvic fin|hindlimb" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:17587327 "Mercader N, Early steps of paired fin development in zebrafish compared with tetrapod limb development. Development, growth and differentiation (2007)" "Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0000152|UBERON:0002103 "pelvic fin|hindlimb" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:22913749 "Don EK, Currie PD, Cole NJ, The evolutionary history of the development of the pelvic fin/hindlimb. J Anat (2013)" "The hindlimbs of tetrapods are derived from the pelvic fins of ancestral fish. These evolutionary origins can be seen in the examination of shared gene and protein expression patterns during the development of pelvic fins and tetrapod hindlimbs." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0000152|UBERON:0002103 "pelvic fin|hindlimb" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:22913749 "Don EK, Currie PD, Cole NJ, The evolutionary history of the development of the pelvic fin/hindlimb. J Anat (2013)" "The hindlimbs of tetrapods are derived from the pelvic fins of ancestral fish. These evolutionary origins can be seen in the examination of shared gene and protein expression patterns during the development of pelvic fins and tetrapod hindlimbs." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0000160 "intestine" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 and Figure 2-11 p.42" "The intestine is a craniate feature. [curator]" bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0000162 "cloaca" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572" "A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0000162 "cloaca" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572" "A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0000164 "primitive urogenital sinus" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0721676678 "Romer AS, Vertebrate body (1970)p.388-89 and Figure 300" "In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0000165 "mouth" 6072 "Eumetazoa" CIO:0000005 "low confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:23103190 "Martin-Duran JM, Janssen R, Wennberg S, Budd GE, Hejnol A, Deuterostomic development in the protostome Priapulus caudatus. Curr Biol (2012) Figure 4" "The expression of bra, cdx, gsc, and foxA indicates the homology between the mouth and the anus of P. caudatus and other bilaterians, as well as the homology of the oral opening of cnidarians and the mouth of bilaterians." bgee ANN 2015-03-12 HOM:0000007 "historical homology" UBERON:0000165 "mouth" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000033 "traceable author statement" PMID:18331892 "Lacalli TC, Basic features of the ancestral chordate brain: a protochordate perspective. Brain Res Bull (2008)" "An account of recent data on dorsoventral inversion is also included, as this bears directly on the question of where the chordate brain originated in relation to other structures. It now appears likely that key components of the ancestral brain were originally located around the mouth. A secondary repositioning of the latter would therefore have been required before a unitary brain could be assembled and internalized. This association between the mouth and the evolving brain reinforces the idea of a fundamental early connection between core brain structures and the control of feeding activity." bgee ANN 2015-02-23 HOM:0000007 "historical homology" UBERON:0000165 "mouth" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/j.semcdb.2007.06.002 "Christiaen L, Jaszczyszyn Y, Kerfant M, Kanob S, Thermes V, Joly JS, Evolutionary modification of mouth position in deuterostomes. Seminars in Cell and Developmental Biology (2007)" "(...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth." bgee ANN 2015-02-23 HOM:0000007 "historical homology" UBERON:0000165 "mouth" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1038/nature07309 "Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)" "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0000165 "mouth" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1111/brv.12229 "Nielsen C, Evolution of deuterostomy - and origin of the chordates. Biol Rev Camb Philos Soc (2017)" "deuterostomy is known to occur in several protostomian groups, such as the chaetognaths and representatives of annelids, molluscs, arthropods and priapulans. This raises the question whether the deuterostomian mouth is in fact homologous with that of the protostomes...A few studies of gene expression show identical expression patterns around mouth and anus in protostomes and deuterostomes. Closer studies of the embryology of ascidians and vertebrates show that the mouth/stomodaeum differentiates from the anterior edge of the neural plate...The conclusion must be that the chordate mouth (and that of the deuterostomes in general) is homologous to the protostomian mouth and that the latest common ancestor of protostomes and deuterostomes developed through amphistomy, as suggested by the trochaea theory." bgee ANN 2017-05-23 HOM:0000007 "historical homology" UBERON:0000165 "mouth" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:25788603 "Janssen R, Joergensen M, Lagebro L, Budd GE, Fate and nature of the onychophoran mouth-anus furrow and its contribution to the blastopore. Proc Biol Sci (2015)" "Based on expression patterns of forkhead (fkh), caudal (cad), brachyury (bra) and wingless (wg/Wnt1), we show that this groove [clear ventral groove during gastrulation of onychophorans] does not correspond to the blastopore, even though both the mouth and anus later develop from it. Rather, the posterior pit appears to be the blastopore; the posterior of the groove later fuses with it to form the definitive anus. Onychophoran development therefore represents a case of 'concealed' deuterostomy. The new data from the onychophorans thus remove one of the key pieces of evidence for the amphistomy theory. Rather, in line with other recent results, it suggests that ancestral bilaterian development was deuterostomic." bgee ANN 2015-03-23 HOM:0000007 "historical homology" UBERON:0000165 "mouth" 33511 "Deuterostomia" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.32" "Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron." bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0000165|UBERON:0001245 "mouth|anus" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:23103190 "Martin-Duran JM, Janssen R, Wennberg S, Budd GE, Hejnol A, Deuterostomic development in the protostome Priapulus caudatus. Curr Biol (2012) Figure 4" "The expression of bra, cdx, gsc, and foxA indicates the homology between the mouth and the anus of P. caudatus and other bilaterians, as well as the homology of the oral opening of cnidarians and the mouth of bilaterians." bgee ANN 2015-03-11 HOM:0000007 "historical homology" UBERON:0000165|UBERON:0001245 "mouth|anus" NOT 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1038/nature07309 "Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)" "we find that the genes caudal, orthopedia and brachyury-which are expressed in various bilaterian hindguts-are expressed in a small region at the posterior end of the animal [the acoel Convolutriloba longifissura], separated from the anterior oral brachyury-expressing region by a dorsal domain of ectodermal bmp2/4 expression. These results contradict the hypothesis that the bilaterian mouth and anus evolved simultaneously from a common blastoporal opening, and suggest that a through gut might have evolved independently in different animal lineages." bgee ANN 2015-03-11 HOM:0000007 "historical homology" UBERON:0000165|UBERON:0001245 "mouth|anus" NOT 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:25788603 "Janssen R, Joergensen M, Lagebro L, Budd GE, Fate and nature of the onychophoran mouth-anus furrow and its contribution to the blastopore. Proc Biol Sci (2015)" "The new data from the onychophorans thus remove one of the key pieces of evidence for the amphistomy theory. Rather, in line with other recent results, it suggests that ancestral bilaterian development was deuterostomic." bgee ANN 2015-03-23 HOM:0000007 "historical homology" UBERON:0000173 "amniotic fluid" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187" "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois." bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0000178 "blood" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1146/annurev.cellbio.22.010605.093317 "Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006)" "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrate phyla. (...)a brief survey of the different types of blood cell lineages among metazoa. There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0000178 "blood" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1146/annurev.cellbio.22.010605.093317 "Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006)" "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrate phyla. (...)a brief survey of the different types of blood cell lineages among metazoa. There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0000203 "pallium" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1007/978-3-540-29678-2_3165 "Jarvis ED, Evolution of the Pallium in Birds and Reptiles. Encyclopedia of Neuroscience (2009) p.1390-1400" "Despite these differences in how the developing pallium is organized, developmentally regulated transcription factors have been used to demonstrate that the dorsal part of the telencephalon is homologous as pallium across vertebrates (Fig. 2)." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0000206 "pharyngeal gill" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/j.cub.2017.01.022 "Gillis JA, Tidswell ORA, The Origin of Vertebrate Gills. Current Biology (2017)" "Pharyngeal gills are a fundamental feature of the vertebrate body plan [1]. However, the evolutionary history of vertebrate gills has been the subject of a long-standing controversy [2, 3, 4, 5, 6, 7, 8]. It is thought that gills evolved independently in cyclostomes (jawless vertebrates-lampreys and hagfish) and gnathostomes (jawed vertebrates-cartilaginous and bony fishes), based on their distinct embryonic origins: the gills of cyclostomes derive from endoderm [9, 10, 11, 12], while gnathostome gills were classically thought to derive from ectoderm [10, 13]. Here, we demonstrate by cell lineage tracing that the gills of a cartilaginous fish, the little skate (Leucoraja erinacea), are in fact endodermally derived. This finding supports the homology of gills in cyclostomes and gnathostomes, and a single origin of pharyngeal gills prior to the divergence of these two ancient vertebrate lineages." bgee ANN 2017-02-13 HOM:0000007 "historical homology" UBERON:0000206|UBERON:0001132 "pharyngeal gill|parathyroid gland" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1111/j.1469-7580.2005.00472.x "Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)" "The evolution of the tetrapods, and the shift from an aquatic to a terrestrial environment, was believed to have required new controls for regulating calcium homeostasis, and thus the evolution of parathyroid glands (...) both the tetrapod parathyroid and the gills of fish contribute to the regulation of extracellular calcium levels. It is therefore reasonable to suggest that the parathyroid gland evolved as a result of the transformation of the gills into the parathyroid glands of tetrapods and the transition from an aquatic to a terrestrial environment. This interpretation would also explain the positioning of the parathyroid gland within the pharynx in the tetrapod body. Were the parathyroid gland to have emerged de novo with the evolution of the tetrapods it could, as an endocrine organ, have been placed anywhere in the body and still exert its effect." bgee ANN 2017-02-13 HOM:0000007 "historical homology" UBERON:0000209 "tetrapod frontal bone" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1038/nrn1221 "Santagati F, Rijli FM, Cranial neural crest and the building of the vertebrate head. Nature Reviews Neuroscience (2003)" "Some bones, including the squamosal (SQ), alisphenoid (AS), and pterygoid (PT), are shown with mixed contribution from different NCC populations. Note that in mammals the frontal (FR) and parietal (PA) bones have been reported to be of neural crest and mesodermal origin, respectively (13). In birds, the frontal and parietal bones have been reported to be either entirely derived from NCCs (12), as shown in the figure, or derived from a dual neural crest/mesodermal origin (7,10)." bgee ANN 2013-09-05 HOM:0000007 "historical homology" UBERON:0000209 "tetrapod frontal bone" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:16313386 "Hanken J, Gross JB, Evolution of cranial development and the role of neural crest: insights from amphibians. J Anat (2005)" "Published data for Xenopus (...) most closely resemble the avian results in which frontal and parietal bones are derived exclusively from neural crest (Couly et al. 1993). Moreover, both these accounts differ from that in the mouse, in which the parietal bone is derived exclusively from mesoderm. This pattern of similarity and difference among taxa might indicate that amphibians and birds share the primitive tetrapod condition of derivation of the skull roof, which was subsequently altered in the clade leading to mammals." bgee ANN 2013-09-05 HOM:0000007 "historical homology" UBERON:0000209 "tetrapod frontal bone" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:16313386 "Hanken J, Gross JB, Evolution of cranial development and the role of neural crest: insights from amphibians. J Anat (2005)" "Published data for Xenopus (...) most closely resemble the avian results in which frontal and parietal bones are derived exclusively from neural crest (Couly et al. 1993). Moreover, both these accounts differ from that in the mouse, in which the parietal bone is derived exclusively from mesoderm. This pattern of similarity and difference among taxa might indicate that amphibians and birds share the primitive tetrapod condition of derivation of the skull roof, which was subsequently altered in the clade leading to mammals." bgee ANN 2013-09-05 HOM:0000007 "historical homology" UBERON:0000210 "tetrapod parietal bone" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" DOI:10.1163/157075606778967801 "Cerny R, Horacek I, Lennart O, The Trabecula cranii: development and homology of an enigmatic vertebrate head structure. Animal Biology (2006)" "It would, for example, be considered strange if a bone of mesodermal origin in one vertebrate is a direct homologue of a bone of neural crest origin in another species. But the parietal bone seems to illustrate just such a case. In the mouse it originates from cephalic paraxial mesoderm (Jiang et al., 2000; Morriss-Kay, 2001), whereas in chicken the parietal bone has been traced back to either mesodermal (Noden, 1978) or, according to improved methodological approach, to neural crest cells (Couly et al., 1992, 1993) (fig. 1). In the clawed frog (Xenopus laevis), the only other animal for which the embryonic origin of a membrane bone is currently known (Gross and Hanken, 2005), a single fronto-parietal bone also originates from neural crest cells, although a contribution from cranial paraxial mesodermal cells cannot be excluded, as these have not yet been fate-mapped. These differences suggest that either the pattern of neural crest contribution to the vertebrate skull has changed significantly during evolution, or that widely accepted skull bone homologies across major clades may be incorrect (Hanken and Gross, 2005)." bgee ANN 2013-09-05 HOM:0000007 "historical homology" UBERON:0000210|UBERON:0004866 "tetrapod parietal bone|actinopterygian frontal bone" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" DOI:10.1163/156853888X00062 "Rocek Z, Origin and evolution of the frontoparietal complex in anurans. Amphibia-Reptilia (1988)" "There has been some dispute concerning the homology of frontal and parietal bones in fishes and tetrapods since Westoll's idea were published (1943). Several criteria have been suggested for this purpose, some of them being later refuted as inappropriate. Reliable in establishing homologies of dermal roofing bones seemed to be their relations to brain (Schowing, 1961; 1968a, b, c; but cf. Moy-Thomas, 1941: 681-682), neuromasts (Allis, 1898: 428-429; 1899; Pehrson, 1922; Schmalhausen, 1950: 179, and many others; however, certain limitations of this character were stated by Devillers and Corsin, 1968: 414, and criticism was expressed e.g. by Moy-Thomas, 1941: 681 and Parrington, 1949; 1950: 544; 1956; 1967), and also to the nerves supplying neuromasts of the sensory lines and possibly to some others nerves and vessels (Jarvik, 1967: 188)" bgee ANN 2013-08-26 HOM:0000007 "historical homology" UBERON:0000210|UBERON:0004866 "tetrapod parietal bone|actinopterygian frontal bone" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:17599725 "Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, Westerfield M, Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zool B Mol Dev Evol (2007)" "There are several lines of evidence to suggest that the so-called frontal bone in actinopterygian fishes (including zebrafish) is the homologue of the parietal bone, and not the 'frontal' bone, in advanced 'piscine' sarcopterygians as well as in 'tetrapod' sarcopterygians such as frog, bird, mouse, or human. The so-called parietal bone of actinopterygians is the homologue of the postparietal bone of piscine sarcopterygians and tetrapods (Jollie, '62; Schultze and Arsenault, '85)." bgee ANN 2013-08-26 HOM:0000007 "historical homology" UBERON:0000211 "ligament" 7742 "Vertebrata" CIO:0000005 "low confidence from single evidence" ECO:0000205 "curator inference" PMID:12712326 "Summers AP, Koob-Emunds MM, Kajiura SM, Koob TJ, A novel fibrocartilaginous tendon from an elasmobranch fish ( Rhinoptera bonasus). Cell Tissue Res (2003)" "Histological and biochemical analyses demonstrated that the fibrocartilage [of sharks] bears similarities to that found in mammals. Although it is not clear that these tissues are homologous, they are certainly functional analogs. Comparative studies of the biochemistry of shark and mammalian connective tissues are in the early stages (Sakaguchi et al. 2001), but there are significant differences between these two lineages." bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0000211 "ligament" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:12712326 "Summers AP, Koob-Emunds MM, Kajiura SM, Koob TJ, A novel fibrocartilaginous tendon from an elasmobranch fish ( Rhinoptera bonasus). Cell Tissue Res (2003)" "Histological and biochemical analyses demonstrated that the fibrocartilage [of sharks] bears similarities to that found in mammals. Although it is not clear that these tissues are homologous, they are certainly functional analogs. Comparative studies of the biochemistry of shark and mammalian connective tissues are in the early stages (Sakaguchi et al. 2001), but there are significant differences between these two lineages." bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0000301 "amniotic cavity" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187" "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois." bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0000305 "amnion" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187" "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0000307 "blastula" 33154 "Opisthokonta" CIO:0000005 "low confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1002/bies.200800214 "Mikhailov KV, Konstantinova AV, Nikitin MA, Troshin PV, Rusin LY, Lyubetsky VA, Panchin YV, Mylnikov AP, Moroz LL, Kumar S, Aleoshin VV, The origin of Metazoa: a transition from temporal to spatial cell differentiation. Bioessays (2009)" "genes that typically control metazoan development, cell differentiation, cell-to-cell adhesion, and cell-to-matrix adhesion are found in various unicellular relatives of the Metazoa, which suggests the origin of the genetic programs of cell differentiation and adhesion in the root of the Opisthokonta. Multicellular stages occurring in the complex life cycles of opisthokont protists (mesomycetozoeans and choanoflagellates) never resemble a blastula. Here, we discuss a more realistic scenario of transition to multicellularity through integration of pre-existing transient cell types into the body of an early metazoon, which possessed a complex life cycle with a differentiated sedentary filter-feeding trophic stage and a non-feeding blastula-like larva, the synzoospore. Choanoflagellates are considered as forms with secondarily simplified life cycles." bgee ANN 2017-06-12 HOM:0000007 "historical homology" UBERON:0000307 "blastula" 33208 "Metazoa" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1002/bies.200800214 "Mikhailov KV, Konstantinova AV, Nikitin MA, Troshin PV, Rusin LY, Lyubetsky VA, Panchin YV, Mylnikov AP, Moroz LL, Kumar S, Aleoshin VV, The origin of Metazoa: a transition from temporal to spatial cell differentiation. Bioessays (2009)" "The presence of a uniform blastula and gastrula with differentiated ectoderm and endoderm were postulated by Haeckel to be the characteristic of all Metazoa. This definition has led to the understanding that the unity of animal organization, and not the discrete embranchments paradigm, is the rightful outcome of a major debate in comparative anatomy of the 19th century held between ƒtienne Geoffroy Saint-Hilaire and George Cuvier.12 In other words, it led to the recognition that the diversity of animal organization is derived from a common ancestor." bgee ANN 2017-06-12 HOM:0000007 "historical homology" UBERON:0000315 "subarachnoid space" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:22100360 "Sakka L, Coll G, Chazal J, Anatomy and physiology of cerebrospinal fluid. Eur Ann Otorhinolaryngol Head Neck Dis (2011)" "In amphibians, reptiles and birds, the meninges comprise a dura mater and a pia mater. The perimeningeal tissue is considerably reduced, persisting at the spinal level in the form of epidural fat. In mammals, the subarachnoid space is clearly distinct from the pia mater." bgee ANN 2015-04-02 HOM:0000007 "historical homology" UBERON:0000319 "cytotrophoblast" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0878932504 "Gilbert SF, Developmental Biology (2006) p. 353-354 and Figure 11.33" "The cytotrophoblast is one of the distinctly mammalian tissues that enable the fetus to survive within the maternal uterus. [curator]" bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0000348 "ophthalmic nerve" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.4067/S0717-95022005000400017 "Casas SAL, Intelizano W, Castro SMF, Mariana BAN, Mandibular Musculature of the Sand Tiger Shark Carcharias taurus (Rafinesque, 1810) (Chondrichthyes: Odontaspididae). International Journal of Morphology (2005)" "The mandibular innervation of C. taurus [shark, Chondrichthyes] is in agreement with the general pattern established for all the vertebrates, in which the trigeminal nerve presents the ophthalmic, maxillary and mandibular divisions (Hildebrand, 1995, Romer et al., 1985)." bgee ANN 2013-06-13 HOM:0000007 "historical homology" UBERON:0000358 "blastocyst" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:9631662 "Gardner RL, Contributions of blastocyst micromanipulation to the study of mammalian development. Bioessays (1998)" "(...) the initial phase of mammalian development is uniquely modified to meet the requirements of viviparity. Thus, in mammals, repeated cleavage of the egg following fertilization culminates in the formation of a structure called a blastocyst rather than a blastula." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0000358 "blastocyst" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:18155829 "Dard N, Breuer M, Maro B, Louvet-Vallee S, Morphogenesis of the mammalian blastocyst. Mol Cell Endocrinol (2008)" "In this review, we first discuss data showing unambiguously that no essential axis of development is set up before the late blastocyst stage, and explain why the pre-patterning described during the early phases (segmentation) of development in other vertebrates cannot apply to mammalian pre-implantation period." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0000369 "corpus striatum" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471210054 "Butler AB, Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.364" "The ventrolateral part of the telencephalon contains a number of structures in all vertebrate groups. A variety of terms have been used for this region in general and also for some of its specific components, including corpus striatum, dorsal striatum, and so on." bgee ANN 2013-06-10 HOM:0000007 "historical homology" UBERON:0000371 "syncytiotrophoblast" 9347 "Eutheria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1016/j.cbpa.2007.01.029 "Mess A, Carter AM, Evolution of the placenta during the early radiation of placental mammals. Comparative Biochemistry and Physiology - Part A: Molecular and Integrative Physiology (2007)" "In the common ancestor of living placental mammals the interhaemal barrier had a syncytiotrophoblast. [curator]" bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0000375 "mandibular nerve" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.4067/S0717-95022005000400017 "Casas SAL, Intelizano W, Castro SMF, Mariana BAN, Mandibular Musculature of the Sand Tiger Shark Carcharias taurus (Rafinesque, 1810) (Chondrichthyes: Odontaspididae). International Journal of Morphology (2005)" "The mandibular innervation of C. taurus [shark, Chondrichthyes] is in agreement with the general pattern established for all the vertebrates, in which the trigeminal nerve presents the ophthalmic, maxillary and mandibular divisions (Hildebrand, 1995, Romer et al., 1985)." bgee ANN 2013-06-13 HOM:0000007 "historical homology" UBERON:0000376 "hindlimb stylopod" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23434323 "Schneider I, Shubin NH, The origin of the tetrapod limb: from expeditions to enhancers. Trends Genet (2013)" "Of the three limb segments (Figure 1a), the stylopod has been hypothesized to have a homolog in the fins of extant fish, being present as a basal segment of the fin in chondrichthyians, basal actinopterygians, and sarcopterygians." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0000377 "maxillary nerve" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.4067/S0717-95022005000400017 "Casas SAL, Intelizano W, Castro SMF, Mariana BAN, Mandibular Musculature of the Sand Tiger Shark Carcharias taurus (Rafinesque, 1810) (Chondrichthyes: Odontaspididae). International Journal of Morphology (2005)" "The mandibular innervation of C. taurus [shark, Chondrichthyes] is in agreement with the general pattern established for all the vertebrates, in which the trigeminal nerve presents the ophthalmic, maxillary and mandibular divisions (Hildebrand, 1995, Romer et al., 1985)." bgee ANN 2013-06-13 HOM:0000007 "historical homology" UBERON:0000378 "tongue muscle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1002/dvdy.20587 "Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005)" "The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP [migratory muscle precursors], especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals)." bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0000378 "tongue muscle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1002/dvdy.20587 "Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005)" "The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP [migratory muscle precursors], especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals)." bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0000378 "tongue muscle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1002/dvdy.20587 "Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005)" "The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP [migratory muscle precursors], especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals)." bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0000395 "cochlear ganglion" 89593 "Craniata" CIO:0000005 "low confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...)" bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0000395 "cochlear ganglion" 89593 "Craniata" CIO:0000005 "low confidence from single evidence" ECO:0000205 "curator inference" http://tolweb.org/Craniata/14826/1997.01.01 "Janvier P, Craniata. Animals with skulls. The Tree of Life Web Project (1997)" "In all craniates, the olfactory (I), optic (II), trigeminal (V), facial (VII), acoustic (VIII), glossopharyngeal (IX) and vagus (X) cranial nerves are present. Additional cranial nerves, the oculomotor (III), trochlear (IV) and abducent (VI) nerves occur only in the Vertebrata. Some consider that the latter have been secondarily lost in hagfishes." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0000397 "colonic epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001155, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0000398 "cartilage tissue of sternum" 8292 "Amphibia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000975, negated: false, taxon ID: 8292 - entity: UBERON:0002418, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0000398 "cartilage tissue of sternum" 8492 "Archosauria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000975, negated: false, taxon ID: 8492 - entity: UBERON:0002418, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0000398 "cartilage tissue of sternum" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000975, negated: false, taxon ID: 8782 - entity: UBERON:0002418, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0000398 "cartilage tissue of sternum" NOT 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000975, negated: true, taxon ID: 32523 - entity: UBERON:0002418, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0000398 "cartilage tissue of sternum" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000975, negated: false, taxon ID: 40674 - entity: UBERON:0002418, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0000400 "jejunal epithelium" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002115, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0000428 "prostate epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002367, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0000457 "cavernous artery" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001532, negated: false, taxon ID: 7742 - entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0001675, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0000468 "multi-cellular organism" 2759 "Eukaryota" CIO:0000005 "low confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:22930590 "Dickinson DJ, Nelson WJ, Weis WI, An epithelial tissue in Dictyostelium challenges the traditional origin of metazoan multicellularity. Bioessays (2012)" "We hypothesize that aspects of animal multicellularity originated before the divergence of metazoans from fungi and social amoebae. Polarized epithelial tissues are a defining feature of metazoans and contribute to the diversity of animal body plans. The recent finding of a polarized epithelium in the non-metazoan social amoeba Dictyostelium discoideum demonstrates that epithelial tissue is not a unique feature of metazoans, and challenges the traditional paradigm that multicellularity evolved independently in social amoebae and metazoans." bgee ANN 2015-03-10 HOM:0000007 "historical homology" UBERON:0000468 "multi-cellular organism" NOT 2759 "Eukaryota" CIO:0000004 "medium confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:23315654 "Parfrey LW, Lahr DJ, Multicellularity arose several times in the evolution of eukaryotes (response to DOI 10.1002/bies.201100187). Bioessays (2013)" "(...) phylogenetic analyses of two key genes reveal patterns inconsistent with a single origin of multicellularity. A single origin in Amorphea would also require loss of multicellularity in each of the many unicellular lineages within this clade. Further, there are numerous other origins of multicellularity within eukaryotes, including three within Amorphea, that are not characterized by these structural and mechanistic similarities. Instead, convergent evolution resulting from similar selective pressures for forming multicellular structures with motile and differentiated cells is the most likely explanation for the observed similarities between animal and dictyostelid cell-cell connections." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0000468 "multi-cellular organism" NOT 2759 "Eukaryota" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:23315654 "Parfrey LW, Lahr DJ, Multicellularity arose several times in the evolution of eukaryotes (response to DOI 10.1002/bies.201100187). Bioessays (2013)" "(...) phylogenetic analyses of two key genes reveal patterns inconsistent with a single origin of multicellularity. A single origin in Amorphea would also require loss of multicellularity in each of the many unicellular lineages within this clade. Further, there are numerous other origins of multicellularity within eukaryotes, including three within Amorphea, that are not characterized by these structural and mechanistic similarities. Instead, convergent evolution resulting from similar selective pressures for forming multicellular structures with motile and differentiated cells is the most likely explanation for the observed similarities between animal and dictyostelid cell-cell connections." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0000468 "multi-cellular organism" NOT 2759 "Eukaryota" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23315654 "Parfrey LW, Lahr DJ, Multicellularity arose several times in the evolution of eukaryotes (response to DOI 10.1002/bies.201100187). Bioessays (2013)" "(...) phylogenetic analyses of two key genes reveal patterns inconsistent with a single origin of multicellularity. A single origin in Amorphea would also require loss of multicellularity in each of the many unicellular lineages within this clade. Further, there are numerous other origins of multicellularity within eukaryotes, including three within Amorphea, that are not characterized by these structural and mechanistic similarities. Instead, convergent evolution resulting from similar selective pressures for forming multicellular structures with motile and differentiated cells is the most likely explanation for the observed similarities between animal and dictyostelid cell-cell connections." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0000468 "multi-cellular organism" 33208 "Metazoa" CIO:0000003 "high confidence from single evidence" ECO:0000033 "traceable author statement" PMID:22930590 "Dickinson DJ, Nelson WJ, Weis WI, An epithelial tissue in Dictyostelium challenges the traditional origin of metazoan multicellularity. Bioessays (2012)" "Phylogenetically, metazoans belong to the unikonts, a group that also includes fungi, social amoebae and a number of unicellular or colonial protists (see Figure 2) [10, 11]. Historically, it was thought that multicellularity evolved independently in animals, fungi and social amoebae, and that epithelial tissue was a unique feature of animals." bgee ANN 2015-03-10 HOM:0000007 "historical homology" UBERON:0000473 "testis" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1146/annurev.cellbio.042308.13350 "DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)" "Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved." bgee ANN 2015-01-28 HOM:0000007 "historical homology" UBERON:0000473 "testis" NOT 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:21672850 "Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007)" "This article considers what is known about gonadogenesis and reproductive strategies in extant metazoans, and searches for phylogenetic patterns that suggest what shared characteristics of these processes Urbilateria might have displayed. I conclude that the data presently available cannot suggest homologies of the somatic components of metazoan gonads, and that convergent evolution has resulted in many different morphological, and possibly molecular genetic, solutions to the various problems posed by sexual reproduction." bgee ANN 2015-01-28 HOM:0000007 "historical homology" UBERON:0000473 "testis" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:21672850 "Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007)" "(...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0000474 "female reproductive system" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0792383369 "Lombardi J, Comparative vertebrate reproduction (1998) p.43" "By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0000478 "extraembryonic structure" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1387/ijdb.092935md "Dobreva MP, Pereira PN, Deprest J, Zwijsen A, On the origin of amniotic stem cells: of mice and men. The International Journal of Developmental Biology (2010)" "A common characteristic of mammals is the development of extraembryonic supporting tissues and organs that are required for embryonic implantation, survival and development in utero." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0000482 "basal lamina of epithelium" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.57" "A basal lamina is certainly present in Bilateria and was evaluated as an autapomorphy of this taxon." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0000483 "epithelium" 2759 "Eukaryota" CIO:0000005 "low confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:22930590 "Dickinson DJ, Nelson WJ, Weis WI, An epithelial tissue in Dictyostelium challenges the traditional origin of metazoan multicellularity. Bioessays (2012)" "We hypothesize that aspects of animal multicellularity originated before the divergence of metazoans from fungi and social amoebae. Polarized epithelial tissues are a defining feature of metazoans and contribute to the diversity of animal body plans. The recent finding of a polarized epithelium in the non-metazoan social amoeba Dictyostelium discoideum demonstrates that epithelial tissue is not a unique feature of metazoans, and challenges the traditional paradigm that multicellularity evolved independently in social amoebae and metazoans...Dictyostelium and metazoan epithelia are structurally and functionally similar tissues, and importantly, they share a degree of homology at the molecular level, since the catenins are required for the epithelial organization and polarity in both systems" bgee ANN 2015-03-10 HOM:0000007 "historical homology" UBERON:0000483 "epithelium" 2759 "Eukaryota" CIO:0000005 "low confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:22930590 "Dickinson DJ, Nelson WJ, Weis WI, An epithelial tissue in Dictyostelium challenges the traditional origin of metazoan multicellularity. Bioessays (2012)" "We hypothesize that aspects of animal multicellularity originated before the divergence of metazoans from fungi and social amoebae. Polarized epithelial tissues are a defining feature of metazoans and contribute to the diversity of animal body plans. The recent finding of a polarized epithelium in the non-metazoan social amoeba Dictyostelium discoideum demonstrates that epithelial tissue is not a unique feature of metazoans, and challenges the traditional paradigm that multicellularity evolved independently in social amoebae and metazoans...Dictyostelium and metazoan epithelia are structurally and functionally similar tissues, and importantly, they share a degree of homology at the molecular level, since the catenins are required for the epithelial organization and polarity in both systems" bgee ANN 2015-03-10 HOM:0000007 "historical homology" UBERON:0000483 "epithelium" NOT 2759 "Eukaryota" CIO:0000005 "low confidence from single evidence" ECO:0000033 "traceable author statement" PMID:22057924 "Leys SP, Riesgo A, Epithelia, an evolutionary novelty of metazoans. J Exp Zool B Mol Dev Evol (2012)" "Tyler (2003) summarizes a widely held view that epithelia are the 'default state of cells in all eumetazoans,' which arose in ""the stem to the Cnidaria."" He says Porifera are not considered to have true epithelia by ""established criteria"" but admits that Porifera ""likely have developed many, if not all, of the mechanisms deemed specific to true epithelium."" This statement highlights a long-standing equivocation on the part of comparative morphologists on the question of whether Porifera can be considered epithelial, and therefore whether epithelia are a novelty of Metazoa or only Eumetazoa." bgee ANN 2015-03-10 HOM:0000007 "historical homology" UBERON:0000483 "epithelium" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000063 "compositional similarity evidence" ISBN:978-0030259821 "Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59" "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals." bgee ANN 2015-03-10 HOM:0000007 "historical homology" UBERON:0000483 "epithelium" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:22057924 "Leys SP, Riesgo A, Epithelia, an evolutionary novelty of metazoans. J Exp Zool B Mol Dev Evol (2012)" "Though in sponges as in other metazoans the epithelium has grades of specialization with varying complexity of junctions and the BM [basement membrane], the main character of a functional epithelium, the ability to seal and control the ionic composition of the internal milieu, is a property of even the simplest sponge epithelium, and therefore the first metazoans likely also had epithelia with these characteristics, which we consider a ""true"" epithelium." bgee ANN 2015-03-10 HOM:0000007 "historical homology" UBERON:0000483 "epithelium" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:21669855 "Leys SP, Nichols SA, Adams ED, Epithelia and integration in sponges. Integrative and Comparative Biology (2009)" "The presence of most, but not all, gene families known to be involved in epithelial development and function also suggests that sponge epithelia function like, and are homologous to, bilaterian epithelia." bgee ANN 2015-03-10 HOM:0000007 "historical homology" UBERON:0000913 "interstitial fluid" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0002391" bgee HOM:0000007 "historical homology" UBERON:0000922 "embryo" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.197-198 and Figure 5.38" bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0000923 "germ layer" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:22431747 "Hynes RO, The evolution of metazoan extracellular matrix. J Cell Biol (2012)" "All eumetazoa have epithelial layers showing apical-basal polarity and underlain by basement membranes. Bilateria have three germ layers (ectoderm, endoderm, and mesoderm) (...)." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0000924 "ectoderm" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:22431747 "Hynes RO, The evolution of metazoan extracellular matrix. J Cell Biol (2012)" "All eumetazoa have epithelial layers showing apical-basal polarity and underlain by basement membranes. Bilateria have three germ layers (ectoderm, endoderm, and mesoderm) (...)." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0000925 "endoderm" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:22431747 "Hynes RO, The evolution of metazoan extracellular matrix. J Cell Biol (2012)" "All eumetazoa have epithelial layers showing apical-basal polarity and underlain by basement membranes. Bilateria have three germ layers (ectoderm, endoderm, and mesoderm) (...)." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0000925|UBERON:0000926 "endoderm|mesoderm" 6072 "Eumetazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:23300467 "Roettinger E, Dahlin P, Martindale MQ, A framework for the establishment of a cnidarian gene regulatory network for ""endomesoderm"" specification: the inputs of beta-catenin/TCF signaling. PLoS Genet (2012)" "One of the best-studied bilaterian GRNs describes endomesoderm specification and predicts that both mesoderm and endoderm arose from a common GRN early in animal evolution. Compelling molecular, genomic, developmental, and evolutionary evidence supports the hypothesis that the bifunctional gastrodermis of the cnidarian-bilaterian ancestor is derived from the same evolutionary precursor of both endodermal and mesodermal germ layers in all other triploblastic bilaterian animals." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0000925|UBERON:0000926 "endoderm|mesoderm" 6072 "Eumetazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23300467 "Roettinger E, Dahlin P, Martindale MQ, A framework for the establishment of a cnidarian gene regulatory network for ""endomesoderm"" specification: the inputs of beta-catenin/TCF signaling. PLoS Genet (2012)" "One of the best-studied bilaterian GRNs describes endomesoderm specification and predicts that both mesoderm and endoderm arose from a common GRN early in animal evolution. Compelling molecular, genomic, developmental, and evolutionary evidence supports the hypothesis that the bifunctional gastrodermis of the cnidarian-bilaterian ancestor is derived from the same evolutionary precursor of both endodermal and mesodermal germ layers in all other triploblastic bilaterian animals." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0000926 "mesoderm" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:24281726 "Brunet T, Bouclet A, Ahmadi P, Mitrossilis D, Driquez B, Brunet AC, Henry L, Serman F, Bealle G, Menager C, Dumas-Bouchiat F, Givord D, Yanicostas C, Le-Roy D, Dempsey NM, Plessis A, Farge E, Evolutionary conservation of early mesoderm specification by mechanotransduction in Bilateria. Nat Commun (2013)" "Here we report a common mechanosensitive beta-catenin (beta-cat) pathway contributing critically to the induction of mesodermal cell fate during the gastrulation of zebrafish and Drosophila, two bilaterian species that diverged more than 570 million years ago. (...) here we find that mechanical induction of Y667/654 phosphorylation of beta-cat in early mesoderm determination is conserved in both species. This suggests that the mechanotransductive beta-cat pathway is more ancient than the protostome-specific or deuterostome-specific pathways previously identified in mesoderm induction, and dates back to the last common ancestor of zebrafish and Drosophila more than 570 million years ago, the period during which the mesoderm is thought to have emerged. A conserved mechanotransductive origin of the mesoderm specification in Bilateria embryos thus suggests that the mesoderm could have developed in diploblastic ancestors through the emergence of the mechanical control of the phosphorylation of the beta-cat Y667/654 site in response to gastrulation morphogenetic movements." bgee ANN 2014-01-13 HOM:0000007 "historical homology" UBERON:0000926 "mesoderm" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:22431747 "Hynes RO, The evolution of metazoan extracellular matrix. J Cell Biol (2012)" "All eumetazoa have epithelial layers showing apical-basal polarity and underlain by basement membranes. Bilateria have three germ layers (ectoderm, endoderm, and mesoderm) (...)." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0000926 "mesoderm" NOT 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:12459924 "Lartillot N, Le Gouar M, Adoutte A, Expression patterns of fork head and goosecoid homologues in the mollusc Patella vulgata supports the ancestry of the anterior mesendoderm across Bilateria. Dev Genes Evol (2002)" "Classically, in Bilateria, three germ layers are recognised: ectoderm, endoderm, mesoderm. The latter is generally defined as the tissue situated between the basement membrane of ectoderm and endoderm, and differentiates into a variety of organs such as muscles, metanephridia, blood vessels, and mesenchymes. From a comparative point of view, however, mesoderm has always been a puzzling aspect of bilaterian evolution, mainly because of the diversity of ways through which mesoderm originates during early development across, and even within, phyla. This has led many authors to argue that mesoderm would probably not be homologous across Bilateria." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0000930 "stomodeum" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1038/nature07309 "Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)" "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0000930 "stomodeum" 33511 "Deuterostomia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.32" "Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0000931 "proctodeum" 50557 "Insecta" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:9609826 "Wu LH, Lengyel JA, Role of caudal in hindgut specification and gastrulation suggests homology between Drosophila amnioproctodeal invagination and vertebrate blastopore. Development (1998)" "The fact that the same four genes are expressed at the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) and the amnioproctodeal invagination of Drosophila suggests that these two highly dynamic domains are homologous. (...) While there continues to be uncertainty in our understanding of 'protostome' and 'deuterostome' phyla, the significant conclusion of the data presented here is that there may be a homology between the blastopore of vertebrates and the amnioproctodeal (posterior) invagination of insects." bgee ANN 2018-03-19 HOM:0000007 "historical homology" UBERON:0000934 "ventral nerve cord" 88770 "Panarthropoda" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" PMID:26933218 "Yang J, Ortega-Hernandez J, Butterfield NJ, Liu Y, Boyan GS, Hou JB, Lan T, Zhang XG, Fuxianhuiid ventral nerve cord and early nervous system evolution in Panarthropoda. Proceedings of the National Academy of Sciences of the United States of America (2016)" "The VNC of C. kunmingensis comprises a homonymous series of condensed ganglia that extend throughout the body, each associated with a pair of biramous limbs. Submillimetric preservation reveals numerous segmental and intersegmental nerve roots emerging from both sides of the VNC, which correspond topologically to the peripheral nerves of extant Priapulida and Onychophora. The fuxianhuiid VNC indicates that ancestral neurological features of Ecdysozoa persisted into derived members of stem-group Euarthropoda but were later lost in crown-group representatives. These findings illuminate the VNC ground pattern in Panarthropoda and suggest the independent secondary loss of cycloneuralian-like neurological characters in Tardigrada and Euarthropoda." bgee ANN 2016-05-02 HOM:0000007 "historical homology" UBERON:0000934 "ventral nerve cord" 88770 "Panarthropoda" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:26933218 "Yang J, Ortega-Hernandez J, Butterfield NJ, Liu Y, Boyan GS, Hou JB, Lan T, Zhang XG, Fuxianhuiid ventral nerve cord and early nervous system evolution in Panarthropoda. Proceedings of the National Academy of Sciences of the United States of America (2016)" "The VNC of C. kunmingensis comprises a homonymous series of condensed ganglia that extend throughout the body, each associated with a pair of biramous limbs. Submillimetric preservation reveals numerous segmental and intersegmental nerve roots emerging from both sides of the VNC, which correspond topologically to the peripheral nerves of extant Priapulida and Onychophora. The fuxianhuiid VNC indicates that ancestral neurological features of Ecdysozoa persisted into derived members of stem-group Euarthropoda but were later lost in crown-group representatives. These findings illuminate the VNC ground pattern in Panarthropoda and suggest the independent secondary loss of cycloneuralian-like neurological characters in Tardigrada and Euarthropoda." bgee ANN 2016-05-02 HOM:0000007 "historical homology" UBERON:0000935 "anterior commissure" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1111/j.1749-6632.1969.tb20432.x "Nieuwenhuys R, A survey of the structure of the forebrain in higher bony fishes (OSTEICHTHYES). Annals of the New York Academy of Sciences (1969)" "In all vertebrates the thin structure that connects the two halves of the telencephalon shows a ridge-like thickening at the basal side known as the anterior commissure." bgee ANN 2013-06-10 HOM:0000007 "historical homology" UBERON:0000935 "anterior commissure" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1111/j.1749-6632.1969.tb20432.x "Nieuwenhuys R, A survey of the structure of the forebrain in higher bony fishes (OSTEICHTHYES). Annals of the New York Academy of Sciences (1969)" "In all vertebrates the thin structure that connects the two halves of the telencephalon shows a ridge-like thickening at the basal side known as the anterior commissure." bgee ANN 2013-06-10 HOM:0000007 "historical homology" UBERON:0000941 "cranial nerve II" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...)" bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0000941 "cranial nerve II" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" http://tolweb.org/Craniata/14826/1997.01.01 "Janvier P, Craniata. Animals with skulls. The Tree of Life Web Project (1997)" "In all craniates, the olfactory (I), optic (II), trigeminal (V), facial (VII), acoustic (VIII), glossopharyngeal (IX) and vagus (X) cranial nerves are present." bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0000945 "stomach" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:24307675 "Castro LF, Goncalves O, Mazan S, Tay BH, Venkatesh B, Wilson JM, Recurrent gene loss correlates with the evolution of stomach phenotypes in gnathostome history. Proc Biol Sci (2013)" "Here, we test the hypothesis that absence of the gastric phenotype is correlated with absence of key gastric genes. We investigate whether the extensive distribution of the agastric phenotype in vertebrate history is paralleled by differences in gene complement, namely the pepsinogens and the Atp4A/Atp4B genes. Taking advantage of full genome sequences from all major vertebrate classes, we show that the lack of a stomach phenotype (acid secretion and pepsin activity) correlates with the targeted deletion or inactivation of the gene repertoire involved in the gastric function, in all of the examined species." bgee ANN 2016-09-12 HOM:0000007 "historical homology" UBERON:0000945 "stomach" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1046/j.1525-142x.2000.00076.x "Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000)" "It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach." bgee ANN 2016-09-12 HOM:0000007 "historical homology" UBERON:0000945 "stomach" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:24307675 "Castro LF, Goncalves O, Mazan S, Tay BH, Venkatesh B, Wilson JM, Recurrent gene loss correlates with the evolution of stomach phenotypes in gnathostome history. Proc Biol Sci (2013)" "The stomach, a hallmark of gnathostome evolution, represents a unique anatomical innovation characterized by the presence of acid- and pepsin-secreting glands....Gastric glands first appeared approximately 450 Myr ago and represent a key functional innovation found exclusively in jawed vertebrates (figure 1) [10]. Invertebrate chordates such as amphioxus and ascidians lack a stomach, as do the jawless lampreys and hagfishes." bgee ANN 2016-09-12 HOM:0000007 "historical homology" UBERON:0000946 "cardial valve" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1161/CIRCRESAHA.109.201566 "Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009)" "The four-chambered vertebrate heart has aortic and pulmonic semilunar (SL) valves at the arterial pole as well as mitral and tricuspid valves separating the atria and ventricles. (...) Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0000947 "aorta" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0000948 "heart" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481" "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0000948 "heart" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481" "Although structurally similar, birds and mammal hearts arose independently from different groups of reptilian ancestor." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0000948 "heart" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481" "Although structurally similar, birds and mammal hearts arose independently from different groups of reptilian ancestor." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0000948|UBERON:0002376 "heart|cranial muscle" 7742 "Vertebrata" CIO:0000005 "low confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:25903628 "Diogo R, Kelly RG, Christiaen L, Levine M, Ziermann JM, Molnar JL, Noden DM, Tzahor E, A new heart for a new head in vertebrate cardiopharyngeal evolution. Nature (2015)" "We discuss emerging evidence for a surprising link between the evolution of head muscles and chambered hearts - both systems arise from a common pool of mesoderm progenitor cells within the cardiopharyngeal field of vertebrate embryos. We consider the origin of this field in non-vertebrate chordates and its evolution in vertebrates." bgee ANN 2016-09-26 HOM:0000007 "historical homology" UBERON:0000949 "endocrine system" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" DOI:10.1073/pnas.1015112108 "Close DA, Yun SS, McCormick SD, Reply to Thornton and Carroll: Lamprey possess a highly specific corticosteroid signaling system. PNAS (2011)" "Although unlikely, it is certainly possible that the endocrine features that we have reported in lamprey represent a derived state. We should not ignore the more likely possibility that the endocrinology of the lamprey is similar to that of basal vertebrates, as it is in many aspects of its morphology, physiology, and genetics" bgee ANN 2013-09-05 HOM:0000007 "historical homology" UBERON:0000949 "endocrine system" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1073/pnas.0812138106 "Markov GV, Tavares R, Dauphin-Villemant C, Demeneix BA, Baker ME, Laudet V, Independent elaboration of steroid hormone signaling pathways in metazoans. PNAS (2009)" "Understanding NR (Nuclear receptors) evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...)." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0000949 "endocrine system" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:21209326 "Thornton JW, Carroll SM, Lamprey endocrinology is not ancestral. PNAS (2011)" "The ancestral receptor's promiscuity is strongly corroborated by the fact that lamprey and hagfish CRs [corticosteroid receptor], like the GRs and MRs [glucocorticoid and mineralocorticoid receptors] of elasmobranchs, are all activated by both mineralocorticoids and glucocorticoids (2, 5). The experiments of Close et al. (1), interesting as they are, do not refute direct evidence of a broad-specificity ancestral CR." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0000949 "endocrine system" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:15229292 "Bertrand S, Brunet FG, Escriva H, Parmentier G, Laudet V, Robinson-Rechavi M, Evolutionary genomics of nuclear receptors: from twenty-five ancestral genes to derived endocrine systems. Mol Biol Evol (2004)" "Bilaterian animals are notably characterized by complex endocrine systems. The receptors for many steroids, retinoids, and other hormones belong to the superfamily of nuclear receptors (...) To obtain the broad picture of bilaterian nuclear hormone receptor evolution, we have characterized the complete set of nuclear receptor genes from nine animal genome sequences and analyzed it in a phylogenetic framework.(...) We show that there were approximately 25 nuclear receptor genes in Urbilateria, the ancestor of bilaterians, at which point the fundamental diversity of the subfamily was already established. Surprisingly, differential gene loss played an important role in the evolution of different nuclear receptor sets in bilaterian lineages. The nuclear receptor distribution was also shaped by periods of gene duplication, essentially in vertebrates, as well as a lineage-specific duplication burst in nematodes. Our results imply that the genes for major receptors such as steroid receptors or thyroid hormone receptors were present in Urbilateria." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0000949 "endocrine system" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:15229292 "Bertrand S, Brunet FG, Escriva H, Parmentier G, Laudet V, Robinson-Rechavi M, Evolutionary genomics of nuclear receptors: from twenty-five ancestral genes to derived endocrine systems. Mol Biol Evol (2004)" "Bilaterian animals are notably characterized by complex endocrine systems. The receptors for many steroids, retinoids, and other hormones belong to the superfamily of nuclear receptors (...) To obtain the broad picture of bilaterian nuclear hormone receptor evolution, we have characterized the complete set of nuclear receptor genes from nine animal genome sequences and analyzed it in a phylogenetic framework.(...) We show that there were approximately 25 nuclear receptor genes in Urbilateria, the ancestor of bilaterians, at which point the fundamental diversity of the subfamily was already established. Surprisingly, differential gene loss played an important role in the evolution of different nuclear receptor sets in bilaterian lineages. The nuclear receptor distribution was also shaped by periods of gene duplication, essentially in vertebrates, as well as a lineage-specific duplication burst in nematodes. Our results imply that the genes for major receptors such as steroid receptors or thyroid hormone receptors were present in Urbilateria." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0000955 "brain" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1007/978-3-642-20763-1_11 "Loesel R, Neurophylogeny : retracing early metazoan brain evolution. Evolutionary Biology - Concepts, Biodiversity, Macroevolution and Genome Evolution (2011)" "The current view of early metazoan phylogeny suggests that the bilaterian body plan arose only once during evolution. This first urbilaterian animal was most likely equipped with an anterior condensation of nerve cells - a brain - from which all brains of modern animals have diverged. Until recently, the ancestor of all bilaterian phyla was viewed as a very simple animal with an accordingly simple brain. Molecular studies, however, demonstrate a multitude of homologous genes that are expressed in similar patterns in the developing brains of vertebrates, insects, and annelids. Taken together, these findings imply that the anatomy of the urbilaterian cerebrum might have been more elaborate than previously assumed." bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0000955 "brain" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1007/978-3-642-20763-1_11 "Loesel R, Neurophylogeny : retracing early metazoan brain evolution. Evolutionary Biology - Concepts, Biodiversity, Macroevolution and Genome Evolution (2011)" "The current view of early metazoan phylogeny suggests that the bilaterian body plan arose only once during evolution. This first urbilaterian animal was most likely equipped with an anterior condensation of nerve cells - a brain - from which all brains of modern animals have diverged. Until recently, the ancestor of all bilaterian phyla was viewed as a very simple animal with an accordingly simple brain. Molecular studies, however, demonstrate a multitude of homologous genes that are expressed in similar patterns in the developing brains of vertebrates, insects, and annelids. Taken together, these findings imply that the anatomy of the urbilaterian cerebrum might have been more elaborate than previously assumed." bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0000956 "cerebral cortex" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1111/j.1749-6632.1969.tb20437.x "Kruger L, Experimental analyses of the reptilian nervous system. Annals of the New York Academy of Sciences (1969)" "Migration of neurons from the basal or striatal portions of the anterior part of the neural tube occurs to varying degrees in different vertebrate classes, but a true cerebral cortex is generally acknowledged to have made its first appearance in reptiles. The definition can be unambiguous, since 'cortex' simply implies the existence of a surface neuronal layer with an overlying 'zonal lamina' or 'molecular' layer containing dendrites and axons, which is separated from the underlying basal 'matrix' by white matter. Although reptilian cerebral cortex does indeed fulfill these conditions in certain locations, the separation from striatal structures is often indistinct, so that it may even be argued that some primitive dipnoans possess a pallium or cortex. Nevertheless, an extensive laminated layer separated by underlying white matter is well represented only in reptiles and mammals." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0000956 "cerebral cortex" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-8184899917 "Sharma VP (editor), Nature at Work - the Ongoing Saga of Evolution (2010) p.330" "How the cerebral cortex of mammals should be compared to that of reptiles and aves is one of the oldest and most intensely debated questions in the field of comparative neurobiology. In this article the neuronal classes of the cerebral cortex of reptiles, aves and mammals have been compared to show homologous structures for evolutionary interpretations." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0000959 "optic chiasma" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" DOI:10.1163/157075611X617102 "de Lussanet MHE, Osse, JWM, An ancestral axial twist explains the contralateral forebrain and the optic chiasm in vertebrates. Animal Biology (2012)" "An ancestral axial twist explains the contralateral forebrain and the optic chiasm in vertebrates. (...) we propose that a 90-deg turn on the left side evolved in a common ancestor of all vertebrates." bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0000961 "thoracic ganglion" 7776 "Gnathostomata" CIO:0000005 "low confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:22046306 "Haeming D, Simoes-Costa M, Uy B, Valencia J, Sauka-Spengler T, Bronner-Fraser M, Expression of sympathetic nervous system genes in Lamprey suggests their recruitment for specification of a new vertebrate feature. PLoS One (2011)" "In the trunk region of gnathostomes, neural crest precursors to sensory and sympathetic ganglia migrate from the dorsal neural tube, along a ventral pathway to coalesce either next to the neural tube, to form dorsal root ganglia, or further ventrally adjacent to the dorsal aorta, to form sympathetic ganglia." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0000964 "cornea" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.426-427 and Figure 12-28" "Cornea is an avascular structure that is present in the eyeballs of representative vertebrates. [curator]" bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0000965 "lens of camera-type eye" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1038/nrn2283 "Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)" "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya." bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0000966 "retina" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" DOI:10.1038/nrn2283 "Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)" "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya." bgee AUC 2013-05-22 HOM:0000007 "historical homology" UBERON:0000966 "retina" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina." bgee AUC 2013-05-22 HOM:0000007 "historical homology" UBERON:0000966 "retina" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1038/nrn2283 "Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)" "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya." bgee AUC 2013-05-22 HOM:0000007 "historical homology" UBERON:0000966 "retina" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1038/nrn2283 "Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)" "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya." bgee AUC 2013-05-22 HOM:0000007 "historical homology" UBERON:0000975 "sternum" 8292 "Amphibia" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.294" "Fishes lack a sternum. (...) A sternum is absent in the first fossil tetrapods, but it is present in modern amphibians. (...) Thus, a sternum occurs in some modern amphibians, birds, mammals and archosaurs. However, its absence in the common ancestors to these groups means that it has arisen independently several times within the field of the midventral connective tissue." bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0000975 "sternum" 8492 "Archosauria" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.294" "Fishes lack a sternum. (...) A sternum is absent in the first fossil tetrapods, but it is present in modern amphibians. (...) Thus, a sternum occurs in some modern amphibians, birds, mammals and archosaurs. However, its absence in the common ancestors to these groups means that it has arisen independently several times within the field of the midventral connective tissue." bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0000975 "sternum" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.294" "Fishes lack a sternum. (...) A sternum is absent in the first fossil tetrapods, but it is present in modern amphibians. (...) Thus, a sternum occurs in some modern amphibians, birds, mammals and archosaurs. However, its absence in the common ancestors to these groups means that it has arisen independently several times within the field of the midventral connective tissue." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0000975 "sternum" NOT 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.294" "Fishes lack a sternum. (...) A sternum is absent in the first fossil tetrapods, but it is present in modern amphibians. (...) Thus, a sternum occurs in some modern amphibians, birds, mammals and archosaurs. However, its absence in the common ancestors to these groups means that it has arisen independently several times within the field of the midventral connective tissue." bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0000975 "sternum" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.294" "Fishes lack a sternum. (...) A sternum is absent in the first fossil tetrapods, but it is present in modern amphibians. (...) Thus, a sternum occurs in some modern amphibians, birds, mammals and archosaurs. However, its absence in the common ancestors to these groups means that it has arisen independently several times within the field of the midventral connective tissue." bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0000976 "humerus" 8287 "Sarcopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000033 "traceable author statement" ISBN:978-0198540472 "Janvier P, Early vertebrates (1996) p.268" "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0000977 "pleura" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1007/s00898-999-0002-1 "Brainerd EL, New perspectives on the evolution of lung ventilation mechanisms in vertebrates. Experimental Biology Online (1999)" "In green iguanas, as in most lepidosaurs, the body cavity is not divided into separate pleural and peritoneal spaces. Instead, the lungs and viscera are contained within a single, 'pleuroperitoneal' cavity. This condition is also seen in air-breathing fishes and amphibians, indicating that an undivided body cavity is the primitive condition for amniotes." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0000978 "leg" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:17587327 "Mercader N, Early steps of paired fin development in zebrafish compared with tetrapod limb development. Development, growth and differentiation (2007)" "Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0000981 "femur" 8287 "Sarcopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000033 "traceable author statement" ISBN:978-0198540472 "Janvier P, Early vertebrates (1996) p.268" "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0000982 "skeletal joint" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.193-195" bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0000988 "pons" 8782 "Aves" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.474" "During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...)." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0000988 "pons" NOT 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.474" "During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...)." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0000988 "pons" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.474" "During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...)." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0000989 "penis" 8459 "Testudines" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1098/rsbl.2004.0161 "Kelly DA, Turtle and mammal penis designs are anatomically convergent. Proceedings of the Royal Society of London (2004)" "Penises are found in four amniote lineages: mammals (Williams-Ashman 1990), turtles (Zug 1966; McDowell 1983), squamates (Dowling & Savage 1960; Conner & Crews 1980) and archosaurs (Liebe 1914; King 1981; McCracken 2000). It has been proposed that a penis is an amniote synapomorphy (Jones 1915; Gauthier et al. 1988). However, anatomical and developmental differences among penises in these groups (Kelly 2002) mapped on independent phylogenetic hypotheses of their relationships (Rieppel & deBraga 1996; Hedges & Poling 1999; Janke et al. 2001) strongly suggest that each penis-bearing group arose independently from ancestors that had internal fertilization without intromission (such as the cloacal apposition seen in Sphenodon (Romer 1970) and passerine birds (Birkhead et al. 1993))." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0000989 "penis" 8459 "Testudines" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1098/rsbl.2004.0161 "Kelly DA, Turtle and mammal penis designs are anatomically convergent. Proceedings of the Royal Society of London (2004)" "Penises are found in four amniote lineages: mammals (Williams-Ashman 1990), turtles (Zug 1966; McDowell 1983), squamates (Dowling & Savage 1960; Conner & Crews 1980) and archosaurs (Liebe 1914; King 1981; McCracken 2000). It has been proposed that a penis is an amniote synapomorphy (Jones 1915; Gauthier et al. 1988). However, anatomical and developmental differences among penises in these groups (Kelly 2002) mapped on independent phylogenetic hypotheses of their relationships (Rieppel & deBraga 1996; Hedges & Poling 1999; Janke et al. 2001) strongly suggest that each penis-bearing group arose independently from ancestors that had internal fertilization without intromission (such as the cloacal apposition seen in Sphenodon (Romer 1970) and passerine birds (Birkhead et al. 1993))." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0000989 "penis" 8492 "Archosauria" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1098/rsbl.2004.0161 "Kelly DA, Turtle and mammal penis designs are anatomically convergent. Proceedings of the Royal Society of London (2004)" "Penises are found in four amniote lineages: mammals (Williams-Ashman 1990), turtles (Zug 1966; McDowell 1983), squamates (Dowling & Savage 1960; Conner & Crews 1980) and archosaurs (Liebe 1914; King 1981; McCracken 2000). It has been proposed that a penis is an amniote synapomorphy (Jones 1915; Gauthier et al. 1988). However, anatomical and developmental differences among penises in these groups (Kelly 2002) mapped on independent phylogenetic hypotheses of their relationships (Rieppel & deBraga 1996; Hedges & Poling 1999; Janke et al. 2001) strongly suggest that each penis-bearing group arose independently from ancestors that had internal fertilization without intromission (such as the cloacal apposition seen in Sphenodon (Romer 1970) and passerine birds (Birkhead et al. 1993))." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0000989 "penis" 8492 "Archosauria" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1098/rsbl.2004.0161 "Kelly DA, Turtle and mammal penis designs are anatomically convergent. Proceedings of the Royal Society of London (2004)" "Penises are found in four amniote lineages: mammals (Williams-Ashman 1990), turtles (Zug 1966; McDowell 1983), squamates (Dowling & Savage 1960; Conner & Crews 1980) and archosaurs (Liebe 1914; King 1981; McCracken 2000). It has been proposed that a penis is an amniote synapomorphy (Jones 1915; Gauthier et al. 1988). However, anatomical and developmental differences among penises in these groups (Kelly 2002) mapped on independent phylogenetic hypotheses of their relationships (Rieppel & deBraga 1996; Hedges & Poling 1999; Janke et al. 2001) strongly suggest that each penis-bearing group arose independently from ancestors that had internal fertilization without intromission (such as the cloacal apposition seen in Sphenodon (Romer 1970) and passerine birds (Birkhead et al. 1993))." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0000989 "penis" 8509 "Squamata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1098/rsbl.2004.0161 "Kelly DA, Turtle and mammal penis designs are anatomically convergent. Proceedings of the Royal Society of London (2004)" "Penises are found in four amniote lineages: mammals (Williams-Ashman 1990), turtles (Zug 1966; McDowell 1983), squamates (Dowling & Savage 1960; Conner & Crews 1980) and archosaurs (Liebe 1914; King 1981; McCracken 2000). It has been proposed that a penis is an amniote synapomorphy (Jones 1915; Gauthier et al. 1988). However, anatomical and developmental differences among penises in these groups (Kelly 2002) mapped on independent phylogenetic hypotheses of their relationships (Rieppel & deBraga 1996; Hedges & Poling 1999; Janke et al. 2001) strongly suggest that each penis-bearing group arose independently from ancestors that had internal fertilization without intromission (such as the cloacal apposition seen in Sphenodon (Romer 1970) and passerine birds (Birkhead et al. 1993))." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0000989 "penis" 8509 "Squamata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1098/rsbl.2004.0161 "Kelly DA, Turtle and mammal penis designs are anatomically convergent. Proceedings of the Royal Society of London (2004)" "Penises are found in four amniote lineages: mammals (Williams-Ashman 1990), turtles (Zug 1966; McDowell 1983), squamates (Dowling & Savage 1960; Conner & Crews 1980) and archosaurs (Liebe 1914; King 1981; McCracken 2000). It has been proposed that a penis is an amniote synapomorphy (Jones 1915; Gauthier et al. 1988). However, anatomical and developmental differences among penises in these groups (Kelly 2002) mapped on independent phylogenetic hypotheses of their relationships (Rieppel & deBraga 1996; Hedges & Poling 1999; Janke et al. 2001) strongly suggest that each penis-bearing group arose independently from ancestors that had internal fertilization without intromission (such as the cloacal apposition seen in Sphenodon (Romer 1970) and passerine birds (Birkhead et al. 1993))." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0000989 "penis" 32524 "Amniota" CIO:0000005 "low confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:26510679 "Sanger TJ, Gredler ML, Cohn MJ, Resurrecting embryos of the tuatara, Sphenodon punctatus, to resolve vertebrate phallus evolution. Biology letters (2015)" "a phallus may have evolved multiple times in amniotes. However, similarities in development across amniote external genitalia suggest that the phallus may have a single evolutionary origin. To resolve the evolutionary history of amniote genitalia, we performed three-dimensional reconstruction of Victorian era tuatara embryos to look for embryological evidence of external genital initiation. Despite the absence of an intromittent phallus in adult tuataras, our observations show that tuatara embryos develop genital anlagen. This illustrates that there is a conserved developmental stage of external genital development among all amniotes and suggests a single evolutionary origin of amniote external genitalia." bgee ANN 2016-05-02 HOM:0000007 "historical homology" UBERON:0000989 "penis" NOT 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000033 "traceable author statement" DOI:10.1098/rsbl.2004.0161 "Kelly DA, Turtle and mammal penis designs are anatomically convergent. Proceedings of the Royal Society of London (2004)" "Current phylogenies suggest that turtles and mammals are very distantly related (Rieppel & deBraga 1996; Hedges & Poling 1999; Janke et al. 2001) and although penile development is controlled by the genes Hoxa13 and Hoxd13 in both groups (Dolle et al. 1993; Loredo et al. 2001) their penises appear to originate from nonhomologous tissues (King 1981; Hunter 1995; Perritin et al. 2002). This difference suggests that while the developmental signal to build a penis is homologous in turtles and mammals, the resulting anatomical structures are not (Raff 1996)." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0000989 "penis" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1098/rsbl.2004.0161 "Kelly DA, Turtle and mammal penis designs are anatomically convergent. Proceedings of the Royal Society of London (2004)" "Penises are found in four amniote lineages: mammals (Williams-Ashman 1990), turtles (Zug 1966; McDowell 1983), squamates (Dowling & Savage 1960; Conner & Crews 1980) and archosaurs (Liebe 1914; King 1981; McCracken 2000). It has been proposed that a penis is an amniote synapomorphy (Jones 1915; Gauthier et al. 1988). However, anatomical and developmental differences among penises in these groups (Kelly 2002) mapped on independent phylogenetic hypotheses of their relationships (Rieppel & deBraga 1996; Hedges & Poling 1999; Janke et al. 2001) strongly suggest that each penis-bearing group arose independently from ancestors that had internal fertilization without intromission (such as the cloacal apposition seen in Sphenodon (Romer 1970) and passerine birds (Birkhead et al. 1993))." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0000989 "penis" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1098/rsbl.2004.0161 "Kelly DA, Turtle and mammal penis designs are anatomically convergent. Proceedings of the Royal Society of London (2004)" "Penises are found in four amniote lineages: mammals (Williams-Ashman 1990), turtles (Zug 1966; McDowell 1983), squamates (Dowling & Savage 1960; Conner & Crews 1980) and archosaurs (Liebe 1914; King 1981; McCracken 2000). It has been proposed that a penis is an amniote synapomorphy (Jones 1915; Gauthier et al. 1988). However, anatomical and developmental differences among penises in these groups (Kelly 2002) mapped on independent phylogenetic hypotheses of their relationships (Rieppel & deBraga 1996; Hedges & Poling 1999; Janke et al. 2001) strongly suggest that each penis-bearing group arose independently from ancestors that had internal fertilization without intromission (such as the cloacal apposition seen in Sphenodon (Romer 1970) and passerine birds (Birkhead et al. 1993))." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0000990 "reproductive system" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:21672850 "Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007)" "Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0000991 "gonad" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1146/annurev.cellbio.042308.13350 "DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)" "Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved." bgee ANN 2015-01-28 HOM:0000007 "historical homology" UBERON:0000991 "gonad" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:24108303 "Lim SL, Tsend-Ayush E, Kortschak RD, Jacob R, Ricciardelli C, Oehler MK, Gruetzner F, Conservation and Expression of PIWI-Interacting RNA Pathway Genes in Male and Female Adult Gonad of Amniotes. Biol Reprod (2013)" "We investigated the evolution and expression of piRNA pathway genes in gonads of amniote species (chicken, platypus, and mouse). Database searches confirm a high level of conservation and revealed lineage-specific gain and loss of Piwi genes in vertebrates. Expression analysis in mammals shows that orthologs of Piwi-like (Piwil) genes, Mael (Maelstrom), Mvh (mouse vasa homolog), and Tdrd1 (Tudor domain-containing protein 1) are expressed in platypus adult testis. In contrast to mouse, Piwil4 is expressed in platypus and human adult testis. We found evidence for Mael and Piwil2 expression in mouse Sertoli cells. Importantly, we show mRNA expression of Piwil2, Piwil4, and Mael in oocytes and supporting cells of human, mouse, and platypus ovary. We found no Piwil1 expression in mouse and chicken ovary. The conservation of gene expression in somatic parts of the gonad and germ cells of species that diverged over 800 million yr ago indicates an important role in adult male and female gonad." bgee ANN 2014-01-15 HOM:0000007 "historical homology" UBERON:0000991 "gonad" NOT 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:21672850 "Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007)" "This article considers what is known about gonadogenesis and reproductive strategies in extant metazoans, and searches for phylogenetic patterns that suggest what shared characteristics of these processes Urbilateria might have displayed. I conclude that the data presently available cannot suggest homologies of the somatic components of metazoan gonads, and that convergent evolution has resulted in many different morphological, and possibly molecular genetic, solutions to the various problems posed by sexual reproduction." bgee ANN 2015-01-28 HOM:0000007 "historical homology" UBERON:0000992 "ovary" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1146/annurev.cellbio.042308.13350 "DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)" "Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved." bgee ANN 2015-01-28 HOM:0000007 "historical homology" UBERON:0000992 "ovary" NOT 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:21672850 "Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007)" "This article considers what is known about gonadogenesis and reproductive strategies in extant metazoans, and searches for phylogenetic patterns that suggest what shared characteristics of these processes Urbilateria might have displayed. I conclude that the data presently available cannot suggest homologies of the somatic components of metazoan gonads, and that convergent evolution has resulted in many different morphological, and possibly molecular genetic, solutions to the various problems posed by sexual reproduction." bgee ANN 2015-01-28 HOM:0000007 "historical homology" UBERON:0000992 "ovary" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:21672850 "Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007)" "(...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0000993 "oviduct" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.687-688" "In all remaining vertebrates (i.e., coelacanths, lungfishes, amphibians, reptiles, birds, and mammals), the oviduct arises in ontogeny as a longitudinal, groovelike invagination of the coelomic epithelium on the lateral surface of the mesonephros." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0000995 "uterus" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" DOI:10.1098/rspb.2004.2848 "Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP, Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings of the Royal Society of London, Series B (2004)" "The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0000995|UBERON:0008975 "uterus|oviduct shell gland" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" http://en.wikipedia.org/wiki/Uterus "uterus on Wikipedia" "the shell gland of birds and reptiles, with which the uterus is homologous" bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0000996 "vagina" NOT 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:16252266 "Wagner GP, Lynch VJ, Molecular evolution of evolutionary novelties: the vagina and uterus of therian mammals. Journal of Experimental Zoology (2005)" "Although divisions of the oviduct in basal amniotes are frequently given names comparable to those used in mammals, the functions differ and, in the case of the vagina, are not homologous." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0000996 "vagina" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" DOI:10.1098/rspb.2004.2848 "Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP, Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings of the Royal Society of London, Series B (2004)" "The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0000998 "seminal vesicle" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.556" "(In mammalian testis) Along the way (the sperm travel), three accessory sex glands, the seminal vesicle, prostate, and bulbourethral (Cowper's) gland, respectively, add their secretions as sperm move from the testes to the urethra." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0001000 "vas deferens" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.670" "The continuation of the archinephric duct, now called the deferent duct, extends caudally to the cloaca or to the part of the mammalian urethra that is derived from the cloaca." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0001003 "skin epidermis" 33208 "Metazoa" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72" "The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell." bgee ANN 2013-07-17 HOM:0000007 "historical homology" UBERON:0001004 "respiratory system" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:15556096 "Duncker HR, Vertebrate lungs: structure, topography and mechanics. A comparative perspective of the progressive integration of respiratory system, locomotor apparatus and ontogenetic development. Respir Physiol Neurobiol (2004)" "Most aquatic lower vertebrates perform gas exchange with the surrounding water by means of a gill system in combination with skin, both to varying degrees, depending on the body size of the animal and the special seasonal and environmental conditions. Very early in their history fishes developed supplementary air-breathing organs, at least independently in two different taxonomic lines, from which the Actinopterygians with the bony fishes and the Sarcopterygians with the lung fishes survived." bgee ANN 2013-09-06 HOM:0000007 "historical homology" UBERON:0001004 "respiratory system" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007), Respiratory systems chapter 11, p.211" "The evolutionary interpretation of respiratory structures appears comparatively obvious. They are barely comparable between larger taxa, and often evolved within taxa in adaptation to either body size increase or to environmental changes. Terrestrialization, especially, requires fundamental changes of the respiratory system, as can be witnessed in molluscs, arthropods, and craniotes." bgee ANN 2013-09-06 HOM:0000007 "historical homology" UBERON:0001007 "digestive system" 33208 "Metazoa" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0721676685 "Sherwood Romer A and Parsons T, Vertebrate body (1977) p.3" "All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it." bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0001008 "renal system" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:21937596 "Scimone ML, Srivastava M, Bell GW, Reddien PW, A regulatory program for excretory system regeneration in planarians. Development (2011)" "The identity or existence of a common genetic regulatory program for excretory systems has not been established. Here, we identify a regeneration program for the planarian tubule-based filtration excretory system. Our results suggest that there existed a genetic program for nephridia formation in the common ancestor of the Bilateria with components still responsible for the formation and function of varied excretory systems in extant" bgee ANN 2015-01-28 HOM:0000007 "historical homology" UBERON:0001009 "circulatory system" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:23809110 "Monahan-Earley R, Dvorak AM, Aird WC, Evolutionary origins of the blood vascular system and endothelium. J Thromb Haemost (2013)" "The blood vascular system consists of blood-filled spaces (vessels, sinuses, hemocoels, and/or pumping organs) within the connective tissue compartment, which is continuous around and between all tissue layers in the body [6]. In invertebrates, the spaces are lined only by matrix. Vertebrates have evolved a secondary cell lining, termed endothelium. (...)The last common ancestor of vertebrates and annelids, or of vertebrates and mollusks was the ancestor of the protostome-deuterostome ancestor, which lived between 600 and 700 million years ago [59]. Although the fossil record is scarce, it is widely believed that this precursor animal was a segmented bilaterian (triploblastic coelomate) [9]. If we are to accept that the blood vascular system evolved as a means to bypass the bulkheads of a segmented animal (see next section), then the first such system likely arose during this time. Flow would have been mediated by peristaltic vessels, perhaps like those described in the annelid. Blood probably percolated through spaces in the extracellular matrix, and thus, the system was by definition closed, albeit primitive. This scenario supports homology of all blood vascular systems." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0001013 "adipose tissue" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1017/S0029665107005423 "Haugen F, Drevon CA, The interplay between nutrients and the adipose tissue. The Proceedings of the Nutrition Society (2007)" "Adipose tissue is unique to vertebrates. It is found in most mammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue." bgee ANN 2013-07-17 HOM:0000007 "historical homology" UBERON:0001013 "adipose tissue" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" DOI:10.1017/S0029665107005423 "Haugen F, Drevon CA, The interplay between nutrients and the adipose tissue. The Proceedings of the Nutrition Society (2007)" "Adipose tissue is unique to vertebrates. It is found in most mammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue." bgee ANN 2013-07-17 HOM:0000007 "historical homology" UBERON:0001015 "musculature" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:23846897 "Kuratani S, Evolution. A muscular perspective on vertebrate evolution. Science 82013)" "If the muscle patterns reported by Trinajstic et al. are found to reflect the general morphology of the placoderms, it would suggest that the developmental bases for the muscle anatomy of modern jawed vertebrates were present, in primitive form, around the time of the appearance of the functional jaw. This would stimulate even greater curiosity about the anatomy of more ancient stem gnathostomes such as ostracoderms, because the beginning of the jawed vertebrate body plan is likely to be buried in the anatomy of these animals." bgee ANN 2013-08-21 HOM:0000007 "historical homology" UBERON:0001016 "nervous system" 6072 "Eumetazoa" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117" "Nervous systems evolved in the ancestor of Eumetazoa." bgee ANN 2013-06-10 HOM:0000007 "historical homology" UBERON:0001017 "central nervous system" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:24098981 "Holland LZ, Carvalho JE, Escriva H, Laudet V, Schubert M, Shimeld SM, Yu JK, Evolution of bilaterian central nervous systems: a single origin? Evodevo (2013)" "The question of whether the ancestral bilaterian had a central nervous system (CNS) or a diffuse ectodermal nervous system has been hotly debated. Considerable evidence supports the theory that a CNS evolved just once. However, an alternative view proposes that the chordate CNS evolved from the ectodermal nerve net of a hemichordate-like ancestral deuterostome, implying independent evolution of the CNS in chordates and protostomes." bgee ANN 2013-10-18 HOM:0000007 "historical homology" UBERON:0001017 "central nervous system" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1016/j.cell.2007.02.040 "Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007)" "Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS" bgee ANN 2013-10-18 HOM:0000007 "historical homology" UBERON:0001017 "central nervous system" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/j.cell.2007.02.040 "Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007)" "Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS" bgee ANN 2013-10-18 HOM:0000007 "historical homology" UBERON:0001017 "central nervous system" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1016/j.cell.2007.02.040 "Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007)" "Comparing nervous system development in annelids to that of other bilaterians could provide valuable information about the common ancestor of all Bilateria. We find that the Platynereis neuroectoderm is subdivided into longitudinal progenitor domains by partially overlapping expression regions of nk and pax genes. These domains match corresponding domains in the vertebrate neural tube and give rise to conserved neural cell types. As in vertebrates, neural patterning genes are sensitive to Bmp signaling. Our data indicate that this mediolateral architecture was present in the last common bilaterian ancestor and thus support a common origin of nervous system centralization in Bilateria." bgee ANN 2013-10-18 HOM:0000007 "historical homology" UBERON:0001021 "nerve" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0001032 "sensory system" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" DOI:10.1073/pnas.97.9.4449 "Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)" "An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages." bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0001040 "yolk sac" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187" "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0001041 "foregut" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0521617147 "Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut." bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0001041 "foregut" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1038/nature07309 "Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)" "Even if there is still incertaincy about which type of gastrulation is ancestral for the Bilateria, expression of the foregut markers bra and gsc in the acoel C. longifissura around the mouth and in the entire antero-ventral ectoderm indicates an homology to the foregut of other bilaterians. [curator]" bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0001042 "chordate pharynx" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0495010333 "Wolfe SL, Hertz PE, Starr C, Biology: The Dynamic Science, Volume 2 w/ PAC: The Dynamic Science, Volume 2 (2007) p.707" "Chordates share several derived characteristics: a notochord; postanal tail; segmentation of body wall and tail muscles; a dorsal, hollow nerve cord; and a perforated pharynx at some stages of the life cycle." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0001042 "chordate pharynx" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.2174/1874196701104010035 "Carvalho O, Goncalves C, Comparative Physiology of the Respiratory System in the Animal Kingdom. The Open Biology Journal (2011)" "The development of the respiratory organs of vertebrates is closely related to the primitive pharynx, since the gills of aquatic vertebrates and the lungs of terrestrial vertebrates and aquatic mammals have pharyngeal embryology origin." bgee ANN 2013-06-27 HOM:0000007 "historical homology" UBERON:0001042 "chordate pharynx" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Box essay 13.1 and Box figure I, p.502-503" "(...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0001042|UBERON:0006562 "chordate pharynx|pharynx" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030259821 "Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.204" "Pharynx is cited as a common feature to Bilateria. [curator]" bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0001042|UBERON:0011288 "chordate pharynx|stomochord" 33511 "Deuterostomia" CIO:0000005 "low confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:25303744 "Satoh N, Tagawa K, Lowe CJ, Yu JK, Kawashima T, Takahashi H, Ogasawara M, Kirschner M, Hisata K, Su YH, Gerhart J, On a possible evolutionary link of the stomochord of hemichordates to pharyngeal organs of chordates. Genesis (2014)" "FoxE that is expressed in the stomochord-forming region in acorn worm juveniles is expressed in the club-shaped gland and in the endostyle of amphioxus, in the endostyle of ascidians, and in the thyroid gland of vertebrates. Based on these findings, together with the anterior endodermal location of the stomochord, we propose that the stomochord has evolutionary relatedness to chordate organs deriving from the anterior pharynx rather than to the notochord." bgee ANN 2018-03-26 HOM:0000007 "historical homology" UBERON:0001043 "esophagus" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1111/j.1096-3642.1996.tb01658.x "Mallatt J, Ventilation and the origin of jawed vertebrates: a new mouth. Zoological Journal of the Linnean Society (1996)" "The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0001043 "esophagus" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030259821 "Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.204" "Oesophagus is cited as a common feature to Bilateria. [curator]" bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0001044 "saliva-secreting gland" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471210054 "Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptationm(2005) p.211" "In air-feeding animals, the lack of water column to lubricate the food has been compensated for by the evolution of the salivary glands. These glands are present only in amniotes and are controlled by the parasympathetic system." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0001045 "midgut" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0521617147 "Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut." bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0001045 "midgut" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000060 "positional similarity evidence" ISBN:978-0030259821 "Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.530" "Like that of most bilaterians, the arthropod gut consits of three regions (the foregut, midgut, and hindgut), each having a characteristic histology, function, and developmental origin. The foregut and hindgut are derived from the ectodermal stomodeum and proctodeum, respectively, and only the midgut is endodermal." bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0001045 "midgut" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030259821 "Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.530" "Like that of most bilaterians, the arthropod gut consits of three regions (the foregut, midgut, and hindgut), each having a characteristic histology, function, and developmental origin. The foregut and hindgut are derived from the ectodermal stomodeum and proctodeum, respectively, and only the midgut is endodermal." bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0001045 "midgut" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030259821 "Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203" "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus" bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0001046 "hindgut" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0521617147 "Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut." bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0001046 "hindgut" NOT 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1038/nature07309 "Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)" "A through gut could have been present in the last common ancestor of all bilaterians and the anus could have been lost independently in both Acoela and Nemertodermatida lineages. The expression of hindgut markers at the posterior pole in C. longifissura would therefore be remnants of a posterior anal opening. The more parsimonious explanation, however, is to assume that the metazoan mouth evolved first and the anal opening arose independently through co-option of hindgut genes in posterior domains at the ectodermal-endodermal interface." bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0001046 "hindgut" NOT 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1038/nature07309 "Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)" "A through gut could have been present in the last common ancestor of all bilaterians and the anus could have been lost independently in both Acoela and Nemertodermatida lineages. The expression of hindgut markers at the posterior pole in C. longifissura would therefore be remnants of a posterior anal opening. The more parsimonious explanation, however, is to assume that the metazoan mouth evolved first and the anal opening arose independently through co-option of hindgut genes in posterior domains at the ectodermal-endodermal interface." bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0001049 "neural tube" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0001049 "neural tube" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0001049 "neural tube" 33511 "Deuterostomia" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:24177053 "Miyamoto N, Wada H, Hemichordate neurulation and the origin of the neural tube. Nat Commun (2013)" "We propose that the origin of the core genetic mechanisms for the development of the notochord and the neural tube date back to the last common deuterostome ancestor." bgee ANN 2014-01-15 HOM:0000007 "historical homology" UBERON:0001049|UBERON:0035602 "neural tube|collar nerve cord" 33511 "Deuterostomia" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:24177053 "Miyamoto N, Wada H, Hemichordate neurulation and the origin of the neural tube. Nat Commun (2013)" "To investigate the potential homology between the collar cord and neural tube, we here examine the development of the collar cord in the enteropneust Balanoglossus simodensis, focusing on the expression patterns of genes known to be critical for the early patterning and formation of the chordate neural tube. We find conserved gene expression patterns between neurulations of hemichordates and chordates. The present results suggest that the origin of genetic mechanisms to form and pattern a tubular nervous system predates the diversification of hemichordates and chordates." bgee ANN 2016-08-29 HOM:0000007 "historical homology" UBERON:0001051 "hypopharynx" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.596 and Figure 18-21" "The synapsid line of evolution culminating in mammals and the sauropsid line to reptiles and birds diverged millions of years ago, near the time of the origin of amniotes. Although mammals, too, evolved an efficient respiratory system, needed by endothermic animals, the mammalian system differs in many ways from that of birds because it evolved its complex design from the generalized amniote condition independently. The evolution of the secondary palate in mammals and their therapsid ancestors made possible a separation of food and respiratory passage." bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0001052 "rectum" NOT 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1038/nature07309 "Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)" "A through gut could have been present in the last common ancestor of all bilaterians and the anus could have been lost independently in both Acoela and Nemertodermatida lineages. The expression of hindgut markers at the posterior pole in C. longifissura would therefore be remnants of a posterior anal opening. The more parsimonious explanation, however, is to assume that the metazoan mouth evolved first and the anal opening arose independently through co-option of hindgut genes in posterior domains at the ectodermal-endodermal interface." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0001063 "flocculus" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471210054 "Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.245" "The auricle is the region of the cerebellum that receives input from the vestibular system. The output from the auricular region is especially influential on those motor neurons that control the muscles that moves the eyes. In tetrapods, the auricle is known as the flocculus." bgee ANN 2017-10-09 HOM:0000007 "historical homology" UBERON:0001072 "posterior vena cava" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455" "Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0001074 "pericardial cavity" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0471090588 "Hildebrand M, Analysis of vertebrate structure (1983) p.205-206" "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present." bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0001075 "bony vertebral centrum" 7776 "Gnathostomata" CIO:0000005 "low confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:25968309 "Fleming A, Kishida MG, Kimmel CB, Keynes RJ, Building the backbone: the development and evolution of vertebral patterning. Development (2015)" "Particular controversy surrounds whether vertebral component structures are homologous across vertebrates, how somite and vertebral patterning are connected, and the developmental origin of vertebral bone-mineralizing cells. Here, we assemble evidence from ichthyologists, palaeontologists and developmental biologists to consider these issues. Vertebral arch elements were present in early stem vertebrates, whereas centra arose later. We argue that centra are homologous among jawed vertebrates, and review evidence in teleosts that the notochord plays an instructive role in segmental patterning, alongside the somites, and contributes to mineralization. By clarifying the evolutionary relationship between centra and arches, and their varying modes of skeletal mineralization, we can better appreciate the detailed mechanisms that regulate and diversify vertebral patterning... centra might have been more easily lost during evolution than re-invented multiple times, and we suggest that multiple loss events is a more parsimonious interpretation of the available phylogenetic evidence." bgee ANN 2017-02-14 HOM:0000007 "historical homology" UBERON:0001075 "bony vertebral centrum" NOT 7776 "Gnathostomata" CIO:0000005 "low confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:25968309 "Fleming A, Kishida MG, Kimmel CB, Keynes RJ, Building the backbone: the development and evolution of vertebral patterning. Development (2015)" "Particular controversy surrounds whether vertebral component structures are homologous across vertebrates, how somite and vertebral patterning are connected, and the developmental origin of vertebral bone-mineralizing cells. Here, we assemble evidence from ichthyologists, palaeontologists and developmental biologists to consider these issues. Vertebral arch elements were present in early stem vertebrates, whereas centra arose later. We argue that centra are homologous among jawed vertebrates, and review evidence in teleosts that the notochord plays an instructive role in segmental patterning, alongside the somites, and contributes to mineralization. By clarifying the evolutionary relationship between centra and arches, and their varying modes of skeletal mineralization, we can better appreciate the detailed mechanisms that regulate and diversify vertebral patterning... centra might have been more easily lost during evolution than re-invented multiple times, and we suggest that multiple loss events is a more parsimonious interpretation of the available phylogenetic evidence." bgee ANN 2017-12-18 HOM:0000007 "historical homology" UBERON:0001075 "bony vertebral centrum" 7778 "Elasmobranchii" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:28144984 "Criswell KE, Coates MI, Gillis JA, Embryonic development of the axial column in the little skate, Leucoraja erinacea. J Morphol (2017)" "The vertebrae of elasmobranchs are distinct among vertebrates, both in terms of their composition (i.e., with centra consisting of up to three tissues layers-an inner cartilage layer, a calcified areolar ring, and an outer layer of hyaline cartilage), and their mode of development (i.e., the subdivision of arch and outer centrum cartilage from an initially continuous layer of hyaline cartilage). Given the evident variation in patterns of vertebral construction, broad taxon sampling, and comparative developmental analyses are required to understand the diversity of mechanisms at work in the developing axial skeleton of vertebrates." bgee ANN 2017-02-14 HOM:0000007 "historical homology" UBERON:0001075 "bony vertebral centrum" 7778 "Elasmobranchii" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:28144984 "Criswell KE, Coates MI, Gillis JA, Embryonic development of the axial column in the little skate, Leucoraja erinacea. J Morphol (2017)" "The vertebrae of elasmobranchs are distinct among vertebrates, both in terms of their composition (i.e., with centra consisting of up to three tissues layers-an inner cartilage layer, a calcified areolar ring, and an outer layer of hyaline cartilage), and their mode of development (i.e., the subdivision of arch and outer centrum cartilage from an initially continuous layer of hyaline cartilage). Given the evident variation in patterns of vertebral construction, broad taxon sampling, and comparative developmental analyses are required to understand the diversity of mechanisms at work in the developing axial skeleton of vertebrates." bgee ANN 2017-02-14 HOM:0000007 "historical homology" UBERON:0001075 "bony vertebral centrum" 7898 "Actinopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:11746457 "Arratia G, Schultze HP, Casciotta J, Vertebral column and associated elements in dipnoans and comparison with other fishes: development and homology. J Morphol (2001)" "A vertebral column formed by a persistent notochord without vertebral centra is the primitive pattern for all vertebrates. The formation of centra, which is not homologous among vertebrate groups, is acquired independently in some lineages of placoderms, most advanced actinopterygians, and some dipnoans and rhipidistians...as we have shown above, the vertebral column in fishes develops differently in different fish groups. our results support once more (see also Arratia and Schultze, 1990, 1991) the idea that fishes may reach similar terminal stages by using different ontogenetic processes and/or sequences. It is a serious error to base conclusions on the assumption that teleostomes have the same development of structures that have been previously assumed to be homologous." bgee ANN 2017-02-14 HOM:0000007 "historical homology" UBERON:0001075 "bony vertebral centrum" 8287 "Sarcopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:11746457 "Arratia G, Schultze HP, Casciotta J, Vertebral column and associated elements in dipnoans and comparison with other fishes: development and homology. J Morphol (2001)" "A vertebral column formed by a persistent notochord without vertebral centra is the primitive pattern for all vertebrates. The formation of centra, which is not homologous among vertebrate groups, is acquired independently in some lineages of placoderms, most advanced actinopterygians, and some dipnoans and rhipidistians...as we have shown above, the vertebral column in fishes develops differently in different fish groups. our results support once more (see also Arratia and Schultze, 1990, 1991) the idea that fishes may reach similar terminal stages by using different ontogenetic processes and/or sequences. It is a serious error to base conclusions on the assumption that teleostomes have the same development of structures that have been previously assumed to be homologous." bgee ANN 2017-02-14 HOM:0000007 "historical homology" UBERON:0001075 "bony vertebral centrum" NOT 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:11746457 "Arratia G, Schultze HP, Casciotta J, Vertebral column and associated elements in dipnoans and comparison with other fishes: development and homology. J Morphol (2001)" "A vertebral column formed by a persistent notochord without vertebral centra is the primitive pattern for all vertebrates. The formation of centra, which is not homologous among vertebrate groups, is acquired independently in some lineages of placoderms, most advanced actinopterygians, and some dipnoans and rhipidistians...as we have shown above, the vertebral column in fishes develops differently in different fish groups. our results support once more (see also Arratia and Schultze, 1990, 1991) the idea that fishes may reach similar terminal stages by using different ontogenetic processes and/or sequences. It is a serious error to base conclusions on the assumption that teleostomes have the same development of structures that have been previously assumed to be homologous." bgee ANN 2017-02-14 HOM:0000007 "historical homology" UBERON:0001081 "endocardium of ventricle" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481" "While bird and mammal 4-chambered hearts arose independently from different groups of reptilian ancestor, the vertebrate chambered heart is commonly considered arising from fishes and then defined as an historical homology relationship. However uncertainty remains on the origin of the heart substructures and tissues. [curator]" bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0001082 "epicardium of ventricle" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002082, negated: false, taxon ID: 7742 - entity: UBERON:0002348, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001083 "myocardium of ventricle" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481" "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0001084 "skin of head" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0000033, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001091 "calcareous tooth" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19266065 "Koussoulakou DS, Margaritis LH, Koussoulakos SL, A curriculum vitae of teeth: evolution, generation, regeneration. International Journal of Biological Sciences (2009)" "The ancestor of recent vertebrate teeth was a tooth-like structure on the outer body surface of jawless fishes.(...) Teeth are highly mineralized appendages found in the entrance of the alimentary canal of both invertebrates and vertebrates." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0001091 "calcareous tooth" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:24132236 "Murdock DJ, Dong XP, Repetski JE, Marone F, Stampanoni M, Donoghue PC, The origin of conodonts and of vertebrate mineralized skeletons. Nature (2013)" "Thus, the precise ontogenetic, structural and topological similarities between conodont elements and vertebrate odontodes appear to be a remarkable instance of convergence. The last common ancestor of conodonts and jawed vertebrates probably lacked mineralized skeletal tissues. The hypothesis that teeth evolved before jaws and the inside-out hypothesis of dental evolution must be rejected; teeth seem to have evolved through the extension of odontogenic competence from the external dermis to internal epithelium soon after the origin of jaws." bgee ANN 2014-01-15 HOM:0000007 "historical homology" UBERON:0001100 "pectoralis minor" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.394 Table 10.2" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0001103 "diaphragm" NOT 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" DOI:10.1016/j.resp.2006.06.003 "Brainerd EL, Owerkowicz T, Functional morphology and evolution of aspiration breathing in tetrapods. Respiratory physiology and neurobiology (2006)" "Crocodylians, mammals and turtles have all evolved accessory respiratory muscles that reduce or eliminate their reliance on costal aspiration. These are all sometimes called diaphragm muscles, presumably by analogy with the mammalian diaphragm muscle, but they are not homologous structures." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0001103 "diaphragm" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0471384618 "Colbert EH, Evolution of the vertebrates: a history of the backboned animals through time (2001) p.278" "The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...)." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0001105 "clavicle bone" 32440 "Chondrostei" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1080/02724634.1984.10012024 "Olsen PE, The skull and pectoral girdle of the parasemionotid fish Watsonulus eugnathoides from the Early Triassic Sakamena Group of Madagascar, with comments on the relationships of the holostean fishes. Journal of Vertebrate Paleontology (1984)" "Watsonulus eugnathoides occupies a critical position within the Neopterygii of Patterson (1 973) because it shares two primitive characters with chondrosteans that are derived in other neopterygians. These are 1) unreduced clavicles, and 2) a preoperculum with a broad dorsal limb. ""Journal of Vertebrate Paleontology (1984)""" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0001105 "clavicle bone" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.330-333 and Figure 9.18" "In early tetrapods, the connecting skull bone, the posttemporal, and adjoining shoulder bones, supracleithrum and postcleithrum (=anocleithrum), are absent, leaving a dermal shoulder girdle composed of the remaining ventral elements: the paired cleithrum and clavicle, and an unpaired midventral interclavicle that joins both halves of the girdle across the midline. (...) Several dermal elements of the shoulder persist in early synapsids. The clavicle and interclavicle are present in therapsids and monotremes, but in marsupials and placentals, the interclavicle is absent, the clavicle often is reduced in size, and the scapula becomes the predominant shoulder element." bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0001111 "intercostal muscle" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0262112789 "Kent RD, The MIT Encyclopedia of Communication Disorders (2003) p.56" "Inspiration by active expansion of the thorax evolved later, in the ancestor of reptiles, birds, and mammals. This was powered originally by the intercostal muscles (as in lizards or crocodilians) and later (in mammals only) by a muscular diaphragm." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0001112 "latissimus dorsi muscle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.394 Table 10.2" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0001116 "quadrate lobe of liver" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1053/ax.2000.7133 "Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000)" "(...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0001117 "caudate lobe of liver" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1053/ax.2000.7133 "Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000)" "(...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0001118 "lobe of thyroid gland" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1210/er.2003-0028 "De Felice M, Di Lauro R, Thyroid development and its disorders: genetics and molecular mechanisms. Endocrine Reviews (2004)" "In mammals and in some reptiles, the thyroid is composed of two lobes connected by an isthmus; in birds and amphibians, the thyroid consists of two isolated lobes. (...) Despite these morphological differences, the ontogeny of the thyroid follows the same pattern in all vertebrates (...)." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0001119 "right lobe of thyroid gland" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001118, negated: false, taxon ID: 32524 - entity: UBERON:0002046, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001120 "left lobe of thyroid gland" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001118, negated: false, taxon ID: 32524 - entity: UBERON:0002046, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001125 "serratus ventralis" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.394 Table 10.2" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0001128 "sternocleidomastoid" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.345" "The sternomastoid and the three parts of the trapezius are branchiomeric muscles that have secondarily acquired an attachment to the pectoral girdle. They evolved from the fish cucullaris." bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0001129 "subscapularis muscle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.394 Table 10.2" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0001130 "vertebral column" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.53" "Vertebrata is characterized by three synapomorphies. First, vertebrates have a backbone composed of vertebrae (...)." bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0001130 "vertebral column" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:23334417 "Pierce SE, Ahlberg PE, Hutchinson JR, Molnar JL, Sanchez S, Tafforeau P, Clack JA, Vertebral architecture in the earliest stem tetrapods. Nature (2013)" "The construction of the vertebral column has been used as a key anatomical character in defining and diagnosing early tetrapod groups. (...) Comparison of Ichthyostega with two other stem tetrapods, Acanthostega and Pederpes, shows that reverse rhachitomous vertebrae may be the ancestral condition for limbed vertebrates. This study fundamentally revises our current understanding of vertebral column evolution in the earliest tetrapods and raises questions about the presumed vertebral architecture of tetrapodomorph fish and later, more crownward, tetrapods." bgee ANN 2013-08-26 HOM:0000007 "historical homology" UBERON:0001132 "parathyroid gland" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1111/j.1469-7580.2005.00472.x "Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)" "The evolution of the tetrapods, and the shift from an aquatic to a terrestrial environment, was believed to have required new controls for regulating calcium homeostasis, and thus the evolution of parathyroid glands (...) both the tetrapod parathyroid and the gills of fish contribute to the regulation of extracellular calcium levels. It is therefore reasonable to suggest that the parathyroid gland evolved as a result of the transformation of the gills into the parathyroid glands of tetrapods and the transition from an aquatic to a terrestrial environment. This interpretation would also explain the positioning of the parathyroid gland within the pharynx in the tetrapod body. Were the parathyroid gland to have emerged de novo with the evolution of the tetrapods it could, as an endocrine organ, have been placed anywhere in the body and still exert its effect." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0001134 "skeletal muscle tissue" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:10368962 "Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999)" "We reconstructed phylogenetic trees of six protein genes that are expressed in muscle tissues and, using a newly developed program, inferred the phylogeny of muscle tissues by superimposition of five of those gene trees. (...)This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA)." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0001134 "skeletal muscle tissue" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:22763458 "Steinmetz PR, Kraus JE, Larroux C, Hammel JU, Amon-Hassenzahl A, Houliston E, Woerheide G, Nickel M, Degnan BM, Technau U, Independent evolution of striated muscles in cnidarians and bilaterians. Nature (2012)" "Striated muscles are present in bilaterian animals (for example, vertebrates, insects and annelids) and some non-bilaterian eumetazoans (that is, cnidarians and ctenophores). The considerable ultrastructural similarity of striated muscles between these animal groups is thought to reflect a common evolutionary origin. Here we show that a muscle protein core set, including a type II myosin heavy chain (MyHC) motor protein characteristic of striated muscles in vertebrates, was already present in unicellular organisms before the origin of multicellular animals." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0001135 "smooth muscle tissue" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1002/jez.b.21416 "Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011)" "The three genes characterized in this study interact in the striated muscles of vertebrates and invertebrates, where troponin I and tropomyosin are key regulators of the contraction of the sarcomere. S. roscoffensis and all other acoels so far described have only smooth muscles, but the molecular architecture of these is the same as that of striated fibers of other bilaterians. Given the proposed basal position of acoels within the Bilateria, we suggest that sarcomeric muscles arose from a smooth muscle type, which had the molecular repertoire of striated musculature already in place." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0001140 "renal vein" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0002113, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001143 "hepatic vein" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0002107, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001144 "testicular vein" 7711 "Chordata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000473, negated: false, taxon ID: 33213 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0001144 "testicular vein" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000473, negated: false, taxon ID: 7742 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0001145 "ovarian vein" 7711 "Chordata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000992, negated: false, taxon ID: 33213 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0001145 "ovarian vein" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000992, negated: false, taxon ID: 7742 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0001146 "suprarenal vein" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0002369, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0001152 "cystic duct" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.526-527 and Figure 13.38" "Cystic duct appears during the embryonic formation of the liver in a mammalian embryo. [curator]" bgee ANN 2013-09-06 HOM:0000007 "historical homology" UBERON:0001153 "caecum" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0521617147 "Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0001154 "vermiform appendix" 38609 "Diprotodontia" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1111/j.1420-9101.2009.01809.x "Smith HF, Fisher RE, Everett ML, Thomas AD, Randal Bollinger R, Parker W, Comparative anatomy and phylogenetic distribution of the mammalian cecal appendix. Journal of Evolutionary Biology (2009)" "A comparative anatomical approach reveals three apparent morphotypes of the cecal appendix, as well as appendix-like structures in some species that lack a true cecal appendix. Cladistic analyses indicate that the appendix has evolved independently at least twice (at least once in diprotodont marsupials and at least once in Euarchontoglires), shows a highly significant (P < 0.0001) phylogenetic signal in its distribution, and has been maintained in mammalian evolution for 80 million years or longer." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0001154 "vermiform appendix" 38609 "Diprotodontia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1111/j.1420-9101.2009.01809.x "Smith HF, Fisher RE, Everett ML, Thomas AD, Randal Bollinger R, Parker W, Comparative anatomy and phylogenetic distribution of the mammalian cecal appendix. Journal of Evolutionary Biology (2009)" "A comparative anatomical approach reveals three apparent morphotypes of the cecal appendix, as well as appendix-like structures in some species that lack a true cecal appendix. Cladistic analyses indicate that the appendix has evolved independently at least twice (at least once in diprotodont marsupials and at least once in Euarchontoglires), shows a highly significant (P < 0.0001) phylogenetic signal in its distribution, and has been maintained in mammalian evolution for 80 million years or longer." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0001154 "vermiform appendix" NOT 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1016/j.crpv.2012.12.001 "Smith HF, Parker W, Kotze SH, Laurin M, Multiple independent appearances of the cecal appendix in mammalian evolution and an investigation of related ecological and anatomical factors. C R Palevol (2013)" "Substantial evidence supports the view that the cecal appendix is an immune structure primarily functioning as a safe-house for beneficial bacteria, and comes from a range of disciplines, including medicine, epidemiology, immunology, and microbiology (Laurin et al., 2011). Corroborating this view that the appendix has an adaptive function is the finding in this study that the appendix has evolved a minimum of 32 times in mammals." bgee ANN 2017-10-24 HOM:0000007 "historical homology" UBERON:0001154 "vermiform appendix" NOT 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1016/j.crpv.2012.12.001 "Smith HF, Parker W, Kotze SH, Laurin M, Multiple independent appearances of the cecal appendix in mammalian evolution and an investigation of related ecological and anatomical factors. C R Palevol (2013)" "Substantial evidence supports the view that the cecal appendix is an immune structure primarily functioning as a safe-house for beneficial bacteria, and comes from a range of disciplines, including medicine, epidemiology, immunology, and microbiology (Laurin et al., 2011). Corroborating this view that the appendix has an adaptive function is the finding in this study that the appendix has evolved a minimum of 32 times in mammals." bgee ANN 2017-10-24 HOM:0000007 "historical homology" UBERON:0001154 "vermiform appendix" 314146 "Euarchontoglires" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1111/j.1420-9101.2009.01809.x "Smith HF, Fisher RE, Everett ML, Thomas AD, Randal Bollinger R, Parker W, Comparative anatomy and phylogenetic distribution of the mammalian cecal appendix. Journal of Evolutionary Biology (2009)" "A comparative anatomical approach reveals three apparent morphotypes of the cecal appendix, as well as appendix-like structures in some species that lack a true cecal appendix. Cladistic analyses indicate that the appendix has evolved independently at least twice (at least once in diprotodont marsupials and at least once in Euarchontoglires), shows a highly significant (P < 0.0001) phylogenetic signal in its distribution, and has been maintained in mammalian evolution for 80 million years or longer." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0001154 "vermiform appendix" 314146 "Euarchontoglires" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1111/j.1420-9101.2009.01809.x "Smith HF, Fisher RE, Everett ML, Thomas AD, Randal Bollinger R, Parker W, Comparative anatomy and phylogenetic distribution of the mammalian cecal appendix. Journal of Evolutionary Biology (2009)" "A comparative anatomical approach reveals three apparent morphotypes of the cecal appendix, as well as appendix-like structures in some species that lack a true cecal appendix. Cladistic analyses indicate that the appendix has evolved independently at least twice (at least once in diprotodont marsupials and at least once in Euarchontoglires), shows a highly significant (P < 0.0001) phylogenetic signal in its distribution, and has been maintained in mammalian evolution for 80 million years or longer." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0001155 "colon" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0521617147 "Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0001160 "fundus of stomach" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0521617147 "Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0001166 "pylorus" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0521617147 "Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0001174 "common bile duct" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.569-571 and Figures 17-9 and 17-10" "In the adults of all vertebrates, the liver is the largest organ in the body cavity, and it occupies most of the space in the abdomen. (...) Minute bile canaliculi lie between hepatic cells and drain bile, the secretion of the hepatic cells, into hepatic ducts that leave the liver and unite to form the common bile duct." bgee ANN 2013-09-06 HOM:0000007 "historical homology" UBERON:0001175 "common hepatic duct" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.569-571 and Figures 17-9 and 17-10" "In the adults of all vertebrates, the liver is the largest organ in the body cavity, and it occupies most of the space in the abdomen. (...) Minute bile canaliculi lie between hepatic cells and drain bile, the secretion of the hepatic cells, into hepatic ducts that leave the liver and unite to form the common bile duct." bgee ANN 2013-09-06 HOM:0000007 "historical homology" UBERON:0001178 "visceral peritoneum" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1007/s00898-999-0002-1 "Brainerd EL, New perspectives on the evolution of lung ventilation mechanisms in vertebrates. Experimental Biology Online (1999)" "In green iguanas, as in most lepidosaurs, the body cavity is not divided into separate pleural and peritoneal spaces. Instead, the lungs and viscera are contained within a single, 'pleuroperitoneal' cavity. This condition is also seen in air-breathing fishes and amphibians, indicating that an undivided body cavity is the primitive condition for amniotes." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0001179 "peritoneal cavity" 8457 "Sauropsida" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.162-163" "In most living diapsids (some lizards, snakes, crocodiles, and birds) as well as all mammals, additional folds of coelomic epithelium separate de paired pleural recesses from the rest of the pleuroperitoneal cavity. The coelom of these animals thus consists of four compartments: the pericardial cavity, two pleural cavities, and the peritoneal cavity. [...] In reptiles and birds, the folds separating the pleural cavities from the peritoneal cavity form the oblique septum. In mammals, the separation between the two pleural cavities and the peritoneal cavity develops by the pleuroperitoneal membranes, which push in from the dorsolateral body wall, and by other folds that extend laterally from the mesenteries and medially from the body wall to meet the pleuroperitoneal membranes." bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0001179 "peritoneal cavity" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0471090588 "Hildebrand M, Analysis of vertebrate structure (1983) p.205-206" "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes." bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0001184 "renal artery" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0002113, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001187 "testicular artery" 7711 "Chordata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000473, negated: false, taxon ID: 33213 - entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0001187 "testicular artery" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000473, negated: false, taxon ID: 7742 - entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0001190 "ovarian artery" 7711 "Chordata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000992, negated: false, taxon ID: 33213 - entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0001190 "ovarian artery" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000992, negated: false, taxon ID: 7742 - entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0001193 "hepatic artery" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0002107, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001194 "splenic artery" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0002106, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0001202 "pyloric sphincter" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1046/j.1525-142x.2000.00076.x "Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000)" "(...) the adult Xenopus stomach exhibits both glandular and aglandular regions and a distinct pyloric sphincter similar to that of the amniotic vertebrates (...)." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0001216 "jejunal vein" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0002115, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0001217 "ileal vein" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0002116, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001221 "transversus abdominis muscle" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:23765280 "Trinajstic K, Sanchez S, Dupret V, Tafforeau P, Long J, Young G, Senden T, Boisvert C, Power N, Ahlberg PE, Fossil musculature of the most primitive jawed vertebrates. Science (2013)" "The placoderm data suggest (...) that transverse abdominal muscles are an innovation of gnathostomes rather than of tetrapods." bgee ANN 2013-08-21 HOM:0000007 "historical homology" UBERON:0001221 "transversus abdominis muscle" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1016/j.resp.2006.06.003 "Brainerd EL, Owerkowicz T, Functional morphology and evolution of aspiration breathing in tetrapods. Respiratory physiology and neurobiology (2006)" "Since the presence of the TA muscle itself is a tetrapod character, it being absent in ray-finned fishes and lungfishes, these findings are best explained by the expiration pump being a shared- derived character of Tetrapoda." bgee ANN 2013-08-21 HOM:0000007 "historical homology" UBERON:0001222 "right ureter" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000056, negated: false, taxon ID: 32524 - entity: UBERON:0000468, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0001223 "left ureter" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000056, negated: false, taxon ID: 32524 - entity: UBERON:0000468, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0001229 "renal corpuscle" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:15376276 "Mobjerg N, Jespersen A, Wilkinson M, Morphology of the kidney in the West African caecilian, Geotrypetes seraphini (Amphibia, Gymnophiona, Caeciliidae). J Morphol (2004)" "Evolutionary events that may have led to the development of the Malpighian corpuscle of the vertebrate nephron: (...)C: The coelomic chamber becomes the capsule of Bowman, which surrounds the glomerulus, and a Malpighian corpuscle is formed. The renal tubule connects to the coelom via ciliated peritoneal funnels. This is the situation in the mesonephros of adult salamanders and caecilians." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0001232 "collecting duct of renal tubule" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:21491542 "Georgas KM, Chiu HS, Lesieur E, Rumballe BA, Little MH, Expression of metanephric nephron-patterning genes in differentiating mesonephric tubules. Developmental dynamics : an official publication of the American Association of Anatomists (2011)" "The metanephros is the functional organ in adult amniotes while the mesonephros degenerates. However, parallel tubulogenetic events are thought to exist between mesonephros and metanephros. Mesonephric tubules are retained in males and differentiate into efferent ducts of the male reproductive tract. By examining the murine mesonephric expression of markers of distinct stages and regions of metanephric nephrons during tubule formation and patterning, we provide further evidence to support this common morphogenetic mechanism." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0001232 "collecting duct of renal tubule" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:21491542 "Georgas KM, Chiu HS, Lesieur E, Rumballe BA, Little MH, Expression of metanephric nephron-patterning genes in differentiating mesonephric tubules. Developmental dynamics : an official publication of the American Association of Anatomists (2011)" "The metanephros is the functional organ in adult amniotes while the mesonephros degenerates. However, parallel tubulogenetic events are thought to exist between mesonephros and metanephros. Mesonephric tubules are retained in males and differentiate into efferent ducts of the male reproductive tract. By examining the murine mesonephric expression of markers of distinct stages and regions of metanephric nephrons during tubule formation and patterning, we provide further evidence to support this common morphogenetic mechanism." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0001235 "adrenal cortex" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9" "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0001236 "adrenal medulla" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9" "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0001245 "anus" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:25788603 "Janssen R, Joergensen M, Lagebro L, Budd GE, Fate and nature of the onychophoran mouth-anus furrow and its contribution to the blastopore. Proc Biol Sci (2015)" "Based on expression patterns of forkhead (fkh), caudal (cad), brachyury (bra) and wingless (wg/Wnt1), we show that this groove [clear ventral groove during gastrulation of onychophorans] does not correspond to the blastopore, even though both the mouth and anus later develop from it. Rather, the posterior pit appears to be the blastopore; the posterior of the groove later fuses with it to form the definitive anus. Onychophoran development therefore represents a case of 'concealed' deuterostomy. The new data from the onychophorans thus remove one of the key pieces of evidence for the amphistomy theory. Rather, in line with other recent results, it suggests that ancestral bilaterian development was deuterostomic." bgee ANN 2015-03-11 HOM:0000007 "historical homology" UBERON:0001245 "anus" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000071 "morphological similarity evidence" http://dpc.uba.uva.nl/ctz/vol73/nr01/art01 "Jenner RA, Towards a phylogeny of the Metazoa: evaluating alternative phylogenetic positions of Platyhelminthes, Nemertea, and Gnathostomulida, with a critical reappraisal of cladistic characters. Contributions to Zoology (2004)" "All comprehensive morphological cladistic analyses support (although not unambiguously in all studies) the evolution of a unidirectional digestive tract with an anus as an autapomorphy for Bilateria (Zrzavy et al., 1998; Giribet et al., 2000; Meglitsch & Schram, 1991; Nielsen, 2001; Peterson & Eernisse, 2001). Consequently, the absence of an anus in taxa such as the platyhelminths (misscored for NI32), pogonophorans, articulate brachiopods, and acanthocephalans must be considered secondary. In contrast, other studies suggested the independent evolution of an anus in the protostomes and deuterostomes (Brusca & Brusca, 1990; Rouse & Fauchald, 1995); Ax, 1989, 1995; see further discussion under Nemertea). However, these studies only considered a restricted set of metazoan phyla, and consequently, their results do not constitute real tests of the homology of anuses throughout the Metazoa." bgee ANN 2015-03-11 HOM:0000007 "historical homology" UBERON:0001245 "anus" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1038/nature07309 "Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)" "The existence of a posterior domain of coordinated expression of 'hindgut' genes in the acoel C. longifissura, however, can be explained in two different ways. A through gut could have been present in the last common ancestor of all bilaterians and the anus could have been lost independently in both Acoela and Nemertodermatida lineages. The expression of hindgut markers at the posterior pole in C. longifissura would therefore be remnants of a posterior anal opening. The more parsimonious explanation, however, is to assume that the metazoan mouth evolved first and the anal opening arose independently through co-option of hindgut genes in posterior domains at the ectodermal-endodermal interface. The region of the posterior expression of bra in the acoel juvenile corresponds to the area at which the gonoduct will form in the mature adult, which also expresses bra (Fig. 2t, u). It is of interest that this position has previously been proposed to represent a common cloacal opening in basal metazoans28." bgee ANN 2015-03-11 HOM:0000007 "historical homology" UBERON:0001245 "anus" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" http://dpc.uba.uva.nl/ctz/vol73/nr01/art01 "Jenner RA, Towards a phylogeny of the Metazoa: evaluating alternative phylogenetic positions of Platyhelminthes, Nemertea, and Gnathostomulida, with a critical reappraisal of cladistic characters. Contributions to Zoology (2004)" "All comprehensive morphological cladistic analyses support (although not unambiguously in all studies) the evolution of a unidirectional digestive tract with an anus as an autapomorphy for Bilateria (Zrzavy et al., 1998; Giribet et al., 2000; Meglitsch & Schram, 1991; Nielsen, 2001; Peterson & Eernisse, 2001). Consequently, the absence of an anus in taxa such as the platyhelminths (misscored for NI32), pogonophorans, articulate brachiopods, and acanthocephalans must be considered secondary. In contrast, other studies suggested the independent evolution of an anus in the protostomes and deuterostomes (Brusca & Brusca, 1990; Rouse & Fauchald, 1995); Ax, 1989, 1995; see further discussion under Nemertea). However, these studies only considered a restricted set of metazoan phyla, and consequently, their results do not constitute real tests of the homology of anuses throughout the Metazoa." bgee ANN 2015-03-11 HOM:0000007 "historical homology" UBERON:0001245 "anus" NOT 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000033 "traceable author statement" http://dpc.uba.uva.nl/ctz/vol73/nr01/art01 "Jenner RA, Towards a phylogeny of the Metazoa: evaluating alternative phylogenetic positions of Platyhelminthes, Nemertea, and Gnathostomulida, with a critical reappraisal of cladistic characters. Contributions to Zoology (2004)" "All comprehensive morphological cladistic analyses support (although not unambiguously in all studies) the evolution of a unidirectional digestive tract with an anus as an autapomorphy for Bilateria (Zrzavy et al., 1998; Giribet et al., 2000; Meglitsch & Schram, 1991; Nielsen, 2001; Peterson & Eernisse, 2001). Consequently, the absence of an anus in taxa such as the platyhelminths (misscored for NI32), pogonophorans, articulate brachiopods, and acanthocephalans must be considered secondary. In contrast, other studies suggested the independent evolution of an anus in the protostomes and deuterostomes (Brusca & Brusca, 1990; Rouse & Fauchald, 1995); Ax, 1989, 1995; see further discussion under Nemertea). However, these studies only considered a restricted set of metazoan phyla, and consequently, their results do not constitute real tests of the homology of anuses throughout the Metazoa." bgee ANN 2015-03-11 HOM:0000007 "historical homology" UBERON:0001245 "anus" NOT 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1038/nature07309 "Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)" "The existence of a posterior domain of coordinated expression of 'hindgut' genes in the acoel C. longifissura, however, can be explained in two different ways. A through gut could have been present in the last common ancestor of all bilaterians and the anus could have been lost independently in both Acoela and Nemertodermatida lineages. The expression of hindgut markers at the posterior pole in C. longifissura would therefore be remnants of a posterior anal opening. The more parsimonious explanation, however, is to assume that the metazoan mouth evolved first and the anal opening arose independently through co-option of hindgut genes in posterior domains at the ectodermal-endodermal interface. The region of the posterior expression of bra in the acoel juvenile corresponds to the area at which the gonoduct will form in the mature adult, which also expresses bra (Fig. 2t, u). It is of interest that this position has previously been proposed to represent a common cloacal opening in basal metazoans28." bgee ANN 2015-03-11 HOM:0000007 "historical homology" UBERON:0001245 "anus" 33511 "Deuterostomia" CIO:0000003 "high confidence from single evidence" ECO:0000033 "traceable author statement" PMID:23031503 "Smith AB, Cambrian problematica and the diversification of deuterostomes. BMC Biol (2012)" "one generally accepted model is that the latest common ancestor of deuterostomes was a worm-like creature with pharyngeal gill slits, a terminal anus, a simple nerve plexus without regionalization, and well-developed circular and longitudinal muscles." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0001247 "falciform ligament" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) Development of the coelomic cavity and mesenteries, p.160 and Figure 4-31" bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0001255 "urinary bladder" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:538956 "Bentley PJ, The vertebrate urinary bladder: osmoregulatory and other uses. Yale J Biol Med (1979)" "Urinary bladders appear to have evolved in vertebrates at least twice, which suggests that they are useful. In tetrapods the bladder is an endodermal structure which arises as an outgrowth of the cloaca. In amniotes it gives rise to the embryonic allantoic membrane, part of which may persist as the bladder in the adult. While a bladder does not occur in birds the allantois remains an important organ during its development in the egg. The fish bladder is embryologically quite different to the tetrapod bladder and is mesodermal in origin, arising as an expansion of the mesonephoric ducts. It is thus really an extension of the kidney." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0001255 "urinary bladder" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.577-78" "In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0001255 "urinary bladder" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:538956 "Bentley PJ, The vertebrate urinary bladder: osmoregulatory and other uses. Yale J Biol Med (1979)" "Urinary bladders appear to have evolved in vertebrates at least twice, which suggests that they are useful. In tetrapods the bladder is an endodermal structure which arises as an outgrowth of the cloaca. In amniotes it gives rise to the embryonic allantoic membrane, part of which may persist as the bladder in the adult. While a bladder does not occur in birds the allantois remains an important organ during its development in the egg. The fish bladder is embryologically quite different to the tetrapod bladder and is mesodermal in origin, arising as an expansion of the mesonephoric ducts. It is thus really an extension of the kidney." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0001255 "urinary bladder" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:538956 "Bentley PJ, The vertebrate urinary bladder: osmoregulatory and other uses. Yale J Biol Med (1979)" "Urinary bladders appear to have evolved in vertebrates at least twice, which suggests that they are useful. In tetrapods the bladder is an endodermal structure which arises as an outgrowth of the cloaca. In amniotes it gives rise to the embryonic allantoic membrane, part of which may persist as the bladder in the adult. While a bladder does not occur in birds the allantois remains an important organ during its development in the egg. The fish bladder is embryologically quite different to the tetrapod bladder and is mesodermal in origin, arising as an expansion of the mesonephoric ducts. It is thus really an extension of the kidney." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0001255 "urinary bladder" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:538956 "Bentley PJ, The vertebrate urinary bladder: osmoregulatory and other uses. Yale J Biol Med (1979)" "Urinary bladders appear to have evolved in vertebrates at least twice, which suggests that they are useful. In tetrapods the bladder is an endodermal structure which arises as an outgrowth of the cloaca. In amniotes it gives rise to the embryonic allantoic membrane, part of which may persist as the bladder in the adult. While a bladder does not occur in birds the allantois remains an important organ during its development in the egg. The fish bladder is embryologically quite different to the tetrapod bladder and is mesodermal in origin, arising as an expansion of the mesonephoric ducts. It is thus really an extension of the kidney." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0001264 "pancreas" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" http://tolweb.org/Craniata/14826/1997.01.01 "Janvier P, Craniata. Animals with skulls. The Tree of Life Web Project (1997)" "All craniates have a pancreas that produces digestive enzymes and hormones (insulin and glucagon) that regulate blood sugar level. The pancreas was ancestrally disseminated along the anterior part of the gut, but becomes condensed into a well-defined organ in the Vertebrata." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0001264 "pancreas" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" DOI:10.1016/j.crvi.2007.03.006 "Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C R Biol (2007)" "In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0001269 "acetabular part of hip bone" 1338369 "Dipnotetrapodomorpha" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:23342976 "Boisvert CA, Joss JM, Ahlberg PE, Comparative pelvic development of the axolotl (Ambystoma mexicanum) and the Australian lungfish (Neoceratodus forsteri): conservation and innovation across the fish-tetrapod transition. Evodevo (2013)" "(...) the fact that the acetabular region is the first part of the pelvis to develop in both Neoceratodus [Dipnoi] and Ambystoma [Tetrapoda] suggests that the acetabulum should instead be regarded as a fixed landmark (grey line, Figure 3). Such a change of perspective makes the evolutionary transformation of the pelvis much easier to understand. As shown in the descriptions above, the principal difference in early pelvic development between salamander and lungfish is that in the salamander, the pubis grows anteriorly and the ischium posteriorly from the acetabular region, whereas in lungfish the pubis grows anteriorly and the ischium is absent; in other words, chondrogenic cells proliferate both anteriorly and posteriorly in the salamander, whereas in the lungfish they only proliferate anteriorly" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0001273 "ilium" 1338369 "Dipnotetrapodomorpha" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:23342976 "Boisvert CA, Joss JM, Ahlberg PE, Comparative pelvic development of the axolotl (Ambystoma mexicanum) and the Australian lungfish (Neoceratodus forsteri): conservation and innovation across the fish-tetrapod transition. Evodevo (2013)" "The fact that the ilium of salamanders slowly extends dorsally during development, only contacting the sacral rib at a late stage when the pelvis is more or less fully formed, means that the ilium passes through a protracted developmental stage when it closely resembles the iliac process of these fishes [tetrapodomorph fishes] (Figure 1). Together with the wide phylogenetic distribution of the iliac process, which suggests that it is a general character for the 'fish' part of the tetrapod stem group [11,12,14,15], this provides strong circumstantial evidence for the homology of the two structures." bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0001273 "ilium" 1338369 "Dipnotetrapodomorpha" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23342976 "Boisvert CA, Joss JM, Ahlberg PE, Comparative pelvic development of the axolotl (Ambystoma mexicanum) and the Australian lungfish (Neoceratodus forsteri): conservation and innovation across the fish-tetrapod transition. Evodevo (2013)" "The fact that the ilium of salamanders slowly extends dorsally during development, only contacting the sacral rib at a late stage when the pelvis is more or less fully formed, means that the ilium passes through a protracted developmental stage when it closely resembles the iliac process of these fishes [tetrapodomorph fishes] (Figure 1). Together with the wide phylogenetic distribution of the iliac process, which suggests that it is a general character for the 'fish' part of the tetrapod stem group [11,12,14,15], this provides strong circumstantial evidence for the homology of the two structures." bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0001276 "epithelium of stomach" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21669855 "Leys SP, Nichols SA, Adams ED, Epithelia and integration in sponges. Integrative and Comparative Biology (2009)" bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0001277 "intestinal epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000160, negated: false, taxon ID: 7742 - entity: UBERON:0000483, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0001278 "epithelium of large intestine" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000059, negated: false, taxon ID: 32523 - entity: UBERON:0000483, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0001280 "liver parenchyma" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1002/ar.20524 "Hardman RC, Volz DC, Kullman SW, Hinton DE, An in vivo look at vertebrate liver architecture: three-dimensional reconstruction from Medaka (Oryzias latipes). The Anatomical Record (2007)" "the (liver) tubular structure (dual layered parenchyma) appears to be conserved among all embryonic vertebrates (...) it is not unlikely that all vertebrate livers share the same fundamental functional unit." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0001280 "liver parenchyma" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1002/ar.20524 "Hardman RC, Volz DC, Kullman SW, Hinton DE, An in vivo look at vertebrate liver architecture: three-dimensional reconstruction from Medaka (Oryzias latipes). The Anatomical Record (2007)" "the (liver) tubular structure (dual layered parenchyma) appears to be conserved among all embryonic vertebrates (...) it is not unlikely that all vertebrate livers share the same fundamental functional unit." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0001281 "hepatic sinusoid" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1053/ax.2000.7133 "Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000)" "(...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0001285 "nephron" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:15376276 "Mobjerg N, Jespersen A, Wilkinson M, Morphology of the kidney in the West African caecilian, Geotrypetes seraphini (Amphibia, Gymnophiona, Caeciliidae). J Morphol (2004)" "The original vertebrate kidney, archinephros or holonephros, is believed to have covered the entire length of the coelom, consisting of paired segmental tubules with associated glomeruli, archinephrons (Price, 1897; Goodrich, 1958). Each tubule opened into the coelom through a ciliated nephrostome and was connected to the archinephric duct, which led to the exterior (Goodrich, 1958). Nephrons were present at some time in all body segments, but later were restricted to the trunk region of the animal. A tendency for the most anterior tubules to develop and function in early life, and for the more posterior tubules to develop and function later in life led to the differentiation into pro-, meso-, and metanephros (Goodrich, 1958)." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0001288 "loop of Henle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" DOI:10.1093/ndt/14.10.2510 "Morel F, The loop of Henle, a turning-point in the history of kidney physiology. Nephrol Dial Transplant (1999)" "(...) in the meantime (1909) Klaus Peter [5] had reported that the loops of Henle are present in the kidney of mammals only, and that they are proportionally more developed in species living in a dry habitat and producing a concentrated urine." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0001288 "loop of Henle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:23338209 "Romagnani P, Lasagni L, Remuzzi G, Renal progenitors: an evolutionary conserved strategy for kidney regeneration. Nat Rev Nephrol (2013)" "Both birds and mammals first develop a pronephros followed by a mesonephros, which ultimately degenerate to be replaced by the mature kidney, the metanephros (Figure 1c).(16) However, birds and mammals developed a modification to the basic structure of the nephron, a novel hairpin loop localized between the proximal and the distal tubule, namely Henle's loop (Figure 2). Henle's loop permitted the generation of an osmolar gradient for water reabsorption in the collecting duct and enabled the concentratation of urine, which contributed to the successful establishment of mammalian life.(16) (...) Avian and mammalian kidneys show a major modification to the basic structure of the nephron-Henle's loop-which enabled urine to be concentrated. Bird kidneys contain two types of nephrons: nephrons with Henle's loop ('mammalian type') and nephrons without Henle's loop ('reptilian type'). By contrast, all nephrons in mammals display Henle's loop, although the lengths of these loops differ both within and between species." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0001295 "endometrium" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.144" "The maternal part of the placenta (of eutherian mammals) is the vascularized and glandular uterine lining, or endometrium." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0001296 "myometrium" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:15471813 "Spencer TE, Bazer FW, Uterine and placental factors regulating conceptus growth in domestic animals. Journal of Animal Science (2004)" "In all mammals, the uterus develops as a specialization of the paramesonephric or Mullerian ducts, which gives rise to the infundibula, oviducts, uterus, cervix, and anterior vagina. Morphogenetic events common to development of all uteri include: 1) differentiation and growth of the myometrium, 2) differentiation and morphogenesis of the endometrial glands, and 3) organization and stratification of endometrial stroma. Uterine development is initiated in the fetus, but is only completed postnatally with differentiation and development of the endometrial glands." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0001299 "glans penis" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1098/rsbl.2004.0161 "Kelly DA, Turtle and mammal penis designs are anatomically convergent. Proceedings of the Royal Society of London (2004)" "Penises are found in four amniote lineages: mammals (Williams-Ashman 1990), turtles (Zug 1966; McDowell 1983), squamates (Dowling & Savage 1960; Conner & Crews 1980) and archosaurs (Liebe 1914; King 1981; McCracken 2000). It has been proposed that a penis is an amniote synapomorphy (Jones 1915; Gauthier et al. 1988). However, anatomical and developmental differences among penises in these groups (Kelly 2002) mapped on independent phylogenetic hypotheses of their relationships (Rieppel & deBraga 1996; Hedges & Poling 1999; Janke et al. 2001) strongly suggest that each penis-bearing group arose independently from ancestors that had internal fertilization without intromission (such as the cloacal apposition seen in Sphenodon (Romer 1970) and passerine birds (Birkhead et al. 1993))." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0001299|UBERON:0002411|UBERON:0004713 "glans penis|clitoris|corpus cavernosum penis" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:23169570 "Puppo V, Anatomy and physiology of the clitoris, vestibular bulbs, and labia minora with a review of the female orgasm and the prevention of female sexual dysfunction. Clin Anat (2013)" "The clitoris is the homologue of the male's glans and corpora cavernosa (Fig. 3) (Puppo et al., 2008b; Standring, 2008; Puppo, 2011a)." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0001301 "epididymis" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.556" "(In mammalian testis) Along the way (the sperm travel), three accessory sex glands, the seminal vesicle, prostate, and bulbourethral (Cowper's) gland, respectively, add their secretions as sperm move from the testes to the urethra." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0001305 "ovarian follicle" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1146/annurev.cellbio.042308.13350 "DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)" "Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved." bgee ANN 2015-01-28 HOM:0000007 "historical homology" UBERON:0001310 "umbilical artery" 9347 "Eutheria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1016/j.cbpa.2007.01.029 "Mess A, Carter AM, Evolution of the placenta during the early radiation of placental mammals. Comparative Biochemistry and Physiology - Part A: Molecular and Integrative Physiology (2007)" "Two umbilical arteries and one vein are characters of the common ancestor of living placental mammals. [curator]" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0001319 "vaginal vein" NOT 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000996, negated: true, taxon ID: 32524 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0001319 "vaginal vein" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000996, negated: false, taxon ID: 40674 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0001322 "sciatic nerve" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21669821 "Lacalli TC, Head organization and the head/trunk relationship in protochordates: problems and prospects. Integrative and Comparative Biology (2008)" "Sciatic nerve is a somatic nerve. [curator]" bgee ANN 2013-06-13 HOM:0000007 "historical homology" UBERON:0001331 "skin of penis" 8459 "Testudines" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0000989, negated: false, taxon ID: 8459" bgee HOM:0000007 "historical homology" UBERON:0001331 "skin of penis" 8492 "Archosauria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0000989, negated: false, taxon ID: 8492" bgee HOM:0000007 "historical homology" UBERON:0001331 "skin of penis" 8509 "Squamata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0000989, negated: false, taxon ID: 8509" bgee HOM:0000007 "historical homology" UBERON:0001331 "skin of penis" 32524 "Amniota" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0000989, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0001331 "skin of penis" NOT 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0000989, negated: true, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0001331 "skin of penis" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0000989, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0001332 "prepuce of penis" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1098/rsbl.2004.0161 "Kelly DA, Turtle and mammal penis designs are anatomically convergent. Proceedings of the Royal Society of London (2004)" "Penises are found in four amniote lineages: mammals (Williams-Ashman 1990), turtles (Zug 1966; McDowell 1983), squamates (Dowling & Savage 1960; Conner & Crews 1980) and archosaurs (Liebe 1914; King 1981; McCracken 2000). It has been proposed that a penis is an amniote synapomorphy (Jones 1915; Gauthier et al. 1988). However, anatomical and developmental differences among penises in these groups (Kelly 2002) mapped on independent phylogenetic hypotheses of their relationships (Rieppel & deBraga 1996; Hedges & Poling 1999; Janke et al. 2001) strongly suggest that each penis-bearing group arose independently from ancestors that had internal fertilization without intromission (such as the cloacal apposition seen in Sphenodon (Romer 1970) and passerine birds (Birkhead et al. 1993))." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0001342 "mesovarium" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Chapter 6, Integument, p.560 and Figure 14.23 p.561" "The mesovarium is part of female reproductive system in all vertebrates and even present in hagfish. [curator]" bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0001342 "mesovarium" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Chapter 6, Integument, p.560 and Figure 14.23 p.561" "The mesovarium is part of female reproductive system in all vertebrates and even present in hagfish. [curator]" bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0001343 "seminiferous tubule of testis" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688 and Figure 21-28" "Frogs among amphibians and the amniotes have males with testes that are composed of seminiferous tubules, which differ from ampullae in being long, highly convoluted ductules." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0001344 "epithelium of vagina" NOT 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000996, negated: true, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0001344 "epithelium of vagina" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000996, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0001359 "cerebrospinal fluid" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19274662 "Lowery LA, Sive H, Totally tubular: the mystery behind function and origin of the brain ventricular system. Bioessays (2009)" "A unique feature of the vertebrate brain is the brain ventricular system, a series of connected cavities which are filled with cerebrospinal fluid (CSF) and surrounded by neuroepithelium." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0001366 "parietal peritoneum" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1007/s00898-999-0002-1 "Brainerd EL, New perspectives on the evolution of lung ventilation mechanisms in vertebrates. Experimental Biology Online (1999)" "In green iguanas, as in most lepidosaurs, the body cavity is not divided into separate pleural and peritoneal spaces. Instead, the lungs and viscera are contained within a single, 'pleuroperitoneal' cavity. This condition is also seen in air-breathing fishes and amphibians, indicating that an undivided body cavity is the primitive condition for amniotes." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0001373 "sartorius muscle" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.391" "The ambiens of reptiles and the iliotibialis of amphibians are likely homologues of the sartorius." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0001373|UBERON:0013511|UBERON:0014888 "sartorius muscle|ambiens muscle|iliotibialis muscle" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.391" "The ambiens of reptiles and the iliotibialis of amphibians are likely homologues of the sartorius." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0001377 "quadriceps femoris" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.394 Table 10.2" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0001388 "gastrocnemius" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.393" "The most prominent ventral muscle of the shank is the gastrocnemius, the 'calf' muscle. In mammals, it has two heads, resulting from the fusion of two different phylogenetic predecessors." bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0001419 "skin of limb" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0002101, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0001422 "facial lymphatic vessel" 32523 "Tetrapoda" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001456, negated: false, taxon ID: 7742 - entity: UBERON:0001473, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0001434 "skeletal system" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:23535660 "Shimada A, Kawanishi T, Kaneko T, Yoshihara H, Yano T, Inohaya K, Kinoshita M, Kamei Y, Tamura K, Takeda H, Trunk exoskeleton in teleosts is mesodermal in origin. Nat Commun (2013)" "The vertebrate mineralized skeleton is known to have first emerged as an exoskeleton that extensively covered the fossil jawless fish. The evolutionary origin of this exoskeleton has long been attributed to the emergence of the neural crest, but experimental evaluation for this is still poor. Here we determine the embryonic origin of scales and fin rays of medaka (teleost trunk exoskeletons) by applying long-term cell labelling methods, and demonstrate that both tissues are mesodermal in origin. Neural crest cells, however, fail to contribute to these tissues. This result suggests that the trunk neural crest has no skeletogenic capability in fish, instead highlighting the dominant role of the mesoderm in the evolution of the trunk skeleton. This further implies that the role of the neural crest in skeletogenesis has been predominant in the cephalic region from the early stage of vertebrate evolution." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0001447 "tarsal bone" 32523 "Tetrapoda" CIO:0000005 "low confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.7717/peerj.2036 "Pineiro G, Nunez Demarco P, Meneghel MD, The ontogenetic transformation of the mesosaurid tarsus: a contribution to the origin of the primitive amniotic astragalus. PeerJ (2016)" "The ontogenetic transformation of the mesosaurid tarsus: a contribution to the origin of the primitive amniotic astragalus... An amniote-like tarsal structure is observed in very basal Carboniferous and Permian tetrapods such as Proterogyrinus, Gephyrostegus, the diadectids Diadectes and Orobates, some microsaurs like Tuditanus and Pantylus and possibly Westlothiana, taxa that were all considered as true amniotes in their original descriptions. Therefore, the structure of the amniotic tarsus, including the configuration of the proximal series formed by the astragalus and the calcaneum, typically a pair of enlarged bones, could have been established well before the first recognized amniote walked on Earth. Accordingly, the tarsus of these taxa does not constitute specialized convergences that appeared in unrelated groups, they might be instead, part of a transformation series that involves taxa closely related to the early amniotes as some hypotheses have suggested." bgee ANN 2017-05-01 HOM:0000007 "historical homology" UBERON:0001447 "tarsal bone" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.7717/peerj.2036 "Pineiro G, Nunez Demarco P, Meneghel MD, The ontogenetic transformation of the mesosaurid tarsus: a contribution to the origin of the primitive amniotic astragalus. PeerJ (2016)" "The ontogenetic transformation of the mesosaurid tarsus: a contribution to the origin of the primitive amniotic astragalus... An amniote-like tarsal structure is observed in very basal Carboniferous and Permian tetrapods such as Proterogyrinus, Gephyrostegus, the diadectids Diadectes and Orobates, some microsaurs like Tuditanus and Pantylus and possibly Westlothiana, taxa that were all considered as true amniotes in their original descriptions. Therefore, the structure of the amniotic tarsus, including the configuration of the proximal series formed by the astragalus and the calcaneum, typically a pair of enlarged bones, could have been established well before the first recognized amniote walked on Earth. Accordingly, the tarsus of these taxa does not constitute specialized convergences that appeared in unrelated groups, they might be instead, part of a transformation series that involves taxa closely related to the early amniotes as some hypotheses have suggested." bgee ANN 2017-05-01 HOM:0000007 "historical homology" UBERON:0001450 "calcaneus" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1002/jez.b.22688 "Reno PL, Kjosness KM, Hines JE, The Role of Hox in Pisiform and Calcaneus Growth Plate Formation and the Nature of the Zeugopod/Autopod Boundary. J Exp Zool B Mol Dev Evol (2016)" "The mammalian calcaneus forms as the combination of two separate condensations which likely shares homology with the fibulare of less derived tetrapods (Cihak, 1972)." bgee ANN 2017-06-12 HOM:0000007 "historical homology" UBERON:0001450 "calcaneus" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1002/jez.b.22688 "Reno PL, Kjosness KM, Hines JE, The Role of Hox in Pisiform and Calcaneus Growth Plate Formation and the Nature of the Zeugopod/Autopod Boundary. J Exp Zool B Mol Dev Evol (2016)" "While there is a general correspondence between developmental gene expression and timing of evolutionary origins with the stylopod, zeugopod, and autopod, the correlation is not perfect. The misalignment is highlighted by the growth potential of the pisiform and calcaneus and their residency within particular Hox expression domains supporting a zeugopodial identity (Fig. 8). Such a view better aligns the developmental identity determined in living tetrapods with the evolutionary origin of the proximal mesopodials in sarcopterygians (Fig. 1) prior to the establishment of distal mesopodials and digits." bgee ANN 2017-06-12 HOM:0000007 "historical homology" UBERON:0001450 "calcaneus" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1002/jez.b.22688 "Reno PL, Kjosness KM, Hines JE, The Role of Hox in Pisiform and Calcaneus Growth Plate Formation and the Nature of the Zeugopod/Autopod Boundary. J Exp Zool B Mol Dev Evol (2016)" "In contrast to the other mesopodials, the mammalian pisiform and calcaneus form true growth plates. We show that these bones, along with other proximal mesopodials, develop within the Hoxa11 and Hoxd11 expression domains." bgee ANN 2017-06-12 HOM:0000007 "historical homology" UBERON:0001456 "face" 7742 "Vertebrata" CIO:0000005 "low confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1242/dev.005132 "Brugmann SA, Goodnough LH, Gregorieff A, Leucht P, ten Berge D, Fuerer C, Clevers H, Nusse R, Helms JA, Wnt signaling mediates regional specification in the vertebrate face. Development (2007)" "We tested the hypothesis that Wnt signaling is an evolutionarily conserved mechanism controlling facial morphogenesis by determining the pattern of Wnt responsiveness in avian faces, and then by evaluating the consequences of Wnt inhibition in the chick face. Collectively, these data elucidate a new role for Wnt signaling in regional specification of the vertebrate face, and suggest possible mechanisms whereby species-specific facial features are generated." bgee ANN 2017-05-01 HOM:0000007 "historical homology" UBERON:0001456 "face" 7742 "Vertebrata" CIO:0000005 "low confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1242/dev.005132 "Brugmann SA, Goodnough LH, Gregorieff A, Leucht P, ten Berge D, Fuerer C, Clevers H, Nusse R, Helms JA, Wnt signaling mediates regional specification in the vertebrate face. Development (2007)" "We tested the hypothesis that Wnt signaling is an evolutionarily conserved mechanism controlling facial morphogenesis by determining the pattern of Wnt responsiveness in avian faces, and then by evaluating the consequences of Wnt inhibition in the chick face. Collectively, these data elucidate a new role for Wnt signaling in regional specification of the vertebrate face, and suggest possible mechanisms whereby species-specific facial features are generated." bgee ANN 2017-05-01 HOM:0000007 "historical homology" UBERON:0001458 "skin of lip" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0001833, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001459 "skin of external ear" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0001691, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0001459 "skin of external ear" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0001691, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0001460 "arm" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:19324642 "Zhu M, Yu X, Stem sarcopterygians have primitive polybasal fin articulation. Biology letters (2009)" "In the fin-limb transition, the origin of the sarcopterygian paired fins triggered new possibilities of fin articulation and movement, and established the proximal segments (stylopod and zeugopod) of the presumptive tetrapod limb." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0001461 "elbow" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:22722854 "Pierce SE, Clack JA, Hutchinson JR, Three-dimensional limb joint mobility in the early tetrapod Ichthyostega. Nature (2012)" "Elbow joint mobility in Ichthyostega is, as far as can be judged from the ulna articulation, comparable to that in the modern tetrapods." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0001464 "hip" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333" "The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0001465 "knee" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000033 "traceable author statement" PMID:22722854 "Pierce SE, Clack JA, Hutchinson JR, Three-dimensional limb joint mobility in the early tetrapod Ichthyostega. Nature (2012)" "This proposed model of hindlimb movement in Ichthyostega is in accordance with the development of broad, paddle-shaped, distal limb bones and expanded pedes (1). It is also further supported by a reduced range of flexion/extension in the knee, which is an essential component of terrestrial locomotion in living tetrapods (18, 19, 20, 21)." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0001466 "pedal digit" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002387, negated: false, taxon ID: 32523 - entity: UBERON:0002544, negated: false, taxon ID: 8782" bgee HOM:0000007 "historical homology" UBERON:0001466 "pedal digit" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002387, negated: false, taxon ID: 32523 - entity: UBERON:0002544, negated: false, taxon ID: 32523 - entity: UBERON:0002544|UBERON:4000172, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0001466 "pedal digit" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002387, negated: false, taxon ID: 32523 - entity: UBERON:0002544, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0001466 "pedal digit" NOT 32524 "Amniota" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002387, negated: false, taxon ID: 32523 - entity: UBERON:0002544, negated: true, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0001466 "pedal digit" NOT 1338369 "Dipnotetrapodomorpha" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002387|UBERON:2000508, negated: false, taxon ID: 8287 - entity: UBERON:0002544|UBERON:2000271, negated: true, taxon ID: 1338369" bgee HOM:0000007 "historical homology" UBERON:0001467 "shoulder" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.332" "(...) endochondral elements of the early tetrapod shoulder develop from two centers of ossification, giving rise to a scapula and a 'coracoid'." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0001468 "intervertebral joint" 7776 "Gnathostomata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0001075, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0001468 "intervertebral joint" NOT 7776 "Gnathostomata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0001075, negated: true, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0001468 "intervertebral joint" 7778 "Elasmobranchii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0001075, negated: false, taxon ID: 7778" bgee HOM:0000007 "historical homology" UBERON:0001468 "intervertebral joint" 7898 "Actinopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0001075, negated: false, taxon ID: 7898" bgee HOM:0000007 "historical homology" UBERON:0001468 "intervertebral joint" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0001075, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0001468 "intervertebral joint" NOT 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0001075, negated: true, taxon ID: 117571" bgee HOM:0000007 "historical homology" UBERON:0001469 "sternoclavicular joint" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000975, negated: false, taxon ID: 40674 - entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0001105, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0001470 "glenohumeral joint" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.193 and Figure 5-14" bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0001471 "skin of prepuce of penis" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1098/rsbl.2004.0161 "Kelly DA, Turtle and mammal penis designs are anatomically convergent. Proceedings of the Royal Society of London (2004)" "Penises are found in four amniote lineages: mammals (Williams-Ashman 1990), turtles (Zug 1966; McDowell 1983), squamates (Dowling & Savage 1960; Conner & Crews 1980) and archosaurs (Liebe 1914; King 1981; McCracken 2000). It has been proposed that a penis is an amniote synapomorphy (Jones 1915; Gauthier et al. 1988). However, anatomical and developmental differences among penises in these groups (Kelly 2002) mapped on independent phylogenetic hypotheses of their relationships (Rieppel & deBraga 1996; Hedges & Poling 1999; Janke et al. 2001) strongly suggest that each penis-bearing group arose independently from ancestors that had internal fertilization without intromission (such as the cloacal apposition seen in Sphenodon (Romer 1970) and passerine birds (Birkhead et al. 1993))." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0001473 "lymphatic vessel" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.627" "Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body." bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0001474 "bone element" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1159/000324245 "Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011)" "The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit' of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate." bgee ANN 2013-08-21 HOM:0000007 "historical homology" UBERON:0001476 "deltoid" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.394 Table 10.2" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0001477 "infraspinatus muscle" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:20807270 "Abdala V, Diogo R, Comparative anatomy, homologies and evolution of the pectoral and forelimb musculature of tetrapods with special attention to extant limbed amphibians and reptiles. J Anat (2010)" "It is now accepted that the mammalian supraspinatus and infraspinatus, which usually connect the dorsal region of the pectoral girdle to the proximal region of the arm, derive from the supracoracoideus (Tables 1 and 2), a muscle that lies ventral, not dorsal, to the pectoral girdle in most other extant tetrapods (e.g. Kardong, 2002; Diogo et al. 2009a)." bgee ANN 2017-02-15 HOM:0000007 "historical homology" UBERON:0001477 "infraspinatus muscle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.394 Table 10.2" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0001477|UBERON:0002383|UBERON:0014840 "infraspinatus muscle|supraspinatus muscle|supracoracoideus muscle" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" ISBN:978-0253018328 "Bonnan MF, The bare bones An unconventional evolutionary history of the skeleton (2016) p.459" "In reptiles and the ancestors of therian mammals, the coracoid was a large element of the shoulder girdle to which the supracoracoideus muscle anchored. As revealed by therian mammal embryology and muscle innervation studies, with the reduction of the coracoid bone, the supracoracoideus gained a new anchorage on the scapula and transformed into the supraspinatus and infraspinatus muscles of the rotator cuff." bgee ANN 2017-02-14 HOM:0000007 "historical homology" UBERON:0001477|UBERON:0002383|UBERON:0014840 "infraspinatus muscle|supraspinatus muscle|supracoracoideus muscle" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0253018328 "Bonnan MF, The bare bones An unconventional evolutionary history of the skeleton (2016) p.459" "In reptiles and the ancestors of therian mammals, the coracoid was a large element of the shoulder girdle to which the supracoracoideus muscle anchored. As revealed by therian mammal embryology and muscle innervation studies, with the reduction of the coracoid bone, the supracoracoideus gained a new anchorage on the scapula and transformed into the supraspinatus and infraspinatus muscles of the rotator cuff." bgee ANN 2017-02-14 HOM:0000007 "historical homology" UBERON:0001478 "teres major muscle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.394 Table 10.2" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0001479 "sesamoid bone" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1016/S1095-6433(02)00241-6 "Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002)" "Sesamoid bones are common in bony fish and also in tetrapods." bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0001483 "skin of shoulder" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0001467, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0001485 "knee joint" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.193 and Figure 5-14" bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0001486 "hip joint" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.193 and Figure 5-14" bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0001487 "pes joint" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0002387, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0001489 "manus joint" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0002398, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0001490 "elbow joint" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.193 and Figure 5-14" bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0001492 "radial nerve" 32523 "Tetrapoda" CIO:0000005 "low confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1046/j.1469-7580.1997.19030447.x "Koizumi M, Sakai T, On the morphology of the brachial plexus of the platypus (Ornithorhynchus anatinus) and the echidna (Tachyglossus aculeatus). Journal of Anatomy (1997)" "Considering the incomplete dorsoventral division of forelimb nerves in some reptiles and urodeles, the caudal half of the monotreme brachial plexus has characteristics in common with those of lower tetrapods." bgee ANN 2013-06-14 HOM:0000007 "historical homology" UBERON:0001494 "ulnar nerve" 32523 "Tetrapoda" CIO:0000005 "low confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1046/j.1469-7580.1997.19030447.x "Koizumi M, Sakai T, On the morphology of the brachial plexus of the platypus (Ornithorhynchus anatinus) and the echidna (Tachyglossus aculeatus). Journal of Anatomy (1997)" "Considering the incomplete dorsoventral division of forelimb nerves in some reptiles and urodeles, the caudal half of the monotreme brachial plexus has characteristics in common with those of lower tetrapods." bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001506 "brachialis muscle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.342-343 and Figure 10-20 and Table 10-7" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0001507 "biceps brachii" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.342-343 and Figure 10-20 and Table 10-7" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0001508 "arch of aorta" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460 and p.461 Figure 12.20" "The double systemic arch arches (left and right) present in amphibians and reptiles become reduced to a single systemic arch - the right in birds, the left in mammals." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0001509 "triceps brachii" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.394 Table 10.2" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0001510 "skin of knee" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0001465, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0001511 "skin of leg" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0000978, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0001513 "skin of pes" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0002387, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0001517 "skin of elbow" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0001461, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0001519 "skin of manus" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0002398, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0001532 "internal carotid artery" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451-454 and Figure 12.11" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0001554 "skin of hip" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0001464, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0001555 "digestive tract" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:11256379 "Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000)" "Although the gut is homologous among different vertebrates, morphological differences exist between different species." bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0001555 "digestive tract" NOT 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:25788603 "Janssen R, Joergensen M, Lagebro L, Budd GE, Fate and nature of the onychophoran mouth-anus furrow and its contribution to the blastopore. Proc Biol Sci (2015)" "The puzzling presence of classical 'protostomes' and 'deuterostomes', in which the blastopore develops either into the mouth (or mouth and anus) or anus, respectively (figure 1a), led some authors to conclude that the through gut evolved at least twice in bilaterians [2]." bgee ANN 2015-03-23 HOM:0000007 "historical homology" UBERON:0001555 "digestive tract" NOT 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1038/nature07309 "Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)" "Most bilaterian animals possess a through gut with a separate mouth and anus. (...) These results (we studied the expression of genes involved in bilaterian foregut and hindgut patterning during the development of the acoel Convolutriloba longifissura) contradict the hypothesis that the bilaterian mouth and anus evolved simultaneously from a common blastoporal opening, and suggest that a through gut might have evolved independently in different animal lineages." bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0001555 "digestive tract" NOT 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1038/nature07309 "Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)" "Most bilaterian animals possess a through gut with a separate mouth and anus. (...) These results (we studied the expression of genes involved in bilaterian foregut and hindgut patterning during the development of the acoel Convolutriloba longifissura) contradict the hypothesis that the bilaterian mouth and anus evolved simultaneously from a common blastoporal opening, and suggest that a through gut might have evolved independently in different animal lineages." bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0001566 "cricothyroid muscle" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001630, negated: false, taxon ID: 33208 - entity: UBERON:0001738, negated: false, taxon ID: 40674 - entity: UBERON:0001759, negated: false, taxon ID: 89593 - entity: UBERON:0002375, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0001571 "genioglossus muscle" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:16252276 "Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Dev Dyn (2005)" "The lamprey head contains another group of muscles, the epi- and hypobranchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP [migratory muscle precursors], especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface (Kuratani et al., 1997). (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals)." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0001571|UBERON:0011151 "genioglossus muscle|jaw depressor muscle" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" DOI:10.1186/1471-213X-8-24 "Diogo R, Hinits Y, Hughes SM, Development of mandibular, hyoid and hypobranchial muscles in the zebrafish: homologies and evolution of these muscles within bony fishes and tetrapods. BMC Developmental Biology (2008)" "according to e.g. Edgeworth [12] the genioglossus of salamanders such as Ambystoma is derived from the coracomandibularis [Probable plesiomorphic osteichthyan condition]" bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0001575 "extrinsic muscle of tongue" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1002/dvdy.20587 "Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005)" "The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals)." bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0001576 "intrinsic muscle of tongue" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1002/dvdy.20587 "Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005)" "The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals)." bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0001579 "olfactory nerve" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...)" bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001579 "olfactory nerve" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" http://tolweb.org/Craniata/14826/1997.01.01 "Janvier P, Craniata. Animals with skulls. The Tree of Life Web Project (1997)" "In all craniates, the olfactory (I), optic (II), trigeminal (V), facial (VII), acoustic (VIII), glossopharyngeal (IX) and vagus (X) cranial nerves are present. Additional cranial nerves, the oculomotor (III), trochlear (IV) and abducent (VI) nerves occur only in the Vertebrata. Some consider that the latter have been secondarily lost in hagfishes." bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001585 "anterior vena cava" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455" "Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0001591 "thymic vein" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0002370, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001592 "bronchial vein" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0002185, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0001597 "masseter muscle" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.333-334 and same reference Table 10-4" "The division of the adductor mandibulae in the various lines of tetrapod evolution correlates with divergences in their methods of feeding. (...) As the jaws become stronger and their movements more complex in the line of evolution toward mammals, the adductor complex becomes divided into several distinct muscles (temporalis, masseter, pterygoideus, tensor tympani, tensor veli palati)." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0001598 "temporalis muscle" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.333-334 and Table 10-4" "The division of the adductor mandibulae in the various lines of tetrapod evolution correlates with divergences in their methods of feeding. (...) As the jaws become stronger and their movements more complex in the line of evolution toward mammals, the adductor complex becomes divided into several distinct muscles (temporalis, masseter, pterygoideus, tensor tympani, tensor veli palati)." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0001599 "stapedius muscle" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.398" "The depressor mandibulae of tetrapods, which opens the jaws, is the homologue of the levator operculi and epihyoidean. In mammals, the depressor mandibulae evolves into the stapedius (...)." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0001599|UBERON:0011647|UBERON:0011649|UBERON:0011650 "stapedius muscle|depressor mandibulae muscle|levator operculi|epihyoidean" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.398" "The depressor mandibulae of tetrapods, which opens the jaws, is the homologue of the levator operculi and epihyoidean. In mammals, the depressor mandibulae evolves into the stapedius (...)." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0001600 "tensor tympani" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.333-334 and same reference Table 10-4" "The division of the adductor mandibulae in the various lines of tetrapod evolution correlates with divergences in their methods of feeding. (...) As the jaws become stronger and their movements more complex in the line of evolution toward mammals, the adductor complex becomes divided into several distinct muscles (temporalis, masseter, pterygoideus, tensor tympani, tensor veli palati)." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0001601 "extra-ocular muscle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.331" "The ability to rotate the eyeball is common to all vertebrates with well-developed eyes, regardless of the habitat in which they live, so these (extrinsic ocular) muscles tend to be conservative. They change little during the course of evolution." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0001601 "extra-ocular muscle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:27081572 "Suzuki DG, Fukumoto Y, Yoshimura M, Yamazaki Y, Kosaka J, Kuratani S, Wada H, Comparative morphology and development of extra-ocular muscles in the lamprey and gnathostomes reveal the ancestral state and developmental patterns of the vertebrate head. Zoological Lett (2016)." "the disposition of the lamprey EOMs [extra-ocular muscles] differs from those the rest of vertebrates, in which the morphological pattern of EOMs is strongly conserved. To better understand the evolution and developmental origins of the vertebrate EOMs, we explored the development of the head mesoderm and EOMs of the lamprey in detail. We found that the disposition of lamprey EOM primordia differed from that in gnathostomes, even during the earliest period of development. We also found that three components of the paraxial head mesoderm could be distinguished genetically (premandibular mesoderm: Gsc+/TbxA-; mandibular mesoderm: Gsc-/TbxA-; hyoid mesoderm: Gsc-/TbxA+), indicating that the genetic mechanisms of EOMs are conserved in all vertebrates. We conclude that the tripartite developmental origin of the EOMs is likely to have been possessed by the latest common ancestor of the vertebrates. This ancestor's EOM developmental pattern was also suggested to have resembled more that of the lamprey, and the gnathostome EOMs' disposition is likely to have been established by a secondary modification that took place in the common ancestor of crown gnathostomes." bgee ANN 2016-10-10 HOM:0000007 "historical homology" UBERON:0001602 "medial rectus extraocular muscle" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.331" "The ability to rotate the eyeball is common to all vertebrates with well-developed eyes, regardless of the habitat in which they live, so these [extrinsic ocular] muscles tend to be conservative. They change little during the course of evolution." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0001603 "lateral rectus extra-ocular muscle" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.331" "The ability to rotate the eyeball is common to all vertebrates with well-developed eyes, regardless of the habitat in which they live, so these [extrinsic ocular] muscles tend to be conservative. They change little during the course of evolution." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0001606 "muscle of iris" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001630, negated: false, taxon ID: 33208 - entity: UBERON:0001769, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001609 "isthmus of thyroid gland" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1210/er.2003-0028 "De Felice M, Di Lauro R, Thyroid development and its disorders: genetics and molecular mechanisms. Endocrine Reviews (2004)" "In mammals and in some reptiles, the thyroid is composed of two lobes connected by an isthmus; in birds and amphibians, the thyroid consists of two isolated lobes. (...) Despite these morphological differences, the ontogeny of the thyroid follows the same pattern in all vertebrates (...)." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0001610 "lingual artery" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0001723, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0001611 "sublingual artery" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0001832, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0001621 "coronary artery" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.618-623" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0001622 "lacrimal artery" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0001817, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0001629 "carotid body" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" PMID:25524981 "Reichert MN, Brink DL, Milsom WK, Evidence for a carotid body homolog in the lizard Tupinambis merianae. J Exp Biol (2015)" "These results provide evidence in lizards for the existence of dispersed chemoreceptor cells at the first carotid bifurcation in the central cardiovascular area that have similar properties to known carotid body homologs, adding to the picture of chemoreceptor evolution in vertebrates." bgee ANN 2015-02-16 HOM:0000007 "historical homology" UBERON:0001630 "muscle organ" 33208 "Metazoa" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75" "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0001633 "basilar artery" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1242/dev.058776 "Fujita M, Cha YR, Pham VN, Sakurai A, Roman BL, Gutkind JS, Weinstein BM, Assembly and patterning of the vascular network of the vertebrate hindbrain. Development (2011)" "The major artery supplying the hindbrain, the basilar artery, runs along the ventral keel of the hindbrain in all vertebrates." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0001637 "artery" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1196/annals.1341.002 "Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)" "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0001638 "vein" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1196/annals.1341.002 "Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)" "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0001643 "oculomotor nerve" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625" "Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII)." bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001643 "oculomotor nerve" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...)" bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001644 "trochlear nerve" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625" "Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII)." bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001644 "trochlear nerve" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...)" bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001645 "trigeminal nerve" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625" "Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII)." bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001645 "trigeminal nerve" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...)" bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001646 "abducens nerve" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625" "Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII)." bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001646 "abducens nerve" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...)" bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001647 "facial nerve" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625" "Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII)." bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001647 "facial nerve" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...)" bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001648 "vestibulocochlear nerve" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...)" bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001648 "vestibulocochlear nerve" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" http://tolweb.org/Craniata/14826/1997.01.01 "Janvier P, Craniata. Animals with skulls. The Tree of Life Web Project (1997)" "In all craniates, the olfactory (I), optic (II), trigeminal (V), facial (VII), acoustic (VIII), glossopharyngeal (IX) and vagus (X) cranial nerves are present. Additional cranial nerves, the oculomotor (III), trochlear (IV) and abducent (VI) nerves occur only in the Vertebrata. Some consider that the latter have been secondarily lost in hagfishes." bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001649 "glossopharyngeal nerve" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625" "Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII)." bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001649 "glossopharyngeal nerve" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...)" bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001650 "hypoglossal nerve" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" http://en.wikipedia.org/wiki/Cranial_nerves "cranial nerves on Wikipedia" "Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0001663 "cerebral vein" NOT 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0001893, negated: true, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0001663 "cerebral vein" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0001893, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001668 "cerebellar vein" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0002037, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0001674 "masseteric vein" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001597, negated: false, taxon ID: 40674 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0001675 "trigeminal ganglion" NOT 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1016/j.brainresbull.2007.10.057 "Murakami Y, Kuratani S, Brain segmentation and trigeminal projections in the lamprey; with reference to vertebrate brain evolution. Brain Research Bulletin (2008)" "amphioxus has neither neuromeres nor a trigeminal system, although a Hox2 expression domain is present in the hindbrain [20]. It seems likely that the link between somatotopy and rhombomeres has been established in the vertebrate ancestor and conserved through the evolutionary process (Fig. 4)." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0001675 "trigeminal ganglion" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1016/j.brainresbull.2007.10.057 "Murakami Y, Kuratani S, Brain segmentation and trigeminal projections in the lamprey; with reference to vertebrate brain evolution. Brain Research Bulletin (2008)" "amphioxus has neither neuromeres nor a trigeminal system, although a Hox2 expression domain is present in the hindbrain [20]. It seems likely that the link between somatotopy and rhombomeres has been established in the vertebrate ancestor and conserved through the evolutionary process (Fig. 4)." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0001678 "temporal bone" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.258 and Table 7-1" bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0001679 "ethmoid bone" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:22020897 "Jankowski R, Revisiting human nose anatomy: phylogenic and ontogenic perspectives. Laryngoscope (2011)" "The ethmoid bone is derived from the cartilaginous nasal capsule of primitive vertebrates and considered to be a highly conserved region among the bony elements of the skull base." bgee ANN 2013-08-27 HOM:0000007 "historical homology" UBERON:0001679 "ethmoid bone" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.259" "The ethmoid region of the chondrocranium and the nasal capsules, which were largely unossified in early tetrapods and ancestral amniotes, are represented in mammals by the ethmoid and turbinates bones, respectively." bgee ANN 2013-08-27 HOM:0000007 "historical homology" UBERON:0001680 "lacrimal bone" 8287 "Sarcopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-3899370805 "Arratia G, Schultze HP, Wilson MVH, Mesozoic Fishes 4 - Homology and Phylogeny (2008) p.23-48" "The infraorbital bone 1 of actinopterygians is homologous with the lacrimal bone (...)." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0001680|UBERON:2000223 "lacrimal bone|infraorbital 1" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-3899370805 "Arratia G, Schultze HP, Wilson MVH, Mesozoic Fishes 4 - Homology and Phylogeny (2008) p.23-48" "The infraorbital bone 1 of actinopterygians is homologous with the lacrimal bone (...)." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0001681 "nasal bone" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" http://www.jstor.org/stable/2460812 "Jollie M, Segment Theory and the Homologizing of Cranial Bones. Am Nat (1981)" "Some note should be taken of the lack of frontal and nasal bones in the crossopterygian (...) the short-headed, large-eyed actinopterygian looks quite different, but the head pattern, like the pectoral girdle, yields to analysis. The cranial roof has a well-developed transverse extrascapular series posteriorly; in front of this, there are the same pairs of roofing bones as in the crossopterygian. In place of the fronto-nasal series there is a single nasal bone, which obviously is not the homologue of the tetrapod bone. Between these fish ""nasals"" is a large internasal corresponding to a group of anamestics on the snout of the crossopterygian." bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0001683 "jugal bone" 8287 "Sarcopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-3899370805 "Arratia G, Schultze HP, Wilson MVH, Mesozoic Fishes 4 - Homology and Phylogeny (2008) p.23-48" "(...) and the infraorbital bone 3 of advanced actinopterygians (is homologous) with the jugal bone of sarcopterygians." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0001683|UBERON:2001408 "jugal bone|infraorbital 3" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-3899370805 "Arratia G, Schultze HP, Wilson MVH, Mesozoic Fishes 4 - Homology and Phylogeny (2008) p.23-48" "(...) and the infraorbital bone 3 of advanced actinopterygians (is homologous) with the jugal bone of sarcopterygians." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0001685 "hyoid bone" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1038/nrn1221 "Santagati F, Rijli FM, Cranial neural crest and the building of the vertebrate head. Nature Reviews Neuroscience (2003)" "[In vertebrates] Hoxa2 expression in NCCs is necessary for the patterning of hyoid skeletal elements." bgee ANN 2013-09-05 HOM:0000007 "historical homology" UBERON:0001686 "auditory ossicle bone" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.695" "Additional structural analysis within a phylogenetic context has led to the remarkable discovery that in synapsids, thought to be ancestral to mammals, both the quadrate and articular have become reduced and less firmly articulated with their surrounding bones, reducing their jaw-joint-bearing role. This trend culminated with the incorporation of the quadrate, the columella (which remains articulated with the quadrate), and the articular into the expanded middle ear in mammals." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0001687 "stapes bone" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "Having three ossicles in the middle ear is one of the defining features of mammals. All reptiles and birds have only one middle ear ossicle, the stapes or columella. How these two additional ossicles came to reside and function in the middle ear of mammals has been studied for the last 200 years and represents one of the classic example of how structures can change during evolution to function in new and novel ways. From fossil data, comparative anatomy and developmental biology it is now clear that the two new bones in the mammalian middle ear, the malleus and incus, are homologous to the quadrate and articular, which form the articulation for the upper and lower jaws in non-mammalian jawed vertebrates." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0001687|UBERON:0011606 "stapes bone|hyomandibular bone" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" DOI:10.1017/S0022215100009087 "Gerrie J, The phylogeny of the mammalian tympanic cavity and auditory ossicles. The Journal of Laryngology and Otology (1948)" "This structure [the hyomandibular], on ontogenic grounds alone, can be considered homologous with the amphibian and reptilian columella and the mammalian stapes." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0001687|UBERON:0011606 "stapes bone|hyomandibular bone" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:19786082 "Manley GA, An evolutionary perspective on middle ears. Hearing research (2010)" "One mechanical strut-stabilizer of these early vertebrate jaws was derived from the upper portion of the second gill arch (hyoid arch) and termed the hyomandibula. The hyomandibula has been traced through vertebrate evolution and is clearly homologous (derived from the same tissues and having the same embryonic origin) to the land-vertebrate columella or stapes." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0001687|UBERON:0011606 "stapes bone|hyomandibular bone" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:19786082 "Manley GA, An evolutionary perspective on middle ears. Hearing research (2010)" "One mechanical strut-stabilizer of these early vertebrate jaws was derived from the upper portion of the second gill arch (hyoid arch) and termed the hyomandibula. The hyomandibula has been traced through vertebrate evolution and is clearly homologous (derived from the same tissues and having the same embryonic origin) to the land-vertebrate columella or stapes." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0001687|UBERON:0011606 "stapes bone|hyomandibular bone" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19786082 "Manley GA, An evolutionary perspective on middle ears. Hearing research (2010)" "One mechanical strut-stabilizer of these early vertebrate jaws was derived from the upper portion of the second gill arch (hyoid arch) and termed the hyomandibula. The hyomandibula has been traced through vertebrate evolution and is clearly homologous (derived from the same tissues and having the same embryonic origin) to the land-vertebrate columella or stapes." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0001688 "incus bone" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1017/S0022215100009087 "Gerrie J, The phylogeny of the mammalian tympanic cavity and auditory ossicles. The Journal of Laryngology and Otology (1948)" "According to this theory [Reichert-Gaupp theory], the mammalian stapes is derived from the reptilian columella, the incus from the quadrate and the malleus from the articular (...)." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0001688 "incus bone" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "Having three ossicles in the middle ear is one of the defining features of mammals. All reptiles and birds have only one middle ear ossicle, the stapes or columella. How these two additional ossicles came to reside and function in the middle ear of mammals has been studied for the last 200 years and represents one of the classic example of how structures can change during evolution to function in new and novel ways. From fossil data, comparative anatomy and developmental biology it is now clear that the two new bones in the mammalian middle ear, the malleus and incus, are homologous to the quadrate and articular, which form the articulation for the upper and lower jaws in non-mammalian jawed vertebrates." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0001688|UBERON:0006597 "incus bone|quadrate bone" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000033 "traceable author statement" DOI:10.1017/S0022215100009087 "Gerrie J, The phylogeny of the mammalian tympanic cavity and auditory ossicles. The Journal of Laryngology and Otology (1948)" "According to this theory [Reichert-Gaupp theory], the mammalian stapes is derived from the reptilian columella, the incus from the quadrate and the malleus from the articular (...)." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0001688|UBERON:0006597 "incus bone|quadrate bone" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "The homologies of the malleus, incus and stapes to the articular, quadrate and columella, and tympanic ring and gonial to the angular and prearticular suggested by comparative anatomy 175 years ago have been recently confirmed by molecular and developmental biology." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0001689 "malleus bone" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "Having three ossicles in the middle ear is one of the defining features of mammals. All reptiles and birds have only one middle ear ossicle, the stapes or columella. How these two additional ossicles came to reside and function in the middle ear of mammals has been studied for the last 200 years and represents one of the classic example of how structures can change during evolution to function in new and novel ways. From fossil data, comparative anatomy and developmental biology it is now clear that the two new bones in the mammalian middle ear, the malleus and incus, are homologous to the quadrate and articular, which form the articulation for the upper and lower jaws in non-mammalian jawed vertebrates." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0001689|UBERON:0004744 "malleus bone|articular/anguloarticular" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000033 "traceable author statement" DOI:10.1017/S0022215100009087 "Gerrie J, The phylogeny of the mammalian tympanic cavity and auditory ossicles. The Journal of Laryngology and Otology (1948)" "According to this theory [Reichert-Gaupp theory], the mammalian stapes is derived from the reptilian columella, the incus from the quadrate and the malleus from the articular (...)." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0001689|UBERON:0004744 "malleus bone|articular/anguloarticular" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "The homologies of the malleus, incus and stapes to the articular, quadrate and columella, and tympanic ring and gonial to the angular and prearticular suggested by comparative anatomy 175 years ago have been recently confirmed by molecular and developmental biology." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0001690 "ear" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" DOI:10.1002/dvdy.20207 "Boekhoff-Falk G, Hearing in Drosophila: Development of Johnston's organ and emerging parallels to vertebrate ear development. Developmental Dynamics (2005)" "Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ." bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0001690 "ear" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" DOI:10.1016/S0378-5955(00)00168-4 "Fay RR, Popper AN, Evolution of hearing in vertebrates: the inner ears and processing. Hearing research (2000)" "(...) considerations have led to our rethinking issues related to the origin of several aspects of vertebrate hearing, and to the view that many basic auditory functions evolved very early in vertebrate history, and that the functions observed in more `advanced' vertebrates, such as birds and mammals, are frequently modifications of themes first encountered in fishes, and perhaps even more ancestral animals." bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0001690 "ear" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:11523832 "Streit A, Origin of the vertebrate inner ear: evolution and induction of the otic placode. J Anat (2001)" "Recent molecular data have challenged the longstanding view that special sense organs such as the inner ear have evolved with the appearance of vertebrates. In addition, it has remained unclear whether the ear originally arose through a modification of the amphibian mechanosensory lateral line system or whether both evolved independently." bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0001691 "external ear" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1007/s00359-008-0327-1 "Schoffelen RLM, Segenhout JM, Van Dijk P, Mechanics of the exceptional anuran ear. Journal of Comparative Physiology A (2008)" "Some species, like Amolops tormotus (Feng et al. 2006) [Anura], have a cavity in front of the tympanic membrane which is considered to be an ear canal and thus an outer ear. (...) The ancestral lineage of amphibians separated from the mammalian lineage, approximately 350 million years ago, in the paleozoic era. Many of the important developments in the auditory systems emerged after the ancestral paths separated (Manley and Clack 2003). This implies that shared features, like the tympanic middle ear, developed independently in different vertebrate lineages." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0001691 "external ear" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0387210933 "Manley GA, Fay RR, Evolution of the Vertebrate Auditory System (2004) p.167 Figure 6.2" "Amphibians do not have an external ear (or pinna) such as seen in mammals. Airborne sounds enter the ear via the middle-ear apparatus, which begins with the tympanum." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0001691 "external ear" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000205 "curator inference" http://www.uni-oldenburg.de/en/neurosciences/cochlea/team/prof-geoffrey-a-manley/manley-ear-evolution/ "Manley GA, The evolution of the hearing organs of amniote vertebrates. Carl von Ossietzky University, Oldenburg (2014)" "An increasing body of evidence indicates that all amniote hearing organs are capable of not only receiving sound stimuli, but also of amplifying weak stimuli. One bi-product of the amplification process is that some of the energy produced escapes the organ and can be measured as sound in the external ear canal. Our work has contributed to the knowledge that not only mammals, as originally thought, but birds and lizards, too, show phenomena associated with an amplification process." bgee ANN 2015-04-14 HOM:0000007 "historical homology" UBERON:0001692 "basioccipital bone" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.237 Table 7.1" bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0001693 "exoccipital bone" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.237 Table 7.1" bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0001694 "petrous part of temporal bone" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.256-258 and Figure 7-24" bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0001695 "squamous part of temporal bone" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.246 and Figure 7-12" bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0001698 "foramen ovale of skull" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0001700 "geniculate ganglion" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1046/j.1469-7580.2001.19910133.x "Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" "These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia." bgee ANN 2013-06-14 HOM:0000007 "historical homology" UBERON:0001701 "glossopharyngeal ganglion" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1046/j.1469-7580.2001.19910133.x "Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" "These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia." bgee ANN 2013-06-14 HOM:0000007 "historical homology" UBERON:0001705 "nail" 9443 "Primates" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p. 225 and p.230-232" "Only primates have nails. In other vertebrates, the keratinizing system at the terminus of each digit produces claws or hooves." bgee ANN 2013-07-17 HOM:0000007 "historical homology" UBERON:0001706 "nasal septum" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1098/rstb.2001.0976 "Kuratani S, Nobusada Y, Horigome N, Shigetani Y, Embryology of the lamprey and evolution of the vertebrate jaw: insights from molecular and developmental perspectives. Philosophical transactions of the Royal Society of London, Series B, Biological sciences (2001)" "Whatever the common ancestor of the lamprey and gnathostomes may have looked like, it most likely possessed a neural-crest-derived premandibular ectomesenchyme closely associated with the NHP [nasohypophyseal plate]. Invention of the jaw subsequently required a space for the nasal septum and maxillary process to develop, which might have been provided by subdivision of the NHP into the nasal placode and the hypophysis (diplorhiny, the state of bilaterally separated nasal openings, would also have been a prerequisite for this)." bgee ANN 2013-06-26 HOM:0000007 "historical homology" UBERON:0001707 "nasal cavity" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1666/04027.1 "Evans DC, Nasal cavity homologies and cranial crest function in lambeosaurine dinosaurs. Paleobiology (2006)" "Despite significant modification to the nasal cavity within Archosauria and its extreme hypertrophy and supraorbital development in Lambeosaurinae, the neural olfactory system and the olfactory region of the nasal cavity proper retain their plesiomorphic positions and associations, suggesting that this system is highly conserved in vertebrate evolution." bgee ANN 2013-06-26 HOM:0000007 "historical homology" UBERON:0001708 "jaw skeleton" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1046/j.1469-7580.2001.19910133.x "Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid." bgee ANN 2013-08-21 HOM:0000007 "historical homology" UBERON:0001708 "jaw skeleton" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "The incorporation of the primary jaw joint into the mammalian middle ear was only possible due to the evolution of a new way to articulate the upper and lower jaws, with the formation of the dentary-squamosal joint, or TMJ in humans. The evolution of the three-ossicle ear in mammals is thus intricately connected with the evolution of a novel jaw joint, the two structures evolving together to create the distinctive mammalian skull." bgee ANN 2013-08-21 HOM:0000007 "historical homology" UBERON:0001709 "upper jaw region" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1046/j.1469-7580.2001.19910133.x "Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid." bgee ANN 2013-08-21 HOM:0000007 "historical homology" UBERON:0001710 "lower jaw region" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1046/j.1469-7580.2001.19910133.x "Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid." bgee ANN 2013-08-21 HOM:0000007 "historical homology" UBERON:0001712 "upper eyelid" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.431" "A tetrapod's eye usually has one or more eyelids that can move across its surface and protect and cleanse it. The eye of lissamphibians has a stationary upper eyelid but a movable and transparent lower one." bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0001713 "lower eyelid" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.431" "A tetrapod's eye usually has one or more eyelids that can move across its surface and protect and cleanse it. The eye of lissamphibians has a stationary upper eyelid but a movable and transparent lower one." bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0001714 "cranial ganglion" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...)" bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0001719 "nucleus ambiguus" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1196/annals.1298.038 "Jarvis ED, Learned birdsong and the neurobiology of human language. Annals of the New York Academy of Sciences (2004)" "Nucleus ambiguous in mammals controls muscles of the vocal organ (the larynx)." bgee ANN 2013-06-07 HOM:0000007 "historical homology" UBERON:0001723 "tongue" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1046/j.1469-7580.2002.00073.x "Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002)" "Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0001727 "taste bud" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1046/j.1469-7580.2001.19910133.x "Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" "Experiments in amphibia have shown that an intrinsic feature of the pharyngeal endoderm is its ability to generate taste buds and this capacity must have been acquired by the endoderm at the origin of the vertebrates." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0001727 "taste bud" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:22512454 "Graham A, Shimeld SM, The origin and evolution of the ectodermal placodes. J Anat (2013)" "Epibranchial placode homologues have also not been identified outside the vertebrates. Indeed, taste buds, one of the structures innervated by epibranchial neurones, are believed to be vertebrate-specific. It should be noted, however, that the epibranchial placodes develop adjacent to the branchial slits, structures which in ascidians form after metamorphosis and are relatively poorly studied." bgee ANN 2015-05-01 HOM:0000007 "historical homology" UBERON:0001728 "nasopharynx" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.596 and Figure 18-21" "The synapsid line of evolution culminating in mammals and the sauropsid line to reptiles and birds diverged millions of years ago, near the time of the origin of amniotes. Although mammals, too, evolved an efficient respiratory system, needed by endothermic animals, the mammalian system differs in many ways from that of birds because it evolved its complex design from the generalized amniote condition independently. The evolution of the secondary palate in mammals and their therapsid ancestors made possible a separation of food and respiratory passage." bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0001729 "oropharynx" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.596 and Figure 18-21" "The synapsid line of evolution culminating in mammals and the sauropsid line to reptiles and birds diverged millions of years ago, near the time of the origin of amniotes. Although mammals, too, evolved an efficient respiratory system, needed by endothermic animals, the mammalian system differs in many ways from that of birds because it evolved its complex design from the generalized amniote condition independently. The evolution of the secondary palate in mammals and their therapsid ancestors made possible a separation of food and respiratory passage." bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0001736 "submandibular gland" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0471210054 "Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptationm(2005) p.211" "In air-feeding animals, the lack of water column to lubricate the food has been compensated for by the evolution of the salivary glands. These glands are present only in amniotes and are controlled by the parasympathetic system." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0001737 "larynx" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.591-592" "Neck lenght increases in reptiles, and the primitive laryngotracheal chamber [found in frogs] becomes divided into a larynx and trachea." bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0001738 "thyroid cartilage" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471090588 "Hildebrand M, Analysis of vertebrate structure (1983) p.239-241" "(In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis." bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0001739 "laryngeal cartilage" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471090588 "Hildebrand M, Analysis of vertebrate structure (1983) p.239-241" "(In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis." bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0001743 "ligament of larynx" 32523 "Tetrapoda" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000211, negated: false, taxon ID: 7742 - entity: UBERON:0001737, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0001743 "ligament of larynx" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000211, negated: false, taxon ID: 40674 - entity: UBERON:0001737, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0001751 "dentine" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1111/j.1469-7580.2012.01495.x "Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)" "Dentine is a bona fide vertebrate novelty, and dentine-secreting odontoblasts represent a cell type that is exclusively derived from the neural crest." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0001751 "dentine" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1002/jez.b.21090 "Donoghue PCJ, Sansom IJ, Downs JP, Early evolution of vertebrate skeletal tissues and cellular interactions, and the canalization of skeletal development. Journal of Experimental Zoology (Mol Dev Evol) (2006) Figure 1" "Origin of dentine predates the evolution of gnathostomes. [curator]" bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0001753 "cementum" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:24023957 "Leblanc AR, Reisz RR, Periodontal ligament, cementum, and alveolar bone in the oldest herbivorous tetrapods, and their evolutionary significance. PLoS One (2013)" "The presence of a tripartite periodontium in diadectids supports the hypothesis that the dental follicle and its derivatives (cementum, alveolar bone, and periodontal ligament) were present in these stem amniotes. We provide the earliest record of a tripartite periodontium in a tetrapod by demonstrating its presence in the Diadectidae, a group that persisted from the Late Pennsylvanian into the Early Permian [27]. The presence of a tripartite periodontium in diadectids and several amniote taxa [2], [3], [8], [11] provides an increasing amount of evidence that all amniotes share the ability to produce the periodontal tissues that have historically been associated with mammalian and crocodilian thecodonty." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0001753|UBERON:0004103|UBERON:0008266|UBERON:0008969 "cementum|alveolar ridge|periodontal ligament|dental follicle" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:24023957 "Leblanc AR, Reisz RR, Periodontal ligament, cementum, and alveolar bone in the oldest herbivorous tetrapods, and their evolutionary significance. PLoS One (2013)" "The presence of a tripartite periodontium in diadectids supports the hypothesis that the dental follicle and its derivatives (cementum, alveolar bone, and periodontal ligament) were present in these stem amniotes. We provide the earliest record of a tripartite periodontium in a tetrapod by demonstrating its presence in the Diadectidae, a group that persisted from the Late Pennsylvanian into the Early Permian [27]. The presence of a tripartite periodontium in diadectids and several amniote taxa [2], [3], [8], [11] provides an increasing amount of evidence that all amniotes share the ability to produce the periodontal tissues that have historically been associated with mammalian and crocodilian thecodonty." bgee ANN 2013-10-08 HOM:0000007 "historical homology" UBERON:0001754 "dental pulp" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1038/nature07304 "Soukup V, Epperlein HH, Horacek I, Cerny R, Dual epithelial origin of vertebrate oral teeth. Nature (2008)" "The oral cavity of vertebrates is generally thought to arise as an ectodermal invagination. Consistent with this, oral teeth are proposed to arise exclusively from ectoderm, contributing to tooth enamel epithelium, and from neural crest derived mesenchyme, contributing to dentin and pulp." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0001756 "middle ear" 8292 "Amphibia" CIO:0000003 "high confidence from single evidence" ECO:0000033 "traceable author statement" DOI:10.1007/s00359-008-0327-1 "Schoffelen RLM, Segenhout JM, Van Dijk P, Mechanics of the exceptional anuran ear. Journal of Comparative Physiology A (2008)" "The ancestral lineage of amphibians separated from the mammalian lineage, approximately 350 million years ago, in the paleozoic era. Many of the important developments in the auditory systems emerged after the ancestral paths separated (Manley and Clack, 2003). This implies that shared features, like the tympanic middle ear, developed independently in different vertebrate lineages." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0001756 "middle ear" 8292 "Amphibia" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.697" "From (the) primitive tetrapod ear, a tympanic ear (enclosed middle ear plus tympanum) subsequently evolved independently at least five times, perhaps more, in later tetrapods. Amphibians, and the related temnospondyls, were the earliest group to evolve a tympanic ear. The tympanum and the enclosed middle ear were inherited by frogs but lost in urodeles and caecilians. Within amniotes, the tympanic ear appears independently in turtles, lepidosaurs, and archosaurs, as well as in mammals." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0001756 "middle ear" 8457 "Sauropsida" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:25902370 "Kitazawa T, Takechi M, Hirasawa T, Adachi N, Narboux-Neme N, Kume H, Maeda K, Hirai T, Miyagawa-Tomita S, Kurihara Y, Hitomi J, Levi G, Kuratani S, Kurihara H, Developmental genetic bases behind the independent origin of the tympanic membrane in mammals and diapsids. Nat Commun (2015)" "The amniote middle ear is a classical example of the evolutionary novelty. Although paleontological evidence supports the view that mammals and diapsids (modern reptiles and birds) independently acquired the middle ear after divergence from their common ancestor, the developmental bases of these transformations remain unknown. Here we show that lower-to-upper jaw transformation induced by inactivation of the Endothelin1-Dlx5/6 cascade involving Goosecoid results in loss of the tympanic membrane in mouse, but causes duplication of the tympanic membrane in chicken. Detailed anatomical analysis indicates that the relative positions of the primary jaw joint and first pharyngeal pouch led to the coupling of tympanic membrane formation with the lower jaw in mammals, but with the upper jaw in diapsids. We propose that differences in connection and release by various pharyngeal skeletal elements resulted in structural diversity, leading to the acquisition of the tympanic membrane in two distinct manners during amniote evolution." bgee ANN 2015-04-29 HOM:0000007 "historical homology" UBERON:0001756 "middle ear" 8459 "Testudines" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.697" "From (the) primitive tetrapod ear, a tympanic ear (enclosed middle ear plus tympanum) subsequently evolved independently at least five times, perhaps more, in later tetrapods. Amphibians, and the related temnospondyls, were the earliest group to evolve a tympanic ear. The tympanum and the enclosed middle ear were inherited by frogs but lost in urodeles and caecilians. Within amniotes, the tympanic ear appears independently in turtles, lepidosaurs, and archosaurs, as well as in mammals." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0001756 "middle ear" 8492 "Archosauria" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.697" "From (the) primitive tetrapod ear, a tympanic ear (enclosed middle ear plus tympanum) subsequently evolved independently at least five times, perhaps more, in later tetrapods. Amphibians, and the related temnospondyls, were the earliest group to evolve a tympanic ear. The tympanum and the enclosed middle ear were inherited by frogs but lost in urodeles and caecilians. Within amniotes, the tympanic ear appears independently in turtles, lepidosaurs, and archosaurs, as well as in mammals." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0001756 "middle ear" 8504 "Lepidosauria" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.697" "From (the) primitive tetrapod ear, a tympanic ear (enclosed middle ear plus tympanum) subsequently evolved independently at least five times, perhaps more, in later tetrapods. Amphibians, and the related temnospondyls, were the earliest group to evolve a tympanic ear. The tympanum and the enclosed middle ear were inherited by frogs but lost in urodeles and caecilians. Within amniotes, the tympanic ear appears independently in turtles, lepidosaurs, and archosaurs, as well as in mammals." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0001756 "middle ear" 9255 "Monotremata" CIO:0000005 "low confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:27563341 "Ramirez-Chaves HE, Weisbecker V, Wroe S, Phillips MJ, Resolving the evolution of the mammalian middle ear using Bayesian inference. Front Zool (2016)" "Resolving the evolution of the mammalian middle ear using Bayesian inference...Our results support a simple, biologically plausible scenario without reversals. The middle ear bones detach from the postdentary trough only twice among mammals, once each in the ancestors of therians and monotremes. Disappearance of Meckel's cartilage occurred independently in numerous lineages from the Late Jurassic to the Late Cretaceous. This final separation is recapitulated during early development of extant mammals, while the earlier-occurring disappearance of a postdentary trough is not" bgee ANN 2016-09-12 HOM:0000007 "historical homology" UBERON:0001756 "middle ear" 9255 "Monotremata" CIO:0000005 "low confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:27228358 "Meng J, Bi S, Zheng X, Wang X, Ear ossicle morphology of the Jurassic euharamiyidan Arboroharamiya and evolution of mammalian middle ear. J Morphol (2016)" "Ear ossicle morphology of the Jurassic euharamiyidan Arboroharamiya and evolution of mammalian middle ear...Given this phylogeny, development of the DMME [definitive mammalian middle ear] took place once in the allotherian clade containing euharamiyidans and multituberculates, probably independent to those of monotremes and therians. Thus, the DMME has evolved at least three times independently in mammals." bgee ANN 2016-09-12 HOM:0000007 "historical homology" UBERON:0001756 "middle ear" NOT 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:25902370 "Kitazawa T, Takechi M, Hirasawa T, Adachi N, Narboux-Neme N, Kume H, Maeda K, Hirai T, Miyagawa-Tomita S, Kurihara Y, Hitomi J, Levi G, Kuratani S, Kurihara H, Developmental genetic bases behind the independent origin of the tympanic membrane in mammals and diapsids. Nat Commun (2015)" "The amniote middle ear is a classical example of the evolutionary novelty. Although paleontological evidence supports the view that mammals and diapsids (modern reptiles and birds) independently acquired the middle ear after divergence from their common ancestor, the developmental bases of these transformations remain unknown. Here we show that lower-to-upper jaw transformation induced by inactivation of the Endothelin1-Dlx5/6 cascade involving Goosecoid results in loss of the tympanic membrane in mouse, but causes duplication of the tympanic membrane in chicken. Detailed anatomical analysis indicates that the relative positions of the primary jaw joint and first pharyngeal pouch led to the coupling of tympanic membrane formation with the lower jaw in mammals, but with the upper jaw in diapsids. We propose that differences in connection and release by various pharyngeal skeletal elements resulted in structural diversity, leading to the acquisition of the tympanic membrane in two distinct manners during amniote evolution." bgee ANN 2015-04-29 HOM:0000007 "historical homology" UBERON:0001756 "middle ear" 32525 "Theria" CIO:0000005 "low confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:27563341 "Ramirez-Chaves HE, Weisbecker V, Wroe S, Phillips MJ, Resolving the evolution of the mammalian middle ear using Bayesian inference. Front Zool (2016)" "Resolving the evolution of the mammalian middle ear using Bayesian inference...Our results support a simple, biologically plausible scenario without reversals. The middle ear bones detach from the postdentary trough only twice among mammals, once each in the ancestors of therians and monotremes. Disappearance of Meckel's cartilage occurred independently in numerous lineages from the Late Jurassic to the Late Cretaceous. This final separation is recapitulated during early development of extant mammals, while the earlier-occurring disappearance of a postdentary trough is not" bgee ANN 2016-09-12 HOM:0000007 "historical homology" UBERON:0001756 "middle ear" 32525 "Theria" CIO:0000005 "low confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:27228358 "Meng J, Bi S, Zheng X, Wang X, Ear ossicle morphology of the Jurassic euharamiyidan Arboroharamiya and evolution of mammalian middle ear. J Morphol (2016)" "Ear ossicle morphology of the Jurassic euharamiyidan Arboroharamiya and evolution of mammalian middle ear...Given this phylogeny, development of the DMME [definitive mammalian middle ear] took place once in the allotherian clade containing euharamiyidans and multituberculates, probably independent to those of monotremes and therians. Thus, the DMME has evolved at least three times independently in mammals." bgee ANN 2016-09-12 HOM:0000007 "historical homology" UBERON:0001756 "middle ear" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.697" "From (the) primitive tetrapod ear, a tympanic ear (enclosed middle ear plus tympanum) subsequently evolved independently at least five times, perhaps more, in later tetrapods. Amphibians, and the related temnospondyls, were the earliest group to evolve a tympanic ear. The tympanum and the enclosed middle ear were inherited by frogs but lost in urodeles and caecilians. Within amniotes, the tympanic ear appears independently in turtles, lepidosaurs, and archosaurs, as well as in mammals." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0001756 "middle ear" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:25902370 "Kitazawa T, Takechi M, Hirasawa T, Adachi N, Narboux-Neme N, Kume H, Maeda K, Hirai T, Miyagawa-Tomita S, Kurihara Y, Hitomi J, Levi G, Kuratani S, Kurihara H, Developmental genetic bases behind the independent origin of the tympanic membrane in mammals and diapsids. Nat Commun (2015)" "The amniote middle ear is a classical example of the evolutionary novelty. Although paleontological evidence supports the view that mammals and diapsids (modern reptiles and birds) independently acquired the middle ear after divergence from their common ancestor, the developmental bases of these transformations remain unknown. Here we show that lower-to-upper jaw transformation induced by inactivation of the Endothelin1-Dlx5/6 cascade involving Goosecoid results in loss of the tympanic membrane in mouse, but causes duplication of the tympanic membrane in chicken. Detailed anatomical analysis indicates that the relative positions of the primary jaw joint and first pharyngeal pouch led to the coupling of tympanic membrane formation with the lower jaw in mammals, but with the upper jaw in diapsids. We propose that differences in connection and release by various pharyngeal skeletal elements resulted in structural diversity, leading to the acquisition of the tympanic membrane in two distinct manners during amniote evolution." bgee ANN 2015-04-29 HOM:0000007 "historical homology" UBERON:0001756 "middle ear" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23396272 "Sienknecht UJ, Developmental origin and fate of middle ear structures. Hearing research (2013)" "Middle ear structures are the result of long evolutionary processes that produced a remarkable transformation of structural to auditory elements. This transformation can be reconstructed from fossil vertebrates by comparison of homologous structures, i.e. structures sharing a common ancestral origin. At least two lineages of development can be resolved when tracing back the components that comprise the middle ears of mammalian and non-mammalian land vertebrates (amniotes): Evolution has led to the formation of three-ossicle middle ears of mammals and a single-ossicle transmission system in other land vertebrates." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0001756 "middle ear" NOT 40674 "Mammalia" CIO:0000005 "low confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:27563341 "Ramirez-Chaves HE, Weisbecker V, Wroe S, Phillips MJ, Resolving the evolution of the mammalian middle ear using Bayesian inference. Front Zool (2016)" "Resolving the evolution of the mammalian middle ear using Bayesian inference...Our results support a simple, biologically plausible scenario without reversals. The middle ear bones detach from the postdentary trough only twice among mammals, once each in the ancestors of therians and monotremes. Disappearance of Meckel's cartilage occurred independently in numerous lineages from the Late Jurassic to the Late Cretaceous. This final separation is recapitulated during early development of extant mammals, while the earlier-occurring disappearance of a postdentary trough is not" bgee ANN 2016-09-12 HOM:0000007 "historical homology" UBERON:0001756 "middle ear" NOT 40674 "Mammalia" CIO:0000005 "low confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:27228358 "Meng J, Bi S, Zheng X, Wang X, Ear ossicle morphology of the Jurassic euharamiyidan Arboroharamiya and evolution of mammalian middle ear. J Morphol (2016)" "Ear ossicle morphology of the Jurassic euharamiyidan Arboroharamiya and evolution of mammalian middle ear...Given this phylogeny, development of the DMME [definitive mammalian middle ear] took place once in the allotherian clade containing euharamiyidans and multituberculates, probably independent to those of monotremes and therians. Thus, the DMME has evolved at least three times independently in mammals." bgee ANN 2016-09-12 HOM:0000007 "historical homology" UBERON:0001757 "pinna" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.420" "Mammals have a third type of tympanic ear. An external flap, the auricle or pinna, helps funnel sound waves down the external acoustic meatus to the tympanic membrane." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0001758 "periodontium" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:24023957 "Leblanc AR, Reisz RR, Periodontal ligament, cementum, and alveolar bone in the oldest herbivorous tetrapods, and their evolutionary significance. PLoS One (2013)" "The presence of a tripartite periodontium in diadectids supports the hypothesis that the dental follicle and its derivatives (cementum, alveolar bone, and periodontal ligament) were present in these stem amniotes. We provide the earliest record of a tripartite periodontium in a tetrapod by demonstrating its presence in the Diadectidae, a group that persisted from the Late Pennsylvanian into the Early Permian [27]. The presence of a tripartite periodontium in diadectids and several amniote taxa [2], [3], [8], [11] provides an increasing amount of evidence that all amniotes share the ability to produce the periodontal tissues that have historically been associated with mammalian and crocodilian thecodonty." bgee ANN 2013-10-08 HOM:0000007 "historical homology" UBERON:0001759 "vagus nerve" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625" "Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII)." bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001759 "vagus nerve" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...)" bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001761 "future foramen cecum" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0006699" bgee HOM:0000007 "historical homology" UBERON:0001763 "odontogenic papilla" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:19266065 "Koussoulakou DS, Margaritis LH, Koussoulakos SL, A curriculum vitae of teeth: evolution, generation, regeneration. International Journal of Biological Sciences (2009)" "The ancestor of recent vertebrate teeth was a tooth-like structure on the outer body surface of jawless fishes.(...) Teeth are highly mineralized appendages found in the entrance of the alimentary canal of both invertebrates and vertebrates." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0001765 "mammary duct" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23681303 "Oftedal OT, Dhouailly D, Evo-devo of the mammary gland. J Mammary Gland Biol Neoplasia (2013)" "While it appears that the mammary ductal tree and secretory tissue (lactocytes and myoepithelial cells) evolved from an ancestral apocrine gland embedded within an APSU [Apo-pilo-sebaceous unit] , the earlier developmental structures, including the ML [Mammary line], MP [Mammary placode], MB [Mammary bulb] and PS [Primary sprout]-and the nipple and gland cistern derived from these structures-have a separate evolutionary origin." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0001766 "anterior chamber of eyeball" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424-428 and Figure 12-25" "Although the eye varies greatly in adaptive details among vertebrates, its basic structure is the same in all. (...) the aqueous humor flows into the anterior chamber, located between the iris and the cornea." bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0001769 "iris" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1038/nrn2283 "Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)" "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya." bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0001771 "pupil" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1038/nrn2283 "Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)" "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya." bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0001772 "corneal epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000964, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001773 "sclera" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.426-427 and Figure 12-28" "Sclera is an opaque and white fibrous tunic that is present in the eyeballs of representative vertebrates. [curator]" bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0001775 "ciliary body" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1038/nrn2283 "Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)" "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya." bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0001776 "optic choroid" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.426-427 and Figure 12-28" "Choroid is a vascular tunic that is present in the eyeballs of representative vertebrates. [curator]" bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0001778 "ciliary epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001775, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001780 "spinal nerve" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0001782 "pigmented layer of retina" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina." bgee AUC 2013-05-15 HOM:0000007 "historical homology" UBERON:0001783 "optic disc" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.428" "Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. (...) Because no photoreceptors are present in the optic disk, this is a blind spot." bgee ANN 2013-04-15 HOM:0000007 "historical homology" UBERON:0001783 "optic disc" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1038/nrn2283 "Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)" "(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya." bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0001785 "cranial nerve" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...)" bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001785 "cranial nerve" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625" "Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII)." bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001786 "fovea centralis" 7742 "Vertebrata" CIO:0000005 "low confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:11193946 "Azuma N, Molecular cell biology on morphogenesis of the fovea and evolution of the central vision. Nihon Ganka Gakkai Zasshi (2000)" "The fovea first appeared in evolution in the temporal retina of fishes. Then, in birds, the nasal fovea and bifoveal system with nasal and temporal foveas developed. The fovea disappeared in primitive mammals, and reappeared in primates. A residue of the fovea is conserved in the visual streak, and the disappearance and reappearance of the fovea, in primitive mammals and primates respectively, correlates with degeneration and restoration of cone pigment genes in photoreceptors." bgee ANN 2013-06-20 HOM:0000007 "historical homology" UBERON:0001786 "fovea centralis" 40674 "Mammalia" CIO:0000005 "low confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1016/S1350-9462(00)00012-4 "Ahnelt PK, Kolb H, The mammalian photoreceptor mosaic-adaptive design. Progress in Retinal and Eye Research (2000)" "Many retinal features (foveas, trichromacy, midget pathways and associated cell types) appear specific to primates. This has led to investigations in parallel with other mammalian models such as cat or rabbit. Correlation of the results often proves to be difficult, since an evolutionary scenario with transitions between the mammalian models is largely lacking." bgee ANN 2013-06-20 HOM:0000007 "historical homology" UBERON:0001787 "photoreceptor layer of retina" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina." bgee ANN 2013-04-15 HOM:0000007 "historical homology" UBERON:0001787|UBERON:0001905 "photoreceptor layer of retina|pineal body" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:16771606 "Mano H, Fukada Y, A median third eye: pineal gland retraces evolution of vertebrate photoreceptive organs. Photochemistry and photobiology (2007)" "In many vertebrates, the pineal gland serves as a photoreceptive neuroendocrine organ. Morphological and functional similarities between the pineal and retinal photoreceptor cells indicate their close evolutionary relationship, and hence the comparative studies on the pineal gland and the retina are the keys to deciphering the evolutionary traces of the vertebrate photoreceptive organs." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0001789 "outer nuclear layer of retina" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina." bgee ANN 2013-04-15 HOM:0000007 "historical homology" UBERON:0001790 "outer plexiform layer of retina" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 and Figure 12-26 p.425" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina." bgee AUC 2013-05-15 HOM:0000007 "historical homology" UBERON:0001791 "inner nuclear layer of retina" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina." bgee ANN 2013-04-15 HOM:0000007 "historical homology" UBERON:0001792 "ganglionic layer of retina" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina." bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0001792 "ganglionic layer of retina" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1038/nrn2283 "Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)" "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya." bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0001793 "nerve fiber layer of retina" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina." bgee AUC 2013-05-15 HOM:0000007 "historical homology" UBERON:0001795 "inner plexiform layer of retina" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 and Figure 12-26 p.425" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina." bgee AUC 2013-05-15 HOM:0000007 "historical homology" UBERON:0001796 "aqueous humor of eyeball" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:19060283 "Gray MP, Smith RS, Soules KA, John SW, Link BA, The aqueous humor outflow pathway of zebrafish. Invest Ophthalmol Vis Sci (2009)" "In the ocular anterior segment of vertebrates, the production and outflow of aqueous humor are important determinants of intraocular pressure and are required to maintain the proper shape and optical parameters of the eye. (...) Despite the unique vectorial flow of aqueous humor of zebrafish, the local anatomic features and cellular ultrastructure of this system have similarities with the aqueous humor pathway of mammals. (...) the description of homologous aqueous humor outflow tissues in zebrafish provides the opportunity for genetic studies to probe the specific molecular and cellular mechanisms that control aqueous humor dynamics and intraocular pressure." bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0001797 "vitreous humor" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424-426" "Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens, and a more gelatinous vitreous body lies behind the lens." bgee ANN 2013-09-06 HOM:0000007 "historical homology" UBERON:0001798 "vitreous body" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424-429" "Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. (...) A watery aqueous humor fills the spaces in the eye in front of the lens, and a more gelatinous vitreous body lies behind the lens." bgee ANN 2013-09-06 HOM:0000007 "historical homology" UBERON:0001803 "epithelium of lens" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000965, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001804 "capsule of lens" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1038/nrn2283 "Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)" "(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya." bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0001804 "capsule of lens" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24" "Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...)." bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0001805 "autonomic ganglion" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000045, negated: false, taxon ID: 33213 - entity: UBERON:0002410, negated: false, taxon ID: 89593" bgee HOM:0000007 "historical homology" UBERON:0001806 "sympathetic ganglion" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000013, negated: false, taxon ID: 7742 - entity: UBERON:0000045, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0001806 "sympathetic ganglion" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000013, negated: false, taxon ID: 32523 - entity: UBERON:0000045, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0001813 "spinal nerve plexus" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1038/ncomms1045 "Ma LH, Gilland E, Bass AH, Baker R, Ancestry of motor innervation to pectoral fin and forelimb. Nature Communication (2010)" "The conserved pectoral innervation pattern among jawed fish shown here, which consists of motoneurons and nerves originating from both the hindbrain and the spinal cord, differs notably from the spinal-only innervation in tetrapods. Our work [anatomical and embryological evidence] in basal and derived actinopterygians supports the hypothesis that a dual hindbrain-spinal origin for pectoral motoneurons in fish evolved into a spinal-only origin for forelimb motoneurons in tetrapods (...) We propose that Oc/Sp [occipital/spinal] pectoral innervation among actinopterygians, sarcopterygians and members of both subclasses of chondrichthyans (the elasmobranch pattern may be derived) represents the ancestral condition for all jawed vertebrates." bgee ANN 2013-06-13 HOM:0000007 "historical homology" UBERON:0001813 "spinal nerve plexus" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1038/ncomms1045 "Ma LH, Gilland E, Bass AH, Baker R, Ancestry of motor innervation to pectoral fin and forelimb. Nature Communication (2010)" "The conserved pectoral innervation pattern among jawed fish shown here, which consists of motoneurons and nerves originating from both the hindbrain and the spinal cord, differs notably from the spinal-only innervation in tetrapods. Our work [anatomical and embryological evidence] in basal and derived actinopterygians supports the hypothesis that a dual hindbrain-spinal origin for pectoral motoneurons in fish evolved into a spinal-only origin for forelimb motoneurons in tetrapods (...) We propose that Oc/Sp [occipital/spinal] pectoral innervation among actinopterygians, sarcopterygians and members of both subclasses of chondrichthyans (the elasmobranch pattern may be derived) represents the ancestral condition for all jawed vertebrates." bgee ANN 2013-06-13 HOM:0000007 "historical homology" UBERON:0001814 "brachial nerve plexus" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.436" "To reach the muscles, dermatomes, and other structures of the limbs, some of the neurons in the spinal nerves come together in the plexus at the base of the limb. Such plexuses occur in all gnathostomes, and they reach their highest complexity among mammals and birds in which the cervical plexus supplies many ventral neck muscles, the brachial plexus supplies the pectoral appendage, a lumbosacral plexus supplies the pelvic appendage, and a coccygeal plexus supplies some of the pelvic muscles." bgee ANN 2013-06-13 HOM:0000007 "historical homology" UBERON:0001815 "lumbosacral nerve plexus" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.436" "To reach the muscles, dermatomes, and other structures of the limbs, some of the neurons in the spinal nerves come together in the plexus at the base of the limb. Such plexuses occur in all gnathostomes, and they reach their highest complexity among mammals and birds in which the cervical plexus supplies many ventral neck muscles, the brachial plexus supplies the pectoral appendage, a lumbosacral plexus supplies the pelvic appendage, and a coccygeal plexus supplies some of the pelvic muscles." bgee ANN 2013-06-13 HOM:0000007 "historical homology" UBERON:0001817 "lacrimal gland" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) The eye of terrestrial vertebrates, p.431-432 and Figure 12-30" "Lacrimal glands are structures of the mammalian lacrimal apparatus. [curator]" bgee ANN 2013-09-05 HOM:0000007 "historical homology" UBERON:0001820 "sweat gland" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471090588 "Hildebrand M, Analysis of vertebrate structure (1983) p.101" "Sweat glands (also called sudoriferous glands) are unique to mammals." bgee ANN 2013-07-17 HOM:0000007 "historical homology" UBERON:0001821 "sebaceous gland" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" http://www1.unifi.it/caryologia/past_volumes/59_2/59-2_1405.pdf "Quagliata1 S, Malentacchi C, Delfino C, Brunasso AMG, Delfino G, Adaptive evolution of secretory cell lines in vertebrate skin. Caryologia (2006)" "In reptilian skin, a novel, successful type of multicellular glands appears that shares several morpho-functional traits with mammalian sebaceous and avian preen glands (Quay 1986a). In this review, they are therefore referred to a common lipogenic class. These glands are exclusive of Amniota and perform similar functions to the syncytial lipid glands in phyllomedusine tree frogs, by providing a hydrophobic shield against terrestrial environs. They differ from the latter in that they are epithelial rather than syncytial in structure, undergo holocrine degeneration during lipogenesis and lack a myoepithelial sheath. Besides waterproofing the body surface and horny skin appendages (feathers and hairs), sebaceous units may play an accessory role as scent (odorous) glands, either as homogeneous secretory organs, or in association with apocrine sweat tubules (in mammals)." bgee ANN 2013-10-10 HOM:0000007 "historical homology" UBERON:0001828 "gingiva" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1007/s00223-002-1076-8 "Sawada T, Inoue S, Mineralization of basement membrane mediates dentogingival adhesion in mammalian and nonmammalian vertebrates. Calcified Tissue International (2003)" "The use of the developing tooth of both the shark and the monkey in this study provided an opportunity for the comparative examination of the internal basement membrane again in the course of the evolution of the tooth. The results show that the strong binding between the organic and mineral phases is established by mineralization of a part of the internal basement membrane in a mammalian as well as in a nonmammalian vertebrate." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0001831 "parotid gland" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0471210054 "Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptationm(2005) p.211" "In air-feeding animals, the lack of water column to lubricate the food has been compensated for by the evolution of the salivary glands. These glands are present only in amniotes and are controlled by the parasympathetic system." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0001832 "sublingual gland" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0471210054 "Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptationm(2005) p.211" "In air-feeding animals, the lack of water column to lubricate the food has been compensated for by the evolution of the salivary glands. These glands are present only in amniotes and are controlled by the parasympathetic system." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0001833 "lip" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1242/dev.01705 "Helms JA, Cordero D, Tapadia MD, New insights into craniofacial morphogenesis. Development (2005) Figure 1" "[During development of the vertebrate craniofacial primordia] The maxillomandibular prominences give rise to the lower jaw (specifically from the mandibular prominences), to the sides of the middle and lower face, to the lateral borders of the lips, and to the secondary palate (from the maxillary prominences)." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0001834 "upper lip" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" DOI:10.1111/j.1096-3642.1996.tb01658.x "Mallatt J, Ventilation and the origin of jawed vertebrates: a new mouth. Zoological Journal of the Linnean Society (1996)"", ISBN:978-0072528305 ""Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Box essay 13.1 and Box figure I, p.502-503" "In the Jon Mallatt's reconstructed model, the upper lips were well developed in the jawless common ancestor of all living vertebrates. [curator]" bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0001835 "lower lip" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001710, negated: false, taxon ID: 7776 - entity: UBERON:0001833, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001839 "bony labyrinth" 9347 "Eutheria" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1080/02724634.2011.557284 "Ekdale EG, Rowe T, Morphology and Variation within the Bony Labyrinth of Zhelestids (Mammalia, Eutheria) and Other Therian Mammals. Journal of Vertebrate Paleontology (2011)" "The morphology of the labyrinth of zhelestids, a group of eutherian mammals from the Late Cretaceous, agrees with that of other extinct eutherians, including Kulbeckia kulbecke, Ukhaatherium gobiensis, and Zalambdalestes lechei. Features of the labyrinth of zhelestids include a cochlea with one and a half turns and a secondary common crus, which are plesiomorphic for eutherians." bgee ANN 2013-06-26 HOM:0000007 "historical homology" UBERON:0001839 "bony labyrinth" 32525 "Theria" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:22404255 "Gunz P, Ramsier M, Kuhrig M, Hublin JJ, Spoor F, The mammalian bony labyrinth reconsidered, introducing a comprehensive geometric morphometric approach. J Anat (2012)" "The bony labyrinth inside the petrous portion of the temporal bone houses the sense organs of hearing and balance. Characterized in therian mammals by three semicircular canals and a coiled cochlea (Luo et al., 2011) its morphology is highly conserved. Nevertheless, the detailed morphology varies even among closely related taxa and carries valuable functional, developmental and phylogenetic information (e.g. Spoor & Zonneveld, 1998; Schmelzle et al., 2007; Lebrun et al., 2010)." bgee ANN 2013-06-26 HOM:0000007 "historical homology" UBERON:0001840 "semicircular canal" 32525 "Theria" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:22404255 "Gunz P, Ramsier M, Kuhrig M, Hublin JJ, Spoor F, The mammalian bony labyrinth reconsidered, introducing a comprehensive geometric morphometric approach. J Anat (2012)" "The bony labyrinth inside the petrous portion of the temporal bone houses the sense organs of hearing and balance. Characterized in therian mammals by three semicircular canals and a coiled cochlea (Luo et al., 2011) its morphology is highly conserved. Nevertheless, the detailed morphology varies even among closely related taxa and carries valuable functional, developmental and phylogenetic information (e.g. Spoor & Zonneveld, 1998; Schmelzle et al., 2007; Lebrun et al., 2010)." bgee ANN 2013-06-26 HOM:0000007 "historical homology" UBERON:0001844 "cochlea" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1016/S0959-4388(98)80033-0 "Manley GA, Koeppl C, Phylogenetic development of the cochlea and its innervation. Current Opinion in Neurobiology (1998)" "Because achieving high sensitivity is generally advantageous for auditory organs, it is not surprising that evidence for cochlear amplification is also seen in nonmammals. Spontaneous otoacoustic emissions (SOAEs) are narrow-band sound signals emitted from the inner ear, and it is generally assumed that their energy derives from the hair-cell molecular motors underlying cochlear amplification. However, all terrestrial vertebrates studied so far (including amphibians) show very similar SOAEs. The most parsimonious explanation for the universality of this phenomena is that some kind of amplifying mechanism is at least as old as land vertebrates themselves." bgee ANN 2017-05-02 HOM:0000007 "historical homology" UBERON:0001844 "cochlea" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1111/joa.12314 "Basch ML, Brown RM 2nd, Jen HI, Groves AK, Where hearing starts: the development of the mammalian cochlea. J Anat (2016)" "Although the term 'cochlea' derives from the Latin description of the coiled snail-like auditory structure in the mammalian inner ear, the term is habitually also applied to the homologous shorter, uncoiled structures in birds, crocodiles and alligators (archosaurs), snakes and lizards (lepidosaurs) and turtles. Regardless of their length and curvature, these outgrowths from the rest of the inner ear contain a patch of sensory epithelium - the basilar papilla - that responds to sound using mechanosensitive hair cells. In mammals, the basilar papilla is more commonly known as the organ of Corti." bgee ANN 2017-05-02 HOM:0000007 "historical homology" UBERON:0001844 "cochlea" 32525 "Theria" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:20667879 "Luo ZX, Ruf I, Schultz JA, Martin T, Fossil evidence on evolution of inner ear cochlea in Jurassic mammals. Proc Biol Sci (2011)" "The coiled cochlea is a key evolutionary innovation of modern therian mammals." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0001844 "cochlea" 32525 "Theria" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:22404255 "Gunz P, Ramsier M, Kuhrig M, Hublin JJ, Spoor F, The mammalian bony labyrinth reconsidered, introducing a comprehensive geometric morphometric approach. J Anat (2012)" "The bony labyrinth inside the petrous portion of the temporal bone houses the sense organs of hearing and balance. Characterized in therian mammals by three semicircular canals and a coiled cochlea (Luo et al., 2011) its morphology is highly conserved. Nevertheless, the detailed morphology varies even among closely related taxa and carries valuable functional, developmental and phylogenetic information (e.g. Spoor & Zonneveld, 1998; Schmelzle et al., 2007; Lebrun et al., 2010)." bgee ANN 2017-05-02 HOM:0000007 "historical homology" UBERON:0001844 "cochlea" 32525 "Theria" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:22404255 "Gunz P, Ramsier M, Kuhrig M, Hublin JJ, Spoor F, The mammalian bony labyrinth reconsidered, introducing a comprehensive geometric morphometric approach. J Anat (2012)" "The bony labyrinth inside the petrous portion of the temporal bone houses the sense organs of hearing and balance. Characterized in therian mammals by three semicircular canals and a coiled cochlea (Luo et al., 2011) its morphology is highly conserved. Nevertheless, the detailed morphology varies even among closely related taxa and carries valuable functional, developmental and phylogenetic information (e.g. Spoor & Zonneveld, 1998; Schmelzle et al., 2007; Lebrun et al., 2010)." bgee ANN 2017-05-02 HOM:0000007 "historical homology" UBERON:0001846 "internal ear" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:11523832 "Streit A, Origin of the vertebrate inner ear: evolution and induction of the otic placode. J Anat (2001)" "Molecular evidence has revealed that lower chordates already possess sensory organs that share homology to the vertebrate inner ear." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0001846 "internal ear" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0471090588 "Hildebrand M, Analysis of vertebrate structure (1983) p.366" "The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0001846 "internal ear" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:11523832 "Streit A, Origin of the vertebrate inner ear: evolution and induction of the otic placode. J Anat (2001)" "Recent molecular data have challenged the longstanding view that special sense organs such as the inner ear have evolved with the appearance of vertebrates." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0001846 "internal ear" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" http://www.uni-oldenburg.de/en/neurosciences/cochlea/team/prof-geoffrey-a-manley/manley-ear-evolution/ "Manley GA, The evolution of the hearing organs of amniote vertebrates. Carl von Ossietzky University, Oldenburg (2014)" "the therian lineages also evolved a specialized, three-ossicle middle-ear system that was pre-adapted to respond to very high frequencies (Manley, 2010a). Thus inner and middle ears evolved congruently, enabling an expansion to the audibility of very high frequencies in most - especially small - mammals." bgee ANN 2015-04-13 HOM:0000007 "historical homology" UBERON:0001846 "internal ear" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:20667879 "Luo ZX, Ruf I, Schultz JA, Martin T, Fossil evidence on evolution of inner ear cochlea in Jurassic mammals. Proc Biol Sci (2011)" "Here, we report the discovery of the precursory structures of the fully coiled cochlea of modern therians in the inner ear of the Late Jurassic mammal Dryolestes leiriensis [17], a 150 Myr old fossil mammal in the cladotherian clade, as defined by the common ancestor of dryolestoids + extant therians (e.g. [3]). Dryolestes is a stem taxon characterized by plesiomorphic dental features, and a near relative to the modern marsupials and placentals. The fine inner ear structures are preserved in a petrosal bone that houses the inner ear in the skull." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0001849 "membranous labyrinth" 32525 "Theria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:22404255 "Gunz P, Ramsier M, Kuhrig M, Hublin JJ, Spoor F, The mammalian bony labyrinth reconsidered, introducing a comprehensive geometric morphometric approach. J Anat (2012)" "The bony labyrinth inside the petrous portion of the temporal bone houses the sense organs of hearing and balance. Characterized in therian mammals by three semicircular canals and a coiled cochlea (Luo et al., 2011) its morphology is highly conserved. Nevertheless, the detailed morphology varies even among closely related taxa and carries valuable functional, developmental and phylogenetic information (e.g. Spoor & Zonneveld, 1998; Schmelzle et al., 2007; Lebrun et al., 2010)." bgee ANN 2013-06-26 HOM:0000007 "historical homology" UBERON:0001853 "utricle of membranous labyrinth" NOT 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19786082 "Manley GA, An evolutionary perspective on middle ears. Hearing research (2010)" "During their evolution, various lineages of fishes developed an auditory ability through co-opting vestibular epithelia (e.g. sacculus, utriculus, lagena) to also respond to sound. By means of these changes, and in some cases supported by accessory structures which increase sensitivity, some modern fish are quite sensitive to frequencies up to several kHz (Ladich and Popper, 2004). These developments are, however, entirely unrelated to hearing in land vertebrates." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0001853 "utricle of membranous labyrinth" 7776 "Gnathostomata" CIO:0000005 "low confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414" "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0001853 "utricle of membranous labyrinth" NOT 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19786082 "Manley GA, An evolutionary perspective on middle ears. Hearing research (2010)" "During their evolution, various lineages of fishes developed an auditory ability through co-opting vestibular epithelia (e.g. sacculus, utriculus, lagena) to also respond to sound. By means of these changes, and in some cases supported by accessory structures which increase sensitivity, some modern fish are quite sensitive to frequencies up to several kHz (Ladich and Popper, 2004). These developments are, however, entirely unrelated to hearing in land vertebrates." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0001853 "utricle of membranous labyrinth" 7898 "Actinopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19786082 "Manley GA, An evolutionary perspective on middle ears. Hearing research (2010)" "During their evolution, various lineages of fishes developed an auditory ability through co-opting vestibular epithelia (e.g. sacculus, utriculus, lagena) to also respond to sound. By means of these changes, and in some cases supported by accessory structures which increase sensitivity, some modern fish are quite sensitive to frequencies up to several kHz (Ladich and Popper, 2004). These developments are, however, entirely unrelated to hearing in land vertebrates." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0001853 "utricle of membranous labyrinth" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19786082 "Manley GA, An evolutionary perspective on middle ears. Hearing research (2010)" "During their evolution, various lineages of fishes developed an auditory ability through co-opting vestibular epithelia (e.g. sacculus, utriculus, lagena) to also respond to sound. By means of these changes, and in some cases supported by accessory structures which increase sensitivity, some modern fish are quite sensitive to frequencies up to several kHz (Ladich and Popper, 2004). These developments are, however, entirely unrelated to hearing in land vertebrates." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0001853 "utricle of membranous labyrinth" NOT 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19786082 "Manley GA, An evolutionary perspective on middle ears. Hearing research (2010)" "During their evolution, various lineages of fishes developed an auditory ability through co-opting vestibular epithelia (e.g. sacculus, utriculus, lagena) to also respond to sound. By means of these changes, and in some cases supported by accessory structures which increase sensitivity, some modern fish are quite sensitive to frequencies up to several kHz (Ladich and Popper, 2004). These developments are, however, entirely unrelated to hearing in land vertebrates." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0001854 "saccule of membranous labyrinth" NOT 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19786082 "Manley GA, An evolutionary perspective on middle ears. Hearing research (2010)" "During their evolution, various lineages of fishes developed an auditory ability through co-opting vestibular epithelia (e.g. sacculus, utriculus, lagena) to also respond to sound. By means of these changes, and in some cases supported by accessory structures which increase sensitivity, some modern fish are quite sensitive to frequencies up to several kHz (Ladich and Popper, 2004). These developments are, however, entirely unrelated to hearing in land vertebrates." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0001854 "saccule of membranous labyrinth" 7776 "Gnathostomata" CIO:0000005 "low confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414" "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. (...) In all gnathostomes, the utriculus connects ventrally with a larger sac, called the sacculus (...) ." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0001854 "saccule of membranous labyrinth" NOT 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19786082 "Manley GA, An evolutionary perspective on middle ears. Hearing research (2010)" "During their evolution, various lineages of fishes developed an auditory ability through co-opting vestibular epithelia (e.g. sacculus, utriculus, lagena) to also respond to sound. By means of these changes, and in some cases supported by accessory structures which increase sensitivity, some modern fish are quite sensitive to frequencies up to several kHz (Ladich and Popper, 2004). These developments are, however, entirely unrelated to hearing in land vertebrates." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0001854 "saccule of membranous labyrinth" 7898 "Actinopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19786082 "Manley GA, An evolutionary perspective on middle ears. Hearing research (2010)" "During their evolution, various lineages of fishes developed an auditory ability through co-opting vestibular epithelia (e.g. sacculus, utriculus, lagena) to also respond to sound. By means of these changes, and in some cases supported by accessory structures which increase sensitivity, some modern fish are quite sensitive to frequencies up to several kHz (Ladich and Popper, 2004). These developments are, however, entirely unrelated to hearing in land vertebrates." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0001854 "saccule of membranous labyrinth" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19786082 "Manley GA, An evolutionary perspective on middle ears. Hearing research (2010)" "During their evolution, various lineages of fishes developed an auditory ability through co-opting vestibular epithelia (e.g. sacculus, utriculus, lagena) to also respond to sound. By means of these changes, and in some cases supported by accessory structures which increase sensitivity, some modern fish are quite sensitive to frequencies up to several kHz (Ladich and Popper, 2004). These developments are, however, entirely unrelated to hearing in land vertebrates." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0001854 "saccule of membranous labyrinth" NOT 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19786082 "Manley GA, An evolutionary perspective on middle ears. Hearing research (2010)" "During their evolution, various lineages of fishes developed an auditory ability through co-opting vestibular epithelia (e.g. sacculus, utriculus, lagena) to also respond to sound. By means of these changes, and in some cases supported by accessory structures which increase sensitivity, some modern fish are quite sensitive to frequencies up to several kHz (Ladich and Popper, 2004). These developments are, however, entirely unrelated to hearing in land vertebrates." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0001855 "cochlear duct of membranous labyrinth" 32525 "Theria" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414" "In most groups of gnathostomes, the caudoventral evagination of the sacculus forms a small lagena, and in some diapsids and mammals the lagena develops into a longer duct. The lagena becomes greatly elongated in therians and coils to form the cochlear duct." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0001855 "cochlear duct of membranous labyrinth" 32525 "Theria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:20667879 "Luo ZX, Ruf I, Schultz JA, Martin T, Fossil evidence on evolution of inner ear cochlea in Jurassic mammals. Proceedings Biological sciences The Royal Society (2011) Figure 1" "The snail-shaped cochlea with its interior complexity is one of the most prominent features of marsupial and placental mammals with significant function and evolutionary consequence." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0001855 "cochlear duct of membranous labyrinth" 32525 "Theria" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414" "In most groups of gnathostomes, the caudoventral evagination of the sacculus forms a small lagena, and in some diapsids and mammals the lagena develops into a longer duct. The lagena becomes greatly elongated in therians and coils to form the cochlear duct." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0001856 "semicircular duct" 32525 "Theria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:22404255 "Gunz P, Ramsier M, Kuhrig M, Hublin JJ, Spoor F, The mammalian bony labyrinth reconsidered, introducing a comprehensive geometric morphometric approach. J Anat (2012)" "The bony labyrinth inside the petrous portion of the temporal bone houses the sense organs of hearing and balance. Characterized in therian mammals by three semicircular canals and a coiled cochlea (Luo et al., 2011) its morphology is highly conserved. Nevertheless, the detailed morphology varies even among closely related taxa and carries valuable functional, developmental and phylogenetic information (e.g. Spoor & Zonneveld, 1998; Schmelzle et al., 2007; Lebrun et al., 2010)." bgee ANN 2013-06-26 HOM:0000007 "historical homology" UBERON:0001857 "anterior semicircular duct" 32525 "Theria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:22404255 "Gunz P, Ramsier M, Kuhrig M, Hublin JJ, Spoor F, The mammalian bony labyrinth reconsidered, introducing a comprehensive geometric morphometric approach. J Anat (2012)" "The bony labyrinth inside the petrous portion of the temporal bone houses the sense organs of hearing and balance. Characterized in therian mammals by three semicircular canals and a coiled cochlea (Luo et al., 2011) its morphology is highly conserved. Nevertheless, the detailed morphology varies even among closely related taxa and carries valuable functional, developmental and phylogenetic information (e.g. Spoor & Zonneveld, 1998; Schmelzle et al., 2007; Lebrun et al., 2010)." bgee ANN 2013-06-26 HOM:0000007 "historical homology" UBERON:0001858 "posterior semicircular duct" 32525 "Theria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:22404255 "Gunz P, Ramsier M, Kuhrig M, Hublin JJ, Spoor F, The mammalian bony labyrinth reconsidered, introducing a comprehensive geometric morphometric approach. J Anat (2012)" "The bony labyrinth inside the petrous portion of the temporal bone houses the sense organs of hearing and balance. Characterized in therian mammals by three semicircular canals and a coiled cochlea (Luo et al., 2011) its morphology is highly conserved. Nevertheless, the detailed morphology varies even among closely related taxa and carries valuable functional, developmental and phylogenetic information (e.g. Spoor & Zonneveld, 1998; Schmelzle et al., 2007; Lebrun et al., 2010)." bgee ANN 2013-06-26 HOM:0000007 "historical homology" UBERON:0001869 "cerebral hemisphere" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1146/annurev.ne.04.030181.001505 "Northcutt RG, Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci. (1981)" "The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor." bgee ANN 2013-06-10 HOM:0000007 "historical homology" UBERON:0001873 "caudate nucleus" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1016/j.cub.2011.05.001 "Stephenson-Jones M, Samuelsson E, Ericsson J, Robertson B, Grillner S, Evolutionary conservation of the basal ganglia as a common vertebrate mechanism for action selection. Current Biology (2011)" "All nuclei of the mammalian basal ganglia are also present in the oldest vertebrates." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0001874 "putamen" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1016/j.cub.2011.05.001 "Stephenson-Jones M, Samuelsson E, Ericsson J, Robertson B, Grillner S, Evolutionary conservation of the basal ganglia as a common vertebrate mechanism for action selection. Current Biology (2011)" "All nuclei of the mammalian basal ganglia are also present in the oldest vertebrates." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0001875 "globus pallidus" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:24776992 "Medina L, Abellan A, Vicario A, Desfilis E, Evolutionary and developmental contributions for understanding the organization of the Basal Ganglia. Brain Behav Evol (2014)" "in the absence of enough connectivity/functional data, it is unclear whether the pallidal domain of lungfishes, ray-finned fishes and cartilaginous fishes is subdivided into dorsal and ventral parts comparable to those in tetrapods, although it seems plausible in lungfishes due to the similarity of their subpallium to that of amphibians [Gonzalez and Northcutt, 2009]. In this sense, a true globus pallidus (dorsal pallidum) may first be seen at the time of origin of tetrapods or perhaps a little earlier (with the common ancestor of lungfishes and tetrapods) and be characterized by the presence of two major neuron types. Nevertheless, data on the neuropeptide content and connections of each one of these cell types in different species are still missing." bgee ANN 2014-05-20 HOM:0000007 "historical homology" UBERON:0001875 "globus pallidus" 1338369 "Dipnotetrapodomorpha" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:24776992 "Medina L, Abellan A, Vicario A, Desfilis E, Evolutionary and developmental contributions for understanding the organization of the Basal Ganglia. Brain Behav Evol (2014)" "in the absence of enough connectivity/functional data, it is unclear whether the pallidal domain of lungfishes, ray-finned fishes and cartilaginous fishes is subdivided into dorsal and ventral parts comparable to those in tetrapods, although it seems plausible in lungfishes due to the similarity of their subpallium to that of amphibians [Gonzalez and Northcutt, 2009]. In this sense, a true globus pallidus (dorsal pallidum) may first be seen at the time of origin of tetrapods or perhaps a little earlier (with the common ancestor of lungfishes and tetrapods) and be characterized by the presence of two major neuron types. Nevertheless, data on the neuropeptide content and connections of each one of these cell types in different species are still missing." bgee ANN 2014-05-20 HOM:0000007 "historical homology" UBERON:0001875 "globus pallidus" 1338369 "Dipnotetrapodomorpha" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:24776992 "Medina L, Abellan A, Vicario A, Desfilis E, Evolutionary and developmental contributions for understanding the organization of the Basal Ganglia. Brain Behav Evol (2014)" "in the absence of enough connectivity/functional data, it is unclear whether the pallidal domain of lungfishes, ray-finned fishes and cartilaginous fishes is subdivided into dorsal and ventral parts comparable to those in tetrapods, although it seems plausible in lungfishes due to the similarity of their subpallium to that of amphibians [Gonzalez and Northcutt, 2009]. In this sense, a true globus pallidus (dorsal pallidum) may first be seen at the time of origin of tetrapods or perhaps a little earlier (with the common ancestor of lungfishes and tetrapods) and be characterized by the presence of two major neuron types. Nevertheless, data on the neuropeptide content and connections of each one of these cell types in different species are still missing." bgee ANN 2014-05-20 HOM:0000007 "historical homology" UBERON:0001876 "amygdala" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0471090588 "Hildebrand M, Analysis of vertebrate structure (1983) p.342" "One part of the striatum is called the archistriatum. (...) The archistriatum of fishes consists of several indistinctly segregated nuclei called the amygdaloid (...) complex. Tetrapods retain the structure, and in mammals the corresponding amygdala is a globular mass that tends to be ventral to the other basal nuclei." bgee ANN 2013-06-07 HOM:0000007 "historical homology" UBERON:0001883 "olfactory tubercle" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1016/0166-2236(95)93932-N "Northcutt RG, Kaas JH, The emergence and evolution of mammalian neocortex. Trends in Neurosciences (1995) Figure 3" "An olfactory tubercle was already present in the ancestor of mammals. [curator]" bgee ANN 2013-06-13 HOM:0000007 "historical homology" UBERON:0001884 "phrenic nerve" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:12539245 "Straus C, Vasilakos K, Wilson RJ, Oshima T, Zelter M, Derenne JP, Similowski T, Whitelaw WA, A phylogenetic hypothesis for the origin of hiccough. Bioessays (2003)" "Hiccoughs are characterized by glottal closure during neuronal inspiration, and by early development in relation to lung ventilation. They are inhibited during hypercapnia and by lung inflation. They can be abolished by baclofen. These properties are shared by ventilatory motor patterns of lower vertebrates, leading to the hypothesis that hiccough is the resurgence of archaic motor patterns and particularly of the motor pattern of gill ventilation in bimodal breathers such as most frogs, at the tadpole stage. A circuit that can generate hiccoughs may persist in mammals because it has permitted the development of pattern generators for other useful functions such as modern eupnea or suckling. Neurone recordings may permit testing of these models by comparing the pattern of neuronal activation during hiccoughs in mammals and during gill ventilation in bimodal breathers." bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0001885 "dentate gyrus of hippocampal formation" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000063 "compositional similarity evidence" DOI:10.1002/cne.23851 "Hevner RF, Evolution of the mammalian dentate gyrus. J Comp Neurol (2016)" "the neuronal morphology and cytoarchitecture of reptilian medial cortex appear similar enough to mammalian DG that a common ancestral form with conserved neuronal composition and trilaminar organization can be inferred. These considerations support the conclusion that a DG precursor was present in the cortical bauplan of early amniotes, and retained certain recognizable features (morphologic and molecular) in derived lineages of reptiles, birds, and mammals." bgee ANN 2017-05-16 HOM:0000007 "historical homology" UBERON:0001885 "dentate gyrus of hippocampal formation" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1002/cne.23851 "Hevner RF, Evolution of the mammalian dentate gyrus. J Comp Neurol (2016)" "the neuronal morphology and cytoarchitecture of reptilian medial cortex appear similar enough to mammalian DG that a common ancestral form with conserved neuronal composition and trilaminar organization can be inferred. These considerations support the conclusion that a DG precursor was present in the cortical bauplan of early amniotes, and retained certain recognizable features (morphologic and molecular) in derived lineages of reptiles, birds, and mammals." bgee ANN 2017-05-16 HOM:0000007 "historical homology" UBERON:0001885 "dentate gyrus of hippocampal formation" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1002/cne.23851 "Hevner RF, Evolution of the mammalian dentate gyrus. J Comp Neurol (2016)" "Comparative analysis of amniotes shows that the mammalian dentate gyrus is distinguished by convolution and non-periventricular adult neurogenesis. Both features arose in stem mammals, by enhanced migration of intermediate progenitors (IPs) and radial glial progenitors (RGPs) in the embryonic dentate migration stream." bgee ANN 2017-05-16 HOM:0000007 "historical homology" UBERON:0001886 "choroid plexus" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0001890 "forebrain" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:8787764 "Holland ND, Panganiban G, Henyey EL, Holland LZ, Sequence and developmental expression of AmphiDll, an amphioxus Distal-less gene transcribed in the ectoderm, epidermis and nervous system: insights into evolution of craniate forebrain and neural crest. Development (1996)" "In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0001891 "midbrain" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/S0959-4388(99)00003-3 "Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)" "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0001891 "midbrain" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1016/S0959-4388(99)00003-3 "Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)" "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0001891 "midbrain" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1016/S0959-4388(99)00003-3 "Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)" "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0001892 "rhombomere" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1006/dbio.2002.0831 "Mazet F, Shimeld SM, The Evolution of Chordate Neural Segmentation. Developmental Biology (2002)" "Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0001893 "telencephalon" NOT 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1016/j.ydbio.2005.02.008 "Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)" "From an evolutionary standpoint, the telencephalon is the most recent brain structure: the amphioxus does not have this structure as a morphological entity. Overt telencephalon is present in the hagfish and lamprey to receive numerous input fibers from various parts of the CNS, similar to gnathostomes." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0001893 "telencephalon" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1016/j.ydbio.2005.02.008 "Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)" "From an evolutionary standpoint, the telencephalon is the most recent brain structure: the amphioxus does not have this structure as a morphological entity. Overt telencephalon is present in the hagfish and lamprey to receive numerous input fibers from various parts of the CNS, similar to gnathostomes." bgee ANN 2015-04-02 HOM:0000007 "historical homology" UBERON:0001894 "diencephalon" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/S0959-4388(99)00003-3 "Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)" "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0001894 "diencephalon" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1016/S0959-4388(99)00003-3 "Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)" "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0001894 "diencephalon" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1016/S0959-4388(99)00003-3 "Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)" "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0001895 "metencephalon" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500" "The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0001896 "medulla oblongata" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1016/j.ydbio.2008.08.017 "Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008)" "Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0001897 "dorsal plus ventral thalamus" 8457 "Sauropsida" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1017/S1472928808000356 "Butler AB, Evolution of the thalamus: a morphological and functional review. Thalamus and Related System (2008)" "Enlargement of the forebrain, including elaboration of the thalamus, has occurred independently within different groups of vertebrates. Dorsal and ventral thalamic territories can be identified in most vertebrates, with variations in the presence of GABAergic neuronal components. An inhibitory thalamic reticular nucleus-like input to the dorsal thalamus might be a common feature, as might the organizational plan of two divisions of the dorsal thalamus, the lemnothalamus and collothalamus. Differential, independent elaboration of these divisions occurred in mammals and sauropsids (reptiles and birds), making their evolutionary relationships challenging to discern. Not all of the crucial features identified for mammalian thalamocortical circuitry are present in other vertebrates, but birds share the most features identified to date." bgee ANN 2013-10-21 HOM:0000007 "historical homology" UBERON:0001897 "dorsal plus ventral thalamus" 8457 "Sauropsida" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1017/S1472928808000356 "Butler AB, Evolution of the thalamus: a morphological and functional review. Thalamus and Related System (2008)" "Enlargement of the forebrain, including elaboration of the thalamus, has occurred independently within different groups of vertebrates. Dorsal and ventral thalamic territories can be identified in most vertebrates, with variations in the presence of GABAergic neuronal components. An inhibitory thalamic reticular nucleus-like input to the dorsal thalamus might be a common feature, as might the organizational plan of two divisions of the dorsal thalamus, the lemnothalamus and collothalamus. Differential, independent elaboration of these divisions occurred in mammals and sauropsids (reptiles and birds), making their evolutionary relationships challenging to discern. Not all of the crucial features identified for mammalian thalamocortical circuitry are present in other vertebrates, but birds share the most features identified to date." bgee ANN 2013-10-21 HOM:0000007 "historical homology" UBERON:0001897 "dorsal plus ventral thalamus" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1017/S1472928808000356 "Butler AB, Evolution of the thalamus: a morphological and functional review. Thalamus and Related System (2008)" "Enlargement of the forebrain, including elaboration of the thalamus, has occurred independently within different groups of vertebrates. Dorsal and ventral thalamic territories can be identified in most vertebrates, with variations in the presence of GABAergic neuronal components. An inhibitory thalamic reticular nucleus-like input to the dorsal thalamus might be a common feature, as might the organizational plan of two divisions of the dorsal thalamus, the lemnothalamus and collothalamus. Differential, independent elaboration of these divisions occurred in mammals and sauropsids (reptiles and birds), making their evolutionary relationships challenging to discern. Not all of the crucial features identified for mammalian thalamocortical circuitry are present in other vertebrates, but birds share the most features identified to date." bgee ANN 2013-06-10 HOM:0000007 "historical homology" UBERON:0001897 "dorsal plus ventral thalamus" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1017/S1472928808000356 "Butler AB, Evolution of the thalamus: a morphological and functional review. Thalamus and Related System (2008)" "Enlargement of the forebrain, including elaboration of the thalamus, has occurred independently within different groups of vertebrates. Dorsal and ventral thalamic territories can be identified in most vertebrates, with variations in the presence of GABAergic neuronal components. An inhibitory thalamic reticular nucleus-like input to the dorsal thalamus might be a common feature, as might the organizational plan of two divisions of the dorsal thalamus, the lemnothalamus and collothalamus. Differential, independent elaboration of these divisions occurred in mammals and sauropsids (reptiles and birds), making their evolutionary relationships challenging to discern. Not all of the crucial features identified for mammalian thalamocortical circuitry are present in other vertebrates, but birds share the most features identified to date." bgee ANN 2013-06-10 HOM:0000007 "historical homology" UBERON:0001898 "hypothalamus" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1016/j.ydbio.2005.02.008 "Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)" "For instance, the vertebrate ventral diencephalon generates the hypothalamus which functions as a major endocrine center in cooperation with the hypophysis, the anterior part of the pituitary gland, located just ventral to the hypothalamus. In the amphioxus brain, the presence of a hypothalamus-like structure has been reported associated with the ventrally located Hatschek's pit, the hypothetical hypophysial homologue. It is thus conceivable that a hypothalamus-like structure originally involved in endocrine functions may have already been present before the establishment of vertebrates." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0001898 "hypothalamus" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1016/j.ydbio.2005.02.008 "Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)" "For instance, the vertebrate ventral diencephalon generates the hypothalamus which functions as a major endocrine center in cooperation with the hypophysis, the anterior part of the pituitary gland, located just ventral to the hypothalamus. In the amphioxus brain, the presence of a hypothalamus-like structure has been reported associated with the ventrally located Hatschek's pit, the hypothetical hypophysial homologue. It is thus conceivable that a hypothalamus-like structure originally involved in endocrine functions may have already been present before the establishment of vertebrates." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0001899 "epithalamus" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1046/j.1469-7580.2001.19910063.x "Concha ML and Wilson SW, Asymmetry in the epithalamus of vertebrates. J Anat (2001)" "The epithalamus has been historically conceived as a distinct neuroanatomical moiety within the diencephalon of all vertebrates. (...) The evolutionary origins of epithalamic structures are uncertain but asymmetry in this region is likely to have existed at the origin of the vertebrate, perhaps even the chordate, lineage." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0001899 "epithalamus" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1046/j.1469-7580.2001.19910063.x "Concha ML and Wilson SW, Asymmetry in the epithalamus of vertebrates. J Anat (2001)" "The epithalamus has been historically conceived as a distinct neuroanatomical moiety within the diencephalon of all vertebrates. (...) The evolutionary origins of epithalamic structures are uncertain but asymmetry in this region is likely to have existed at the origin of the vertebrate, perhaps even the chordate, lineage." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0001901 "epithelium of trachea" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21669855 "Leys SP, Nichols SA, Adams ED, Epithelia and integration in sponges. Integrative and Comparative Biology (2009)" bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0001902 "epithelium of small intestine" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002108, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0001905 "pineal body" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:16771606 "Mano H, Fukada Y, A median third eye: pineal gland retraces evolution of vertebrate photoreceptive organs. Photochemistry and photobiology (2007)" "In many vertebrates, the pineal gland serves as a photoreceptive neuroendocrine organ." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0001911 "mammary gland" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:23681303 "Oftedal OT, Dhouailly D, Evo-devo of the mammary gland. J Mammary Gland Biol Neoplasia (2013)" "Mammary development proceeds through homologous phases across taxa, but evolutionary modifications in early development produce different final morphologies." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0001911 "mammary gland" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:12751889 "Oftedal OT, The mammary gland and its origin during synapsid evolution. J Mammary Gland Biol Neoplasia (2002)" "The synapsid branch of the amniote tree that separated from other taxa in the Pennsylvanian (>310 million years ago) evolved a glandular rather than scaled integument. Repeated radiations of synapsids produced a gradual accrual of mammalian features. The mammary gland apparently derives from an ancestral apocrine-like gland that was associated with hair follicles. This association is retained by monotreme mammary glands and is evident as vestigial mammary hair during early ontogenetic development of marsupials." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0001911 "mammary gland" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.224" "The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0001911 "mammary gland" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.224" "The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0001911 "mammary gland" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:12751889 "Oftedal OT, The mammary gland and its origin during synapsid evolution. J Mammary Gland Biol Neoplasia (2002)" "The synapsid branch of the amniote tree that separated from other taxa in the Pennsylvanian (>310 million years ago) evolved a glandular rather than scaled integument. Repeated radiations of synapsids produced a gradual accrual of mammalian features. The mammary gland apparently derives from an ancestral apocrine-like gland that was associated with hair follicles. This association is retained by monotreme mammary glands and is evident as vestigial mammary hair during early ontogenetic development of marsupials." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0001913 "milk" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23681303 "Oftedal OT, Dhouailly D, Evo-devo of the mammary gland. J Mammary Gland Biol Neoplasia (2013)" "The origin of the mammary gland (MG) is buried deep in time, as many of its evolutionary novelties-such as caseins and other milk-specific proteins, and the method of sugar synthesis- appear to have originated more than 300 million years ago (mya) in the Carboniferous geological period [1, 2]. This was a time (Fig. 1) when the first fully terrestrial vertebrates, the basal amniotes, were evolving from earlier tetrapods (ancestors of amphibians and other terrestrial forms) from which they inherited a glandular integument-long before the first appearance of mammals (ca. 190 mya) or even of dinosaurs (ca. 230 mya)." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0001915 "endothelium of capillary" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001982, negated: false, taxon ID: 7711 - entity: UBERON:0001986, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001916 "endothelium of arteriole" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001980, negated: false, taxon ID: 7742 - entity: UBERON:0001986, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001917 "endothelium of artery" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0001986, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001918 "endothelium of venule" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001979, negated: false, taxon ID: 7742 - entity: UBERON:0001986, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001919 "endothelium of vein" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0001986, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001936 "tuberomammillary nucleus" 314146 "Euarchontoglires" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1038/nrn1299 "Vann SD, Aggleton JP, The mammillary bodies: two memory systems in one? Nature reviews, Neuroscience (2004)" "Both lateral and medial mammillary bodies are also innervated by the supramammillary nuclei, the tuberomammillary nucleus and the septal region. As far as can be determined, this overall pattern of connections, which has been most studied in the rat brain, is also found in the primate brain." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0001938 "lateral mammillary nucleus" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.651 and Figure 16.41" "In vertebrates mammillary bodies develop within the hypothalamus and contain medial mammillary nuclei and lateral mammillary nuclei. [curator]" bgee FRB 2013-05-22 HOM:0000007 "historical homology" UBERON:0001939 "medial mammillary nucleus" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.651 and Figure 16.41" "In vertebrates mammillary bodies develop within the hypothalamus and contain medial mammillary nuclei and lateral mammillary nuclei. [curator]" bgee FRB 2013-05-22 HOM:0000007 "historical homology" UBERON:0001941 "lateral habenular nucleus" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1523/JNEUROSCI.3690-09.2010 "Amo R, Aizawa H, Takahoko M, Kobayashi M, Takahashi R, Aoki T, Okamoto H, Identification of the Zebrafish ventral habenula as a homolog of the mammalian lateral habenula. The Journal of Neuroscience (2010)" "Identification of the Zebrafish ventral habenula as a homolog of the mammalian lateral habenula (...) Gene expression analyses revealed that the ventromedially positioned ventral habenula in the adult originated from the region of primordium lateral to the dorsal habenula during development. This suggested that zebrafish habenulae emerge during development with mediolateral orientation similar to that of the mammalian medial and lateral habenulae. These findings indicated that the lateral habenular pathways are evolutionarily conserved pathways and might control adaptive behaviors in vertebrates through the regulation of monoaminergic activities." bgee ANN 2015-04-14 HOM:0000007 "historical homology" UBERON:0001941|ZFA:0000302 "lateral habenular nucleus|ventral habenular nucleus (Danio)" 117571 "Euteleostomi" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1523/JNEUROSCI.3690-09.2010 "Amo R, Aizawa H, Takahoko M, Kobayashi M, Takahashi R, Aoki T, Okamoto H, Identification of the Zebrafish ventral habenula as a homolog of the mammalian lateral habenula. The Journal of Neuroscience (2010)" "Identification of the Zebrafish ventral habenula as a homolog of the mammalian lateral habenula (...) Gene expression analyses revealed that the ventromedially positioned ventral habenula in the adult originated from the region of primordium lateral to the dorsal habenula during development. This suggested that zebrafish habenulae emerge during development with mediolateral orientation similar to that of the mammalian medial and lateral habenulae. These findings indicated that the lateral habenular pathways are evolutionarily conserved pathways and might control adaptive behaviors in vertebrates through the regulation of monoaminergic activities." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0001941|ZFA:0000302 "lateral habenular nucleus|ventral habenular nucleus (Danio)" 117571 "Euteleostomi" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1523/JNEUROSCI.3690-09.2010 "Amo R, Aizawa H, Takahoko M, Kobayashi M, Takahashi R, Aoki T, Okamoto H, Identification of the Zebrafish ventral habenula as a homolog of the mammalian lateral habenula. The Journal of Neuroscience (2010)" "Identification of the Zebrafish ventral habenula as a homolog of the mammalian lateral habenula (...) Gene expression analyses revealed that the ventromedially positioned ventral habenula in the adult originated from the region of primordium lateral to the dorsal habenula during development. This suggested that zebrafish habenulae emerge during development with mediolateral orientation similar to that of the mammalian medial and lateral habenulae. These findings indicated that the lateral habenular pathways are evolutionarily conserved pathways and might control adaptive behaviors in vertebrates through the regulation of monoaminergic activities." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0001943 "midbrain tegmentum" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/j.brainresbull.2005.05.001 "Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005)" "Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny." bgee ANN 2013-06-07 HOM:0000007 "historical homology" UBERON:0001943 "midbrain tegmentum" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1016/j.brainresbull.2005.05.001 "Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005)" "Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny." bgee ANN 2013-06-07 HOM:0000007 "historical homology" UBERON:0001947 "red nucleus" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471210054 "Butler AB, Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.292" "A red nucleus is present in cartilaginous fishes, ray-finned fishes, lungfishes, amphibians, and amniotes and is thus plesiomorphic for jawed vertebrates." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0001949 "gingival epithelium" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001828, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0001950 "neocortex" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:26029038 "Luzzati F, A hypothesis for the evolution of the upper layers of the neocortex through co-option of the olfactory cortex developmental program. Front Neurosci (2015)" "The neocortex is unique to mammals and its evolutionary origin is still highly debated. The neocortex is generated by the dorsal pallium ventricular zone, a germinative domain that in reptiles give rise to the dorsal cortex. Whether this latter allocortical structure contains homologs of all neocortical cell types it is unclear. Recently we described a population of DCX+/Tbr1+ cells that is specifically associated with the layer II of higher order areas of both the neocortex and of the more evolutionary conserved piriform cortex. In a reptile similar cells are present in the layer II of the olfactory cortex and the DVR but not in the dorsal cortex. These data are consistent with the proposal that the reptilian dorsal cortex is homologous only to the deep layers of the neocortex while the upper layers are a mammalian innovation." bgee ANN 2015-08-17 HOM:0000007 "historical homology" UBERON:0001950 "neocortex" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000033 "traceable author statement" PMID:24671134 "Nomura T, Murakami Y, Gotoh H, Ono K, Reconstruction of ancestral brains: exploring the evolutionary process of encephalization in amniotes. Neurosci Res (2014)" "Extant amniotes have homologous regions in their dorsal part of the telencephalon, namely the pallium. The pallium is subdivided into four regions including the medial, dorsal, lateral and ventral pallium. In mammals, the dorsal and lateral pallium increased its their size and the neocortex was elaborated with a six-layered laminar structure (Nieuwenhuys, 1994 and Puelles et al., 2000). These cortical characteristics are unique to three mammalian groups, including eutheria (placental mammals), marsupials and monotremes, which suggests that the neocortex was acquired in the common ancestors of modern mammalian groups (Nieuwenhuys, 1994 and Puzzolo and Mallamaci, 2010)." bgee ANN 2016-09-20 HOM:0000007 "historical homology" UBERON:0001950 "neocortex" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:26029038 "Luzzati F, A hypothesis for the evolution of the upper layers of the neocortex through co-option of the olfactory cortex developmental program. Front Neurosci (2015)" "The neocortex is unique to mammals and its evolutionary origin is still highly debated. The neocortex is generated by the dorsal pallium ventricular zone, a germinative domain that in reptiles give rise to the dorsal cortex. Whether this latter allocortical structure contains homologs of all neocortical cell types it is unclear. Recently we described a population of DCX+/Tbr1+ cells that is specifically associated with the layer II of higher order areas of both the neocortex and of the more evolutionary conserved piriform cortex. In a reptile similar cells are present in the layer II of the olfactory cortex and the DVR but not in the dorsal cortex. These data are consistent with the proposal that the reptilian dorsal cortex is homologous only to the deep layers of the neocortex while the upper layers are a mammalian innovation." bgee ANN 2015-08-17 HOM:0000007 "historical homology" UBERON:0001951 "epithelium of nasopharynx" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21669855 "Leys SP, Nichols SA, Adams ED, Epithelia and integration in sponges. Integrative and Comparative Biology (2009)" bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0001952 "epithelium of oropharynx" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001729, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0001954 "Ammon's horn" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000033 "traceable author statement" PMID:23754432 "Allen TA, Fortin NJ, The evolution of episodic memory. Proceedings of the National Academy of Sciences of the United States of America (2013)" "The hippocampus has been identified in many species, including a large breadth of mammals (57, 58), birds (59, 60), reptiles [medial cortex, (61)], and teleost fish [dorsolateral telencephalon (61, 62)]. The neurobiological and functional evidence strongly suggests that the hippocampus is a homologous structure across species." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0001954 "Ammon's horn" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1007/978-3-540-29678-2_3165 "Jarvis ED, Evolution of the Pallium in Birds and Reptiles. Encyclopedia of Neuroscience (2009) p.1390-1400" "pallial regions that are widely recognized to be homologous among birds, reptiles, mammals and other vertebrates: the hippocampus, olfactory cortex, and olfactory bulb" bgee ANN 2013-06-14 HOM:0000007 "historical homology" UBERON:0001954 "Ammon's horn" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:11923018 "Rodriguez F, Lopez JC, Vargas JP, Broglio C, Gomez Y, Salas C, Spatial memory and hippocampal pallium through vertebrate evolution: insights from reptiles and teleost fish. Brain research bulletin (2002)" "the close functional similarity among the hippocampus of mammals and birds, the medial cortex of reptiles, and the lateral pallium of teleost fish suggest that early in the evolution of vertebrates, the medial pallium of an ancestral fish group that lived some 400 million years ago and gave rise to these extant vertebrate groups became specialized for encoding and processing complex spatial information, possibly as a navigational device that has been conserved through the evolution of each independent vertebrate lineage" bgee ANN 2013-06-14 HOM:0000007 "historical homology" UBERON:0001970 "bile" 7776 "Gnathostomata" CIO:0000005 "low confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1194/jlr.R000042 "Hofmann AF, Hagey LR, Krasowski MD, Bile salts of vertebrates: structural variation and possible evolutionary significance. J Lipid Res (2010)" "It is tempting to infer what the ancestral bile salt profile was at some of the major nodes on the tree in Fig. 2. As discussed above, the earliest ancestral vertebrates are predicted to have produced only C27 bile alcohols as their major bile salts. The more difficult question is, when did the ability to synthesize C24 bile acids first appear. There are two main possibilities here. First, the last common ancestor to fish and mammals (basal gnathostome) already had the ability to synthesize C24 bile acids. In this case, the observation of extant gnathostomes (e.g., lobe-finned fish, salamanders, some frogs) that secrete only C27 bile alcohols would reflect lineage-specific loss of the ability to synthesize C24 bile acids during evolution. Alternatively, the basal gnathostome had only C27 bile alcohols and the ability to synthesize C24 bile acids has occurred multiple times in vertebrate evolution (i.e., convergent evolution)." bgee ANN 2017-10-10 HOM:0000007 "historical homology" UBERON:0001976 "epithelium of esophagus" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001043, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001976 "epithelium of esophagus" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001043, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0001979 "venule" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.604-606" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0001980 "arteriole" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.604-606" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0001981 "blood vessel" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1196/annals.1341.002 "Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)" "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0001982 "capillary" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1196/annals.1341.002 "Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)" "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0001985 "corneal endothelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000964, negated: false, taxon ID: 7742 - entity: UBERON:0001986, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0001986 "endothelium" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23809110 "Monahan-Earley R, Dvorak AM, Aird WC, Evolutionary origins of the blood vascular system and endothelium. J Thromb Haemost (2013)" "The endothelium evolved in an ancestral vertebrate some 540-510 million years ago to optimize flow dynamics and barrier function, and/or to localize immune and coagulation functions." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0001987 "placenta" 9347 "Eutheria" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1038/35054550 "Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O'Brien SJ, Molecular phylogenetics and the origins of placental mammals. Nature (2001)" "Phylogenetic analyses of the concatenated data set using maximum parsimony, maximum likelihood and distance based (neighbour joining) methods all converged on a nearly identical, well supported topology defining four principal eutherian lineages. The results affirm monophyly of traditional placental orders (except Artiodactyla and Insectivora), and also support some previously proposed, as well as new, superordinal clades." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0001987 "placenta" 9347 "Eutheria" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:16492730 "Wildman DE, Chen C, Erez O, Grossman LI, Goodman M, Romero R, Evolution of the mammalian placenta revealed by phylogenetic analysis. Proc Natl Acad Sci U S A (2006)" "Phylogenetic estimations of the ancestral placental shape suggest this character had a minimum of seven state changes during eutherian evolution (Fig. 2 B). A discoid placenta is clearly ancestral for Eutheria (and probably for Metatheria + Eutheria) and is still maintained in most clades." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0001987 "placenta" 32525 "Theria" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:16492730 "Wildman DE, Chen C, Erez O, Grossman LI, Goodman M, Romero R, Evolution of the mammalian placenta revealed by phylogenetic analysis. Proc Natl Acad Sci U S A (2006)" "Phylogenetic estimations of the ancestral placental shape suggest this character had a minimum of seven state changes during eutherian evolution (Fig. 2 B). A discoid placenta is clearly ancestral for Eutheria (and probably for Metatheria + Eutheria) and is still maintained in most clades." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0001997 "olfactory epithelium" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19590178 "Zeiske E, Bartsch P, Hansen A, Early ontogeny of the olfactory organ in a basal actinopterygian fish: polypterus. Brain Behav Evol (2009)" "Formation of the olfactory epithelium with an exclusively epidermal contribution of supporting cells as seen in Acipenser and Xenopus is phylogenetically considered a plesiomorphic (primitive) osteichthyan or at least a basal actinopterygian character, as opposed to the apomorphic (derived) mode found in teleosts." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0001999 "iliopsoas" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.394 Table 10.2" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0002000 "gluteal muscle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.394 Table 10.2" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0002011 "thoracodorsal artery" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001112, negated: false, taxon ID: 40674 - entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0002012 "pulmonary artery" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" "On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0002012 "pulmonary artery" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:23378277 "Longo S, Riccio M, McCune AR, Homology of lungs and gas bladders: insights from arterial vasculature. J Morphol (2013)" "Our data reveal that Acipenser and Polyodon [both Actinopterygii] have paired posterior branches of the fourth efferent branchial arteries, which are thus similar in origin to pulmonary arteries. We hypothesize that these arteries are vestigial pulmonary arteries that have been coopted for new functions due to the dorsal shift of the AO and/or the loss of respiration in these taxa. Ancestral state reconstructions support pulmonary arteries as a synapomorphy of the Osteichthyes, provide the first concrete evidence for the retention of pulmonary arteries in Amia, and support the homology of lungs and gas bladders due to a shared vascular supply." bgee ANN 2013-10-08 HOM:0000007 "historical homology" UBERON:0002012 "pulmonary artery" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" PMID:23378277 "Longo S, Riccio M, McCune AR, Homology of lungs and gas bladders: insights from arterial vasculature. J Morphol (2013)" "Based on the topographic similarity of their origin to that of pulmonary arteries in Protopterus, Polypterus, Amia, and tetrapods, we propose that the paired branches of the fourth efferent branchial arteries in Polyodon and Acipenser [both Actinopterygii] are not novel arteries, but vestigial pulmonary arteries that have found new targets in the Acipenseriformes." bgee ANN 2013-10-08 HOM:0000007 "historical homology" UBERON:0002012 "pulmonary artery" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23378277 "Longo S, Riccio M, McCune AR, Homology of lungs and gas bladders: insights from arterial vasculature. J Morphol (2013)" "Our data reveal that Acipenser and Polyodon [both Actinopterygii] have paired posterior branches of the fourth efferent branchial arteries, which are thus similar in origin to pulmonary arteries. We hypothesize that these arteries are vestigial pulmonary arteries that have been coopted for new functions due to the dorsal shift of the AO and/or the loss of respiration in these taxa. Ancestral state reconstructions support pulmonary arteries as a synapomorphy of the Osteichthyes, provide the first concrete evidence for the retention of pulmonary arteries in Amia, and support the homology of lungs and gas bladders due to a shared vascular supply." bgee ANN 2013-10-08 HOM:0000007 "historical homology" UBERON:0002016 "pulmonary vein" 8287 "Sarcopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" "On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0002018 "synovial membrane of synovial joint" 8287 "Sarcopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:11068553 "O'Connel JX, Pathology of the synovium. American Journal of Clinical Pathology (2000)" "Phylogenetically, synovium is one of the newer attributes of the vertebrate locomotor apparatus. The first synovial joints developed in the piscine jaw of ancestors of modern lungfish by an evolutionary process that modified preexisting fibrous and cartilaginous joints, which were the predominant articulation of the early sea- and land-dwelling vertebrates." bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0002019 "accessory XI nerve" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" http://en.wikipedia.org/wiki/Cranial_nerves "cranial nerves on Wikipedia" "Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0002020 "gray matter" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:16389299 "Wen Q, Chklovskii DB, Segregation of the brain into gray and white matter: a design minimizing conduction delays. PLoS Comput Biol (2005)" "A ubiquitous feature of the vertebrate brain is its segregation into white and gray matter. Gray matter contains neuron somata, synapses, and local wiring, such as dendrites and mostly nonmyelinated axons." bgee ANN 2013-06-10 HOM:0000007 "historical homology" UBERON:0002023 "claustrum of brain" 32525 "Theria" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1159/000066698 "Butler AB, Molnar Z, Manger PR, Apparent absence of claustrum in monotremes: implications for forebrain evolution in amniotes. Brain, Behavior and Evolution (2002)" "A claustrum might have been present in ancestral mammals and lost in the monotreme clade, or it might have been gained at the origin of therian mammals." bgee ANN 2013-06-10 HOM:0000007 "historical homology" UBERON:0002023 "claustrum of brain" 40674 "Mammalia" CIO:0000005 "low confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1159/000066698 "Butler AB, Molnar Z, Manger PR, Apparent absence of claustrum in monotremes: implications for forebrain evolution in amniotes. Brain, Behavior and Evolution (2002)" "A claustrum might have been present in ancestral mammals and lost in the monotreme clade, or it might have been gained at the origin of therian mammals." bgee ANN 2013-06-10 HOM:0000007 "historical homology" UBERON:0002028 "hindbrain" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/S0959-4388(99)00003-3 "Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)" "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0002028 "hindbrain" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1016/S0959-4388(99)00003-3 "Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)" "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0002028 "hindbrain" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1016/S0959-4388(99)00003-3 "Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)" "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0002029 "epithelium of gall bladder" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002110, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0002031 "epithelium of bronchus" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002185, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0002036 "striated muscle tissue" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:22763458 "Steinmetz PR, Kraus JE, Larroux C, Hammel JU, Amon-Hassenzahl A, Houliston E, Woerheide G, Nickel M, Degnan BM, Technau U, Independent evolution of striated muscles in cnidarians and bilaterians. Nature (2012)" "Striated muscles are present in bilaterian animals (for example, vertebrates, insects and annelids) and some non-bilaterian eumetazoans (that is, cnidarians and ctenophores). The considerable ultrastructural similarity of striated muscles between these animal groups is thought to reflect a common evolutionary origin. Here we show that a muscle protein core set, including a type II myosin heavy chain (MyHC) motor protein characteristic of striated muscles in vertebrates, was already present in unicellular organisms before the origin of multicellular animals." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0002037 "cerebellum" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1016/j.ydbio.2005.02.008 "Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)" "However, although the lamprey possesses a region comparable to the cerebellum and display expression of LjFgf8/17 at the MHB (midbrain hindbrain boundary), it does not have Purkinje cells and cerebellar nuclei, as well as components of the rhombic lip-derived cerebellar and pre-cerebellar systems. It is noteworthy that the latter structures require specific expression of Pax6 in the rhombic lip of the gnathostome hindbrain. Interestingly, the lamprey rhombic lip does not express Pax6. Thus, it is tempting to speculate that in vertebrate evolution the rostral hindbrain is incapable of differentiating into the cerebellum before the co-option of Pax6 in that region. In other words, cerebellum has been brought about as an evolutionary innovation in gnathostomes, based on exaptation of MHB, rhombic lip, and some regulatory gene expression already present in the vertebrate common ancestor." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0002038 "substantia nigra" 7777 "Chondrichthyes" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471210054 "Butler AB, Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.303" "(...) nuclei identified as the ventral tegmental area and substantia nigra are present only in two groups: the sharks, skates, and rays (but not in ratfishes) and the amniotes. The absence of these structures in all ray-finned fishes, lungfishes, and amphibians implies that they have been independently evolved in cartilaginous fishes and in amniotes." bgee ANN 2013-10-21 HOM:0000007 "historical homology" UBERON:0002038 "substantia nigra" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471210054 "Butler AB, Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.303" "(...) nuclei identified as the ventral tegmental area and substantia nigra are present only in two groups: the sharks, skates, and rays (but not in ratfishes) and the amniotes. The absence of these structures in all ray-finned fishes, lungfishes, and amphibians implies that they have been independently evolved in cartilaginous fishes and in amniotes." bgee ANN 2013-06-10 HOM:0000007 "historical homology" UBERON:0002038|UBERON:2000633 "substantia nigra|caudal tuberculum" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:19439422 "Flinn L, Mortiboys H, Volkmann K, Koster RW, Ingham PW, Bandmann O, Complex I deficiency and dopaminergic neuronal cell loss in parkin-deficient zebrafish (Danio rerio). Brain (2009)" "The zebrafish Parkin protein is 62% identical to its human counterpart with 78% identity in functionally relevant regions. The parkin gene is expressed throughout zebrafish development and ubiquitously in adult zebrafish tissue. Abrogation of Parkin activity leads to a significant decrease in the number of ascending dopaminergic neurons in the posterior tuberculum (homologous to the substantia nigra in humans), an effect enhanced by exposure to MPP+." bgee ANN 2016-04-25 HOM:0000007 "historical homology" UBERON:0002042 "lymphatic vessel endothelium" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001473, negated: false, taxon ID: 32523 - entity: UBERON:0001986, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0002045 "cuneate nucleus" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471210054 "Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.150" "In mammals the dorsal column is divided into two segments: a medial segment (fasciculus gracilis), which is present throughout the cord, and a lateral segment (fasciculus cuneatus), which is present only at the thoracic and cervical regions. The dorsal column nuclei are therefore also known as the nucleus gracilis and the nucleus cuneatus." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0002046 "thyroid gland" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...)." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0002046 "thyroid gland" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...)." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0002046 "thyroid gland" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:15592682 "Kluge B, Renault N, Rohr KB, Anatomical and molecular reinvestigation of lamprey endostyle development provides new insight into thyroid gland evolution. Development genes and evolution (2005)" "The thyroid gland of vertebrates is considered to be homologous to the endostyle of non-vertebrate chordates (cephalochordates, urochordates), a key character for understanding the origin and evolution of the chordate body plan." bgee ANN 2013-07-01 HOM:0000007 "historical homology" UBERON:0002046|UBERON:0006870 "thyroid gland|endostyle" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:15592682 "Kluge B, Renault N, Rohr KB, Anatomical and molecular reinvestigation of lamprey endostyle development provides new insight into thyroid gland evolution. Development genes and evolution (2005)" "The thyroid gland of vertebrates is considered to be homologous to the endostyle of non-vertebrate chordates (cephalochordates, urochordates), a key character for understanding the origin and evolution of the chordate body plan." bgee ANN 2013-07-01 HOM:0000007 "historical homology" UBERON:0002048|UBERON:0006860 "lung|swim bladder" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000033 "traceable author statement" DOI:10.1016/j.acthis.2012.01.003 "Zaccone D, Sengar M, Lauriano ER, Pergolizzi S, Macri' F, Salpietro L, Favaloro A, Satora L, Dabrowski K, Zaccone G, Morphology and innervation of the teleost physostome swim bladders and their functional evolution in non-teleostean lineages. Acta histochemica (2012)" "Swim bladders and lungs are homologous structures (for reviews see: Faenge, 1983, Kapoor and Khanna, 2004, Zaccone et al., 2006 and Zaccone et al., 2007) since they emerge embryologically from a single or paired pouches of the cranial part of the digestive tube and during the course of evolution these outgrowths that comprise the respiratory pharynx originally were used as a site for aerial gas exchange." bgee ANN 2015-04-14 HOM:0000007 "historical homology" UBERON:0002048|UBERON:0006860 "lung|swim bladder" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/j.acthis.2012.01.003 "Zaccone D, Sengar M, Lauriano ER, Pergolizzi S, Macri' F, Salpietro L, Favaloro A, Satora L, Dabrowski K, Zaccone G, Morphology and innervation of the teleost physostome swim bladders and their functional evolution in non-teleostean lineages. Acta histochemica (2012)" "Swim bladders and lungs are homologous structures (for reviews see: Faenge, 1983, Kapoor and Khanna, 2004, Zaccone et al., 2006 and Zaccone et al., 2007) since they emerge embryologically from a single or paired pouches of the cranial part of the digestive tube and during the course of evolution these outgrowths that comprise the respiratory pharynx originally were used as a site for aerial gas exchange." bgee ANN 2015-04-14 HOM:0000007 "historical homology" UBERON:0002048|UBERON:0006860 "lung|swim bladder" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1371/journal.pone.0024019 "Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011)" "Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. (...) Several prominent transcription factor genes in the swimbladder including hoxc4a, hoxc6a, hoxc8a and foxf1 were identified and their expressions in developing swimbladder during embryogenesis were confirmed. By comparison of enriched transcripts in the swimbladder with those in human and mouse lungs, we established the resemblance of transcriptome of the zebrafish swimbladder and mammalian lungs." bgee ANN 2015-04-14 HOM:0000007 "historical homology" UBERON:0002048|UBERON:0006860 "lung|swim bladder" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1016/j.acthis.2012.01.003 "Zaccone D, Sengar M, Lauriano ER, Pergolizzi S, Macri' F, Salpietro L, Favaloro A, Satora L, Dabrowski K, Zaccone G, Morphology and innervation of the teleost physostome swim bladders and their functional evolution in non-teleostean lineages. Acta histochemica (2012)" "Swim bladders and lungs are homologous structures (for reviews see: Faenge, 1983, Kapoor and Khanna, 2004, Zaccone et al., 2006 and Zaccone et al., 2007) since they emerge embryologically from a single or paired pouches of the cranial part of the digestive tube and during the course of evolution these outgrowths that comprise the respiratory pharynx originally were used as a site for aerial gas exchange." bgee ANN 2015-04-14 HOM:0000007 "historical homology" UBERON:0002048|UBERON:0006860 "lung|swim bladder" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210" "Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata [bony vertebrates, Euteleostomi]. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ." bgee ANN 2015-04-14 HOM:0000007 "historical homology" UBERON:0002049|UBERON:0007798 "vasculature|vascular system" 33208 "Metazoa" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:22474612 "Lammert E, Axnick J, Vascular lumen formation. Cold Spring Harb Perspect Med (2012)" "The vascular system developed early in evolution. It is required in large multicellular organisms for the transport of nutrients, oxygen, and waste products to and from tissues. (...) Invertebrates have various different vascular systems. Porifera and Cnidaria, for example, have a body cavity with apical cilia that serves both for nutrient and oxygen uptake, and therefore, it is sometimes called the gastrovascular cavity." bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0002051 "epithelium of bronchiole" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002186, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0002058 "main ciliary ganglion" 117571 "Euteleostomi" CIO:0000005 "low confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1016/j.autneu.2010.03.002 "Young HM, Cane KN, Anderson CR, Development of the autonomic nervous system: A comparative view. Autonomic Neuroscience : basic and clinical (2010)" "Little is known about the development of parasympathetic neurons apart from the ciliary ganglion in chicks. Although there are considerable gaps in our knowledge, some of the mechanisms controlling sympathetic and enteric neuron development appear to be conserved between mammals, avians and zebrafish." bgee ANN 2013-06-14 HOM:0000007 "historical homology" UBERON:0002059 "submandibular ganglion" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000045, negated: false, taxon ID: 33213 - entity: UBERON:0001736, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0002062 "endocardial cushion" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1038/35047564 "Stainier DYR, Zebrafish genetics and vertebrate heart formation. Nature Reviews Genetics (2001) Figure 3" "(Cardiac valve formation in vertebrates) In response to a myocardial signal, endocardial cells at chamber boundaries take on a mesenchymal character, delaminate and migrate into the cardiac jelly. There, they form an endocardial cushion that is later remodelled into a valve." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0002063 "sinus venosus" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1152/physrev.00006.2003 "Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)" "Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002063 "sinus venosus" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0721676678 "Romer AS, Vertebrate body (1970) p.428" "In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002064 "common cardinal vein" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.462" "In primitive vertebrates, the basic early embryonic pattern is retained, and blood from anterior and posterior systemic tissues is returned in anterior and posterior cardinal veins, both pairs of veins uniting in common cardinal veins near the heart. In derived vertebrates, the cardinals appear but usually persist only in the embryo, being functionally replaced by alternative adult vessels, the precava and postcava (anterior and posterior venae cavae)." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0002065 "posterior cardinal vein" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.462" "In primitive vertebrates, the basic early embryonic pattern is retained, and blood from anterior and posterior systemic tissues is returned in anterior and posterior cardinal veins, both pairs of veins uniting in common cardinal veins near the heart. In derived vertebrates, the cardinals appear but usually persist only in the embryo, being functionally replaced by alternative adult vessels, the precava and postcava (anterior and posterior venae cavae)." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0002067 "dermis" 7711 "Chordata" CIO:0000005 "low confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:23535660 "Shimada A, Kawanishi T, Kaneko T, Yoshihara H, Yano T, Inohaya K, Kinoshita M, Kamei Y, Tamura K, Takeda H, Trunk exoskeleton in teleosts is mesodermal in origin. Nat Commun (2013)" "amphioxus was found to have Pax3/7-positive satellite-like cells, suggesting that they have already acquired an evolutionary precursor of somite-derived dermomyotome, a tissue that produces dermis" bgee ANN 2013-07-17 HOM:0000007 "historical homology" UBERON:0002067 "dermis" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1111/j.1469-7580.2008.01043.x "Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)" "Although often overlooked, the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes but most details of their evolution and development remain confused and uncertain." bgee ANN 2013-07-17 HOM:0000007 "historical homology" UBERON:0002073 "hair follicle" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" ISBN:978-4431998051 "Morioka K, Hair follicle: differentiation under the electron microscope, An atlas (2005) p.3" "The earliest reliable record of hair is found in a fossil of the Paleocene period, in which the structure of hair cuticles is preserved. Its appearance suggests that the complicated structure of the hair follicle, closely similar to that of present-day mammals, had already appeared at this time." bgee ANN 2013-07-17 HOM:0000007 "historical homology" UBERON:0002078 "right cardiac atrium" 7711 "Chordata" CIO:0000005 "low confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:17223594 "Davidson B, Ciona intestinalis as a model for cardiac development. Ciona intestinalis as a model for cardiac development. Semin Cell Dev Biol (2007)" "in Ciona the RA [right atrium] metabolic gene RALDH2 is expressed specifically in the posterior sister lineage to the embryonic heart field (the anterior tail muscle lineage) [34]. This provides preliminary support for the hypothesis that a newly recruited atrial lineage carried a distinct genetic signature that was subsequently exploited for patterning of two distinct chambers (Fig. 4). Further characterization of the role of RA in Ciona heart development and the relationship between the Ciona heart lineage and the posterior sister lineage will provide a test of this highly speculative scenario." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002078 "right cardiac atrium" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002079 "left cardiac atrium" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002080 "heart right ventricle" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1126/science.1190181 "Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010)" "The vertebrate heart is formed from diverse embryonic territories, including the first and second heart fields. The second heart field (SHF) gives rise to the right ventricle and outflow tract, yet its evolutionary origins are unclear. We found that heart progenitor cells of the simple chordate Ciona intestinalis also generate precursors of the atrial siphon muscles (ASMs). (...) We propose that the last common ancestor of tunicates and vertebrates possessed multipotent cardiopharyngeal muscle precursors, and that their reallocation might have contributed to the emergence of the SHF." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0002080 "heart right ventricle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1126/science.1190181 "Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010)" "The vertebrate heart is formed from diverse embryonic territories, including the first and second heart fields. The second heart field (SHF) gives rise to the right ventricle and outflow tract, yet its evolutionary origins are unclear. (...) SHF-like territories have been identified in frog, zebrafish, and lamprey, yet evidence for a deeper evolutionary origin remains obscured by the absence of a clear SHF in invertebrates." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002080 "heart right ventricle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1126/science.1190181 "Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010)" "The vertebrate heart is formed from diverse embryonic territories, including the first and second heart fields. The second heart field (SHF) gives rise to the right ventricle and outflow tract, yet its evolutionary origins are unclear. (...) SHF-like territories have been identified in frog, zebrafish, and lamprey, yet evidence for a deeper evolutionary origin remains obscured by the absence of a clear SHF in invertebrates." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002081 "cardiac atrium" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1152/physrev.00006.2003 "Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)" "Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002082 "cardiac ventricle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1152/physrev.00006.2003 "Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)" "Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002083 "ductus venosus" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.485-487 and Figure 12.42" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0002084 "heart left ventricle" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000063 "compositional similarity evidence" DOI:10.1126/science.1190181 "Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010)" "The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002084 "heart left ventricle" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:17223594 "Davidson B, Ciona intestinalis as a model for cardiac development. Ciona intestinalis as a model for cardiac development. Semin Cell Dev Biol (2007)" "It has recently become apparent that amniote (avian, reptilian and mammalian) hearts are constructed from at least two distinct fields [32]. The left ventricle and atrial chambers arise from a primary field. (...) The ancestral chordate heart has been proposed to be equivalent to the primary heart field with the resulting left ventricle representing the ancestral single chamber. Studies of primary heart field patterning indicate that the default fate of this lineage is ventricular and that the atrial fate is the result of secondary patterning events, including a critical role for RA [right atrium] signaling [33]. Thus the Ciona heart is probably homologous to the vertebrate left ventricular field." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0002084|UBERON:0004140 "heart left ventricle|primary heart field" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:17223594 "Davidson B, Ciona intestinalis as a model for cardiac development. Ciona intestinalis as a model for cardiac development. Semin Cell Dev Biol (2007)" "It has recently become apparent that amniote (avian, reptilian and mammalian) hearts are constructed from at least two distinct fields [32]. The left ventricle and atrial chambers arise from a primary field. (...) The ancestral chordate heart has been proposed to be equivalent to the primary heart field with the resulting left ventricle representing the ancestral single chamber. Studies of primary heart field patterning indicate that the default fate of this lineage is ventricular and that the atrial fate is the result of secondary patterning events, including a critical role for RA [right atrium] signaling [33]. Thus the Ciona heart is probably homologous to the vertebrate left ventricular field." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002085 "interatrial septum" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002087 "atrioventricular canal" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/j.ddmec.2004.08.004 "Haramis APG, Clevers HC, Holehearted: genetic approaches to congenital cardiac valve malformations. Drug Discovery Today: Disease Mechanisms (2004)" "The heart is the first organ to form and function in a vertebrate. (...) Septation of the AV canal is initiated with the formation of inferior and superior endocardial cushions in response to signaling from the overlying myocardium. (...) Analysis of zebrafish mutants with cardiovascular defects uncovered a previously unexpected level of conservation between zebrafish and human cardiovascular physiology." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0002089 "thoracodorsal vein" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001112, negated: false, taxon ID: 40674 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0002090 "postcranial axial skeleton" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1186/1742-9994-8-4 "Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011)" "The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0002091 "appendicular skeleton" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1002/jemt.10217 "Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy reasearch and technique (2002)" "Origin of an appendicular skeleton predates the evolution of gnathostomes. [curator]" bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0002092 "brain dura mater" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000955, negated: false, taxon ID: 33213 - entity: UBERON:0002363, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0002094 "interventricular septum" 8782 "Aves" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.618" "Superficially, the mammalian heart resembles those of birds and crocodiles, but the interventricular septum evolved independently and develops embryonically in a slightly different way, so it is not homologous to the interventricular septum of these vertebrates." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002094 "interventricular septum" 8782 "Aves" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.618" "Superficially, the mammalian heart resembles those of birds and crocodiles, but the interventricular septum evolved independently and develops embryonically in a slightly different way, so it is not homologous to the interventricular septum of these vertebrates." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002094 "interventricular septum" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" DOI:10.1038/nature08324 "Koshiba-Takeuchi K, Mori AD, Kaynak BL, Cebra-Thomas J, Sukonnik T, Georges RO, Latham S, Beck L, Henkelman RM, Black BL, Olson EN, Wade J, Takeuchi JK, Nemer M, Gilbert SF, Bruneau BG, Reptilian heart development and the molecular basis of cardiac chamber evolution. Nature (2009)" "Amphibians have a three-chambered heart, whereas mammalian, crocodilian and avian hearts have four chambers, two each for pulmonary and systemic circulations. The acquisition of a fully septated ventricle has evolved independently in birds, mammals and crocodilians, and is an important example of convergent evolution." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0002094 "interventricular septum" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1038/nature08324 "Koshiba-Takeuchi K, Mori AD, Kaynak BL, Cebra-Thomas J, Sukonnik T, Georges RO, Latham S, Beck L, Henkelman RM, Black BL, Olson EN, Wade J, Takeuchi JK, Nemer M, Gilbert SF, Bruneau BG, Reptilian heart development and the molecular basis of cardiac chamber evolution. Nature (2009)" "Amphibians have a three-chambered heart, whereas mammalian, crocodilian and avian hearts have four chambers, two each for pulmonary and systemic circulations. The acquisition of a fully septated ventricle has evolved independently in birds, mammals and crocodilians, and is an important example of convergent evolution." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0002094 "interventricular septum" NOT 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.618" "Superficially, the mammalian heart resembles those of birds and crocodiles, but the interventricular septum evolved independently and develops embryonically in a slightly different way, so it is not homologous to the interventricular septum of these vertebrates." bgee ANN 2013-09-06 HOM:0000007 "historical homology" UBERON:0002094 "interventricular septum" NOT 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.618" "Superficially, the mammalian heart resembles those of birds and crocodiles, but the interventricular septum evolved independently and develops embryonically in a slightly different way, so it is not homologous to the interventricular septum of these vertebrates." bgee ANN 2013-09-06 HOM:0000007 "historical homology" UBERON:0002094 "interventricular septum" NOT 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" DOI:10.1038/nature08324 "Koshiba-Takeuchi K, Mori AD, Kaynak BL, Cebra-Thomas J, Sukonnik T, Georges RO, Latham S, Beck L, Henkelman RM, Black BL, Olson EN, Wade J, Takeuchi JK, Nemer M, Gilbert SF, Bruneau BG, Reptilian heart development and the molecular basis of cardiac chamber evolution. Nature (2009)" "Amphibians have a three-chambered heart, whereas mammalian, crocodilian and avian hearts have four chambers, two each for pulmonary and systemic circulations. The acquisition of a fully septated ventricle has evolved independently in birds, mammals and crocodilians, and is an important example of convergent evolution." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0002094 "interventricular septum" NOT 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1038/nature08324 "Koshiba-Takeuchi K, Mori AD, Kaynak BL, Cebra-Thomas J, Sukonnik T, Georges RO, Latham S, Beck L, Henkelman RM, Black BL, Olson EN, Wade J, Takeuchi JK, Nemer M, Gilbert SF, Bruneau BG, Reptilian heart development and the molecular basis of cardiac chamber evolution. Nature (2009)" "Amphibians have a three-chambered heart, whereas mammalian, crocodilian and avian hearts have four chambers, two each for pulmonary and systemic circulations. The acquisition of a fully septated ventricle has evolved independently in birds, mammals and crocodilians, and is an important example of convergent evolution." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0002094 "interventricular septum" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.618" "Superficially, the mammalian heart resembles those of birds and crocodiles, but the interventricular septum evolved independently and develops embryonically in a slightly different way, so it is not homologous to the interventricular septum of these vertebrates." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002094 "interventricular septum" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.618" "Superficially, the mammalian heart resembles those of birds and crocodiles, but the interventricular septum evolved independently and develops embryonically in a slightly different way, so it is not homologous to the interventricular septum of these vertebrates." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002094 "interventricular septum" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" DOI:10.1038/nature08324 "Koshiba-Takeuchi K, Mori AD, Kaynak BL, Cebra-Thomas J, Sukonnik T, Georges RO, Latham S, Beck L, Henkelman RM, Black BL, Olson EN, Wade J, Takeuchi JK, Nemer M, Gilbert SF, Bruneau BG, Reptilian heart development and the molecular basis of cardiac chamber evolution. Nature (2009)" "Amphibians have a three-chambered heart, whereas mammalian, crocodilian and avian hearts have four chambers, two each for pulmonary and systemic circulations. The acquisition of a fully septated ventricle has evolved independently in birds, mammals and crocodilians, and is an important example of convergent evolution." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0002094 "interventricular septum" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1038/nature08324 "Koshiba-Takeuchi K, Mori AD, Kaynak BL, Cebra-Thomas J, Sukonnik T, Georges RO, Latham S, Beck L, Henkelman RM, Black BL, Olson EN, Wade J, Takeuchi JK, Nemer M, Gilbert SF, Bruneau BG, Reptilian heart development and the molecular basis of cardiac chamber evolution. Nature (2009)" "Amphibians have a three-chambered heart, whereas mammalian, crocodilian and avian hearts have four chambers, two each for pulmonary and systemic circulations. The acquisition of a fully septated ventricle has evolved independently in birds, mammals and crocodilians, and is an important example of convergent evolution." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0002094 "interventricular septum" 1294634 "Crocodylia" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" DOI:10.1038/nature08324 "Koshiba-Takeuchi K, Mori AD, Kaynak BL, Cebra-Thomas J, Sukonnik T, Georges RO, Latham S, Beck L, Henkelman RM, Black BL, Olson EN, Wade J, Takeuchi JK, Nemer M, Gilbert SF, Bruneau BG, Reptilian heart development and the molecular basis of cardiac chamber evolution. Nature (2009)" "Amphibians have a three-chambered heart, whereas mammalian, crocodilian and avian hearts have four chambers, two each for pulmonary and systemic circulations. The acquisition of a fully septated ventricle has evolved independently in birds, mammals and crocodilians, and is an important example of convergent evolution." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0002094 "interventricular septum" 1294634 "Crocodylia" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1038/nature08324 "Koshiba-Takeuchi K, Mori AD, Kaynak BL, Cebra-Thomas J, Sukonnik T, Georges RO, Latham S, Beck L, Henkelman RM, Black BL, Olson EN, Wade J, Takeuchi JK, Nemer M, Gilbert SF, Bruneau BG, Reptilian heart development and the molecular basis of cardiac chamber evolution. Nature (2009)" "Amphibians have a three-chambered heart, whereas mammalian, crocodilian and avian hearts have four chambers, two each for pulmonary and systemic circulations. The acquisition of a fully septated ventricle has evolved independently in birds, mammals and crocodilians, and is an important example of convergent evolution." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0002101 "limb" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23256837 "Yano T, Tamura K, The making of differences between fins and limbs. J Anat (2013)" "Fish and tetrapods have many homologous organs, which are sometimes altered for the organism's adaptation to a specific environment. The paired fins in fish and limbs in tetrapods are a good example of homologous organs." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0002101|UBERON:0002534 "limb|paired fin" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:23256837 "Yano T, Tamura K, The making of differences between fins and limbs. J Anat (2013)" "Fish and tetrapods have many homologous organs, which are sometimes altered for the organism's adaptation to a specific environment. The paired fins in fish and limbs in tetrapods are a good example of homologous organs." bgee ANN 2013-07-12 HOM:0000007 "historical homology" UBERON:0002102 "forelimb" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:17587327 "Mercader N, Early steps of paired fin development in zebrafish compared with tetrapod limb development. Development, growth and differentiation (2007)" "Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0002103 "hindlimb" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:17587327 "Mercader N, Early steps of paired fin development in zebrafish compared with tetrapod limb development. Development, growth and differentiation (2007)" "Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0002106 "spleen" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0781765190 "Paul WE, Fundamental Immunology (2008) p.94" "With the advent of clonal selection, the accumulation and segregation of T and B cells in specialized organs for antigen presentation became necessary, and indeed the spleen is found in all jawed vertebrates, but not in agnathans or invertebrates." bgee ANN 2013-07-01 HOM:0000007 "historical homology" UBERON:0002107 "liver" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" DOI:10.1053/ax.2000.7133 "Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000)" "(...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0002107 "liver" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1053/ax.2000.7133 "Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000)" "(...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0002107 "liver" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:21052758 "Wang Y, Zhang S, Identification and expression of liver-specific genes after LPS challenge in amphioxus: the hepatic cecum as liver-like organ and (pre-hepatic) acute phase response. Functional and integrative genomics (2011)" "Liver is present in all vertebrates and central to many physiological processes including processing of nutrients from ingested food, plasma protein synthesis, hormone production, and detoxification. However, its evolutionary origin remains open to date. Liver is also the principal organ of acute phase response (APR) but when the vertebrate-like APR regulatory network emerges during the chordate evolution is unknown. (...) These similarities in liver/hepatic cecum-specific genes, APR, and regulatory networks between amphioxus and zebrafish supports the idea that hepatic cecum in amphioxus is the ""pre-hepatic"" organ homologous to vertebrate liver and acts as an immunological organ, playing an important role in APR. (...) In this study, by combining global genome survey and qRT-PCR data sets, we clearly demonstrate the presence of 58 vertebrate (zebrafish) liver-specific genes in amphioxus (hepatic cecum-specific genes), including genes encoding metabolic or catabolic enzymes and blood components, which are expressed in atissue-specific manner in the hepatic cecum." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0002107|UBERON:0012474 "liver|hepatic cecum" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:21052758 "Wang Y, Zhang S, Identification and expression of liver-specific genes after LPS challenge in amphioxus: the hepatic cecum as liver-like organ and (pre-hepatic) acute phase response. Functional and integrative genomics (2011)" "Liver is present in all vertebrates and central to many physiological processes including processing of nutrients from ingested food, plasma protein synthesis, hormone production, and detoxification. However, its evolutionary origin remains open to date. Liver is also the principal organ of acute phase response (APR) but when the vertebrate-like APR regulatory network emerges during the chordate evolution is unknown. (...) These similarities in liver/hepatic cecum-specific genes, APR, and regulatory networks between amphioxus and zebrafish supports the idea that hepatic cecum in amphioxus is the ""pre-hepatic"" organ homologous to vertebrate liver and acts as an immunological organ, playing an important role in APR. (...) In this study, by combining global genome survey and qRT-PCR data sets, we clearly demonstrate the presence of 58 vertebrate (zebrafish) liver-specific genes in amphioxus (hepatic cecum-specific genes), including genes encoding metabolic or catabolic enzymes and blood components, which are expressed in atissue-specific manner in the hepatic cecum." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0002108 "small intestine" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566" "Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0002110 "gall bladder" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1002/(SICI)1097-0029(19970915)38:6<571::AID-JEMT3>3.0.CO;2-I "Oldham-Ott CK, Gilloteaux J, Comparative morphology of the gallbladder and biliary tract in vertebrates: Variation in structure, homology in function and gallstones. Microscopy research and technique (1997)" "The presence of a gallbladder appears to be a primitive trait. It is found in most fish and all adult reptiles and amphibians and has been well conserved in mammals, for the most part." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0002111 "artery smooth muscle tissue" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0002112 "smooth muscle of esophagus" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001043, negated: false, taxon ID: 7742 - entity: UBERON:0001135, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0002112 "smooth muscle of esophagus" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001043, negated: false, taxon ID: 33213 - entity: UBERON:0001135, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0002113 "kidney" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-3540428541 "Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406" "Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions." bgee ANN 2015-01-28 HOM:0000007 "historical homology" UBERON:0002113 "kidney" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-3540428541 "Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406" "Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions." bgee ANN 2015-01-28 HOM:0000007 "historical homology" UBERON:0002114 "duodenum" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.567 and Figure 17-3 p.562" "Duodenum is present in the digestive tracts of primitive tetrapods. [curator]" bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0002115 "jejunum" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.567 and Figure 17-4 p.562" "[In birds and mammals] The small intestine can be differentiated into a duodenum, jejunum, and ileum." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0002116 "ileum" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0521617147 "Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0002118 "right ovary" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000468, negated: false, taxon ID: 33208 - entity: UBERON:0000992, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0002118 "right ovary" NOT 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000468, negated: false, taxon ID: 33208 - entity: UBERON:0000992, negated: true, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0002118 "right ovary" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000468, negated: false, taxon ID: 33208 - entity: UBERON:0000992, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0002119 "left ovary" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000468, negated: false, taxon ID: 33208 - entity: UBERON:0000992, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0002119 "left ovary" NOT 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000468, negated: false, taxon ID: 33208 - entity: UBERON:0000992, negated: true, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0002119 "left ovary" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000468, negated: false, taxon ID: 33208 - entity: UBERON:0000992, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0002120 "pronephros" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.637" "In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0002127 "inferior olivary complex" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471210054 "Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.256" "The inferior olive appears to be present in all vertebrate classes and is particularly well developed in species with a well-developed cerebellum." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0002129 "cerebellar cortex" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0002131 "anterior lobe of cerebellum" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0002132 "dentate nucleus" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471210054 "Butler AB, Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.260-261" "One or more deep cerebellar nuclei appear in agnathans, sharks, ropefishes, lungfishes, Latimeria, and amphibians. Reptiles have two nuclei (a medial and a lateral), and birds and mammals have three nuclei (a medial, a lateral, and an interposed nucleus). The medial nucleus of mammals is known as the fastigial nucleus, and the lateral nucleus is known as the dentate nucleus." bgee ANN 2013-06-07 HOM:0000007 "historical homology" UBERON:0002133 "atrioventricular valve" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1152/physrev.00006.2003 "Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)" "The conus arteriosus is the most distal part of the primitive fish heart and forms the connection between the ventricle and the ventral aorta. At the sinoatrial, the atrioventricular, and the ventriculoconal junctions, valves developed to prevent backflow of blood during relaxation of the preceding compartment." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0002133|UBERON:0005998|UBERON:0014854 "atrioventricular valve|tricuspid valve cusp|anterior leaflet of mitral valve" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:23755108 "Jensen B, van den Berg G, van den Doel R, Oostra RJ, Wang T, Moorman AF, Development of the hearts of lizards and snakes and perspectives to cardiac evolution. PLoS One (2013)" "The mesenchyme of the atrioventricular canal is strikingly similar in amniotes with a large cushion dorsally and ventrally. This suggests that the fully formed left and right atrioventricular valve of the reptilian heart are homologous to the septal leaflet of the right-sided tricuspid valve and the aortic leaflet of the left-sided mitral valve of the mammalian heart." bgee ANN 2013-10-18 HOM:0000007 "historical homology" UBERON:0002134 "tricuspid valve" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000063 "compositional similarity evidence" DOI:10.1161/CIRCRESAHA.109.201566 "Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009)" "The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0002134 "tricuspid valve" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1161/CIRCRESAHA.109.201566 "Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009)" "The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0002134 "tricuspid valve" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1161/CIRCRESAHA.109.201566 "Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009)" "The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0002135 "mitral valve" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000063 "compositional similarity evidence" DOI:10.1161/CIRCRESAHA.109.201566 "Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009)" "The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0002135 "mitral valve" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1161/CIRCRESAHA.109.201566 "Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009)" "The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0002135 "mitral valve" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1161/CIRCRESAHA.109.201566 "Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009)" "The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0002137 "aortic valve" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1161/CIRCRESAHA.109.201566 "Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009)" "The four-chambered vertebrate heart has aortic and pulmonic semilunar (SL) valves at the arterial pole as well as mitral and tricuspid valves separating the atria and ventricles. (...) Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0002140 "parabigeminal nucleus" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1002/cne.22364 "Volkmann K, Chen YY, Harris MP, Wullimann MF, Koester RW, The zebrafish cerebellar upper rhombic lip generates tegmental hindbrain nuclei by long-distance migration in an evolutionary conserved manner. The Journal of Comparative Neurology (2010)" "In sum, our results show that the origin of neurons of some tegmental hindbrain nuclei, namely, nucleus isthmi/superior reticular nucleus and secondary gustatory/viscerosensory nucleus is in the URL (upper rhombic lip), and that the temporal order of cell types produced by the URL and their developmental program are conserved among vertebrate species." bgee ANN 2013-06-07 HOM:0000007 "historical homology" UBERON:0002140 "parabigeminal nucleus" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471210054 "Butler AB, Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.272" "Nucleus isthmi is present in the isthmus in most vertebrates. It is called the parabigeminal nucleus in mammals" bgee ANN 2013-06-07 HOM:0000007 "historical homology" UBERON:0002146 "pulmonary valve" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1161/CIRCRESAHA.109.201566 "Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009)" "The four-chambered vertebrate heart has aortic and pulmonic semilunar (SL) valves at the arterial pole as well as mitral and tricuspid valves separating the atria and ventricles. (...) Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0002153 "fastigial nucleus" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471210054 "Butler AB, Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.260-261" "One or more deep cerebellar nuclei appear in agnathans, sharks, ropefishes, lungfishes, Latimeria, and amphibians. Reptiles have two nuclei (a medial and a lateral), and birds and mammals have three nuclei (a medial, a lateral, and an interposed nucleus). The medial nucleus of mammals is known as the fastigial nucleus, and the lateral nucleus is known as the dentate nucleus." bgee ANN 2013-06-07 HOM:0000007 "historical homology" UBERON:0002161 "gracile nucleus" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471210054 "Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.150" "In mammals the dorsal column is divided into two segments: a medial segment (fasciculus gracilis), which is present throughout the cord, and a lateral segment (fasciculus cuneatus), which is present only at the thoracic and cervical regions. The dorsal column nuclei are therefore also known as the nucleus gracilis and the nucleus cuneatus." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0002165 "endocardium" NOT 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:17223594 "Davidson B, Ciona intestinalis as a model for cardiac development. Ciona intestinalis as a model for cardiac development. Semin Cell Dev Biol (2007)" "There is no discernible endocardium in the Ciona heart." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002165 "endocardium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481" "While bird and mammal 4-chambered hearts arose independently from different groups of reptilian ancestor, the vertebrate chambered heart is commonly considered arising from fishes and then defined as an historical homology relationship. However uncertainty remains on the origin of the heart substructures and tissues. [curator]" bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002166 "endocardium of atrium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481" "While bird and mammal 4-chambered hearts arose independently from different groups of reptilian ancestor, the vertebrate chambered heart is commonly considered arising from fishes and then defined as an historical homology relationship. However uncertainty remains on the origin of the heart substructures and tissues. [curator]" bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002170 "upper lobe of right lung" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.596 and Figure 18-21" "The synapsid line of evolution culminating in mammals and the sauropsid line to reptiles and birds diverged millions of years ago, near the time of the origin of amniotes. Although mammals, too, evolved an efficient respiratory system, needed by endothermic animals, the mammalian system differs in many ways from that of birds because it evolved its complex design from the generalized amniote condition independently. The evolution of the secondary palate in mammals and their therapsid ancestors made possible a separation of food and respiratory passage." bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0002171 "lower lobe of right lung" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.596 and Figure 18-21" "The synapsid line of evolution culminating in mammals and the sauropsid line to reptiles and birds diverged millions of years ago, near the time of the origin of amniotes. Although mammals, too, evolved an efficient respiratory system, needed by endothermic animals, the mammalian system differs in many ways from that of birds because it evolved its complex design from the generalized amniote condition independently. The evolution of the secondary palate in mammals and their therapsid ancestors made possible a separation of food and respiratory passage." bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0002182 "main bronchus" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.592 and Figure 18-15" "(...) must reptiles have lungs that are relatively more compartmentalized and larger than are those of amphibians (Fig. 18-15). A wide central bronchus leads fom the trachea into each lung, secondary bronchi branch from it, and alveolar sacs of varying size bud off them." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0002184 "segmental bronchus" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.596 and Figure 18-21" "The synapsid line of evolution culminating in mammals and the sauropsid line to reptiles and birds diverged millions of years ago, near the time of the origin of amniotes. Although mammals, too, evolved an efficient respiratory system, needed by endothermic animals, the mammalian system differs in many ways from that of birds because it evolved its complex design from the generalized amniote condition independently. The evolution of the secondary palate in mammals and their therapsid ancestors made possible a separation of food and respiratory passage." bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0002185 "bronchus" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.592 and Figure 18-15" "(...) must reptiles have lungs that are relatively more compartmentalized and larger than are those of amphibians (Fig. 18-15). A wide central bronchus leads fom the trachea into each lung, secondary bronchi branch from it, and alveolar sacs of varying size bud off them." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0002186 "bronchiole" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.596 and Figure 18-21" "The synapsid line of evolution culminating in mammals and the sauropsid line to reptiles and birds diverged millions of years ago, near the time of the origin of amniotes. Although mammals, too, evolved an efficient respiratory system, needed by endothermic animals, the mammalian system differs in many ways from that of birds because it evolved its complex design from the generalized amniote condition independently. The evolution of the secondary palate in mammals and their therapsid ancestors made possible a separation of food and respiratory passage." bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0002192 "ventricular system choroidal fissure" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0002196 "adenohypophysis" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5" "It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0002197 "median eminence of neurohypophysis" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-4B" "In mammals, the neurohypophysis consists of a median evidence, next to the brain, and a narrow infundibular stalk, which leads to the expanded pars nervosa." bgee ANN 2013-06-07 HOM:0000007 "historical homology" UBERON:0002198 "neurohypophysis" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5" "It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0002200 "vasculature of head" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 7742 - entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0002200 "vasculature of head" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 33213 - entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0002203 "vasculature of eye" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000019, negated: false, taxon ID: 7742 - entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0002204 "musculoskeletal system" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1002/jez.b.21246 "Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009)" "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0002206 "mammillary body" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.651 and Figure 16.41" "In vertebrates mammillary bodies develop within the hypothalamus and contain medial mammillary nuclei and lateral mammillary nuclei. [curator]" bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0002218 "tympanic ring" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "Developmental biology can also help identify the homologous elements for the associated membranous bones of the ear. The tympanic ring and gonial, for example have been suggested to be homologous to the angular bone and prearticular, respectively. Again, by following the position and relative timing of these bones as they develop, clear homologies can be identified (Fig. 2). Bapx1 is also expressed around these membraneous bones in both chick and mouse (Tucker et al. 2004)." bgee ANN 2015-04-02 HOM:0000007 "historical homology" UBERON:0002218|UBERON:0011079 "tympanic ring|angular bone" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "Developmental biology can also help identify the homologous elements for the associated membranous bones of the ear. The tympanic ring and gonial, for example have been suggested to be homologous to the angular bone and prearticular, respectively. Again, by following the position and relative timing of these bones as they develop, clear homologies can be identified (Fig. 2). Bapx1 is also expressed around these membraneous bones in both chick and mouse (Tucker et al. 2004)." bgee ANN 2015-04-02 HOM:0000007 "historical homology" UBERON:0002218|UBERON:0011079 "tympanic ring|angular bone" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "Developmental biology can also help identify the homologous elements for the associated membranous bones of the ear. The tympanic ring and gonial, for example have been suggested to be homologous to the angular bone and prearticular, respectively. Again, by following the position and relative timing of these bones as they develop, clear homologies can be identified (Fig. 2). Bapx1 is also expressed around these membraneous bones in both chick and mouse (Tucker et al. 2004)." bgee ANN 2015-04-02 HOM:0000007 "historical homology" UBERON:0002223 "endolymphatic sac" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414 and Figure 12-15" "Endolymphatic sac is a structure described in the inner ear of a typical gnathostome. [curator]" bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0002227 "spiral organ of cochlea" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:19786082 "Manley GA, An evolutionary perspective on middle ears. Hearing research (2010)" "Comparative and paleontological studies suggest that a dedicated hair-cell epithelium for 'hearing' - a basilar papilla - already existed in stem amniotes but was small (Manley, 2000 and Manley and Koeppl, 1998). One piece of evidence in this regard is from a relative of the ancestors of land-living vertebrates, the so-called ""living fossil"" coelacanth fish Latimeria. A study of their inner ears revealed the presence of an epithelium that in its characteristics suggested a homology to the basilar papilla of amniotes (Fritzsch, 1987). A second reason is the fact that all modern amniotes and their sister group, the amphibians (Smothermann and Narins, 2004; but their papillae are of uncertain homology) have a hearing organ suggests that it is a plesiomorphic feature - i.e., present in the common ancestor." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0002227 "spiral organ of cochlea" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19786082 "Manley GA, An evolutionary perspective on middle ears. Hearing research (2010)" "Comparative and paleontological studies suggest that a dedicated hair-cell epithelium for 'hearing' - a basilar papilla - already existed in stem amniotes but was small (Manley, 2000 and Manley and Koeppl, 1998). One piece of evidence in this regard is from a relative of the ancestors of land-living vertebrates, the so-called ""living fossil"" coelacanth fish Latimeria. A study of their inner ears revealed the presence of an epithelium that in its characteristics suggested a homology to the basilar papilla of amniotes (Fritzsch, 1987). A second reason is the fact that all modern amniotes and their sister group, the amphibians (Smothermann and Narins, 2004; but their papillae are of uncertain homology) have a hearing organ suggests that it is a plesiomorphic feature - i.e., present in the common ancestor." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0002227 "spiral organ of cochlea" NOT 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:19786082 "Manley GA, An evolutionary perspective on middle ears. Hearing research (2010)" "Comparative and paleontological studies suggest that a dedicated hair-cell epithelium for 'hearing' - a basilar papilla - already existed in stem amniotes but was small (Manley, 2000 and Manley and Koeppl, 1998). One piece of evidence in this regard is from a relative of the ancestors of land-living vertebrates, the so-called ""living fossil"" coelacanth fish Latimeria. A study of their inner ears revealed the presence of an epithelium that in its characteristics suggested a homology to the basilar papilla of amniotes (Fritzsch, 1987). A second reason is the fact that all modern amniotes and their sister group, the amphibians (Smothermann and Narins, 2004; but their papillae are of uncertain homology) have a hearing organ suggests that it is a plesiomorphic feature - i.e., present in the common ancestor." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0002227 "spiral organ of cochlea" NOT 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19786082 "Manley GA, An evolutionary perspective on middle ears. Hearing research (2010)" "Comparative and paleontological studies suggest that a dedicated hair-cell epithelium for 'hearing' - a basilar papilla - already existed in stem amniotes but was small (Manley, 2000 and Manley and Koeppl, 1998). One piece of evidence in this regard is from a relative of the ancestors of land-living vertebrates, the so-called ""living fossil"" coelacanth fish Latimeria. A study of their inner ears revealed the presence of an epithelium that in its characteristics suggested a homology to the basilar papilla of amniotes (Fritzsch, 1987). A second reason is the fact that all modern amniotes and their sister group, the amphibians (Smothermann and Narins, 2004; but their papillae are of uncertain homology) have a hearing organ suggests that it is a plesiomorphic feature - i.e., present in the common ancestor." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0002227 "spiral organ of cochlea" 32523 "Tetrapoda" CIO:0000005 "low confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19786082 "Manley GA, An evolutionary perspective on middle ears. Hearing research (2010)" "the fact that all modern amniotes and their sister group, the amphibians (Smothermann and Narins, 2004; but their papillae are of uncertain homology) have a hearing organ suggests that it is a plesiomorphic feature - i.e., present in the common ancestor." bgee ANN 2015-04-02 HOM:0000007 "historical homology" UBERON:0002227 "spiral organ of cochlea" NOT 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:21236326 "Manley GA, Fuchs PA, Recent advances in comparative hearing. Hearing research (2011)" "Most amphibians have, uniquely among terrestrial vertebrates, two auditory papillae, the amphibian and the basilar papillae and it is possible that neither of these is truly homologous to the basilar papilla-organ of Corti of reptiles, birds and mammals." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0002227 "spiral organ of cochlea" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19786082 "Manley GA, An evolutionary perspective on middle ears. Hearing research (2010)" "Comparative and paleontological studies suggest that a dedicated hair-cell epithelium for 'hearing' - a basilar papilla - already existed in stem amniotes but was small (Manley, 2000 and Manley and Koeppl, 1998)." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0002227|UBERON:0013731 "spiral organ of cochlea|basilar papilla" NOT 8292 "Amphibia" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" DOI:10.1007/s10162-016-0579-3 "Manley GA, Comparative Auditory Neuroscience: Understanding the Evolution and Function of Ears. J Assoc Res Otolaryngol (2017)" "Where the basilar papilla of non-mammalian amniotes (and its later relative, the mammalian organ of Corti) came from and when it originated is still an open question. One of the reasons the present discussion does not deal with the (fascinating!) group of amphibians is that neither of their one or two hearing organs is clearly homologous to the amniote basilar papilla (Smothermann and Narins 2004). Thus, the modern amphibians, that are placed in their own group (Lissamphibia) and differ in many respects from the ancestral amphibians from which the amniotes arose, are no help in deciding on the origin of the basilar papilla. The amniote basilar papilla is defined as a patch of sensory hair cells that is supported on a free basilar membrane and lies (at least originally) between the saccular and lagenar maculae." bgee ANN 2017-05-02 HOM:0000007 "historical homology" UBERON:0002227|UBERON:0013731 "spiral organ of cochlea|basilar papilla" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000033 "traceable author statement" DOI:10.1007/s10162-016-0579-3 "Manley GA, Comparative Auditory Neuroscience: Understanding the Evolution and Function of Ears. J Assoc Res Otolaryngol (2017)" "Where the basilar papilla of non-mammalian amniotes (and its later relative, the mammalian organ of Corti) came from and when it originated is still an open question. One of the reasons the present discussion does not deal with the (fascinating!) group of amphibians is that neither of their one or two hearing organs is clearly homologous to the amniote basilar papilla (Smothermann and Narins 2004). Thus, the modern amphibians, that are placed in their own group (Lissamphibia) and differ in many respects from the ancestral amphibians from which the amniotes arose, are no help in deciding on the origin of the basilar papilla. The amniote basilar papilla is defined as a patch of sensory hair cells that is supported on a free basilar membrane and lies (at least originally) between the saccular and lagenar maculae." bgee ANN 2017-05-02 HOM:0000007 "historical homology" UBERON:0002229 "interparietal bone" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:22891324 "Koyabu D, Maier W, Sanchez-Villagra MR, Paleontological and developmental evidence resolve the homology and dual embryonic origin of a mammalian skull bone, the interparietal. Proc Natl Acad Sci U S A (2012)" "Although the interparietal has been regarded as being lost in various lineages, our investigation on embryos demonstrates its presence in all extant mammalian ""orders."" The generally accepted paradigm has regarded the interparietal as consisting of two elements that are homologized to the postparietals of basal amniotes. The tabular bones have been postulated as being lost during the rise of modern mammals. However, our results demonstrate that the interparietal consists not of two but of four elements. We propose that the tabulars of basal amniotes are conserved as the lateral interparietal elements, which quickly fuse to the medial elements at the embryonic stage, and that the postparietals are homologous to the medial elements. Hence, the dual developmental origin of the mammalian interparietal can be explained as the evolutionary consequence of the fusion between the crest-derived ""postparietals"" and the mesoderm-derived ""tabulars.""" bgee ANN 2013-08-27 HOM:0000007 "historical homology" UBERON:0002229 "interparietal bone" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:22891324 "Koyabu D, Maier W, Sanchez-Villagra MR, Paleontological and developmental evidence resolve the homology and dual embryonic origin of a mammalian skull bone, the interparietal. Proc Natl Acad Sci U S A (2012)" "Although the interparietal has been regarded as being lost in various lineages, our investigation on embryos demonstrates its presence in all extant mammalian ""orders."" The generally accepted paradigm has regarded the interparietal as consisting of two elements that are homologized to the postparietals of basal amniotes. The tabular bones have been postulated as being lost during the rise of modern mammals. However, our results demonstrate that the interparietal consists not of two but of four elements. We propose that the tabulars of basal amniotes are conserved as the lateral interparietal elements, which quickly fuse to the medial elements at the embryonic stage, and that the postparietals are homologous to the medial elements. Hence, the dual developmental origin of the mammalian interparietal can be explained as the evolutionary consequence of the fusion between the crest-derived ""postparietals"" and the mesoderm-derived ""tabulars.""" bgee ANN 2013-08-27 HOM:0000007 "historical homology" UBERON:0002241 "chondrocranium" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1002/jemt.10217 "Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy reasearch and technique (2002) Fig.7" "Chondrocranium origin is reported in Vertebrata, and described as a significant event in the vertebrate skeletal system. [curator]" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0002244 "premaxilla" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:24067611 "Zhu M, Yu X, Ahlberg PE, Choo B, Lu J, Qiao T, Qu Q, Zhao W, Jia L, Blom H, Zhu Y, A Silurian placoderm with osteichthyan-like marginal jaw bones. Nature (2013)" "Here we describe a three-dimensionally preserved 419-million-year-old placoderm fish from the Silurian of China that represents the first stem gnathostome with dermal marginal jaw bones (premaxilla, maxilla and dentary), features previously restricted to Osteichthyes." bgee ANN 2013-10-09 HOM:0000007 "historical homology" UBERON:0002254 "thyroglossal duct" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1007/s00427-004-0450-0 "Kluge B, Renault N, Rohr KB, Anatomical and molecular reinvestigation of lamprey endostyle development provides new insight into thyroid gland evolution. Development genes and evolution (2005)" "Analysing lamprey endostyle development using semi-thin histological sections, immunohistochemical detection of thyroid hormone, and the molecular marker thyroid transcription factor1 (Ttf1) refines our current view of the homology between endostyle and thyroid gland. In contrast to earlier literature, we find that a duct always persists to connect the endostyle lumen to the pharynx, a structure that resembles the thyroglossal duct in thyroid development and could further support the homology between endostyle and thyroid." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0002254|UBERON:0014475 "thyroglossal duct|endostylar duct" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1007/s00427-004-0450-0 "Kluge B, Renault N, Rohr KB, Anatomical and molecular reinvestigation of lamprey endostyle development provides new insight into thyroid gland evolution. Development genes and evolution (2005)" "Analysing lamprey endostyle development using semi-thin histological sections, immunohistochemical detection of thyroid hormone, and the molecular marker thyroid transcription factor1 (Ttf1) refines our current view of the homology between endostyle and thyroid gland. In contrast to earlier literature, we find that a duct always persists to connect the endostyle lumen to the pharynx, a structure that resembles the thyroglossal duct in thyroid development and could further support the homology between endostyle and thyroid." bgee ANN 2013-07-01 HOM:0000007 "historical homology" UBERON:0002254|UBERON:0014475 "thyroglossal duct|endostylar duct" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1007/s00427-004-0450-0 "Kluge B, Renault N, Rohr KB, Anatomical and molecular reinvestigation of lamprey endostyle development provides new insight into thyroid gland evolution. Development genes and evolution (2005)" "Analysing lamprey endostyle development using semi-thin histological sections, immunohistochemical detection of thyroid hormone, and the molecular marker thyroid transcription factor1 (Ttf1) refines our current view of the homology between endostyle and thyroid gland. In contrast to earlier literature, we find that a duct always persists to connect the endostyle lumen to the pharynx, a structure that resembles the thyroglossal duct in thyroid development and could further support the homology between endostyle and thyroid." bgee ANN 2013-07-01 HOM:0000007 "historical homology" UBERON:0002254|UBERON:0014475 "thyroglossal duct|endostylar duct" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1007/s00427-004-0450-0 "Kluge B, Renault N, Rohr KB, Anatomical and molecular reinvestigation of lamprey endostyle development provides new insight into thyroid gland evolution. Development genes and evolution (2005)" "Analysing lamprey endostyle development using semi-thin histological sections, immunohistochemical detection of thyroid hormone, and the molecular marker thyroid transcription factor1 (Ttf1) refines our current view of the homology between endostyle and thyroid gland. In contrast to earlier literature, we find that a duct always persists to connect the endostyle lumen to the pharynx, a structure that resembles the thyroglossal duct in thyroid development and could further support the homology between endostyle and thyroid." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0002255 "vomeronasal organ" 32523 "Tetrapoda" CIO:0000005 "low confidence from single evidence" ECO:0000060 "positional similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.669" "(...) the vomeronasal organ is known only in some tetrapods. It is absent in most turtles, crocodiles, birds, some bats, and aquatic mammals. In amphibians, it is in a recessed area off the main nasal cavity. (...) In mammals possesing this organ, it is an isolated area of olfactory membrane within the nasal cavity that is usually connected to the mouth via the nasopalatine duct." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0002255 "vomeronasal organ" 32523 "Tetrapoda" CIO:0000005 "low confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.669" "(...) the vomeronasal organ is known only in some tetrapods. It is absent in most turtles, crocodiles, birds, some bats, and aquatic mammals. In amphibians, it is in a recessed area off the main nasal cavity. (...) In mammals possesing this organ, it is an isolated area of olfactory membrane within the nasal cavity that is usually connected to the mouth via the nasopalatine duct." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0002255 "vomeronasal organ" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23348039 "Brykczynska U, Tzika AC, Rodriguez I, Milinkovitch MC, Contrasted evolution of the vomeronasal receptor repertoires in mammals and squamate reptiles. Genome Biol Evol (2013)" "The vomeronasal organ (VNO) is an olfactory structure that detects pheromones and environmental cues. It consists of sensory neurons that express evolutionary unrelated groups of transmembrane chemoreceptors. The predominant V1R and V2R receptor repertoires are believed to detect airborne and water-soluble molecules, respectively.It has been suggested that the shift in habitat of early tetrapods from water to land is reflected by an increase in the ratio of V1R/V2R genes. (...) Our results do not support the hypothesis that the shift to a vomeronasal receptor repertoire dominated by V1Rs in mammals reflects the evolutionary transition of early tetrapods from water to land. This study sheds light on the evolutionary dynamics of the vomeronasal receptor families in vertebrates and reveals how mammals and squamates differentially adapted the same ancestral vomeronasal repertoire to succeed in a terrestrial environment." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0002255 "vomeronasal organ" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1046/j.1469-7580.2001.19810077.x "Smith TD, Siegel MI, Bonar CJ, Bhatnagar KP, Mooney MP, Burrows AM, Smith MA, Maico LM, The existence of the vomeronasal organ in postnatal chimpanzees and evidence for its homology with that of humans. J Anat (2001)" "(...) the best evidence for the homology of the human VNO to that of other primates (and of mammals in general) is ontogenetic in nature, based on a common embryonic origin from a thickening (vomeronasal primordium) on the medial aspect of each olfactory pit." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0002256 "dorsal horn of spinal cord" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 and Figure 16.27" "The vertebrate spinal cord, like the brain, is organized into two regions and named because of their appearance in fresh preparations. The gray matter of the spinal cord includes nerve cell bodies that lie within the core of the spinal cord. Dorsal and ventral extensions of the gray matter are the dorsal horns and the ventral horns, respectively." bgee ANN 2013-06-14 HOM:0000007 "historical homology" UBERON:0002257 "ventral horn of spinal cord" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 and Figure 16.27" "The vertebrate spinal cord, like the brain, is organized into two regions and named because of their appearance in fresh preparations. The gray matter of the spinal cord includes nerve cell bodies that lie within the core of the spinal cord. Dorsal and ventral extensions of the gray matter are the dorsal horns and the ventral horns, respectively." bgee ANN 2013-06-14 HOM:0000007 "historical homology" UBERON:0002264 "olfactory bulb" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1146/annurev.ne.04.030181.001505 "Northcutt RG, Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci. (1981)" "The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor." bgee ANN 2013-06-07 HOM:0000007 "historical homology" UBERON:0002264 "olfactory bulb" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-3540237358 "Binder MD, Hirokawa N, Windhorst U (editors), Encyclopedia of Neuroscience (2009) p.1390-1400, Jarvis ED, Evolution of the Pallium in Birds and Reptiles" "pallial regions that are widely recognized to be homologous among birds, reptiles, mammals and other vertebrates: the hippocampus, olfactory cortex, and olfactory bulb" bgee ANN 2013-06-07 HOM:0000007 "historical homology" UBERON:0002268 "olfactory organ" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:23428778 "Nakamuta N, Nakamuta S, Taniguchi K, Taniguchi K, Analysis of Glycoproteins Produced by the Associated Gland in the Olfactory Organ of Lungfish. J Vet Med Sci (2013)" "Many vertebrates have two distinct olfactory organs, the olfactory epithelium (OE) and the vomeronasal organ (VNO) for detecting chemical substances in the environment. (...) In the olfactory organ of lungfish, the recess epithelium corresponding to the VNO of tetrapods is equipped with the associated glands, while the lamellar OE corresponding to the OE of ordinary fish is not." bgee ANN 2013-06-26 HOM:0000007 "historical homology" UBERON:0002268 "olfactory organ" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:26108469 "Saraiva LR, Ahuja G, Ivandic I, Syed AS, Marioni JC, Korsching SI, Logan DW, Molecular and neuronal homology between the olfactory systems of zebrafish and mouse. Scientific reports (2015)" "We conducted an analysis of the transcriptional profile of the single zebrafish olfactory organ, and compared it to the transcriptomes of the segregated olfactory sub-systems of the mouse: the olfactory mucosa and vomeronasal organ...Taken together we conclude that the basic molecular mechanisms underlying vertebrate olfaction and all but one of the currently known sensory neuron classes that detect odors and pheromones were already present in the MRCA of the teleost and tetrapod lineages." bgee ANN 2016-05-02 HOM:0000007 "historical homology" UBERON:0002280 "otolith" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" https://www.researchgate.net/publication/285864971 "Lychakov DV, Study on structure of the otolith membrane in the lamprey Lampetra fluviatilis in the context of otolith and otoconium evolution. J Evol Biochem Physiol (1995)" "the otolith membrane of the river lamprey contains an otolith and a thin otoconial layer, i.e., exactly the two main structures that evolve subsequently in a series of fish and tetrapods [1,2]" bgee ANN 2017-05-02 HOM:0000007 "historical homology" UBERON:0002280 "otolith" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0415233705 "Janvier P, Ostracoderms and the shaping of the gnathostome characters (2001) p.173-175" "Among living craniates, the gnathostomes share a large number of unique anatomical and physiological characters...The following list (partly taken from Maisey 1986) only concerns the gnathostome characters that are likely to be preserved in fossils...9 Horizontal semicircular canal and utricular recess; statoconiae or otolith composed of calcium carbonate" bgee ANN 2017-05-02 HOM:0000007 "historical homology" UBERON:0002280 "otolith" 117571 "Euteleostomi" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1007/s10162-008-0137-8 "Kang YJ, Stevenson AK, Yau PM, Kollmar R, Sparc protein is required for normal growth of zebrafish otoliths. J Assoc Res Otolaryngol (2008)" "Otoliths ('ear stones') and the homologous otoconia ('ear dust') are essential to the sense of balance; they convey linear accelerations, including gravity, to sensory hair cells in the inner ear (Hudspeth 1989). Their loss or dislocation causes various forms of disequilibrium, including benign paroxysmal positional vertigo, the most common balance disorder in humans (Brandt 2001). The ear of actinopterygii (ray-finned fishes) contains only three large otoliths - the lapillus in the utricle, the sagitta in the saccule, and the asteriscus in the lagena - each with a distinctive and species-specific shape (Nolf 1985). In contrast, the vestibular organs of sarcopterygii (lobe-finned fishes or higher vertebrates) hold innumerable small and barrel-shaped otoconia. Otoconial growth is completed during early postnatal stages, whereas otoliths continue to grow throughout life under the influence of circadian and seasonal rhythms; the resulting growth rings form a stable record of a fish's life history (Campana and Thorrold 2001)." bgee ANN 2017-05-02 HOM:0000007 "historical homology" UBERON:0002285 "telencephalic ventricle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500" "The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0002286 "third ventricle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500" "The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0002287 "optic recess of third ventricle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:17341136 "Staudt N, Houart C, The prethalamus is established during gastrulation and influences diencephalic regionalization. PLoS Biol (2007)" "The vertebrate brain is divided caudal to rostral into the hind-, mid-, and forebrain. These territories are further developing into highly specialised structures. In the case of the hindbrain, subdivisions are easy to detect morphologically, because rhombomeres are marked by visible borders during the course of development [1]. By contrast, the partition of the embryonic forebrain is not as obvious. The optic recess creates a border between the dorso-rostral telencephalon and the diencephalon." bgee ANN 2013-09-06 HOM:0000007 "historical homology" UBERON:0002288 "choroid plexus of third ventricle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001886, negated: false, taxon ID: 7711 - entity: UBERON:0002286, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0002289 "midbrain cerebral aqueduct" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500" "The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0002290 "choroid plexus of fourth ventricle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001886, negated: false, taxon ID: 7711 - entity: UBERON:0002422, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0002298 "brainstem" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "no:id Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0002299 "alveolus of lung" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.596 and Figure 18-21" "The synapsid line of evolution culminating in mammals and the sauropsid line to reptiles and birds diverged millions of years ago, near the time of the origin of amniotes. Although mammals, too, evolved an efficient respiratory system, needed by endothermic animals, the mammalian system differs in many ways from that of birds because it evolved its complex design from the generalized amniote condition independently. The evolution of the secondary palate in mammals and their therapsid ancestors made possible a separation of food and respiratory passage." bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0002302 "myocardium of atrium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481" "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0002307 "choroid plexus of lateral ventricle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001886, negated: false, taxon ID: 7711 - entity: UBERON:0002285, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0002314 "midbrain tectum" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1371/journal.pone.0003582 "Maximino C, Evolutionary Changes in the Complexity of the Tectum of Nontetrapods: A Cladistic Approach. PLoS One (2008)" "The tectum - a multisensory, topologically mapped structure in the roof of the midbrain presents a remarkable degree of conservation in all vertebrate radiations; although it varies in the extent of its development in different vertebrate classes, there is considerable evidence now to deem its layered structure, its cell types, and its hodological pattern as homologous in all vertebrates." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0002314 "midbrain tectum" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" DOI:10.1371/journal.pone.0003582 "Maximino C, Evolutionary Changes in the Complexity of the Tectum of Nontetrapods: A Cladistic Approach. PLoS One (2008)" "The tectum - a multisensory, topologically mapped structure in the roof of the midbrain presents a remarkable degree of conservation in all vertebrate radiations; although it varies in the extent of its development in different vertebrate classes, there is considerable evidence now to deem its layered structure, its cell types, and its hodological pattern as homologous in all vertebrates." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0002314 "midbrain tectum" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1371/journal.pone.0003582 "Maximino C, Evolutionary Changes in the Complexity of the Tectum of Nontetrapods: A Cladistic Approach. PLoS One (2008)" "The tectum - a multisensory, topologically mapped structure in the roof of the midbrain presents a remarkable degree of conservation in all vertebrate radiations; although it varies in the extent of its development in different vertebrate classes, there is considerable evidence now to deem its layered structure, its cell types, and its hodological pattern as homologous in all vertebrates." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0002314 "midbrain tectum" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1371/journal.pone.0003582 "Maximino C, Evolutionary Changes in the Complexity of the Tectum of Nontetrapods: A Cladistic Approach. PLoS One (2008)" "The tectum - a multisensory, topologically mapped structure in the roof of the midbrain presents a remarkable degree of conservation in all vertebrate radiations; although it varies in the extent of its development in different vertebrate classes, there is considerable evidence now to deem its layered structure, its cell types, and its hodological pattern as homologous in all vertebrates." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0002316 "white matter" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" DOI:10.1038/nature09614 "Nave KA, Myelination and support of axonal integrity by glia. Nature (2010)" "The myelination of axons by glial cells was the last major step in the evolution of cells in the vertebrate nervous system, and white-matter tracts are key to the architecture of the mammalian brain." bgee ANN 2013-06-10 HOM:0000007 "historical homology" UBERON:0002325 "epithelium of urethra" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000057, negated: false, taxon ID: 40674 - entity: UBERON:0000483, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0002328 "notochord" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...)." bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0002328 "notochord" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...)." bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0002328 "notochord" 33511 "Deuterostomia" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:24177053 "Miyamoto N, Wada H, Hemichordate neurulation and the origin of the neural tube. Nat Commun (2013)" "We propose that the origin of the core genetic mechanisms for the development of the notochord and the neural tube date back to the last common deuterostome ancestor." bgee ANN 2014-01-15 HOM:0000007 "historical homology" UBERON:0002328|UBERON:0011288 "notochord|stomochord" 33511 "Deuterostomia" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:25903626 "Holland ND, Holland LZ, Holland PW, Scenarios for the making of vertebrates. Nature (2015)" "Miyamoto and Wada found that the endoderm of the enteropneust stomochord and the roof of the buccal cavity are sources of Hedgehog signals that evidently induce and pattern the collar nerve cord. This parallels Hedgehog signalling from the notochord to the nascent neural tube during vertebrate development. Their data could be interpreted to mean that dorsoventral inversion did not take place during the enteropneust-to-vertebrate transition, that the stomochord is homologous to a notochord, and that the collar cord corresponds to at least part of the vertebrate CNS. These conclusions are close to those reached by Bateson in his original scenario, although Miyamoto and Wada acknowledge that co-option of gene networks cannot be ruled out." bgee ANN 2016-08-29 HOM:0000007 "historical homology" UBERON:0002328|UBERON:0011288 "notochord|stomochord" NOT 33511 "Deuterostomia" CIO:0000005 "low confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:25303744 "Satoh N, Tagawa K, Lowe CJ, Yu JK, Kawashima T, Takahashi H, Ogasawara M, Kirschner M, Hisata K, Su YH, Gerhart J, On a possible evolutionary link of the stomochord of hemichordates to pharyngeal organs of chordates. Genesis (2014)" "Here we review recent progress related to this question (homology of hemichordate stomochord and chordate notochord). First, the developmental mode of the stomochord completely differs from that of the notochord. Second, comparison of expression profiles of genes including Brachyury, a key regulator of notochord formation in chordates, does not support the stomochord/notochord homology." bgee ANN 2018-03-26 HOM:0000007 "historical homology" UBERON:0002328|UBERON:0011288 "notochord|stomochord" NOT 33511 "Deuterostomia" CIO:0000005 "low confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:25303744 "Satoh N, Tagawa K, Lowe CJ, Yu JK, Kawashima T, Takahashi H, Ogasawara M, Kirschner M, Hisata K, Su YH, Gerhart J, On a possible evolutionary link of the stomochord of hemichordates to pharyngeal organs of chordates. Genesis (2014)" "Here we review recent progress related to this question (homology of hemichordate stomochord and chordate notochord). First, the developmental mode of the stomochord completely differs from that of the notochord. Second, comparison of expression profiles of genes including Brachyury, a key regulator of notochord formation in chordates, does not support the stomochord/notochord homology." bgee ANN 2018-03-26 HOM:0000007 "historical homology" UBERON:0002328|UBERON:0011288|UBERON:0035147 "notochord|stomochord|axochord" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000205 "curator inference" PMID:26446368 "Annona G, Holland ND, D'Aniello S, Evolution of the notochord. Evodevo (2015)" "current molecular approaches have actually stimulated the revival of two of the old proposals: first that the notochord is a novelty that arose in the chordates, and second that it is derived from a homologous structure, the axochord, that was present in annelid-like ancestors. In the long term, choosing whether the notochord is a chordate novelty or a legacy from an ancient annelid (or perhaps an evolutionary derivative from precursors yet to be proposed) will probably require descriptions of gene regulatory networks involved in the development of notochords and notochord-like structures in a wide spectrum of animals. For now, one-way forward will be studies of all aspects of the biology of enteropneust hemichordates, a group widely thought to be the key to understanding the evolutionary origin of the chordates." bgee ANN 2018-01-15 HOM:0000007 "historical homology" UBERON:0002328|UBERON:0035147 "notochord|axochord" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" PMID:25214631 "Lauri A, Brunet T, Handberg-Thorsager M, Fischer AH, Simakov O, Steinmetz PR, Tomer R, Keller PJ, Arendt D, Development of the annelid axochord: insights into notochord evolution. Science (2014)" "Our study of annelid development reveals a population of mesodermal cells that converge and extend along the ventral midline and express a combination of transcription factors, signaling molecules, and guidance factors that closely matches that of the vertebrate chordamesoderm. These comparative data suggest that a similar population of mesodermal midline cells already existed in urbilaterian ancestors but leave open its ancient developmental fate. In annelids, these cells differentiate into an axochord; our investigation of chaetognath musculature and an ancestral state reconstruction based on comparative anatomy (fig. S14) suggest that a similar paired longitudinal muscle existed in protostome ancestors." bgee ANN 2018-01-15 HOM:0000007 "historical homology" UBERON:0002328|UBERON:0035147 "notochord|axochord" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:25214631 "Lauri A, Brunet T, Handberg-Thorsager M, Fischer AH, Simakov O, Steinmetz PR, Tomer R, Keller PJ, Arendt D, Development of the annelid axochord: insights into notochord evolution. Science (2014)" "Our study of annelid development reveals a population of mesodermal cells that converge and extend along the ventral midline and express a combination of transcription factors, signaling molecules, and guidance factors that closely matches that of the vertebrate chordamesoderm. These comparative data suggest that a similar population of mesodermal midline cells already existed in urbilaterian ancestors but leave open its ancient developmental fate. In annelids, these cells differentiate into an axochord; our investigation of chaetognath musculature and an ancestral state reconstruction based on comparative anatomy (fig. S14) suggest that a similar paired longitudinal muscle existed in protostome ancestors." bgee ANN 2018-01-15 HOM:0000007 "historical homology" UBERON:0002328|UBERON:0035147 "notochord|axochord" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:25214631 "Lauri A, Brunet T, Handberg-Thorsager M, Fischer AH, Simakov O, Steinmetz PR, Tomer R, Keller PJ, Arendt D, Development of the annelid axochord: insights into notochord evolution. Science (2014)" "Our study of annelid development reveals a population of mesodermal cells that converge and extend along the ventral midline and express a combination of transcription factors, signaling molecules, and guidance factors that closely matches that of the vertebrate chordamesoderm. These comparative data suggest that a similar population of mesodermal midline cells already existed in urbilaterian ancestors but leave open its ancient developmental fate. In annelids, these cells differentiate into an axochord; our investigation of chaetognath musculature and an ancestral state reconstruction based on comparative anatomy (fig. S14) suggest that a similar paired longitudinal muscle existed in protostome ancestors." bgee ANN 2018-01-15 HOM:0000007 "historical homology" UBERON:0002329 "somite" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40" "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...)." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0002329 "somite" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:22037675 "Hannibal RL, Price AL, Patel NH, The functional relationship between ectodermal and mesodermal segmentation in the crustacean, Parhyale hawaiensis. Developmental biology (2012)" "There is considerable debate on whether trunk segmentation in the arthropods, annelids and chordates is homologous, since each phylum is more closely related to unsegmented phyla than to each other (Davis and Patel, 1999, Peel and Akam, 2003 and Seaver, 2003)." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0002329 "somite" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1093/icb/43.1.137 "Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003)" "The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0002329 "somite" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:23430316 "Chesebro JE, Pueyo JI, Couso JP, Interplay between a Wnt-dependent organiser and the Notch segmentation clock regulates posterior development in Periplaneta americana. Biol Open (2013)" "Delta expression maintains Wnt1, maintaining this posterior gene network until all segments have formed. This feedback between caudal, Wnt and Notch-signalling in regulating growth and segmentation seems conserved in other arthropods, with some aspects found even in vertebrates. Thus our findings not only support an ancestral Wnt posterior organiser, but also impinge on the proposals for a common origin of segmentation in arthropods, annelids and vertebrates." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0002329 "somite" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:23430316 "Chesebro JE, Pueyo JI, Couso JP, Interplay between a Wnt-dependent organiser and the Notch segmentation clock regulates posterior development in Periplaneta americana. Biol Open (2013)" "Delta expression maintains Wnt1, maintaining this posterior gene network until all segments have formed. This feedback between caudal, Wnt and Notch-signalling in regulating growth and segmentation seems conserved in other arthropods, with some aspects found even in vertebrates. Thus our findings not only support an ancestral Wnt posterior organiser, but also impinge on the proposals for a common origin of segmentation in arthropods, annelids and vertebrates." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0002329 "somite" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1073/pnas.0808774105 "De Robertis EM, The molecular ancestry of segmentation mechanisms. PNAS (2008)" "The ancestry of segmentation will be resolved (...) when additional genes are found to play conserved roles in segment formation in multiple phyla. In the ideal case, new homologies might be found between the segmentation of vertebrates and that of Drosophila, the species that initiated the molecular dissection of metamerism." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0002333 "pulmonary trunk" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481" "As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0002336 "corpus callosum" 9347 "Eutheria" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1111/j.1749-6632.1969.tb20447.x "Ebner FF, A comparison of primitive forebrain organization in metatherian and eutherian mammals. Annals of the New York Academy of Sciences (1969)" "In addition to the anterior commissure, placental mammals have a phylogenetically new forebrain commissure, the corpus callosum, which primarily interconnects the neocortex of the cerebral hemispheres." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0002340 "epithelium of main bronchus" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21669855 "Leys SP, Nichols SA, Adams ED, Epithelia and integration in sponges. Integrative and Comparative Biology (2009)" bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0002341 "epithelium of segmental bronchus" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002184, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0002342 "neural crest" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)." bgee ANN 2013-06-13 HOM:0000007 "historical homology" UBERON:0002346 "neurectoderm" 33208 "Metazoa" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1046/j.1469-7580.2001.19910133.x "Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0002348 "epicardium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481" "While bird and mammal 4-chambered hearts arose independently from different groups of reptilian ancestor, the vertebrate chambered heart is commonly considered arising from fishes and then defined as an historical homology relationship. However uncertainty remains on the origin of the heart substructures and tissues. [curator]" bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002349 "myocardium" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:17223594 "Davidson B, Ciona intestinalis as a model for cardiac development. Ciona intestinalis as a model for cardiac development. Semin Cell Dev Biol (2007)" "In early juveniles [of tunicate Ciona intestinalis], the heart rudiment consists of a seemingly unstructured mass of cells (B. D. unpublished observations). In diagrams made from sectioned juveniles, researchers have described the formation of two distinct hollow tubes that fuse into a single tube [25]. An invagination along the dorsal surface of this tube gives rise to the myocardium while the outer surface differentiates as pericardium. Further studies are required to confirm these classic observations of post-larval cardiogenesis. If these observations prove accurate, they indicate that Ciona heart morphogenesis may exhibit some ancestral chordate characteristics. In Xenopus and the basal chordate amphioxus, the myocardium is also derived from a dorsal invagination [26, 27]. Whether this process is actually homologous among the chordates must await more detailed molecular characterizations." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002349 "myocardium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481" "While bird and mammal 4-chambered hearts arose independently from different groups of reptilian ancestor, the vertebrate chambered heart is commonly considered arising from fishes and then defined as an historical homology relationship. However uncertainty remains on the origin of the heart substructures and tissues. [curator]" bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002350 "conducting system of heart" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1152/physrev.00006.2003 "Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)" "The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0002352 "atrioventricular node" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1152/physrev.00006.2003 "Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)" "Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus. Furthermore, within the ventricular component a compact outer myocardial component and an interiorly localized extensive trabecular component can be distinguished. The specific activation of the ventricle adds to its complexity as follows. The depolarizing impulse travels rapidly from the atrioventricular node toward the apex and then toward the conal region, achieving activation from apex to base." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002358 "peritoneum" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030259821 "Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.205" "Peritoneum is cited as a common feature to Bilateria. [curator]" bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0002360 "meninx" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0002361 "pia mater" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0002362 "arachnoid mater" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0002363 "dura mater" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0002364 "tympanic membrane" 8292 "Amphibia" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.418" "In particular, a tympanic membrane was not present in the earliest tetrapods (...). An ear utilizing a tympanic membrane evolved independently at least three times in tetrapods: (1) in the lineage that leads to anurans (frogs), (2) in the line of evolution to turtles and diapsids, and (3) in the late synapsid lineage that gave rise to mammals." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0002364 "tympanic membrane" 8457 "Sauropsida" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.418" "In particular, a tympanic membrane was not present in the earliest tetrapods (...). An ear utilizing a tympanic membrane evolved independently at least three times in tetrapods: (1) in the lineage that leads to anurans (frogs), (2) in the line of evolution to turtles and diapsids, and (3) in the late synapsid lineage that gave rise to mammals." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0002364 "tympanic membrane" NOT 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.418" "In particular, a tympanic membrane was not present in the earliest tetrapods (...). An ear utilizing a tympanic membrane evolved independently at least three times in tetrapods: (1) in the lineage that leads to anurans (frogs), (2) in the line of evolution to turtles and diapsids, and (3) in the late synapsid lineage that gave rise to mammals." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0002364 "tympanic membrane" 32524 "Amniota" CIO:0000005 "low confidence from single evidence" ECO:0000033 "traceable author statement" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "Whether the mammalian and non-mammalian tympanic membranes are homologous is still an area of dispute, with discrepancies involving the position of the muscles in relation to the Eustachian tube indicating that the two ear drums may not be homologous (reviewed in (Takechi & Kuratani, 2010))." bgee ANN 2015-04-02 HOM:0000007 "historical homology" UBERON:0002364 "tympanic membrane" NOT 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "Whether the mammalian and non-mammalian tympanic membranes are homologous is still an area of dispute, with discrepancies involving the position of the muscles in relation to the Eustachian tube indicating that the two ear drums may not be homologous (reviewed in (Takechi & Kuratani, 2010))." bgee ANN 2015-04-02 HOM:0000007 "historical homology" UBERON:0002364 "tympanic membrane" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "Whether the mammalian and non-mammalian tympanic membranes are homologous is still an area of dispute, with discrepancies involving the position of the muscles in relation to the Eustachian tube indicating that the two ear drums may not be homologous (reviewed in (Takechi & Kuratani, 2010))." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0002364 "tympanic membrane" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.418" "In particular, a tympanic membrane was not present in the earliest tetrapods (...). An ear utilizing a tympanic membrane evolved independently at least three times in tetrapods: (1) in the lineage that leads to anurans (frogs), (2) in the line of evolution to turtles and diapsids, and (3) in the late synapsid lineage that gave rise to mammals." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0002367 "prostate gland" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.556" "(In mammalian testis) Along the way (the sperm travel), three accessory sex glands, the seminal vesicle, prostate, and bulbourethral (Cowper's) gland, respectively, add their secretions as sperm move from the testes to the urethra." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0002369 "adrenal gland" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9" "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0002370 "thymus" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.558" "A thymus develops in all vertebrates from the endodermal epithelium of certain pharyngeal pouches and from the adjacent ectodermal epithelium. In fishes, all the pouches, or the first four, contribute to thymus formation, but in tetrapods, the number is more restricted. In mammals, only the third and fourth are involved, and the contribution of the third is by far the greater." bgee ANN 2013-07-01 HOM:0000007 "historical homology" UBERON:0002371 "bone marrow" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1146/annurev.cellbio.22.010605.093317 "Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006)" "The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney." bgee ANN 2013-07-01 HOM:0000007 "historical homology" UBERON:0002375 "cricoid cartilage" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471090588 "Hildebrand M, Analysis of vertebrate structure (1983) p.239-241" "(In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis." bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0002376 "cranial muscle" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1111/j.1095-8312.2008.00963.x "Anderson PS, Cranial muscle homology across modern gnathostomes. Biological Journal of the Linnean Society (2008)" "Cranial muscle homology across modern gnathostomes" bgee ANN 2018-03-27 HOM:0000007 "historical homology" UBERON:0002380 "trapezius muscle" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.345" "The sternomastoid and the three parts of the trapezius are branchiomeric muscles that have secondarily acquired an attachment to the pectoral girdle. They evolved from the fish cucullaris." bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0002381 "pectoralis major" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.394 Table 10.2" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0002382 "rectus abdominis muscle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.340-342 and Figure 10-19" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0002383 "supraspinatus muscle" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:20807270 "Abdala V, Diogo R, Comparative anatomy, homologies and evolution of the pectoral and forelimb musculature of tetrapods with special attention to extant limbed amphibians and reptiles. J Anat (2010)" "It is now accepted that the mammalian supraspinatus and infraspinatus, which usually connect the dorsal region of the pectoral girdle to the proximal region of the arm, derive from the supracoracoideus (Tables 1 and 2), a muscle that lies ventral, not dorsal, to the pectoral girdle in most other extant tetrapods (e.g. Kardong, 2002; Diogo et al. 2009a)." bgee ANN 2017-02-15 HOM:0000007 "historical homology" UBERON:0002383 "supraspinatus muscle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.394 Table 10.2" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0002386 "forelimb zeugopod" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:19324642 "Zhu M, Yu X, Stem sarcopterygians have primitive polybasal fin articulation. Biology letters (2009)" "In the fin-limb transition, the origin of the sarcopterygian paired fins triggered new possibilities of fin articulation and movement, and established the proximal segments (stylopod and zeugopod) of the presumptive tetrapod limb." bgee ANN 2013-07-12 HOM:0000007 "historical homology" UBERON:0002387 "pes" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:17849442 "Johanson Z, Joss J, Boisvert CA, Ericsson R, Sutija M, Ahlberg PE, Fish fingers: digit homologues in sarcopterygian fish fins. J Exp Zool B Mol Dev Evol (2007)" "the autopod evolved before the origin of tetrapods, represented by the more distal region of the sarcopterygian fin, with the 'origin of digits' simply representing a modest repatterning of this region rather than the origin of a new structure." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0002387|UBERON:2000508 "pes|pelvic fin radial bone" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:17849442 "Johanson Z, Joss J, Boisvert CA, Ericsson R, Sutija M, Ahlberg PE, Fish fingers: digit homologues in sarcopterygian fish fins. J Exp Zool B Mol Dev Evol (2007)" "the autopod evolved before the origin of tetrapods, represented by the more distal region of the sarcopterygian fin, with the 'origin of digits' simply representing a modest repatterning of this region rather than the origin of a new structure." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0002389 "manual digit" 8782 "Aves" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000024|UBERON:0002102, negated: false, taxon ID: 32524 - entity: UBERON:0002544, negated: false, taxon ID: 8782" bgee HOM:0000007 "historical homology" UBERON:0002389 "manual digit" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000024|UBERON:0002102, negated: false, taxon ID: 32523 - entity: UBERON:0002102, negated: false, taxon ID: 32523 - entity: UBERON:0002544, negated: false, taxon ID: 32523 - entity: UBERON:0002544|UBERON:4000172, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0002389 "manual digit" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000024|UBERON:0002102, negated: false, taxon ID: 32524 - entity: UBERON:0002544, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0002389 "manual digit" NOT 32524 "Amniota" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000024|UBERON:0002102, negated: false, taxon ID: 32524 - entity: UBERON:0002544, negated: true, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0002389 "manual digit" NOT 1338369 "Dipnotetrapodomorpha" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000151|UBERON:0002102, negated: false, taxon ID: 7742 - entity: UBERON:0002544|UBERON:2000271, negated: true, taxon ID: 1338369" bgee HOM:0000007 "historical homology" UBERON:0002390 "hematopoietic system" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/j.coph.2010.05.004 "Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010)" "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways." bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0002391 "lymph" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.627-628 and Figure 19-20" "Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body." bgee ANN 2013-07-01 HOM:0000007 "historical homology" UBERON:0002392 "nasolacrimal duct" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0470671788 "Schoch RR, Amphibian Evolution: The Life of Early Land Vertebrates (2014) p.49" "Superfluous secretions are taken away by the nasolacrimal duct, which is also a novel structure [in Tetrapoda]. This canal connects the periphery of the eye with the nasal sac." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0002392|UBERON:2001426 "nasolacrimal duct|posterior naris" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.256" "The nasolacrimal duct is probably homologous to the posterior (excurrent) naris of actinopterygian fishes." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0002393 "pharyngotympanic tube" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.417" "The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0002393|UBERON:0010019 "pharyngotympanic tube|spiracle (sensu Vertebrata)" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.417" "The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0002394 "bile duct" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1053/ax.2000.7133 "Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000)" "(...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0002397 "maxilla" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:24067611 "Zhu M, Yu X, Ahlberg PE, Choo B, Lu J, Qiao T, Qu Q, Zhao W, Jia L, Blom H, Zhu Y, A Silurian placoderm with osteichthyan-like marginal jaw bones. Nature (2013)" "Here we describe a three-dimensionally preserved 419-million-year-old placoderm fish from the Silurian of China that represents the first stem gnathostome with dermal marginal jaw bones (premaxilla, maxilla and dentary), features previously restricted to Osteichthyes." bgee ANN 2013-10-09 HOM:0000007 "historical homology" UBERON:0002398 "manus" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:17849442 "Johanson Z, Joss J, Boisvert CA, Ericsson R, Sutija M, Ahlberg PE, Fish fingers: digit homologues in sarcopterygian fish fins. J Exp Zool B Mol Dev Evol (2007)" "the autopod evolved before the origin of tetrapods, represented by the more distal region of the sarcopterygian fin, with the 'origin of digits' simply representing a modest repatterning of this region rather than the origin of a new structure." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0002398|UBERON:2001586 "manus|pectoral fin radial bone" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:17849442 "Johanson Z, Joss J, Boisvert CA, Ericsson R, Sutija M, Ahlberg PE, Fish fingers: digit homologues in sarcopterygian fish fins. J Exp Zool B Mol Dev Evol (2007)" "the autopod evolved before the origin of tetrapods, represented by the more distal region of the sarcopterygian fin, with the 'origin of digits' simply representing a modest repatterning of this region rather than the origin of a new structure." bgee ANN 2013-07-12 HOM:0000007 "historical homology" UBERON:0002398|UBERON:2001586 "manus|pectoral fin radial bone" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1002/jmor.10264 "Davis MC, Shubin NH, Force A, Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus. Journal of Morphology (2004)" "While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia." bgee ANN 2013-07-12 HOM:0000007 "historical homology" UBERON:0002399 "lesser omentum" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1007/s00898-999-0002-1 "Brainerd EL, New perspectives on the evolution of lung ventilation mechanisms in vertebrates. Experimental Biology Online (1999)" "In green iguanas, as in most lepidosaurs, the body cavity is not divided into separate pleural and peritoneal spaces. Instead, the lungs and viscera are contained within a single, 'pleuroperitoneal' cavity. This condition is also seen in air-breathing fishes and amphibians, indicating that an undivided body cavity is the primitive condition for amniotes." bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0002400 "parietal pleura" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.193 and Figure 5.34" bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0002401 "visceral pleura" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.193 and Figure 5.34" bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0002402 "pleural cavity" 8457 "Sauropsida" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.162-163" "In most living diapsids (some lizards, snakes, crocodiles, and birds) as well as all mammals, additional folds of coelomic epithelium separate de paired pleural recesses from the rest of the pleuroperitoneal cavity. The coelom of these animals thus consists of four compartments: the pericardial cavity, two pleural cavities, and the peritoneal cavity. [...] In reptiles and birds, the folds separating the pleural cavities from the peritoneal cavity form the oblique septum. In mammals, the separation between the two pleural cavities and the peritoneal cavity develops by the pleuroperitoneal membranes, which push in from the dorsolateral body wall, and by other folds that extend laterally from the mesenteries and medially from the body wall to meet the pleuroperitoneal membranes." bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0002402 "pleural cavity" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.162-163" "In most living diapsids (some lizards, snakes, crocodiles, and birds) as well as all mammals, additional folds of coelomic epithelium separate de paired pleural recesses from the rest of the pleuroperitoneal cavity. The coelom of these animals thus consists of four compartments: the pericardial cavity, two pleural cavities, and the peritoneal cavity. [...] In reptiles and birds, the folds separating the pleural cavities from the peritoneal cavity form the oblique septum. In mammals, the separation between the two pleural cavities and the peritoneal cavity develops by the pleuroperitoneal membranes, which push in from the dorsolateral body wall, and by other folds that extend laterally from the mesenteries and medially from the body wall to meet the pleuroperitoneal membranes." bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0002402 "pleural cavity" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0471090588 "Hildebrand M, Analysis of vertebrate structure (1983) p.205-206" "In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes." bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0002403 "internal intercostal muscle" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0471090588 "Hildebrand M, Analysis of vertebrate structure (1983) p.193" "Behind the thorax, the lateral group (of muscles in reptiles and mammals) remains essentially as for amphibians. (It breaks into three sheet-like layers: external oblique muscle, the internal oblique, and the transversus). More anteriorly, however, the ribs, now enlarged, penetrate and alter this group of muscles. The transversus is excluded from the thorax and the external and internal obliques become, respectively, the external and internal intercostal muscles, which contribute to the new function of ventilation of the lungs." bgee ANN 2013-08-21 HOM:0000007 "historical homology" UBERON:0002405 "immune system" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:21046016 "Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010)" "The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes." bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0002407 "pericardium" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000033 "traceable author statement" DOI:10.1007/s00435-008-0076-2 "Stach TG, Anatomy of the trunk mesoderm in tunicates: homology considerations and phylogenetic interpretation. Zoomorphology (2008)" "Electron microscopic investigations of developmental stages in ascidians, cephalochordates, and craniates showed that the coelomic epithelium, surrounding the major blood vessel that resides in the extracellular matrix, is the plesiomorphic source of contractile myocytes in the chordate heart (Hirakow 1989; Oliphant and Cavey 1972; Stach 1998). Thus, the hypothesis of a general homology of the pericardium-heart in chordates is well established (Davidson and Levine 2003; Hirakow 1989)." bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0002407 "pericardium" 33511 "Deuterostomia" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1007/s00435-011-0125-0 "Kaul-Strehlow S, Stach T, The pericardium in the deuterostome Saccoglossus kowalevskii (Enteropneusta) develops from the ectoderm via schizocoely. Zoomorphology (2011)" "(...) we show that the pericardium of the deuterostome Saccoglossus kowalevskii, an enteropneust, is ontogenetically derived from the ectoderm and develops by schizocoely. (...) The differentiated pericardium possesses a cavity and surrounds a central blood vessel, the heart, situated in the basal extracellular matrix. The pericardium is an integral part of the anterior excretory complex, and comparisons to other deuterostomes indicate that pericardia are homologous despite differing ontogenies." bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0002408 "parietal serous pericardium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481" "While bird and mammal 4-chambered hearts arose independently from different groups of reptilian ancestor, the vertebrate chambered heart is commonly considered arising from fishes and then defined as an historical homology relationship. However uncertainty remains on the origin of the heart substructures and tissues. [curator]" bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002410 "autonomic nervous system" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1002/1097-0185(20000615)261:3<111::AID-AR6>3.0.CO;2-F "Butler AB, Chordate evolution and the origin of craniates: An old brain in a new head. AnaT Rec (New Anat) (2000)" "From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system." bgee ANN 2013-06-10 HOM:0000007 "historical homology" UBERON:0002411 "clitoris" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/j.ydbio.2008.03.017 "Seifert AW, Harfe BD, Cohn MJ, Cell lineage analysis demonstrates an endodermal origin of the distal urethra and perineum. Developmental Biology (2008)" "In both male and female mammalian embryos, development of the external genitalia begins with the emergence of the paired genital swellings immediately above the cloaca (see Perriton et al. 2002 for a detailed description of normal external genitalia development in mouse). These swellings fuse medially and give rise to the bipotential genital tubercle, which can be masculinized to form the penis or feminized to form the clitoris. As the genital tubercle grows out, the ventral side of the cloacal endoderm forms a bilaminar urethral plate that extends into the genital tubercle, and this structure later cavitates in a proximal to distal direction to form the urethral tube (Hynes and Fraher, 2004a; Perriton et al., 2002)." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0002416 "integumental system" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1111/j.1469-7580.2008.01043.x "Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)" "Although often overlooked, the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes but most details of their evolution and development remain confused and uncertain." bgee ANN 2013-07-17 HOM:0000007 "historical homology" UBERON:0002418 "cartilage tissue" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1111/j.1525-142X.2011.00520.x "Hall BK, Parallelism, deep homology, and evo-devo. Evolution and Development (2012)" "Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution." bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0002418 "cartilage tissue" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1111/j.1525-142X.2011.00520.x "Hall BK, Parallelism, deep homology, and evo-devo. Evolution and Development (2012)" "Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution." bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0002422 "fourth ventricle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500" "The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0002423 "hepatobiliary system" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.42-43 and Figure 2-11" "Liver and pancreas are described as major organ systems of craniates. [curator]" bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0002425 "visceral serous pericardium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481" "While bird and mammal 4-chambered hearts arose independently from different groups of reptilian ancestor, the vertebrate chambered heart is commonly considered arising from fishes and then defined as an historical homology relationship. However uncertainty remains on the origin of the heart substructures and tissues. [curator]" bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0002427 "arm skin" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0001460, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0002428 "limb bone" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001474, negated: false, taxon ID: 7742 - entity: UBERON:0002101, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0002432 "pars intermedia of adenohypophysis" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5" "Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. The adenohypophysis forms a thick pars distalis and, in most vertebrates, a pars intermedia, which lies between the pars distalis and the neurohypophysis." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0002433 "pars tuberalis of adenohypophysis" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5" "Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. The adenohypophysis forms a thick pars distalis and, in most vertebrates, a pars intermedia, which lies between the pars distalis and the neurohypophysis. The lumen of Rathke's pouch may persit as a narrow cleft between the pars distalis and the pars intermedia. A pars tuberalis may extend from the pars distalis along the infundibular stalk." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0002434 "pituitary stalk" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-4" "It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0002435 "striatum" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1146/annurev.ne.04.030181.001505 "Northcutt RG, Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci. (1981)" "Thus, certain telencephalic characters - such as the presence of a pallium divided into lateral, dorsal, and medial formations and a subpallium divided into striatum and septum - appear to characterize all vertebrates. They are primitive characters and are homologous among all vertebrates." bgee ANN 2013-06-10 HOM:0000007 "historical homology" UBERON:0002435 "striatum" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1146/annurev.ne.04.030181.001505 "Northcutt RG, Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci. (1981)" "Thus, certain telencephalic characters - such as the presence of a pallium divided into lateral, dorsal, and medial formations and a subpallium divided into striatum and septum - appear to characterize all vertebrates. They are primitive characters and are homologous among all vertebrates." bgee ANN 2013-06-10 HOM:0000007 "historical homology" UBERON:0002436 "primary visual cortex" 314146 "Euarchontoglires" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" PMID:25071460 "Homman-Ludiye J, Bourne JA, Mapping arealisation of the visual cortex of non-primate species: lessons for development and evolution. Front Neural Circuits (2014)" "it was believed that the organization of visual areas into a dorsal stream, specialized in interpreting information relating to the position of an object, and a ventral stream dedicated to object recognition (Mishkin and Ungerleider, 1982; Ungerleider and Haxby, 1994) was exclusively present in primate species. The recent discovery of two processing streams in the mouse visual cortex (Wang et al., 2012) suggests that this trait is homologous in rodents and primates and probably appeared early on in evolution." bgee ANN 2018-03-26 HOM:0000007 "historical homology" UBERON:0002436|UBERON:0014756 "primary visual cortex|Wulst" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" PMID:26554047 "Karten HJ, Vertebrate brains and evolutionary connectomics: on the origins of the mammalian 'neocortex'. Philos Trans R Soc Lond B Biol Sci (2015)" "In birds, a separate pallial region, the dorsomedial 'wulst' or 'bump' shares many properties with the mammalian striate cortex, though with the output layer lying most externally...Wulst, 'bump' homologous to mammalian striate cortex" bgee ANN 2016-09-20 HOM:0000007 "historical homology" UBERON:0002437 "cerebral hemisphere white matter" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001869, negated: false, taxon ID: 7742 - entity: UBERON:0002316, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0002443 "choroidal blood vessel" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001776, negated: false, taxon ID: 7742 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0002444 "lens fiber" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000205 "curator inference" PMID:14985284 "Sivak JG, Through the lens clearly: phylogeny and development, The Proctor lecture. Investigative ophthalmology and visual science (2004)" "The development of the avian lens follows the usual vertebrate pattern, involving the formation and then filling of the lens vesicle and the continued development of new fibers (the secondary fibers) from the equatorial (germinative zone) epithelial cells." bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0002446 "patella" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000981, negated: false, taxon ID: 8287 - entity: UBERON:0001465, negated: false, taxon ID: 32523 - entity: UBERON:0001474, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0002457 "intersomitic artery" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.612" "Few changes of evolutionary significance occur in the branching pattern of the dorsal aorta. All vertebrates have (...) paired intersegmental arteries to the trunk, tail, and paired appendages." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0002460 "vesical vein" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001255, negated: false, taxon ID: 32523 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0002460 "vesical vein" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001255, negated: false, taxon ID: 32524 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0002462 "erector spinae muscle group" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.339-341 and Figure 10-17" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0002463 "muscle of posterior compartment of hindlimb stylopod" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1666/0094-8373(2000)026<0734:AAATEO>2.0.CO;2 "Hutchinson JR, Gatesy SM, Adductors, abductors, and the evolution of archosaur locomotion. Paleobiology (2000)" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0002465 "lymphoid system" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.627" "Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body." bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0002470 "autopod region" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:23598338 "Amemiya CT, Alfoeldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, Gerdol M, Aken B, Biscotti MA, Barucca M, Baurain D, Berlin AM, Blatch GL, Buonocore F, Burmester T, Campbell MS, Canapa A, Cannon JP, Christoffels A, De Moro G, Edkins AL, Fan L, Fausto AM, Feiner N, Forconi M, Gamieldien J, Gnerre S, Gnirke A, Goldstone JV, Haerty W, Hahn ME, Hesse U, Hoffmann S, Johnson J, Karchner SI, Kuraku S, Lara M, Levin JZ, Litman GW, Mauceli E, Miyake T, Mueller MG, Nelson DR, Nitsche A, Olmo E, Ota T, Pallavicini A, Panji S, Picone B, Ponting CP, Prohaska SJ, Przybylski D, Saha NR, Ravi V, Ribeiro FJ, Sauka-Spengler T, Scapigliati G, Searle SM, Sharpe T, Simakov O, Stadler PF, Stegeman JJ, Sumiyama K, Tabbaa D, Tafer H, Turner-Maier J, van Heusden P, White S, Williams L, Yandell M, Brinkmann H, Volff JN, Tabin CJ, Shubin N, Schartl M, Jaffe DB, Postlethwait JH, Venkatesh B, Di Palma F, Lander ES, Meyer A, Lindblad-Toh K, The African coelacanth genome provides insights into tetrapod evolution. Nature (2013)" "There are two major hypotheses about the origins of the autopod; that it was a novel feature of tetrapods, and that it has antecedents in the fins of fish." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0002470 "autopod region" NOT 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:23598338 "Amemiya CT, Alfoeldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, Gerdol M, Aken B, Biscotti MA, Barucca M, Baurain D, Berlin AM, Blatch GL, Buonocore F, Burmester T, Campbell MS, Canapa A, Cannon JP, Christoffels A, De Moro G, Edkins AL, Fan L, Fausto AM, Feiner N, Forconi M, Gamieldien J, Gnerre S, Gnirke A, Goldstone JV, Haerty W, Hahn ME, Hesse U, Hoffmann S, Johnson J, Karchner SI, Kuraku S, Lara M, Levin JZ, Litman GW, Mauceli E, Miyake T, Mueller MG, Nelson DR, Nitsche A, Olmo E, Ota T, Pallavicini A, Panji S, Picone B, Ponting CP, Prohaska SJ, Przybylski D, Saha NR, Ravi V, Ribeiro FJ, Sauka-Spengler T, Scapigliati G, Searle SM, Sharpe T, Simakov O, Stadler PF, Stegeman JJ, Sumiyama K, Tabbaa D, Tafer H, Turner-Maier J, van Heusden P, White S, Williams L, Yandell M, Brinkmann H, Volff JN, Tabin CJ, Shubin N, Schartl M, Jaffe DB, Postlethwait JH, Venkatesh B, Di Palma F, Lander ES, Meyer A, Lindblad-Toh K, The African coelacanth genome provides insights into tetrapod evolution. Nature (2013)" "There are two major hypotheses about the origins of the autopod; that it was a novel feature of tetrapods, and that it has antecedents in the fins of fish." bgee ANN 2015-02-03 HOM:0000007 "historical homology" UBERON:0002470 "autopod region" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:23598338 "Amemiya CT, Alfoeldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, Gerdol M, Aken B, Biscotti MA, Barucca M, Baurain D, Berlin AM, Blatch GL, Buonocore F, Burmester T, Campbell MS, Canapa A, Cannon JP, Christoffels A, De Moro G, Edkins AL, Fan L, Fausto AM, Feiner N, Forconi M, Gamieldien J, Gnerre S, Gnirke A, Goldstone JV, Haerty W, Hahn ME, Hesse U, Hoffmann S, Johnson J, Karchner SI, Kuraku S, Lara M, Levin JZ, Litman GW, Mauceli E, Miyake T, Mueller MG, Nelson DR, Nitsche A, Olmo E, Ota T, Pallavicini A, Panji S, Picone B, Ponting CP, Prohaska SJ, Przybylski D, Saha NR, Ravi V, Ribeiro FJ, Sauka-Spengler T, Scapigliati G, Searle SM, Sharpe T, Simakov O, Stadler PF, Stegeman JJ, Sumiyama K, Tabbaa D, Tafer H, Turner-Maier J, van Heusden P, White S, Williams L, Yandell M, Brinkmann H, Volff JN, Tabin CJ, Shubin N, Schartl M, Jaffe DB, Postlethwait JH, Venkatesh B, Di Palma F, Lander ES, Meyer A, Lindblad-Toh K, The African coelacanth genome provides insights into tetrapod evolution. Nature (2013)" "There are two major hypotheses about the origins of the autopod; that it was a novel feature of tetrapods, and that it has antecedents in the fins of fish." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0002478 "orbitosphenoid" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.237 Table 7.1" bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0002494 "papillary muscle of heart" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" PMID:16758044 "Gumusalan Y, Ozbag D, Ozden H, Saruhan BG, Demirant A, The comparative investigation of left ventricle papillary muscle arteries in different species. Saudi Med J (2006)" "On the internal or parietal surface of the left ventricle in man and in mammals are two papillary muscles, which are almost identical and well developed." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0002506 "iris epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001769, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0002518 "otolith organ" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:11581521 "Moorman SJ, Development of sensory systems in zebrafish (Danio rerio). ILAR Journal (2001)" "In fishes, as in other vertebrates, the vestibular end-organs are divided into a gravity receptor system, with three subdivisions and an angular acceleration receptor system. The gravity receptor system on each side consists of utricular, saccular, and lagenar maculae, each covered by an otolith." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0002518 "otolith organ" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:11581521 "Moorman SJ, Development of sensory systems in zebrafish (Danio rerio). ILAR Journal (2001)" "In fishes, as in other vertebrates, the vestibular end-organs are divided into a gravity receptor system, with three subdivisions and an angular acceleration receptor system. The gravity receptor system on each side consists of utricular, saccular, and lagenar maculae, each covered by an otolith." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0002527 "pancreatic lymph node" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000029, negated: false, taxon ID: 40674 - entity: UBERON:0001264, negated: false, taxon ID: 89593" bgee HOM:0000007 "historical homology" UBERON:0002532 "epiblast (generic)" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1146/annurev.cellbio.042308.113344 "Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009)" "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0002533 "post-anal tail bud" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (5) a larva or embryo with a postanal tail." bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0002534 "paired fin" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:24677573 "Freitas R, Gomez-Skarmeta JL, Rodrigues PN, New frontiers in the evolution of fin development. J Exp Zool B Mol Dev Evol (2014)" "Paleontological data suggest that a pair of fin-like structures appeared in the lineage of jawless fishes that led to the gnathostome stem group in the Silurian period (Coates, 1994; Janvier, 1996; Johanson, 2010). This major clade was then generally characterized by two sets of paired fins emerging from the lateral plate mesoderm (LPM)." bgee ANN 2015-04-15 HOM:0000007 "historical homology" UBERON:0002534|UBERON:2000040 "paired fin|median fin fold" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:16878142 "Freitas R, Zhang G, Cohn MJ, Evidence that mechanisms of fin development evolved in the midline of early vertebrates. Nature (2006)" "Conservation of the embryonic origin and the patterns of Hox and Tbx gene expression in shark and lamprey median fins suggests that the molecular mechanisms of fin development evolved in the midline before the origin of paired fins. Our finding that median fin mesenchyme arises predominantly from somites suggests that these cells may acquire their positional identities, in the form of Hox and Tbx expression, during regionalization of paraxial mesoderm. We suggest that the origin of paired appendages from lateral plate mesoderm involved re-deployment of mechanisms that were originally restricted to paraxial mesoderm, where they regulated development of cartilage (Hox9-Hox13, Tbx18), muscle (Pax7, Paraxis) and tendon (Scleraxis) in the axial skeleton and median fins. Reports of Msx and Dlx expression in paired and median fins of zebrafish (28, 29) may reflect additional evolutionary signatures of this co-option. It is possible that the mechanisms of fin and limb development were established in median finfolds even before the origin of vertebrates. Analysis of median finfold development in cephalochordates will further test the hypothesis that these mechanisms emerged early in chordate evolution." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0002539 "pharyngeal arch" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1111/j.1469-7580.2005.00472.x "Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)" "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0002540 "lateral line system" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471210054 "Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.195" "The mechanosensory lateral line system is widely distributed in aquatic anamniotes. It was apparently present in the earliest vertebrates, as it has been identified in agnathans, cartilaginous fishes, bony fishes, lungfishes, the crossopterygian Latimeria, and aquatic amphibians." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0002544 "digit" 8782 "Aves" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1101/224147 "Stewart TA, Liang C, Cotney J, Noonan JP, Sanger T, Wagner G, Evidence against tetrapod-wide digit identities and for a limited frame shift in bird wings. Biorxiv pre-print December 5 (2017)" "Studies that aim to test digit homology assume that developmental identities (1) were present in a common ancestor, (2) are conserved among the descendent lineages, and (3) are reflected in gene expression profiles. Here we present comparative transcriptomic data from five species that challenge these assumptions among amniotes by documenting a surprising diversity of digital gene expression profiles. Analyses further reveal a core set of transcription factor genes differentially expressed among digits and suggest a new model for the evolution of the bird wing." bgee ANN 2017-12-11 HOM:0000007 "historical homology" UBERON:0002544 "digit" 8782 "Aves" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:21892187 "Wang Z, Young RL, Xue H, Wagner GP, Transcriptomic analysis of avian digits reveals conserved and derived digit identities in birds. Nature (2011)" "Transcriptomic analysis of avian digits reveals conserved and derived digit identities in birds.(...) Here we use transcriptomic data to address a long-standing uncertainty in evolutionary biology, the identity of avian wing digits." bgee ANN 2018-03-05 HOM:0000007 "historical homology" UBERON:0002544 "digit" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:17849442 "Johanson Z, Joss J, Boisvert CA, Ericsson R, Sutija M, Ahlberg PE, Fish fingers: digit homologues in sarcopterygian fish fins. J Exp Zool B Mol Dev Evol (2007)" "the autopod evolved before the origin of tetrapods, represented by the more distal region of the sarcopterygian fin, with the 'origin of digits' simply representing a modest repatterning of this region rather than the origin of a new structure." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0002544 "digit" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:20100248 "Uejima A1 Amano T, Nomura N, Noro M, Yasue T, Shiroishi T, Ohta K, Yokoyama H, Tamura K, Anterior shift in gene expression precedes anteriormost digit formation in amniote limbs. Dev Growth Differ (2010)" "In this study, we investigated the spatiotemporal expression patterns of Mkp3, Sef, and TSK during autopod formation. At chick stage 25-26, when the prospective autopod region is being formed, Mkp3, Sef, and TSK showed unique patterns of gene expression, with strong expression in the region of the prospective anteriormost digit. These gene expression patterns and their sensitivity to Shh signaling are conserved among amniotes." bgee ANN 2018-03-05 HOM:0000007 "historical homology" UBERON:0002544 "digit" NOT 32524 "Amniota" CIO:0000005 "low confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1101/224147 "Stewart TA, Liang C, Cotney J, Noonan JP, Sanger T, Wagner G, Evidence against tetrapod-wide digit identities and for a limited frame shift in bird wings. Biorxiv pre-print December 5 (2017)" "Studies that aim to test digit homology assume that developmental identities (1) were present in a common ancestor, (2) are conserved among the descendent lineages, and (3) are reflected in gene expression profiles. Here we present comparative transcriptomic data from five species that challenge these assumptions among amniotes by documenting a surprising diversity of digital gene expression profiles. Analyses further reveal a core set of transcription factor genes differentially expressed among digits and suggest a new model for the evolution of the bird wing." bgee ANN 2017-12-11 HOM:0000007 "historical homology" UBERON:0002544|UBERON:2000271 "digit|radial bone" 1338369 "Dipnotetrapodomorpha" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:23434323 "Schneider I, Shubin NH, The origin of the tetrapod limb: from expeditions to enhancers. Trends Genet (2013)" "bony radials of lungfish fins have been compared to digits, but these notions have been controversial" bgee ANN 2013-07-12 HOM:0000007 "historical homology" UBERON:0002544|UBERON:2000271 "digit|radial bone" 1338369 "Dipnotetrapodomorpha" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:17849442 "Johanson Z, Joss J, Boisvert CA, Ericsson R, Sutija M, Ahlberg PE, Fish fingers: digit homologues in sarcopterygian fish fins. J Exp Zool B Mol Dev Evol (2007)" "in the Neoceratodus (Osteichthyes: Sarcopterygii) fin, expression of Hoxd13 closely matches late expression patterns observed in the tetrapod autopod. This evidence suggests that Neoceratodus fin radials and tetrapod digits may be patterned by shared mechanisms distinct from those patterning the proximal fin/limb elements, and in that sense are homologous. The presence of independently developing radials in the distal part of the pectoral (and pelvic) fin may be a general feature of the Sarcopterygii." bgee ANN 2013-07-12 HOM:0000007 "historical homology" UBERON:0002544|UBERON:2000271 "digit|radial bone" NOT 1338369 "Dipnotetrapodomorpha" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:23434323 "Schneider I, Shubin NH, The origin of the tetrapod limb: from expeditions to enhancers. Trends Genet (2013)" "bony radials of lungfish fins have been compared to digits, but these notions have been controversial" bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0002544|UBERON:4000172 "digit|lepidotrichium" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:27533041 "Nakamura T, Gehrke AR, Lemberg J, Szymaszek J, Shubin NH, Digits and fin rays share common developmental histories. Nature (2016)" "Digits and fin rays share common developmental histories." bgee ANN 2018-03-26 HOM:0000007 "historical homology" UBERON:0002544|UBERON:4000172 "digit|lepidotrichium" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:27533041 "Nakamura T, Gehrke AR, Lemberg J, Szymaszek J, Shubin NH, Digits and fin rays share common developmental histories. Nature (2016)" "Here, we provide a functional analysis, using CRISPR/Cas9 and fate mapping, of 5' hox genes and enhancers in zebrafish that are indispensable for the development of the wrists and digits of tetrapods. We show that cells marked by the activity of an autopodial hoxa13 enhancer exclusively form elements of the fin fold, including the osteoblasts of the dermal rays. In hox13 knockout fish, we find that a marked reduction and loss of fin rays is associated with an increased number of endochondral distal radials. These discoveries reveal a cellular and genetic connection between the fin rays of fish and the digits of tetrapods and suggest that digits originated via the transition of distal cellular fates." bgee ANN 2018-03-26 HOM:0000007 "historical homology" UBERON:0002546 "cranial placode" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:25903628 "Diogo R, Kelly RG, Christiaen L, Levine M, Ziermann JM, Molnar JL, Noden DM, Tzahor E, A new heart for a new head in vertebrate cardiopharyngeal evolution. Nature (2015)" "The pan-placodal regulatory gene Six1/2 is expressed in a crescent of cells straddling the anterior-most region of the developing neural tube in C. intestinalis embryos, comparable with the sites of origin of cranial placodes in the fate maps of vertebrates. Ectodermal thickenings derived from this domain express placodal regulatory genes, including Six3/6, Pitx and Eya. For example, the atrial siphon placode shares extensive similarities with the vertebrate otic placode (Fig. 4), whereas the stomodeum (the oral siphon primordium) expresses regulatory genes implicated in the specification of the vertebrate olfactory and adenohypophyseal placodes, including Six, Eya and the anterior placode markers Pitx and Dlx. These new findings argue for homologies between urochordate siphon primordia and vertebrate placodes and suggest that; although certain placodes (profundal, maxillomandibular, epibranchial and lens) evolved by diversification within the vertebrate lineage, others (adenohypophyseal, olfactory and otic) appeared before the separation of vertebrates and urochordates (Figs 3, 4)." bgee ANN 2015-05-01 HOM:0000007 "historical homology" UBERON:0002546|UBERON:0009894 "cranial placode|siphon primordium" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:25903628 "Diogo R, Kelly RG, Christiaen L, Levine M, Ziermann JM, Molnar JL, Noden DM, Tzahor E, A new heart for a new head in vertebrate cardiopharyngeal evolution. Nature (2015)" "The pan-placodal regulatory gene Six1/2 is expressed in a crescent of cells straddling the anterior-most region of the developing neural tube in C. intestinalis embryos, comparable with the sites of origin of cranial placodes in the fate maps of vertebrates. Ectodermal thickenings derived from this domain express placodal regulatory genes, including Six3/6, Pitx and Eya. For example, the atrial siphon placode shares extensive similarities with the vertebrate otic placode (Fig. 4), whereas the stomodeum (the oral siphon primordium) expresses regulatory genes implicated in the specification of the vertebrate olfactory and adenohypophyseal placodes, including Six, Eya and the anterior placode markers Pitx and Dlx. These new findings argue for homologies between urochordate siphon primordia and vertebrate placodes and suggest that; although certain placodes (profundal, maxillomandibular, epibranchial and lens) evolved by diversification within the vertebrate lineage, others (adenohypophyseal, olfactory and otic) appeared before the separation of vertebrates and urochordates (Figs 3, 4)." bgee ANN 2015-05-01 HOM:0000007 "historical homology" UBERON:0002546|UBERON:0009894 "cranial placode|siphon primordium" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:25903628 "Diogo R, Kelly RG, Christiaen L, Levine M, Ziermann JM, Molnar JL, Noden DM, Tzahor E, A new heart for a new head in vertebrate cardiopharyngeal evolution. Nature (2015)" "The pan-placodal regulatory gene Six1/2 is expressed in a crescent of cells straddling the anterior-most region of the developing neural tube in C. intestinalis embryos, comparable with the sites of origin of cranial placodes in the fate maps of vertebrates. Ectodermal thickenings derived from this domain express placodal regulatory genes, including Six3/6, Pitx and Eya. For example, the atrial siphon placode shares extensive similarities with the vertebrate otic placode (Fig. 4), whereas the stomodeum (the oral siphon primordium) expresses regulatory genes implicated in the specification of the vertebrate olfactory and adenohypophyseal placodes, including Six, Eya and the anterior placode markers Pitx and Dlx. These new findings argue for homologies between urochordate siphon primordia and vertebrate placodes and suggest that; although certain placodes (profundal, maxillomandibular, epibranchial and lens) evolved by diversification within the vertebrate lineage, others (adenohypophyseal, olfactory and otic) appeared before the separation of vertebrates and urochordates (Figs 3, 4)." bgee ANN 2015-05-01 HOM:0000007 "historical homology" UBERON:0002548 "larva" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000069, negated: false, taxon ID: 33213 - entity: UBERON:0000468, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0002812 "left cerebral hemisphere" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000955, negated: false, taxon ID: 33213 - entity: UBERON:0001869, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0002813 "right cerebral hemisphere" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000955, negated: false, taxon ID: 33213 - entity: UBERON:0001869, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0002824 "vestibular ganglion" 89593 "Craniata" CIO:0000005 "low confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...)" bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0002824 "vestibular ganglion" 89593 "Craniata" CIO:0000005 "low confidence from single evidence" ECO:0000205 "curator inference" http://tolweb.org/Craniata/14826/1997.01.01 "Janvier P, Craniata. Animals with skulls. The Tree of Life Web Project (1997)" "In all craniates, the olfactory (I), optic (II), trigeminal (V), facial (VII), acoustic (VIII), glossopharyngeal (IX) and vagus (X) cranial nerves are present. Additional cranial nerves, the oculomotor (III), trochlear (IV) and abducent (VI) nerves occur only in the Vertebrata. Some consider that the latter have been secondarily lost in hagfishes." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0002827 "vestibulocochlear ganglion" 89593 "Craniata" CIO:0000005 "low confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...)" bgee ANN 2013-06-14 HOM:0000007 "historical homology" UBERON:0002835 "thoracic dorsal root ganglion" 7776 "Gnathostomata" CIO:0000005 "low confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:22046306 "Haeming D, Simoes-Costa M, Uy B, Valencia J, Sauka-Spengler T, Bronner-Fraser M, Expression of sympathetic nervous system genes in Lamprey suggests their recruitment for specification of a new vertebrate feature. PLoS One (2011)" "In the trunk region of gnathostomes, neural crest precursors to sensory and sympathetic ganglia migrate from the dorsal neural tube, along a ventral pathway to coalesce either next to the neural tube, to form dorsal root ganglia, or further ventrally adjacent to the dorsal aorta, to form sympathetic ganglia." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0002894 "olfactory cortex" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-3540237358 "Binder MD, Hirokawa N, Windhorst U (editors), Encyclopedia of Neuroscience (2009) p.1390-1400, Jarvis ED, Evolution of the Pallium in Birds and Reptiles" "pallial regions that are widely recognized to be homologous among birds, reptiles, mammals and other vertebrates: the hippocampus, olfactory cortex, and olfactory bulb" bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0002961 "archicortex" 32524 "Amniota" CIO:0000005 "low confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1038/nrn1606 "Jarvis ED, Gunturkun O, Bruce L, Csillag A, Karten H, Kuenzel W, Medina L, Paxinos G, Perkel DJ, Shimizu T, Striedter G, Wild JM, Ball GF, Dugas-Ford J, Durand SE, Hough GE, Husband S, Kubikova L, Lee DW, Mello CV, Powers A, Siang C, Smulders TV, Wada K, White SA, Yamamoto K, Yu J, Reiner A, Butler AB, Avian Brain Nomenclature Consortium, Avian brains and a new understanding of vertebrate brain evolution. Nat Rev Neurosci (2005)" "The fish pallium was named 'palaeocortex', and was proposed to be the antecedent of the human olfactory cortex. Reptiles were thought to have evolved an 'archicortex', also thought to be olfactory and primitive, that was said to be the antecedent of the human hippocampus. Birds were thought not to have evolved any further pallial regions. By contrast, mammals were thought to have evolved the latest and greatest achievement, a 'neocortex', from the palaeocortex and/or archicortex6. The archicortex and/or palaeocortex, with their 2_3 cell layers, were assumed to be primitive; the neocortex, with its 6 layers, was assumed to be more recently evolved and a substrate for more sophisticated behaviour." bgee ANN 2017-05-15 HOM:0000007 "historical homology" UBERON:0002961 "archicortex" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1002/cne.23851 "Hevner RF, Evolution of the mammalian dentate gyrus. J Comp Neurol (2016)" "Along with paleocortex (likewise 3-layered), archicortex is one form of allocortex (non-neocortex). In mammals, allocortex surrounds the neocortex, which arose from reptilian dorsal cortex like an island (Puelles, 2001, 2011; Medina and Abellan, 2009). While evolutionary growth and transformation of the neocortex are well known, it is less appreciated that evolution also transformed the mammalian archicortex, which came to contain a large, convoluted gyrus: the DG." bgee ANN 2017-05-16 HOM:0000007 "historical homology" UBERON:0002961 "archicortex" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1002/cne.23851 "Hevner RF, Evolution of the mammalian dentate gyrus. J Comp Neurol (2016)" "Along with paleocortex (likewise 3-layered), archicortex is one form of allocortex (non-neocortex). In mammals, allocortex surrounds the neocortex, which arose from reptilian dorsal cortex like an island (Puelles, 2001, 2011; Medina and Abellan, 2009). While evolutionary growth and transformation of the neocortex are well known, it is less appreciated that evolution also transformed the mammalian archicortex, which came to contain a large, convoluted gyrus: the DG." bgee ANN 2017-05-16 HOM:0000007 "historical homology" UBERON:0003050 "olfactory placode" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:25903628 "Diogo R, Kelly RG, Christiaen L, Levine M, Ziermann JM, Molnar JL, Noden DM, Tzahor E, A new heart for a new head in vertebrate cardiopharyngeal evolution. Nature (2015)" "The pan-placodal regulatory gene Six1/2 is expressed in a crescent of cells straddling the anterior-most region of the developing neural tube in C. intestinalis embryos, comparable with the sites of origin of cranial placodes in the fate maps of vertebrates. Ectodermal thickenings derived from this domain express placodal regulatory genes, including Six3/6, Pitx and Eya. For example, the atrial siphon placode shares extensive similarities with the vertebrate otic placode (Fig. 4), whereas the stomodeum (the oral siphon primordium) expresses regulatory genes implicated in the specification of the vertebrate olfactory and adenohypophyseal placodes, including Six, Eya and the anterior placode markers Pitx and Dlx. These new findings argue for homologies between urochordate siphon primordia and vertebrate placodes and suggest that; although certain placodes (profundal, maxillomandibular, epibranchial and lens) evolved by diversification within the vertebrate lineage, others (adenohypophyseal, olfactory and otic) appeared before the separation of vertebrates and urochordates (Figs 3, 4)." bgee ANN 2016-09-05 HOM:0000007 "historical homology" UBERON:0003050 "olfactory placode" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...)." bgee ANN 2016-09-05 HOM:0000007 "historical homology" UBERON:0003051 "ear vesicle" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413 and Figure 12-14" "The inner ear develops embryonically in all vertebrates as an invagination of the ectodermal otic placode to form an otic vesicle." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0003052 "midbrain-hindbrain boundary" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1016/j.ydbio.2005.02.008 "Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)" "Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0003053 "ventricular zone" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "no:id Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0003054 "roof plate" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.6064/2012/475017 "Robertshaw E, Kiecker C, Phylogenetic Origins of Brain Organisers. Scientifica (2012)" "The signalling centres that regulate DV [dorso-ventral] patterning in vertebrates-notochord, prechordal plate, floor plate, MGE [medial ganglionic eminence], and roof plate-seem to have evolved more recently as they are only found in the chordate lineage." bgee ANN 2013-06-12 HOM:0000007 "historical homology" UBERON:0003055 "periderm" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:17532799 "Alibardi L, Gill BJ, Epidermal differentiation in embryos of the tuatara Sphenodon punctatus (Reptilia, Sphenodontidae) in comparison with the epidermis of other reptiles. J Anat (2007)" "In conclusion, despite the variable stratification in the embryonic epidermis of different reptiles, including the relatively primitive S. punctatus, these layers undergo a peculiar form of alpha-keratinization while beta-keratin is absent or very scarce. The latter derives from the dispersion of matrix material in coarse granules of the embryonic epidermis, as previously seen in periderm granules of avian embryonic epidermis or in the embryonic keratohyalin granules of mammalian embryonic epidermis (Alibardi, 2003, 2006). The dispersion of material derived from the coarse filaments in cornifying periderm and inner periderm cells suggests that this process was present in the epidermis of early amniotes." bgee ANN 2013-07-17 HOM:0000007 "historical homology" UBERON:0003056 "pre-chordal neural plate" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0003057 "chordal neural plate" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0003058 "hypochord" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:21172337 "Dal-Pra S, Thisse C, Thisse B, FoxA transcription factors are essential for the development of dorsal axial structures. Developmental biology (2011)" "In vertebrates, embryonic structures present at the dorsal midline, prechordal plate, notochord, hypochord and floor plate share a common embryonic origin. In zebrafish, they derive from a pool of progenitors located within the embryonic shield at the onset of gastrulation. The molecular mechanisms responsible for the common development of these structures remain unknown." bgee ANN 2013-06-10 HOM:0000007 "historical homology" UBERON:0003058 "hypochord" 7742 "Vertebrata" CIO:0000005 "low confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:10648245 "Cleaver O, Seufert DW, Krieg PA, Endoderm patterning by the notochord: development of the hypochord in Xenopus. Development (2000)" "The hypochord, or subnotochordal rod, is an endodermally derived tissue that exists transiently in the embryos of fish, lampreys and amphibians." bgee ANN 2013-06-10 HOM:0000007 "historical homology" UBERON:0003059 "presomitic mesoderm" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1006/dbio.2001.0460 "Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001)" "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0003060 "pronephric duct" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686" "(...) in all craniates, the archinephric duct develops in embryogeny." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0003061 "blood island" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:22204590 "Teixeira V, Arede N, Gardner R, Rodriguez-Leon J, Tavares AT, Targeting the hemangioblast with a novel cell type-specific enhancer. BMC Dev Biol (2011)" "In the early vertebrate embryo, both hematopoietic and endothelial lineages derive from aggregates of mesodermal cells that form the blood islands in the extraembryonic yolk sac [1]. This observation led to the hypothesis that both lineages derive from a common precursor named the hemangioblast [2]. Although still debatable, the existence of hemangioblasts is mainly supported by in vitro differentiation studies [3,4] as well as by evidence that blood and endothelial progenitors express a number of genes in common, such as VEGFR2, GATA2, Lmo2 and Scl/Tal1 [5], some of which regulate the differentiation of both cell lineages" bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0003061 "blood island" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:22204590 "Teixeira V, Arede N, Gardner R, Rodriguez-Leon J, Tavares AT, Targeting the hemangioblast with a novel cell type-specific enhancer. BMC Dev Biol (2011)" "In the early vertebrate embryo, both hematopoietic and endothelial lineages derive from aggregates of mesodermal cells that form the blood islands in the extraembryonic yolk sac [1]. This observation led to the hypothesis that both lineages derive from a common precursor named the hemangioblast [2]. Although still debatable, the existence of hemangioblasts is mainly supported by in vitro differentiation studies [3,4] as well as by evidence that blood and endothelial progenitors express a number of genes in common, such as VEGFR2, GATA2, Lmo2 and Scl/Tal1 [5], some of which regulate the differentiation of both cell lineages" bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0003062 "primitive knot" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1046/j.1525-142x.2000.00073.x "Neidert AH, Panopoulou G and Langeland JA, Amphioxus goosecoid and the evolution of the head organizer and prechordal plate. Evolution and Development (2008)" "The organizer is a central feature of vertebrate embryogenesis. It was first characterized in functional terms in amphibians by Spemann and Mangold (1924), and homologous tissues have since been identified in representatives of most other vertebrate classes, including mammals (the node), birds (Henson's node) and teleost fish (the embryonic shield)." bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0003062 "primitive knot" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:22689359 "Bode HR, The head organizer in Hydra. The International journal of developmental biology (2012)" "During bud formation, Hydra's mode of asexual reproduction, a head organizer based on the canonical Wnt pathway is set up to initiate and control the development of a new Hydra. As this pathway plays a central role in vertebrate embryonic organizers, its presence and activity in Hydra indicate that the molecular basis of the organizer arose early in metazoan evolution." bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0003063 "prechordal plate" NOT 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:11256375 "Neidert AH, Panopoulou G and Langeland JA, Amphioxus goosecoid and the evolution of the head organizer and prechordal plate. Evolution and Development (2000)" "Amphioxus, it is important to note, lacks a prechordal plate in that the notochord extends to the extreme anterior end of the animal, and lacks elaborate differentiation of its forebrain." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0003063 "prechordal plate" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:10357898 "Kuratani S, Horigome N, Hirano S, Developmental morphology of the head mesoderm and reevaluation of segmental theories of the vertebrate head: evidence from embryos of an agnathan vertebrate, Lampetra japonica. Dev Biol (1999)" "The prechordal plate is commonly observed in early embryos of vertebrates. It is in essence the roof of the foregut, caudally continuous with the developing notochord (Jacob et al., 1984). The prechordal plate in the lamprey is a single cell layer located beneath the neural tube rostral to the notochord (Hatta, 1891; de Selys-Longchamps, 1910)." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0003064 "intermediate mesoderm" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/j.ydbio.2004.03.034 "Wilm B, James RG, Schultheiss TM, Hogan BL, The forkhead genes, Foxc1 and Foxc2, regulate paraxial versus intermediate mesoderm cell fate. Developmental biology (2004)" "During vertebrate embryogenesis, the newly formed mesoderm is allocated to the paraxial, intermediate, and lateral domains, each giving rise to different cell and tissue types. Here, we provide evidence that the forkhead genes, Foxc1 and Foxc2, play a role in the specification of mesoderm to paraxial versus intermediate fates." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0003064 "intermediate mesoderm" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1016/j.ydbio.2004.03.034 "Wilm B, James RG, Schultheiss TM, Hogan BL, The forkhead genes, Foxc1 and Foxc2, regulate paraxial versus intermediate mesoderm cell fate. Developmental biology (2004)" "During vertebrate embryogenesis, the newly formed mesoderm is allocated to the paraxial, intermediate, and lateral domains, each giving rise to different cell and tissue types. Here, we provide evidence that the forkhead genes, Foxc1 and Foxc2, play a role in the specification of mesoderm to paraxial versus intermediate fates." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0003065 "ciliary marginal zone" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1159/000057571 "Reh TA, Fischer AJ, Stem cells in the vertebrate retina. Brain Behav Evol (2001)" "The retina of all vertebrates develops via similar mechanisms. Toward the end of retinal histogenesis, proliferating progenitors and newly generated cells are confined to peripheral regions of the retina. In fish and amphibians, this region is maintained after embryonic development and becomes the CMZ (ciliary margin zone). A CMZ exists in birds but compared to that of fish and amphibians this region produces much less new retina as the globe of the eye expands postnatally. At least some of the molecular mechanisms that regulate the addition of new cells in this zone appear to have been conserved from fish to birds." bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0003067 "dorsolateral placode" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1073/pnas.97.9.4449 "Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)" "In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals." bgee ANN 2013-06-13 HOM:0000007 "historical homology" UBERON:0003068 "axial mesoderm" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1002/dvdy.21177 "Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)" "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0003069 "otic placode" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:11523832 "Streit A, Origin of the vertebrate inner ear: evolution and induction of the otic placode. J Anat (2001)" "Molecular evidence has revealed that lower chordates already possess sensory organs that share homology to the vertebrate inner ear. As the pathways that govern the development of the vertebrate otic placode are discovered, it will be interesting to investigate their conservation in lower chordates. A similar approach may also resolve the question of whether the inner ear is derived from the lateral line or whether it evolved independently." bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0003069 "otic placode" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:25903628 "Diogo R, Kelly RG, Christiaen L, Levine M, Ziermann JM, Molnar JL, Noden DM, Tzahor E, A new heart for a new head in vertebrate cardiopharyngeal evolution. Nature (2015)" "The pan-placodal regulatory gene Six1/2 is expressed in a crescent of cells straddling the anterior-most region of the developing neural tube in C. intestinalis embryos, comparable with the sites of origin of cranial placodes in the fate maps of vertebrates. Ectodermal thickenings derived from this domain express placodal regulatory genes, including Six3/6, Pitx and Eya. For example, the atrial siphon placode shares extensive similarities with the vertebrate otic placode (Fig. 4), whereas the stomodeum (the oral siphon primordium) expresses regulatory genes implicated in the specification of the vertebrate olfactory and adenohypophyseal placodes, including Six, Eya and the anterior placode markers Pitx and Dlx. These new findings argue for homologies between urochordate siphon primordia and vertebrate placodes and suggest that; although certain placodes (profundal, maxillomandibular, epibranchial and lens) evolved by diversification within the vertebrate lineage, others (adenohypophyseal, olfactory and otic) appeared before the separation of vertebrates and urochordates (Figs 3, 4)." bgee ANN 2016-09-05 HOM:0000007 "historical homology" UBERON:0003069 "otic placode" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:11523832 "Streit A, Origin of the vertebrate inner ear: evolution and induction of the otic placode. J Anat (2001)" "Recent molecular data have challenged the longstanding view that special sense organs such as the inner ear have evolved with the appearance of vertebrates. (...) During embryonic development, the inner ear arises from a simple epithelium adjacent to the hindbrain, the otic placode, that is specified through inductive interactions with surrounding tissues. (...) the hypothesis is discussed that induction of all sensory placodes initially shares a common molecular pathway, which may have been responsible to generate an 'ancestral placode' during evolution." bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0003069 "otic placode" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...)." bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0003070 "trigeminal placode complex" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1073/pnas.97.9.4449 "Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)" "The dorsolateral placodes (trigeminal and vestibular) develop from ectoderm lateral to the brain (...). In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals." bgee ANN 2013-06-13 HOM:0000007 "historical homology" UBERON:0003070 "trigeminal placode complex" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1073/pnas.97.9.4449 "Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)" "The dorsolateral placodes (trigeminal and vestibular) develop from ectoderm lateral to the brain (...). In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals." bgee ANN 2013-06-13 HOM:0000007 "historical homology" UBERON:0003072 "optic cup" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup." bgee ANN 2013-04-15 HOM:0000007 "historical homology" UBERON:0003073 "lens placode" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens." bgee AUC 2013-05-15 HOM:0000007 "historical homology" UBERON:0003075 "neural plate" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0003075 "neural plate" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0003076 "posterior neural tube" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0003077 "paraxial mesoderm" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1002/dvdy.21177 "Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)" "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0003078 "epibranchial placode" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1046/j.1469-7580.2001.19910133.x "Graham A, The development and evolution of the pharyngeal arches. J Anat (2001)" "These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0003078 "epibranchial placode" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1046/j.1469-7580.2001.19910133.x "Graham A, The development and evolution of the pharyngeal arches. J Anat (2001)" "These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0003078 "epibranchial placode" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1073/pnas.97.9.4449 "Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)" "In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0003078 "epibranchial placode" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:22512454 "Graham A, Shimeld SM, The origin and evolution of the ectodermal placodes. J Anat (2013)" "Epibranchial placode homologues have also not been identified outside the vertebrates. Indeed, taste buds, one of the structures innervated by epibranchial neurones, are believed to be vertebrate-specific. It should be noted, however, that the epibranchial placodes develop adjacent to the branchial slits, structures which in ascidians form after metamorphosis and are relatively poorly studied." bgee ANN 2015-05-01 HOM:0000007 "historical homology" UBERON:0003078 "epibranchial placode" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...)." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0003079 "floor plate" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1016/S0959-4388(99)00003-3 "Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)" "In summary, the available data for tunicates, amphioxus, and vertebrates indicate that a floorplate-like structure was already present in the proximate invertebrate ancestor of the vertebrates and that the genetic mechanisms for DV patterning of the nerve cord were also largely in place." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0003080 "anterior neural tube" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0003081 "lateral plate mesoderm" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1073/pnas.97.9.4449 "Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) Figure 3" "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0003081 "lateral plate mesoderm" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1073/pnas.97.9.4449 "Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) Figure 3" "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0003082 "myotome" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1038/sj.embor.embor920 "Hollway GE, Currie PD, Myotome meanderings. Cellular morphogenesis and the making of muscle. EMBO Rep.(2003)" "In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0003083 "trunk neural crest" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0003085 "ventral aorta" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0003087 "anterior cardinal vein" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.462" "In primitive vertebrates, the basic early embryonic pattern is retained, and blood from anterior and posterior systemic tissues is returned in anterior and posterior cardinal veins, both pairs of veins uniting in common cardinal veins near the heart. In derived vertebrates, the cardinals appear but usually persist only in the embryo, being functionally replaced by alternative adult vessels, the precava and postcava (anterior and posterior venae cavae)." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0003089 "sclerotome" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:23401412 "Ota KG, Fujimoto S, Oisi Y, Kuratani S, Late development of hagfish vertebral elements. J Exp Zool B Mol Dev Evol (2013)" "It has been demonstrated recently that hagfishes, one of two groups of extant jawless vertebrates, have cartilaginous vertebral elements. Embryological and gene expression analyses have also shown that this group of animals develops a sclerotome, the potential primordium of the axial skeleton." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0003089 "sclerotome" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:23401412 "Ota KG, Fujimoto S, Oisi Y, Kuratani S, Late development of hagfish vertebral elements. J Exp Zool B Mol Dev Evol (2013)" "It has been demonstrated recently that hagfishes, one of two groups of extant jawless vertebrates, have cartilaginous vertebral elements. Embryological and gene expression analyses have also shown that this group of animals develops a sclerotome, the potential primordium of the axial skeleton." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0003089 "sclerotome" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1073/pnas.97.9.4449 "Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)" "The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0003091 "thyroid primordium" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0002046 - UBERON:0002046" bgee HOM:0000007 "historical homology" UBERON:0003091 "thyroid primordium" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0002046" bgee HOM:0000007 "historical homology" UBERON:0003092 "ultimobranchial body" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:5094232 "Clark NB, The ultimobranchial body of reptiles. J Exp Zool (1971)" "Reptilian ultimobranchial bodies, located anterior to the heart in the region of the thyroid and parathyroid glands, are composed of cell cords and follicles. The cells show secretory activity and are similar histologically and ultrastructurally to ultimobranchial tissue from other vertebrate classes." bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0003092 "ultimobranchial body" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.523" "(...) ultimobranchial bodies that develop in all vertebrates from the ventral or posterior surface of the last pair of pharyngeal pouches. The ultimobranchial bodies are vestigial in most mammals (...)." bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0003092 "ultimobranchial body" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.523" "(...) ultimobranchial bodies that develop in all vertebrates from the ventral or posterior surface of the last pair of pharyngeal pouches. The ultimobranchial bodies are vestigial in most mammals (...)." bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0003098 "optic stalk" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup." bgee ANN 2013-04-15 HOM:0000007 "historical homology" UBERON:0003099 "cranial neural crest" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0003104 "mesenchyme" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.122-123 and Figure 4-5" "Epithelium is the tissue phenotype of early embryos and primitive adults of the chordate phylum. A second tissue type, however, is produced by epithelial-mesenchymal transformation (EMT) in higher chordates, such as vertebrata. Mesenchymal cells have the ability, which true epithelia do not, to invade and migrate through the extracellular matrix (ECM) to create dramatic cell transpositions." bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0003107 "Meckel's cartilage" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0878932504 "Gilbert SF, Developmental Biology (2006) p.16-17" "In all jawed vertebrates, including fish, the first pharyngeal arch generates the jaw apparatus. The neural crest cells of this arch migrate to form Meckel's cartilage, the precursor of the jaw." bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0003113 "dermatocranium" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1002/jemt.10217 "Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy reasearch and technique (2002) Fig.7" "Origin of a dermal skeleton predates the evolution of gnathostomes. [curator]" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0003124 "chorion" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187" "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0003125 "vitelline membrane" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.159" "Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0003126 "trachea" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.591-592" "Neck lenght increases in reptiles, and the primitive laryngotracheal chamber [found in frogs] becomes divided into a larynx and trachea." bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0003128 "cranium" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.41 and Figure 2-11 p.42" bgee ANN 2013-08-21 HOM:0000007 "historical homology" UBERON:0003129 "skull" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "The incorporation of the primary jaw joint into the mammalian middle ear was only possible due to the evolution of a new way to articulate the upper and lower jaws, with the formation of the dentary-squamosal joint, or TMJ in humans. The evolution of the three-ossicle ear in mammals is thus intricately connected with the evolution of a novel jaw joint, the two structures evolving together to create the distinctive mammalian skull." bgee ANN 2013-08-21 HOM:0000007 "historical homology" UBERON:0003217 "neural lobe of neurohypophysis" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5" "It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0003220 "metanephric mesenchyme" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0878932504 "Gilbert SF, Developmental Biology (2006) p.462" "When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0003224 "chorion syncytiotrophoblast" 9347 "Eutheria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000371, negated: false, taxon ID: 9347 - entity: UBERON:0000478, negated: false, taxon ID: 40674 - entity: UBERON:0003124, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0003229 "epithelium of elbow" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001461, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003231 "epithelium of hip" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001464, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0003232 "epithelium of knee" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001465, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003233 "epithelium of shoulder" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001467, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003235 "epithelium of upper jaw" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001709, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0003236 "epithelium of lower jaw" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21669855 "Leys SP, Nichols SA, Adams ED, Epithelia and integration in sponges. Integrative and Comparative Biology (2009)" bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0003238 "epithelium of superior semicircular canal" 32525 "Theria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:22404255 "Gunz P, Ramsier M, Kuhrig M, Hublin JJ, Spoor F, The mammalian bony labyrinth reconsidered, introducing a comprehensive geometric morphometric approach. J Anat (2012)" "The bony labyrinth inside the petrous portion of the temporal bone houses the sense organs of hearing and balance. Characterized in therian mammals by three semicircular canals and a coiled cochlea (Luo et al., 2011) its morphology is highly conserved. Nevertheless, the detailed morphology varies even among closely related taxa and carries valuable functional, developmental and phylogenetic information (e.g. Spoor & Zonneveld, 1998; Schmelzle et al., 2007; Lebrun et al., 2010)." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0003239 "epithelium of posterior semicircular canal" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21669855 "Leys SP, Nichols SA, Adams ED, Epithelia and integration in sponges. Integrative and Comparative Biology (2009)" bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0003240 "epithelium of lateral semicircular canal" 32525 "Theria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:22404255 "Gunz P, Ramsier M, Kuhrig M, Hublin JJ, Spoor F, The mammalian bony labyrinth reconsidered, introducing a comprehensive geometric morphometric approach. J Anat (2012)" "The bony labyrinth inside the petrous portion of the temporal bone houses the sense organs of hearing and balance. Characterized in therian mammals by three semicircular canals and a coiled cochlea (Luo et al., 2011) its morphology is highly conserved. Nevertheless, the detailed morphology varies even among closely related taxa and carries valuable functional, developmental and phylogenetic information (e.g. Spoor & Zonneveld, 1998; Schmelzle et al., 2007; Lebrun et al., 2010)." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0003241 "epithelium of utricle" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19786082 "Manley GA, An evolutionary perspective on middle ears. Hearing research (2010)" "During their evolution, various lineages of fishes developed an auditory ability through co-opting vestibular epithelia (e.g. sacculus, utriculus, lagena) to also respond to sound. By means of these changes, and in some cases supported by accessory structures which increase sensitivity, some modern fish are quite sensitive to frequencies up to several kHz (Ladich and Popper, 2004). These developments are, however, entirely unrelated to hearing in land vertebrates." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0003242 "epithelium of saccule" NOT 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001854, negated: true, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003242 "epithelium of saccule" 7776 "Gnathostomata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001854, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0003242 "epithelium of saccule" NOT 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001854, negated: true, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0003242 "epithelium of saccule" 7898 "Actinopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001854, negated: false, taxon ID: 7898" bgee HOM:0000007 "historical homology" UBERON:0003242 "epithelium of saccule" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001854, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003242 "epithelium of saccule" NOT 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001854, negated: true, taxon ID: 117571" bgee HOM:0000007 "historical homology" UBERON:0003243 "epithelium of cochlear duct" 32525 "Theria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:20667879 "Luo ZX, Ruf I, Schultz JA, Martin T, Fossil evidence on evolution of inner ear cochlea in Jurassic mammals. Proceedings Biological sciences The Royal Society (2011) Figure 1" "The snail-shaped cochlea with its interior complexity is one of the most prominent features of marsupial and placental mammals with significant function and evolutionary consequence." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0003244 "epithelium of mammary gland" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:23681303 "Oftedal OT, Dhouailly D, Evo-devo of the mammary gland. J Mammary Gland Biol Neoplasia (2013)" "Mammary development proceeds through homologous phases across taxa, but evolutionary modifications in early development produce different final morphologies." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0003246 "epithelium of endolymphatic sac" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21669855 "Leys SP, Nichols SA, Adams ED, Epithelia and integration in sponges. Integrative and Comparative Biology (2009)" bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0003247 "epithelium of forearm" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002386, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0003249 "epithelium of otic placode" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:11523832 "Streit A, Origin of the vertebrate inner ear: evolution and induction of the otic placode. J Anat (2001)" "Molecular evidence has revealed that lower chordates already possess sensory organs that share homology to the vertebrate inner ear. As the pathways that govern the development of the vertebrate otic placode are discovered, it will be interesting to investigate their conservation in lower chordates. A similar approach may also resolve the question of whether the inner ear is derived from the lateral line or whether it evolved independently." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0003257 "yolk sac endoderm" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000925, negated: false, taxon ID: 33213 - entity: UBERON:0001040, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0003257|UBERON:0012275 "yolk sac endoderm|meso-epithelium" 6072 "Eumetazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000925|UBERON:0000926, negated: false, taxon ID: 6072" bgee HOM:0000007 "historical homology" UBERON:0003262 "amniotic mesoderm" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000305, negated: false, taxon ID: 32524 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003265 "chorionic mesenchyme" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0003104, negated: false, taxon ID: 7711 - entity: UBERON:0003124, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0003267 "tooth of upper jaw" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001091, negated: false, taxon ID: 7776 - entity: UBERON:0001709, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0003268 "tooth of lower jaw" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001091, negated: false, taxon ID: 7776 - entity: UBERON:0001710, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0003269 "skeletal muscle tissue of eye" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000019, negated: false, taxon ID: 7742 - entity: UBERON:0001134, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0003274 "mesothelium of omental bursa" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1007/s00898-999-0002-1 "Brainerd EL, New perspectives on the evolution of lung ventilation mechanisms in vertebrates. Experimental Biology Online (1999)" "In green iguanas, as in most lepidosaurs, the body cavity is not divided into separate pleural and peritoneal spaces. Instead, the lungs and viscera are contained within a single, 'pleuroperitoneal' cavity. This condition is also seen in air-breathing fishes and amphibians, indicating that an undivided body cavity is the primitive condition for amniotes." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0003277 "skeleton of upper jaw" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101" "The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof." bgee ANN 2013-08-21 HOM:0000007 "historical homology" UBERON:0003277 "skeleton of upper jaw" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "The incorporation of the primary jaw joint into the mammalian middle ear was only possible due to the evolution of a new way to articulate the upper and lower jaws, with the formation of the dentary-squamosal joint, or TMJ in humans. The evolution of the three-ossicle ear in mammals is thus intricately connected with the evolution of a novel jaw joint, the two structures evolving together to create the distinctive mammalian skull." bgee ANN 2013-08-21 HOM:0000007 "historical homology" UBERON:0003278 "skeleton of lower jaw" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101" "The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof." bgee ANN 2013-08-21 HOM:0000007 "historical homology" UBERON:0003278 "skeleton of lower jaw" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "The incorporation of the primary jaw joint into the mammalian middle ear was only possible due to the evolution of a new way to articulate the upper and lower jaws, with the formation of the dentary-squamosal joint, or TMJ in humans. The evolution of the three-ossicle ear in mammals is thus intricately connected with the evolution of a novel jaw joint, the two structures evolving together to create the distinctive mammalian skull." bgee ANN 2013-08-21 HOM:0000007 "historical homology" UBERON:0003279 "endothelium of trachea" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001986, negated: false, taxon ID: 7742 - entity: UBERON:0003126, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003280 "endothelium of main bronchus" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001986, negated: false, taxon ID: 7742 - entity: UBERON:0002182, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003281 "mesentery of stomach" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1046/j.1525-142x.2000.00076.x "Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000)" "It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach." bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0003282 "mesentery of heart" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) Development of the coelomic cavity and mesenteries, p.159-164" bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0003283 "mesentery of oesophagus" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0521617147 "Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0003284 "mesentery of midgut" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0521617147 "Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut." bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0003288 "meninx of midbrain" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001891, negated: false, taxon ID: 7711 - entity: UBERON:0002360, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003289 "meninx of telencephalon" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001893, negated: false, taxon ID: 7742 - entity: UBERON:0002360, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003290 "meninx of diencephalon" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001894, negated: false, taxon ID: 7711 - entity: UBERON:0002360, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003291 "meninx of hindbrain" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002028, negated: false, taxon ID: 7711 - entity: UBERON:0002360, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003294 "gland of foregut" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0521617147 "Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut." bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0003297 "gland of integumental system" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1111/j.1469-7580.2008.01043.x "Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)" "Although often overlooked, the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes but most details of their evolution and development remain confused and uncertain." bgee ANN 2013-07-17 HOM:0000007 "historical homology" UBERON:0003304 "mesoderm blood island" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000926, negated: false, taxon ID: 33213 - entity: UBERON:0003061, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003312 "mesenchyme of testis" 7711 "Chordata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000473, negated: false, taxon ID: 33213 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003312 "mesenchyme of testis" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000473, negated: false, taxon ID: 7742 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003314 "eye mesenchyme" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000019, negated: false, taxon ID: 7742 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003315 "mesenchyme of ovary" 7711 "Chordata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000992, negated: false, taxon ID: 33213 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003315 "mesenchyme of ovary" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000992, negated: false, taxon ID: 7742 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003316 "mesenchyme of yolk sac" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001040, negated: false, taxon ID: 32524 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003318 "mesenchyme of elbow" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001461, negated: false, taxon ID: 32523 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003320 "mesenchyme of hip" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001464, negated: false, taxon ID: 7776 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003321 "mesenchyme of knee" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001465, negated: false, taxon ID: 32523 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003322 "mesenchyme of shoulder" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001467, negated: false, taxon ID: 32523 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003323 "mesenchyme of upper jaw" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001709, negated: false, taxon ID: 7776 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003324 "mesenchyme of lower jaw" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001710, negated: false, taxon ID: 7776 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003325 "mesenchyme of pinna" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001757, negated: false, taxon ID: 40674 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003326 "mesenchyme of mammary gland" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001911, negated: false, taxon ID: 40674 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003327 "mesenchyme of forearm" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002386, negated: false, taxon ID: 8287 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003338 "ganglion of peripheral nervous system" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000010, negated: false, taxon ID: 7711 - entity: UBERON:0000045, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0003339 "ganglion of central nervous system" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000045, negated: false, taxon ID: 33213 - entity: UBERON:0001017, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0003351 "pharyngeal epithelium" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001042, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003351 "pharyngeal epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001042, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003352 "epithelium of midgut" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0521617147 "Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0003353 "epithelium of hindgut" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0521617147 "Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0003354 "epithelium of rectum" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21669855 "Leys SP, Nichols SA, Adams ED, Epithelia and integration in sponges. Integrative and Comparative Biology (2009)" bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0003356 "epithelium of nasal septum" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001706, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0003357 "epithelium of tongue" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001723, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003359 "epithelium of submandibular gland" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21669855 "Leys SP, Nichols SA, Adams ED, Epithelia and integration in sponges. Integrative and Comparative Biology (2009)" bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0003360 "epithelium of parotid gland" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21669855 "Leys SP, Nichols SA, Adams ED, Epithelia and integration in sponges. Integrative and Comparative Biology (2009)" bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0003361 "epithelium of sublingual gland" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21669855 "Leys SP, Nichols SA, Adams ED, Epithelia and integration in sponges. Integrative and Comparative Biology (2009)" bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0003367 "epithelium of vomeronasal organ" 32523 "Tetrapoda" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002255, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003367 "epithelium of vomeronasal organ" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002255, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0003367 "epithelium of vomeronasal organ" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002255, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0003374 "chorionic ectoderm" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000478, negated: false, taxon ID: 40674 - entity: UBERON:0000924, negated: false, taxon ID: 33213 - entity: UBERON:0003124, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0003379 "cardiac muscle of right atrium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.604-605 and p.618-622" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0003380 "cardiac muscle of left atrium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.604-605 and p.618-622" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0003381|UBERON:0006567 "cardiac muscle of right ventricle|right ventricle myocardium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450-451" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0003382|UBERON:0006566 "cardiac muscle of left ventricle|left ventricle myocardium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450-451" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0003383 "cardiac muscle tissue of interventricular septum" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.618" "Superficially, the mammalian heart resembles those of birds and crocodiles, but the interventricular septum evolved independently and develops embryonically in a slightly different way, so it is not homologous to the interventricular septum of these vertebrates." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0003383 "cardiac muscle tissue of interventricular septum" NOT 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.618" "Superficially, the mammalian heart resembles those of birds and crocodiles, but the interventricular septum evolved independently and develops embryonically in a slightly different way, so it is not homologous to the interventricular septum of these vertebrates." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0003383 "cardiac muscle tissue of interventricular septum" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.618" "Superficially, the mammalian heart resembles those of birds and crocodiles, but the interventricular septum evolved independently and develops embryonically in a slightly different way, so it is not homologous to the interventricular septum of these vertebrates." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0003384 "skeletal muscle tissue of pharynx" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001042, negated: false, taxon ID: 7711 - entity: UBERON:0001134, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0003384 "skeletal muscle tissue of pharynx" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001042, negated: false, taxon ID: 7742 - entity: UBERON:0001134, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0003386 "smooth muscle of eye" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000019, negated: false, taxon ID: 7742 - entity: UBERON:0001135, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0003387 "smooth muscle of trachea" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0003126, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003403 "skin of forearm" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0002386, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0003415 "mesenchyme of nasal septum" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001706, negated: false, taxon ID: 7776 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003416 "mesenchyme of tongue" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001723, negated: false, taxon ID: 32523 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003418 "mesenchyme of submandibular gland" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001736, negated: false, taxon ID: 32524 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003419 "mesenchyme of parotid" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001831, negated: false, taxon ID: 32524 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003420 "mesenchyme of sublingual gland" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001832, negated: false, taxon ID: 32524 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003421 "mesenchyme of vomeronasal organ" 32523 "Tetrapoda" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002255, negated: false, taxon ID: 32523 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003421 "mesenchyme of vomeronasal organ" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002255, negated: false, taxon ID: 32524 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003421 "mesenchyme of vomeronasal organ" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002255, negated: false, taxon ID: 40674 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003425 "renal lymph node" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000029, negated: false, taxon ID: 40674 - entity: UBERON:0002113, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003426 "dermis adipose tissue" 7711 "Chordata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001013, negated: false, taxon ID: 33213 - entity: UBERON:0002067, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003426 "dermis adipose tissue" 7742 "Vertebrata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001013, negated: false, taxon ID: 7742 - entity: UBERON:0002067, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003426 "dermis adipose tissue" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001013, negated: false, taxon ID: 7742 - entity: UBERON:0002067, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0003431 "leg nerve" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000978, negated: false, taxon ID: 32523 - entity: UBERON:0001021, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003433 "arm nerve" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0001460, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003436 "shoulder nerve" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0001467, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003438 "iris nerve" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0001769, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003440 "limb nerve" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0002101, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003441 "forelimb nerve" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000024|UBERON:0002102, negated: false, taxon ID: 32523 - entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0002102, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003441 "forelimb nerve" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000024|UBERON:0002102, negated: false, taxon ID: 32524 - entity: UBERON:0001021, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003442 "hindlimb nerve" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0002103, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003445 "pes nerve" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0002387, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003448 "manus nerve" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0002398, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003456 "respiratory system lymphatic vessel" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001004, negated: false, taxon ID: 7742 - entity: UBERON:0001473, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003457 "head bone" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 7742 - entity: UBERON:0001474, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003460 "arm bone" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001460, negated: false, taxon ID: 32523 - entity: UBERON:0001474, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003464 "hindlimb bone" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001474, negated: false, taxon ID: 7742 - entity: UBERON:0002103, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003466 "forelimb zeugopod bone" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001474, negated: false, taxon ID: 7742 - entity: UBERON:0002386, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0003468 "ureteric segment of renal artery" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000056, negated: false, taxon ID: 32524 - entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003469 "respiratory system artery" 7711 "Chordata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001004, negated: false, taxon ID: 33213 - entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003469 "respiratory system artery" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001004, negated: false, taxon ID: 7742 - entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003470 "artery of upper lip" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0001834, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003472 "cerebellar artery" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0002037, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0003474 "meningeal artery" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0002360, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003475 "ureteric vein" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000056, negated: false, taxon ID: 32524 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003476 "respiratory system venous blood vessel" 7711 "Chordata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001004, negated: false, taxon ID: 33213 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003476 "respiratory system venous blood vessel" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001004, negated: false, taxon ID: 7742 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003477 "vein of upper lip" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0001834, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003480 "vein of clitoris" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001299|UBERON:0002411|UBERON:0004713, negated: false, taxon ID: 40674 - entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0002411, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0003484 "eye sebaceous gland" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000019, negated: false, taxon ID: 7742 - entity: UBERON:0001821, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0003485 "vagina sebaceous gland" NOT 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000996, negated: true, taxon ID: 32524 - entity: UBERON:0001821, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0003485 "vagina sebaceous gland" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000996, negated: false, taxon ID: 40674 - entity: UBERON:0001821, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0003487 "skin sebaceous gland" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471090588 "Hildebrand M, Analysis of vertebrate structure (1983) p.102" "Sebaceous glands are also limited to mammals." bgee ANN 2013-10-10 HOM:0000007 "historical homology" UBERON:0003494 "respiratory system venule" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001004, negated: false, taxon ID: 7742 - entity: UBERON:0001979, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003495 "respiratory system arteriole" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001004, negated: false, taxon ID: 7742 - entity: UBERON:0001980, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003496 "head blood vessel" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 33213 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003496 "head blood vessel" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 7742 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003498 "heart blood vessel" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 7742 - entity: UBERON:0000948|UBERON:0002376, negated: false, taxon ID: 7742 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003498 "heart blood vessel" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 8782 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003498 "heart blood vessel" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 40674 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003499 "brain blood vessel" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000955, negated: false, taxon ID: 33213 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003500 "corneal blood vessel" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000964, negated: false, taxon ID: 7742 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003501 "retina blood vessel" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000966, negated: false, taxon ID: 7742 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003503 "leg blood vessel" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000978, negated: false, taxon ID: 32523 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003504 "respiratory system blood vessel" 7711 "Chordata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001004, negated: false, taxon ID: 33213 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003504 "respiratory system blood vessel" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001004, negated: false, taxon ID: 7742 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003505 "trachea blood vessel" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0003126, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003507 "arm blood vessel" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001460, negated: false, taxon ID: 32523 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003509 "arterial blood vessel" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0004572, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003511 "iris blood vessel" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001769, negated: false, taxon ID: 7742 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003512 "lung blood vessel" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0002048|UBERON:0006860, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0003514 "limb blood vessel" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0002101, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003515 "forelimb blood vessel" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000024|UBERON:0002102, negated: false, taxon ID: 32523 - entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0002102, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003515 "forelimb blood vessel" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000024|UBERON:0002102, negated: false, taxon ID: 32524 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003516 "hindlimb blood vessel" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0002103, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003517 "kidney blood vessel" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0002113, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003518 "main bronchus blood vessel" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0002182, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003521 "pes blood vessel" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0002387, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003523 "manus blood vessel" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0002398, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003526 "respiratory system capillary" 7711 "Chordata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001004, negated: false, taxon ID: 33213 - entity: UBERON:0001982, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003526 "respiratory system capillary" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001004, negated: false, taxon ID: 7742 - entity: UBERON:0001982, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003527 "kidney capillary" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001982, negated: false, taxon ID: 7711 - entity: UBERON:0002113, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003528 "brain gray matter" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000955, negated: false, taxon ID: 33213 - entity: UBERON:0002020, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003531 "forelimb skin" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0000024|UBERON:0002102, negated: false, taxon ID: 32523 - entity: UBERON:0002102, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003531|UBERON:0010855 "forelimb skin|skin of forelimb wing" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0000024|UBERON:0002102, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003531|UBERON:0010855 "forelimb skin|skin of forelimb wing" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0000024|UBERON:0002102, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0003532 "hindlimb skin" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0002103, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003535 "vagus X nerve trunk" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625" "Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII)." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0003544 "brain white matter" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000955, negated: false, taxon ID: 33213 - entity: UBERON:0002316, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003547 "brain meninx" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000955, negated: false, taxon ID: 33213 - entity: UBERON:0002360, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003548 "forebrain meninges" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001890, negated: false, taxon ID: 7711 - entity: UBERON:0002360, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003549 "brain pia mater" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000955, negated: false, taxon ID: 33213 - entity: UBERON:0002361, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0003550 "forebrain pia mater" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0003551 "midbrain pia mater" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001891, negated: false, taxon ID: 7711 - entity: UBERON:0002361, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0003552 "telencephalon pia mater" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001893, negated: false, taxon ID: 7742 - entity: UBERON:0002361, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0003553 "diencephalon pia mater" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001894, negated: false, taxon ID: 7711 - entity: UBERON:0002361, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0003554 "hindbrain pia mater" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002028, negated: false, taxon ID: 7711 - entity: UBERON:0002361, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0003556 "forebrain arachnoid mater" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001890, negated: false, taxon ID: 7711 - entity: UBERON:0002362, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0003557 "midbrain arachnoid mater" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001891, negated: false, taxon ID: 7711 - entity: UBERON:0002362, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0003558 "diencephalon arachnoid mater" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001894, negated: false, taxon ID: 7711 - entity: UBERON:0002362, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0003559 "hindbrain arachnoid mater" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002028, negated: false, taxon ID: 7711 - entity: UBERON:0002362, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0003561 "forebrain dura mater" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001890, negated: false, taxon ID: 7711 - entity: UBERON:0002363, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003562 "midbrain dura mater" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001891, negated: false, taxon ID: 7711 - entity: UBERON:0002363, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003563 "telencephalon dura mater" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001893, negated: false, taxon ID: 7742 - entity: UBERON:0002363, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003564 "diencephalon dura mater" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001894, negated: false, taxon ID: 7711 - entity: UBERON:0002363, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003565 "hindbrain dura mater" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002028, negated: false, taxon ID: 7711 - entity: UBERON:0002363, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003657 "limb joint" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0002101, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003700 "temporomandibular joint" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0001695, negated: false, taxon ID: 40674 - entity: UBERON:0004742, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0003704 "intrahepatic bile duct" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002107, negated: false, taxon ID: 7742 - entity: UBERON:0002394, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003721 "lingual nerve" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0001723, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003723 "vestibular nerve" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...)" bgee ANN 2013-06-13 HOM:0000007 "historical homology" UBERON:0003723 "vestibular nerve" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" http://tolweb.org/Craniata/14826/1997.01.01 "Janvier P, Craniata. Animals with skulls. The Tree of Life Web Project (1997)" "In all craniates, the olfactory (I), optic (II), trigeminal (V), facial (VII), acoustic (VIII), glossopharyngeal (IX) and vagus (X) cranial nerves are present. Additional cranial nerves, the oculomotor (III), trochlear (IV) and abducent (VI) nerves occur only in the Vertebrata. Some consider that the latter have been secondarily lost in hagfishes." bgee ANN 2013-06-13 HOM:0000007 "historical homology" UBERON:0003822 "forelimb stylopod" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23434323 "Schneider I, Shubin NH, The origin of the tetrapod limb: from expeditions to enhancers. Trends Genet (2013)" "Of the three limb segments (Figure 1a), the stylopod has been hypothesized to have a homolog in the fins of extant fish, being present as a basal segment of the fin in chondrichthyians, basal actinopterygians, and sarcopterygians." bgee ANN 2013-07-12 HOM:0000007 "historical homology" UBERON:0003822 "forelimb stylopod" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:19324642 "Zhu M, Yu X, Stem sarcopterygians have primitive polybasal fin articulation. Biology letters (2009)" "Here we describe three-dimensionally preserved shoulder girdles of two stem sarcopterygians (Psarolepis and Achoania) from the Lower Devonian of Yunnan, which demonstrate that stem sarcopterygians have polybasal pectoral fin articulation as in basal actinopterygians. This finding provides a phylogenetic and temporal constraint for studying the origin of the stylopod, which must have originated within the stem sarcopterygian lineage through the loss of the propterygium and mesopterygium." bgee ANN 2013-07-12 HOM:0000007 "historical homology" UBERON:0003823 "hindlimb zeugopod" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:19324642 "Zhu M, Yu X, Stem sarcopterygians have primitive polybasal fin articulation. Biology letters (2009)" "In the fin-limb transition, the origin of the sarcopterygian paired fins triggered new possibilities of fin articulation and movement, and established the proximal segments (stylopod and zeugopod) of the presumptive tetrapod limb." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0003826 "upper leg bone" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000376, negated: false, taxon ID: 7776 - entity: UBERON:0001474, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003831 "respiratory system muscle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001004, negated: false, taxon ID: 7742 - entity: UBERON:0001630, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0003831 "respiratory system muscle" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001004, negated: false, taxon ID: 33213 - entity: UBERON:0001630, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0003832 "esophagus muscle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001043, negated: false, taxon ID: 7742 - entity: UBERON:0001630, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0003832 "esophagus muscle" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001043, negated: false, taxon ID: 33213 - entity: UBERON:0001630, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0003839 "forelimb joint" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000024|UBERON:0002102, negated: false, taxon ID: 32523 - entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0002102, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003839 "forelimb joint" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000024|UBERON:0002102, negated: false, taxon ID: 32524 - entity: UBERON:0000982, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003840 "hindlimb joint" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0002103, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003841 "autopod joint" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0002470, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003841 "autopod joint" NOT 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0002470, negated: true, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003841 "autopod joint" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0002470, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0003842 "neural tube lumen" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0003842 "neural tube lumen" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0003843 "dental epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21669855 "Leys SP, Nichols SA, Adams ED, Epithelia and integration in sponges. Integrative and Comparative Biology (2009)" bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0003844 "upper eyelid epithelium" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.431" "A tetrapod's eye usually has one or more eyelids that can move across its surface and protect and cleanse it. The eye of lissamphibians has a stationary upper eyelid but a movable and transparent lower one." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0003845 "lower eyelid epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21669855 "Leys SP, Nichols SA, Adams EDM, Epithelia and integration in sponges. Integrative and Comparative Biology (2009)" bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0003846 "thymus epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002370, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003847 "thyroid artery" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0002046, negated: false, taxon ID: 7711 - entity: UBERON:0002046|UBERON:0006870, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003847 "thyroid artery" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0002046, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003848 "gonadal vein" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000991, negated: false, taxon ID: 7742 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003848 "gonadal vein" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000991, negated: false, taxon ID: 32524 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003849 "mesencephalic neural crest" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0003850 "telencephalon neural crest" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0003851 "diencephalon neural crest" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0003852 "rhombencephalon neural crest" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0003853 "spinal cord neural crest" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0003854 "spinal cord neural plate" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0003854 "spinal cord neural plate" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0003855 "gonad mesenchyme" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000991, negated: false, taxon ID: 7742 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003855 "gonad mesenchyme" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000991, negated: false, taxon ID: 32524 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003857 "upper eyelid mesenchyme" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001712, negated: false, taxon ID: 32523 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003858 "lower eyelid mesenchyme" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001713, negated: false, taxon ID: 32523 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003859 "forelimb mesenchyme" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000024|UBERON:0002102, negated: false, taxon ID: 32523 - entity: UBERON:0002102, negated: false, taxon ID: 32523 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003859 "forelimb mesenchyme" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000024|UBERON:0002102, negated: false, taxon ID: 32524 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003859|UBERON:0003934 "forelimb mesenchyme|mesenchyme pectoral fin" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000151|UBERON:0002102, negated: false, taxon ID: 7742 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003860 "hindlimb mesenchyme" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002103, negated: false, taxon ID: 32523 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003860|UBERON:0003935 "hindlimb mesenchyme|mesenchyme pelvic fin" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000152|UBERON:0002103, negated: false, taxon ID: 7742 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003861 "neural arch" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" DOI:10.1016/j.cub.2011.07.014 "Janvier P, Comparative anatomy: all vertebrates do have vertebrae. Current Biology (2011)" "(...) lampreys clearly possess a series of cartilaginous elements that flank the notochord and spinal cord dorsally, and are regarded as homologous to the similarly-positioned elements (basidorsals and interdorsals) of gnathostomes, which give rise to the vertebral neural arches" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0003869 "presumptive ganglion" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0000045" bgee HOM:0000007 "historical homology" UBERON:0003887 "intraembryonic coelom" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166" "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota)." bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0003888 "extraembryonic coelomic cavity" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:23050970 "Sheng G, Foley AC, Diversification and conservation of the extraembryonic tissues in mediating nutrient uptake during amniote development. Annals of the New York Academy of Sciences (2012)" "Although all amniotes start with a similar ""tool kit"" of extraembryonic tissues, an enormous diversity of extraembryonic tissue formation has evolved to accommodate embryological and physiological constraints unique to their developmental programs. (...) All amniotes contain the following four extraembryonic components: the amnion, chorion, yolk sac, and allantois (Fig. 1C). Like the intraembryonic tissues, these extraembryonic tissues are composed of cells representing the three germ layers: ectoderm, mesoderm, and endoderm.(...) A comparative knowledge of these extraembryonic tissues and their role in nutrient uptake during development is required to fully appreciate the adaptive changes in placental mammals. (...) The chorion marks the external boundary of the embryo. The space between the amnion and the chorion is the extraembryonic coelomic (body) cavity." bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0003890 "Mullerian duct" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:17070514 "Guioli S, Sekido R, Lovell-Badge R, The origin of the Mullerian duct in chick and mouse. Developmental biology (2007)" "The female reproductive tract represents a tubular structure of obvious importance to the continuation of a species. Its anatomy varies markedly among vertebrates, depending on the type of fertilisation, mode of reproduction, type of placentation and other factors. Anatomical differences can even be observed within a species. Despite the extremely high degree of specialisation of the adult structures, the internal genital tracts derive, with few exceptions such as the Teleost fish (Suzuki and Shibata, 2004), from a pair of tubular structures called Mullerian ducts or paramesonephric ducts." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0003890 "Mullerian duct" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.559" "In females, the archinephric (mesonephric) ducts tend to function only within the urinary systems. The muellerian duct arises embryologically next to the archinephric (wolffian) duct. In males, the muellerian duct regresses if it appears at all, but in females, the muellerian ducts become the oviducts of the reproductive system." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0003902 "retinal neural layer" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina." bgee AUC 2013-05-15 HOM:0000007 "historical homology" UBERON:0003906 "cardiac jelly" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:16675702 "Forouhar AS, Liebling M, Hickerson A, Nasiraei-Moghaddam A, Tsai HJ, Hove JR, Fraser SE, Dickinson ME, Gharib M, The embryonic vertebrate heart tube is a dynamic suction pump. Science (2006)" "The cardiovascular system is the first functional organ system to develop in vertebrate embryos. In its earliest stages, it consists of a primitive heart tube that drives blood through a simple vascular network. (...) The zebrafish offers a powerful vertebrate model for cardiogenetic studies (4-7) with multiple advantages for in vivo imaging: Eggs are externally fertilized; embryos are nearly transparent, providing optical access to the earliest stages of cardiogenesis; and many GFP (green fluorescent protein)-labeled transgenic strains have been derived. (...)The heart tube stems from the surface of the spherical yolk sac, acutely narrows to about 30 um, and becomes lined by an additional layer of cells (myocardium) and cardiac jelly that alters the elasticity of the heart tube at the inflow boundary." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0003911 "choroid plexus epithelium" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001886, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003918 "kidney mesenchyme" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002113, negated: false, taxon ID: 7742 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003920 "venous blood vessel" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0004582, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003925 "photoreceptor inner segment layer" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina." bgee ANN 2013-04-15 HOM:0000007 "historical homology" UBERON:0003926 "photoreceptor outer segment layer" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina." bgee ANN 2013-04-15 HOM:0000007 "historical homology" UBERON:0003929 "digestive tract epithelium" 6072 "Eumetazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:24844197 "Leininger S, Adamski M, Bergum B, Guder C, Liu J, Laplante M, Brate J, Hoffmann F, Fortunato S, Jordal S, Rapp HT, Adamska M, Developmental gene expression provides clues to relationships between sponge and eumetazoan body plans. Nat Commun (2014)" "Morphological and phylogenetic evidence makes the cnidarian polyps an ideal proxy to the 'prebilaterian eumetazoan' body organization, and cnidarian model systems reveal evolutionary ancestry of bilaterian characters15, 16. The polyps are overtly radially symmetrical with a (generally) blind gut (gastrodermis) and apical oral opening." bgee ANN 2015-04-14 HOM:0000007 "historical homology" UBERON:0003930 "atrioventricular canal endocardium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002087, negated: false, taxon ID: 7742 - entity: UBERON:0002165, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003931 "diencephalic white matter" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001894, negated: false, taxon ID: 7711 - entity: UBERON:0002316, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0003934 "mesenchyme pectoral fin" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000151, negated: false, taxon ID: 7776 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003934 "mesenchyme pectoral fin" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000151|UBERON:0001460, negated: false, taxon ID: 8287 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003935 "mesenchyme pelvic fin" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000152, negated: false, taxon ID: 7776 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003935 "mesenchyme pelvic fin" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000152|UBERON:0000978, negated: false, taxon ID: 8287 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0003963 "otic ganglion" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001649, negated: false, taxon ID: 89593 - entity: UBERON:0001714, negated: false, taxon ID: 89593 - entity: UBERON:0001831, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0003966 "gonial bone" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "Developmental biology can also help identify the homologous elements for the associated membranous bones of the ear. The tympanic ring and gonial, for example have been suggested to be homologous to the angular bone and prearticular, respectively. Again, by following the position and relative timing of these bones as they develop, clear homologies can be identified (Fig. 2). Bapx1 is also expressed around these membraneous bones in both chick and mouse (Tucker et al. 2004)." bgee ANN 2015-04-02 HOM:0000007 "historical homology" UBERON:0003966|UBERON:0011637 "gonial bone|prearticular bone" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "Developmental biology can also help identify the homologous elements for the associated membranous bones of the ear. The tympanic ring and gonial, for example have been suggested to be homologous to the angular bone and prearticular, respectively. Again, by following the position and relative timing of these bones as they develop, clear homologies can be identified (Fig. 2). Bapx1 is also expressed around these membraneous bones in both chick and mouse (Tucker et al. 2004)." bgee ANN 2015-04-02 HOM:0000007 "historical homology" UBERON:0003966|UBERON:0011637 "gonial bone|prearticular bone" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "Developmental biology can also help identify the homologous elements for the associated membranous bones of the ear. The tympanic ring and gonial, for example have been suggested to be homologous to the angular bone and prearticular, respectively. Again, by following the position and relative timing of these bones as they develop, clear homologies can be identified (Fig. 2). Bapx1 is also expressed around these membraneous bones in both chick and mouse (Tucker et al. 2004)." bgee ANN 2015-04-02 HOM:0000007 "historical homology" UBERON:0003983 "conus arteriosus" 7777 "Chondrichthyes" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1152/physrev.00006.2003 "Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)" "The conus arteriosus is considered a component part of the heart because it has a myocardial wall and lies within the pericardial cavity. It is a feature of the evolutionary primitive state. In amphibians it is called the bulbus cordis, a term that is also used for its equivalent in mammalian embryos. The more derived extant bony fish, like the zebrafish, do not have this cardiac compartment. They have a so-called bulbus arteriosus, which is not enclosed by cardiac muscle, but by elastic tissue and smooth muscle, and therefore is considered to be a specialization of the proximal part of the ventral aorta. However, similar to the mammalian condition, the bulbus arteriosus in zebrafish embryonic hearts is surrounded by myocardium that disappears with development. The bony fish bulbus arteriosus might thus be homologous to the shark conus arteriosus and amphibian/mammalian bulbus cordis." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0003983|UBERON:0004152|UBERON:0004706 "conus arteriosus|bulbus arteriosus|bulbus cordis" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1152/physrev.00006.2003 "Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)" "The conus arteriosus is considered a component part of the heart because it has a myocardial wall and lies within the pericardial cavity. It is a feature of the evolutionary primitive state. In amphibians it is called the bulbus cordis, a term that is also used for its equivalent in mammalian embryos. The more derived extant bony fish, like the zebrafish, do not have this cardiac compartment. They have a so-called bulbus arteriosus, which is not enclosed by cardiac muscle, but by elastic tissue and smooth muscle, and therefore is considered to be a specialization of the proximal part of the ventral aorta. However, similar to the mammalian condition, the bulbus arteriosus in zebrafish embryonic hearts is surrounded by myocardium that disappears with development. The bony fish bulbus arteriosus might thus be homologous to the shark conus arteriosus and amphibian/mammalian bulbus cordis." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0003983|UBERON:0004152|UBERON:0004706 "conus arteriosus|bulbus arteriosus|bulbus cordis" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1152/physrev.00006.2003 "Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)" "The conus arteriosus is considered a component part of the heart because it has a myocardial wall and lies within the pericardial cavity. It is a feature of the evolutionary primitive state. In amphibians it is called the bulbus cordis, a term that is also used for its equivalent in mammalian embryos. The more derived extant bony fish, like the zebrafish, do not have this cardiac compartment. They have a so-called bulbus arteriosus, which is not enclosed by cardiac muscle, but by elastic tissue and smooth muscle, and therefore is considered to be a specialization of the proximal part of the ventral aorta. However, similar to the mammalian condition, the bulbus arteriosus in zebrafish embryonic hearts is surrounded by myocardium that disappears with development. The bony fish bulbus arteriosus might thus be homologous to the shark conus arteriosus and amphibian/mammalian bulbus cordis." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0003983|UBERON:0004152|UBERON:0004706 "conus arteriosus|bulbus arteriosus|bulbus cordis" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1152/physrev.00006.2003 "Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)" "The conus arteriosus is considered a component part of the heart because it has a myocardial wall and lies within the pericardial cavity. It is a feature of the evolutionary primitive state. In amphibians it is called the bulbus cordis, a term that is also used for its equivalent in mammalian embryos. The more derived extant bony fish, like the zebrafish, do not have this cardiac compartment. They have a so-called bulbus arteriosus, which is not enclosed by cardiac muscle, but by elastic tissue and smooth muscle, and therefore is considered to be a specialization of the proximal part of the ventral aorta. However, similar to the mammalian condition, the bulbus arteriosus in zebrafish embryonic hearts is surrounded by myocardium that disappears with development. The bony fish bulbus arteriosus might thus be homologous to the shark conus arteriosus and amphibian/mammalian bulbus cordis." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0004062 "neural tube marginal layer" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0004063 "spinal cord alar plate" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:10867629 "Butler AB, Chordate evolution and the origin of craniates: an old brain in a new head. Anat Rec (2000)" "During embryological development of the craniate brain, the hollow nerve tube comprises a ventrally situated basal plate and a dorsally situated alar plate (...) The alar plate constitutes the sensory-receptive part of the nervous system." bgee ANN 2017-12-19 HOM:0000007 "historical homology" UBERON:0004064 "neural tube basal plate" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:10867629 "Butler AB, Chordate evolution and the origin of craniates: an old brain in a new head. Anat Rec (2000)" "During embryological development of the craniate brain, the hollow nerve tube comprises a ventrally situated basal plate and a dorsally situated alar plate (...) The alar plate constitutes the sensory-receptive part of the nervous system." bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0004103 "alveolar ridge" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:24023957 "Leblanc AR, Reisz RR, Periodontal ligament, cementum, and alveolar bone in the oldest herbivorous tetrapods, and their evolutionary significance. PLoS One (2013)" "The presence of a tripartite periodontium in diadectids supports the hypothesis that the dental follicle and its derivatives (cementum, alveolar bone, and periodontal ligament) were present in these stem amniotes. We provide the earliest record of a tripartite periodontium in a tetrapod by demonstrating its presence in the Diadectidae, a group that persisted from the Late Pennsylvanian into the Early Permian [27]. The presence of a tripartite periodontium in diadectids and several amniote taxa [2], [3], [8], [11] provides an increasing amount of evidence that all amniotes share the ability to produce the periodontal tissues that have historically been associated with mammalian and crocodilian thecodonty." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0004113 "muscle of auditory ossicle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001630, negated: false, taxon ID: 33208 - entity: UBERON:0001686, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004117 "pharyngeal pouch" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1111/j.1469-7580.2005.00472.x "Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)" "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0004117|UBERON:0008815 "pharyngeal pouch|pharyngeal slit" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:23020903 "Graham A, Richardson J, Developmental and evolutionary origins of the pharyngeal apparatus. Evodevo (2012)." "Given that the presence of a series of pharyngeal slits is a defining chordate feature, homology between vertebrate pharyngeal pouches and amphioxus pharyngeal perforations is perhaps to be anticipated. However, it has also become clear that pharyngeal development built around endodermal outpocketing is more ancient and that it is probably a deuterostome characteristic" bgee ANN 2015-02-24 HOM:0000007 "historical homology" UBERON:0004117|UBERON:0008815 "pharyngeal pouch|pharyngeal slit" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:23020903 "Graham A, Richardson J, Developmental and evolutionary origins of the pharyngeal apparatus. Evodevo (2012)." "Homology between the formation of these gill slits and pharyngeal pouch formation in vertebrates can be assessed via an analysis of the expression of amphioxus orthologues of key players in the development of the vertebrate pharyngeal pouches. Prominent amongst these are a Pax-Six-Eya regulatory network...the expression domains of these orthologues of key pharyngeal genes provide strong evidence for homology between pharyngeal development in vertebrates and amphioxus." bgee ANN 2015-02-24 HOM:0000007 "historical homology" UBERON:0004118 "vasculature of iris" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001769, negated: false, taxon ID: 7742 - entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0004122 "genitourinary system" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.633" "Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0004122 "genitourinary system" 7898 "Actinopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:11875667 "Wrobel KH, Hees I, Schimmel M, Stauber E, The genus Acipenser as a model system for vertebrate urogenital development: nephrostomial tubules and their significance for the origin of the gonad. Anat Embryol (Berl) (2002)" "The subfamily Acipenserinae comprises 19 closely related, extant sturgeon species (Birstein and DeSalle 1998). This phylogenetically very old group of ray-finned chondrostean fishes displays a number of primitive generalized features. Study of the urogenital system of Acipenser, particularly of the male, thus helps us to understand the evolution of more advanced and specialized urogenital systems realized on the one hand by modern teleosts and on the other hand by amniote vertebrates including mammals and man. For instance, males of the genus Acipenser simultanously display an opisthonephric (Wolffian) duct, which is used for the elimination of urine and spermatozoa, a non-regressed Muellerian duct and in addition a pair of abdominal pores (Semon 1891; Baschmakoff 1916; Marinelli and Strenger 1973)." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0004122 "genitourinary system" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:11875667 "Wrobel KH, Hees I, Schimmel M, Stauber E, The genus Acipenser as a model system for vertebrate urogenital development: nephrostomial tubules and their significance for the origin of the gonad. Anat Embryol (Berl) (2002)" "The subfamily Acipenserinae comprises 19 closely related, extant sturgeon species (Birstein and DeSalle 1998). This phylogenetically very old group of ray-finned chondrostean fishes displays a number of primitive generalized features. Study of the urogenital system of Acipenser, particularly of the male, thus helps us to understand the evolution of more advanced and specialized urogenital systems realized on the one hand by modern teleosts and on the other hand by amniote vertebrates including mammals and man. For instance, males of the genus Acipenser simultanously display an opisthonephric (Wolffian) duct, which is used for the elimination of urine and spermatozoa, a non-regressed Muellerian duct and in addition a pair of abdominal pores (Semon 1891; Baschmakoff 1916; Marinelli and Strenger 1973)." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0004128 "optic vesicle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles." bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0004139 "cardiogenic plate" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:15611355 "Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005)" "(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0004140 "primary heart field" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:17223594 "Davidson B, Ciona intestinalis as a model for cardiac development. Ciona intestinalis as a model for cardiac development. Semin Cell Dev Biol (2007)" "It has recently become apparent that amniote (avian, reptilian and mammalian) hearts are constructed from at least two distinct fields [32]. The left ventricle and atrial chambers arise from a primary field. (...) The ancestral chordate heart has been proposed to be equivalent to the primary heart field with the resulting left ventricle representing the ancestral single chamber. Studies of primary heart field patterning indicate that the default fate of this lineage is ventricular and that the atrial fate is the result of secondary patterning events, including a critical role for RA [right atrium] signaling [33]. Thus the Ciona heart is probably homologous to the vertebrate left ventricular field." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0004145 "outflow tract" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1126/science.1190181 "Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010)" "The vertebrate heart is formed from diverse embryonic territories, including the first and second heart fields. The second heart field (SHF) gives rise to the right ventricle and outflow tract, yet its evolutionary origins are unclear. (...) SHF-like territories have been identified in frog, zebrafish, and lamprey, yet evidence for a deeper evolutionary origin remains obscured by the absence of a clear SHF in invertebrates." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0004145 "outflow tract" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1126/science.1190181 "Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010)" "The vertebrate heart is formed from diverse embryonic territories, including the first and second heart fields. The second heart field (SHF) gives rise to the right ventricle and outflow tract, yet its evolutionary origins are unclear. (...) SHF-like territories have been identified in frog, zebrafish, and lamprey, yet evidence for a deeper evolutionary origin remains obscured by the absence of a clear SHF in invertebrates." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0004148 "cardiac vein" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 7742 - entity: UBERON:0000948|UBERON:0002376, negated: false, taxon ID: 7742 - entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0002349, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004148 "cardiac vein" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 8782 - entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0002349, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004148 "cardiac vein" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 40674 - entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0002349, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004152 "bulbus arteriosus" 117571 "Euteleostomi" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1152/physrev.00006.2003 "Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)" "The conus arteriosus is considered a component part of the heart because it has a myocardial wall and lies within the pericardial cavity. It is a feature of the evolutionary primitive state. In amphibians it is called the bulbus cordis, a term that is also used for its equivalent in mammalian embryos. The more derived extant bony fish, like the zebrafish, do not have this cardiac compartment. They have a so-called bulbus arteriosus, which is not enclosed by cardiac muscle, but by elastic tissue and smooth muscle, and therefore is considered to be a specialization of the proximal part of the ventral aorta. However, similar to the mammalian condition, the bulbus arteriosus in zebrafish embryonic hearts is surrounded by myocardium that disappears with development. The bony fish bulbus arteriosus might thus be homologous to the shark conus arteriosus and amphibian/mammalian bulbus cordis." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0004154 "atrial septum primum" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0004154 "atrial septum primum" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21513818 "Dzialowski EM, Sirsat T, van der Sterren S, Villamor E, Prenatal cardiovascular shunts in amniotic vertebrates. Respir Physiol Neurobiol (2011)" "During amniotic vertebrate development, the embryo and fetus employ a number of cardiovascular shunts. These shunts provide a right-to-left shunt of blood and are essential components of embryonic life ensuring proper blood circulation to developing organs and fetal gas exchanger, as well as bypassing the pulmonary circuit and the unventilated, fluid filled lungs." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0004155 "atrial septum secundum" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0004155 "atrial septum secundum" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21513818 "Dzialowski EM, Sirsat T, van der Sterren S, Villamor E, Prenatal cardiovascular shunts in amniotic vertebrates. Respir Physiol Neurobiol (2011)" "During amniotic vertebrate development, the embryo and fetus employ a number of cardiovascular shunts. These shunts provide a right-to-left shunt of blood and are essential components of embryonic life ensuring proper blood circulation to developing organs and fetal gas exchanger, as well as bypassing the pulmonary circuit and the unventilated, fluid filled lungs." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0004161 "septum transversum" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0471090588 "Hildebrand M, Analysis of vertebrate structure (1983) p.205-206" "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0004178 "aorta smooth muscle tissue" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000947, negated: false, taxon ID: 7742 - entity: UBERON:0001135, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004180 "mammary gland fat" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001013, negated: false, taxon ID: 7742 - entity: UBERON:0001911, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004208 "nephrogenic mesenchyme" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001285, negated: false, taxon ID: 7742 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0004211 "nephron epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001285, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004214 "upper leg nerve" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000376, negated: false, taxon ID: 7776 - entity: UBERON:0001021, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0004216 "lower arm nerve" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0002386, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0004217 "upper arm nerve" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0003822, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0004217 "upper arm nerve" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0003822, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0004218 "lower leg nerve" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0003823, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0004219 "urethra smooth muscle layer" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000057, negated: false, taxon ID: 40674 - entity: UBERON:0001135, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004220 "large intestine smooth muscle" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000059, negated: false, taxon ID: 32523 - entity: UBERON:0001135, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004221 "intestine smooth muscle" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000160, negated: false, taxon ID: 7742 - entity: UBERON:0001135, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004222 "stomach smooth muscle" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000945, negated: false, taxon ID: 7776 - entity: UBERON:0001135, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004223 "vagina smooth muscle" NOT 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000996, negated: true, taxon ID: 32524 - entity: UBERON:0001135, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004223 "vagina smooth muscle" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000996, negated: false, taxon ID: 40674 - entity: UBERON:0001135, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004225 "respiratory system smooth muscle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001004, negated: false, taxon ID: 7742 - entity: UBERON:0001135, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004225 "respiratory system smooth muscle" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001004, negated: false, taxon ID: 33213 - entity: UBERON:0001135, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004228 "urinary bladder smooth muscle" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0001255, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0004228 "urinary bladder smooth muscle" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0001255, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0004232 "lymphatic vessel smooth muscle" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0001473, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0004234 "iris smooth muscle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0001769, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004235 "mammary gland smooth muscle" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0001911, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004236 "arteriole smooth muscle" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0001980, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004237 "blood vessel smooth muscle" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0004238 "spleen smooth muscle" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0002106, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0004239 "small intestine smooth muscle" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0002108, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0004240 "gall bladder smooth muscle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0002110, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004241 "main bronchus smooth muscle" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0002182, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0004242 "bronchus smooth muscle" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0002185, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0004243 "prostate gland smooth muscle" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0002367, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004246 "outflow tract smooth muscle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0004145, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004250 "upper arm bone" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001474, negated: false, taxon ID: 7742 - entity: UBERON:0003822, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0004250 "upper arm bone" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001474, negated: false, taxon ID: 7742 - entity: UBERON:0003822, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0004251 "hindlimb zeugopod bone" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001474, negated: false, taxon ID: 7742 - entity: UBERON:0003823, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0004253 "skin muscle" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001630, negated: false, taxon ID: 33208 - entity: UBERON:0002416, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0004257 "upper leg blood vessel" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000376, negated: false, taxon ID: 7776 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0004259 "lower arm blood vessel" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0002386, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0004260 "upper arm blood vessel" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0003822, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0004260 "upper arm blood vessel" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0003822, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0004261 "lower leg blood vessel" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0003823, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0004262 "upper leg skin" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0000376, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0004263 "upper arm skin" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0003822, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0004263 "upper arm skin" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0003822, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0004264 "lower leg skin" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0003823, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0004265 "outflow tract myocardium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:9187138 "Fishman MC, Chien KR, Fashioning the vertebrate heart: earliest embryonic decisions. Development (1997)" "(...) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (...) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0004271 "outflow tract pericardium" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002407, negated: false, taxon ID: 7711 - entity: UBERON:0004145, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004277 "eye muscle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000019, negated: false, taxon ID: 7742 - entity: UBERON:0001630, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0004288 "skeleton" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:23535660 "Shimada A, Kawanishi T, Kaneko T, Yoshihara H, Yano T, Inohaya K, Kinoshita M, Kamei Y, Tamura K, Takeda H, Trunk exoskeleton in teleosts is mesodermal in origin. Nat Commun (2013)" "The vertebrate mineralized skeleton is known to have first emerged as an exoskeleton that extensively covered the fossil jawless fish. The evolutionary origin of this exoskeleton has long been attributed to the emergence of the neural crest, but experimental evaluation for this is still poor. Here we determine the embryonic origin of scales and fin rays of medaka (teleost trunk exoskeletons) by applying long-term cell labelling methods, and demonstrate that both tissues are mesodermal in origin. Neural crest cells, however, fail to contribute to these tissues. This result suggests that the trunk neural crest has no skeletogenic capability in fish, instead highlighting the dominant role of the mesoderm in the evolution of the trunk skeleton. This further implies that the role of the neural crest in skeletogenesis has been predominant in the cephalic region from the early stage of vertebrate evolution." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0004290 "dermomyotome" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1111/j.1525-142X.2006.05079.x "Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006)" "Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0004290 "dermomyotome" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" DOI:10.1111/j.1525-142X.2006.05079.x "Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006)" "Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0004290 "dermomyotome" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1111/j.1525-142X.2006.05079.x "Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006)" "Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0004293 "parasympathetic nerve" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0004339 "vault of skull" 8287 "Sarcopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.256" "The earliest tetrapods arose from rhipidistian ancestors and retained many of their skull features, including most of the bones of the dermatocranium." bgee ANN 2013-08-26 HOM:0000007 "historical homology" UBERON:0004340 "allantois" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187" "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0004341 "primitive streak" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:17928866 "Voiculescu O, Bertocchini F, Wolpert L, Keller RE, Stern CD, The amniote primitive streak is defined by epithelial cell intercalation before gastrulation. Nature (2007)" "We propose that the amniote primitive streak evolved from the ancestral blastopore by acquisition of an additional medio-lateral intercalation event, preceding gastrulation and acting independently of mesendoderm formation to position the primitive streak at the midline." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0004344 "cardinal vein" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.462" "In primitive vertebrates, the basic early embryonic pattern is retained, and blood from anterior and posterior systemic tissues is returned in anterior and posterior cardinal veins, both pairs of veins uniting in common cardinal veins near the heart. In derived vertebrates, the cardinals appear but usually persist only in the embryo, being functionally replaced by alternative adult vessels, the precava and postcava (anterior and posterior venae cavae)." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0004345 "trophectoderm" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0721676685 "Romer AS, Parsons TS, Vertebrate body (1977) p.105-106" "(...) the trophoblast develops rapidly so that contact may be made with the maternal uterine tissues when conditions are appropriate. We have here an excellent example of an embryonic adaptation, the development of a structure never present in either adult or embryo of 'lower' vertebrates." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0004356 "apical ectodermal ridge" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:17587327 "Mercader N, Early steps of paired fin development in zebrafish compared with tetrapod limb development. Development, growth and differentiation (2007)" "The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0004356 "apical ectodermal ridge" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:17587327 "Mercader N, Early steps of paired fin development in zebrafish compared with tetrapod limb development. Development, growth and differentiation (2007)" "The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0004356 "apical ectodermal ridge" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:17587327 "Mercader N, Early steps of paired fin development in zebrafish compared with tetrapod limb development. Development, growth and differentiation (2007)" "The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0004363 "pharyngeal arch artery" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0004365 "vitelline blood vessel" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001040, negated: false, taxon ID: 32524 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0004374 "vitelline vasculature" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001040, negated: false, taxon ID: 32524 - entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0004449 "cerebral artery" NOT 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0001893, negated: true, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0004449 "cerebral artery" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0001893, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004461 "skeletal musculature of head" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 7742 - entity: UBERON:0001015, negated: false, taxon ID: 7776 - entity: UBERON:0003129, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004463 "musculature of hindlimb stylopod" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000376, negated: false, taxon ID: 7776 - entity: UBERON:0001015, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0004466 "musculature of leg" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000978, negated: false, taxon ID: 32523 - entity: UBERON:0001015, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0004468 "set of muscles of vertebral column" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001015, negated: false, taxon ID: 7776 - entity: UBERON:0001130, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004468 "set of muscles of vertebral column" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001015, negated: false, taxon ID: 7776 - entity: UBERON:0001130, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0004473 "musculature of face" 7776 "Gnathostomata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001015, negated: false, taxon ID: 7776 - entity: UBERON:0001456, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004474 "musculature of arm" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001015, negated: false, taxon ID: 7776 - entity: UBERON:0001460, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0004478 "musculature of larynx" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001015, negated: false, taxon ID: 7776 - entity: UBERON:0001737, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0004480 "musculature of limb" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001015, negated: false, taxon ID: 7776 - entity: UBERON:0002101, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0004481 "musculature of upper limb" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000024|UBERON:0002102, negated: false, taxon ID: 32523 - entity: UBERON:0001015, negated: false, taxon ID: 7776 - entity: UBERON:0002102, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0004481 "musculature of upper limb" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000024|UBERON:0002102, negated: false, taxon ID: 32524 - entity: UBERON:0001015, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0004482 "musculature of lower limb" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001015, negated: false, taxon ID: 7776 - entity: UBERON:0002103, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0004487 "musculature of forelimb zeugopod" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001015, negated: false, taxon ID: 7776 - entity: UBERON:0002386, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0004488 "musculature of pes" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001015, negated: false, taxon ID: 7776 - entity: UBERON:0002387, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0004489 "musculature of manus" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001015, negated: false, taxon ID: 7776 - entity: UBERON:0002398, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0004495 "skeletal muscle tissue of diaphragm" NOT 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001103, negated: true, taxon ID: 32524 - entity: UBERON:0001134, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004495 "skeletal muscle tissue of diaphragm" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001103, negated: false, taxon ID: 40674 - entity: UBERON:0001134, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004498 "skeletal muscle tissue of quadriceps femoris" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001134, negated: false, taxon ID: 33213 - entity: UBERON:0001377, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004500 "skeletal muscle tissue of deltoid" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001134, negated: false, taxon ID: 33213 - entity: UBERON:0001476, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004501 "skeletal muscle tissue of teres major" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001134, negated: false, taxon ID: 33213 - entity: UBERON:0001478, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004502 "skeletal muscle tissue of biceps brachii" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001134, negated: false, taxon ID: 33213 - entity: UBERON:0001507, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004506 "skeletal muscle tissue of masseter" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001134, negated: false, taxon ID: 33213 - entity: UBERON:0001597, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004507 "skeletal muscle tissue of temporalis" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001134, negated: false, taxon ID: 33213 - entity: UBERON:0001598, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004509 "skeletal muscle tissue of trapezius" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001134, negated: false, taxon ID: 33213 - entity: UBERON:0002380, negated: false, taxon ID: 117571" bgee HOM:0000007 "historical homology" UBERON:0004510 "skeletal muscle tissue of pectoralis major" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001134, negated: false, taxon ID: 33213 - entity: UBERON:0002381, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004511 "skeletal muscle tissue of rectus abdominis" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001134, negated: false, taxon ID: 33213 - entity: UBERON:0002382, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004512 "skeletal muscle tissue of supraspinatus" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001134, negated: false, taxon ID: 33213 - entity: UBERON:0002383, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004513 "skeletal muscle tissue of internal intercostal muscle" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001134, negated: false, taxon ID: 33213 - entity: UBERON:0002403, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0004515 "smooth muscle tissue of bronchiole" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0002186, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004520 "striated muscle tissue of prostate" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002036, negated: false, taxon ID: 33213 - entity: UBERON:0002367, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004521 "vasculature of muscle organ" 33208 "Metazoa" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001630, negated: false, taxon ID: 33208 - entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0004522 "vasculature of musculoskeletal system" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208 - entity: UBERON:0002204, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004523 "papillary muscle of right ventricle" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002080, negated: false, taxon ID: 7742 - entity: UBERON:0002494, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004524 "papillary muscle of left ventricle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002084, negated: false, taxon ID: 32524 - entity: UBERON:0002494, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004527 "alveolar process of maxilla" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002397, negated: false, taxon ID: 7776 - entity: UBERON:0004103, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0004533 "left testis" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000473, negated: false, taxon ID: 7742 - entity: UBERON:0000990, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004533 "left testis" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000473, negated: false, taxon ID: 33213 - entity: UBERON:0000990, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004534 "right testis" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000473, negated: false, taxon ID: 7742 - entity: UBERON:0000990, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004534 "right testis" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000473, negated: false, taxon ID: 33213 - entity: UBERON:0000990, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004535 "cardiovascular system" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1254/jjp.87.253 "Shigei T, Tsuru H, Ishikawa N, Yoshioka K, Absence of endothelium in invertebrate blood vessels: significance of endothelium and sympathetic nerve/medial smooth muscle in the vertebrate vascular system. Japanese Journal of Pharmacology (2001)" "It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0004535 "cardiovascular system" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451" "The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0004535 "cardiovascular system" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:19125185 "Kucera T, Strilic B, Regener K, Schubert M, Laudet V, Lammert E, Ancestral vascular lumen formation via basal cell surfaces. PLoS One (2009)" "The cardiovascular system of bilaterians developed from a common ancestor. However, no endothelial cells exist in invertebrates demonstrating that primitive cardiovascular tubes do not require this vertebrate-specific cell type in order to form. This raises the question of how cardiovascular tubes form in invertebrates? Here we discovered that in the invertebrate cephalochordate amphioxus, the basement membranes of endoderm and mesoderm line the lumen of the major vessels, namely aorta and heart. (...) our experiments suggest a mechanism of blood vessel formation via basal cell surfaces in amphioxus and possibly in other invertebrates that do not have any endothelial cells." bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0004536 "lymph vasculature" 32443 "Teleostei" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1002/bdrc.20155 "Butler MG, Isogai S, Weinstein BM, Lymphatic development. Birth Defects Res C Embryo Today (2009)" "Comparative phylogenetic analysis has shown that a true lymphatic vascular system is present only in the vertebrates (Isogai et al., 2009; Kampmeier, 1969). A lymphatic-like secondary vascular system is found in primitive fish, but it contains blood and is still considered to be part of the circulatory system. Teleost fish are arguably the first vertebrates with an anatomically distinct lymphatic system (Isogai et al., 2009; Yaniv et al., 2006)." bgee ANN 2017-10-24 HOM:0000007 "historical homology" UBERON:0004536 "lymph vasculature" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1152/japplphysiol.00201.2013 "Hedrick MS, Hillman SS, Drewes RC, Withers PC, Lymphatic regulation in nonmammalian vertebrates. Journal of applied physiology (2013)" "The evolutionary origin of the vertebrate lymphatic system is not clear, but recent advances suggest common developmental factors for lymphangiogenesis in teleost fishes, amphibians, and mammals with some significant changes in the water-land transition." bgee ANN 2017-10-24 HOM:0000007 "historical homology" UBERON:0004537 "blood vasculature" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0004538 "left kidney" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000468, negated: false, taxon ID: 33208 - entity: UBERON:0002113, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004539 "right kidney" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000468, negated: false, taxon ID: 33208 - entity: UBERON:0002113, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004552 "digital artery" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0002544, negated: false, taxon ID: 8782" bgee HOM:0000007 "historical homology" UBERON:0004552 "digital artery" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0002544, negated: false, taxon ID: 32523 - entity: UBERON:0002544|UBERON:4000172, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0004552 "digital artery" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0002544, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0004552 "digital artery" NOT 32524 "Amniota" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0002544, negated: true, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0004552 "digital artery" NOT 1338369 "Dipnotetrapodomorpha" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0002544|UBERON:2000271, negated: true, taxon ID: 1338369" bgee HOM:0000007 "historical homology" UBERON:0004572 "arterial system" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1254/jjp.87.253 "Shigei T, Tsuru H, Ishikawa N, Yoshioka K, Absence of endothelium in invertebrate blood vessels: significance of endothelium and sympathetic nerve/medial smooth muscle in the vertebrate vascular system. Japanese Journal of Pharmacology (2001)" "It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0004582 "venous system" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1254/jjp.87.253 "Shigei T, Tsuru H, Ishikawa N, Yoshioka K, Absence of endothelium in invertebrate blood vessels: significance of endothelium and sympathetic nerve/medial smooth muscle in the vertebrate vascular system. Japanese Journal of Pharmacology (2001)" "It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0004637 "otic capsule" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.235" "A second specialization that may prevent ambient pressure transmission to the balance organs is the encapsulation of the labyrinth in a rigid otic capsule. This feature appeared early in the evolution of vertebrates. The petromyzont inner ear is completely encased in cartilage except for the medial foramen for the acoustic nerve and associated blood vessels (de Burlet,1934). However, otic capsule rigidity was not uniformly retained in subsequent evolution." bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0004637 "otic capsule" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.235" "Otic capsules develop around the parts of the ear that lie within the chondrocranium. This part of the ear, known as the inner ear, is composed of the semicircular ducts and associated sacs that contain the receptive cells for equilibrium and hearing." bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0004638 "blood vessel endothelium" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0001986, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004666 "interventricular septum membranous part" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.618" "Superficially, the mammalian heart resembles those of birds and crocodiles, but the interventricular septum evolved independently and develops embryonically in a slightly different way, so it is not homologous to the interventricular septum of these vertebrates." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0004666 "interventricular septum membranous part" NOT 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.618" "Superficially, the mammalian heart resembles those of birds and crocodiles, but the interventricular septum evolved independently and develops embryonically in a slightly different way, so it is not homologous to the interventricular septum of these vertebrates." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0004666 "interventricular septum membranous part" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.618" "Superficially, the mammalian heart resembles those of birds and crocodiles, but the interventricular septum evolved independently and develops embryonically in a slightly different way, so it is not homologous to the interventricular septum of these vertebrates." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0004686 "gastro-splenic ligament" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) Development of the coelomic cavity and mesenteries, p.159-164" bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0004692 "external naris epithelium" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0005928, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0004692 "external naris epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0005928|UBERON:0013477, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004695 "arterial system smooth muscle" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0004572, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004696 "venous system smooth muscle" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0004582, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004699 "outflow tract endothelium" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23809110 "Monahan-Earley R, Dvorak AM, Aird WC, Evolutionary origins of the blood vascular system and endothelium. J Thromb Haemost (2013)" "The endothelium evolved in an ancestral vertebrate some 540-510 million years ago to optimize flow dynamics and barrier function, and/or to localize immune and coagulation functions." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0004700 "arterial system endothelium" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23809110 "Monahan-Earley R, Dvorak AM, Aird WC, Evolutionary origins of the blood vascular system and endothelium. J Thromb Haemost (2013)" "The endothelium evolved in an ancestral vertebrate some 540-510 million years ago to optimize flow dynamics and barrier function, and/or to localize immune and coagulation functions." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0004701 "venous system endothelium" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23809110 "Monahan-Earley R, Dvorak AM, Aird WC, Evolutionary origins of the blood vascular system and endothelium. J Thromb Haemost (2013)" "The endothelium evolved in an ancestral vertebrate some 540-510 million years ago to optimize flow dynamics and barrier function, and/or to localize immune and coagulation functions." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0004706 "bulbus cordis" 8292 "Amphibia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1152/physrev.00006.2003 "Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)" "The conus arteriosus is considered a component part of the heart because it has a myocardial wall and lies within the pericardial cavity. It is a feature of the evolutionary primitive state. In amphibians it is called the bulbus cordis, a term that is also used for its equivalent in mammalian embryos. The more derived extant bony fish, like the zebrafish, do not have this cardiac compartment. They have a so-called bulbus arteriosus, which is not enclosed by cardiac muscle, but by elastic tissue and smooth muscle, and therefore is considered to be a specialization of the proximal part of the ventral aorta. However, similar to the mammalian condition, the bulbus arteriosus in zebrafish embryonic hearts is surrounded by myocardium that disappears with development. The bony fish bulbus arteriosus might thus be homologous to the shark conus arteriosus and amphibian/mammalian bulbus cordis." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0004706 "bulbus cordis" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1152/physrev.00006.2003 "Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)" "The conus arteriosus is considered a component part of the heart because it has a myocardial wall and lies within the pericardial cavity. It is a feature of the evolutionary primitive state. In amphibians it is called the bulbus cordis, a term that is also used for its equivalent in mammalian embryos. The more derived extant bony fish, like the zebrafish, do not have this cardiac compartment. They have a so-called bulbus arteriosus, which is not enclosed by cardiac muscle, but by elastic tissue and smooth muscle, and therefore is considered to be a specialization of the proximal part of the ventral aorta. However, similar to the mammalian condition, the bulbus arteriosus in zebrafish embryonic hearts is surrounded by myocardium that disappears with development. The bony fish bulbus arteriosus might thus be homologous to the shark conus arteriosus and amphibian/mammalian bulbus cordis." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0004707 "pharyngula stage" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:12116482 "Collazo A, Developmental variation, homology, and the pharyngula stage. Syst Biol (2000)" "(...) modern cell and molecular biology are providing a better and more detailed understanding of development, even at an embryonic stage (the pharyngula) that is thought to be highly conserved across vertebrates. (...) The pharyngula, the phylotypic and zootypic stage of vertebrates, has been thought to be highly conserved, but looking at the development of the neural crest reveals interspecific variation." bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0004707 "pharyngula stage" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:23637639 "Piasecka B, Lichocki P, Moretti S, Bergmann S, Robinson-Rechavi M, The hourglass and the early conservation models--co-existing patterns of developmental constraints in vertebrates. PLoS Genet (2013)" "mid-developmental processes have extremely high conservation of regulation. This conservation could translate into observed common traits of the phylum expressed at the phenotypic level during mid-development. In addition, core developmental genes are known to be present in different taxa (e.g., nematodes, insects and vertebrates), in each of which they have a conserved regulation that evolved in parallel [47]. This could explain why the phylotypic stage is observed not only in vertebrates [49], but also in other phyla, e.g., in arthropods [4], [12]." bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0004710 "pectoral appendage" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:2362486 "Davis MC, The Deep Homology of the Autopod: Insights from Hox Gene Regulation. Integrative and comparative biology (2013)" "Analysis of HoxA/D expression in a basal actinopterygian, the North American paddlefish, Polyodon spathula, reveals patterns of expression long considered to be a unique developmental signature of the autopod (hands/feet, digits) and shown in tetrapods to be controlled by a ""digit enhancer"" regulatory landscape. These data, along with recent interspecific transgenic experiments, expression results from chondrichthyans, and data from fossils support the notion that the autopod shares a deep homology with the distal endoskeleton of the fin (distal radials) of other gnathostomes." bgee ANN 2013-07-12 HOM:0000007 "historical homology" UBERON:0004710 "pectoral appendage" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1002/jmor.10264 "Davis MC, Shubin NH, Force A, Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus. Journal of Morphology (2004)" "While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.(...) Teleosts and tetrapods have different mechanisms by which the pectoral endoskeleton is patterned during development." bgee ANN 2013-07-12 HOM:0000007 "historical homology" UBERON:0004713 "corpus cavernosum penis" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:23169570 "Puppo V, Anatomy and physiology of the clitoris, vestibular bulbs, and labia minora with a review of the female orgasm and the prevention of female sexual dysfunction. Clin Anat (2013)" "The clitoris is the homologue of the male's glans and corpora cavernosa (Fig. 3) (Puppo et al., 2008b; Standring, 2008; Puppo, 2011a)." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0004727 "cochlear nerve" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...)" bgee ANN 2013-06-13 HOM:0000007 "historical homology" UBERON:0004727 "cochlear nerve" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" http://tolweb.org/Craniata/14826/1997.01.01 "Janvier P, Craniata. Animals with skulls. The Tree of Life Web Project (1997)" "In all craniates, the olfactory (I), optic (II), trigeminal (V), facial (VII), acoustic (VIII), glossopharyngeal (IX) and vagus (X) cranial nerves are present. Additional cranial nerves, the oculomotor (III), trochlear (IV) and abducent (VI) nerves occur only in the Vertebrata. Some consider that the latter have been secondarily lost in hagfishes." bgee ANN 2013-06-13 HOM:0000007 "historical homology" UBERON:0004734 "gastrula" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000109, negated: false, taxon ID: 33213 - entity: UBERON:0000468, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0004735 "archenteron" 33511 "Deuterostomia" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1098/rspb.2008.1659 "Morris VB, Selvakumaraswamy P, Whan R, Byrne M, Development of the five primary podia from the coeloms of a sea star larva: homology with the echinoid echinoderms and other deuterostomes. Proc Biol Sci (2009)" "Morphological homology among the deuterostomes is obscure, mostly because the body plans are very different. Echinoderms have a radial body plan that contrasts with the bilateral body plans of the two other principal phyla, the hemichordates and chordates. The approach we take to identify the homology is developmental. The intention is to use evidence of the development of the five primary podia, which are core structures of the echinoderm body plan, to explore whether variation in the development of the primary podia between the echinoderm classes assists in identifying homologous structures in the other phyla....Extending the idea of a conserved regional specialization of the inner archenteron to other deuterostome phyla gives a source for the homology between the deuterostome phyla, leading to inferences of homologous structures." bgee ANN 2017-05-23 HOM:0000007 "historical homology" UBERON:0004736 "metanephric glomerulus" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543" "The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0004737 "metanephric collecting duct" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639" "The ureteric bud itself forms the collecting tubules and the ureter that drain the adult kidney. This type of kidney, called the metanephros, occurs in all adult amniotes." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0004739 "pronephric glomerulus" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1111/j.1096-3642.2007.00311.x "Ditrich H, The origin of vertebrates: a hypothesis based on kidney development. Zoological Journal of the Linnean Society (2007)" "In hagfish, as well as in lampreys and in all gnathostomes, the anterior portion of the kidney, the pronephros, initially shows a segmental arrangement. Nephrostomes and comparatively large glomeruli are present in the hagfish pronephros (Table 1) (...) the hypothetical 'stem-kidney' was developed from a series of nephric tubules opening into the coelom (or into a nephric chamber in a more evolved state), each with a ciliated nephrostome, vis-a-vis to a glomerulus. These tubules would laterally join a common duct that runs caudally to open near the anus (cf. Fig. 1A). This model is strongly modified in all extant vertebrates. However, in males that have a urogenital connection, the nephrons that later participate in seminal transport outline this pattern during differentiation." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0004739 "pronephric glomerulus" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.636" "This variation in nephron types [with external glomeruli that open into the coelom and with internal glomeruli that do not connect with the coelom] and their pattern of distribution suggest an evolutionary sequence. Ancestral craniates probably had an external glomerulus and nephrostomes, as do the first few to develop in very primitive craniates. (...) The mechanism would become more efficient as the coelomic recess into which each glomerulus discharged became a part of the tubule, that is, grew around the glomerulus as a renal capsule. The glomerulus becomes internal. The nephrostomes were lost during subsequent evolution, leaving the type of renal tubule found in most vertebrates." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0004741 "cleithrum" 8342 "Anura" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:16034409 "Matsuoka T, Ahlberg PE, Kessaris N, Iannarelli P, Dennehy U, Richardson WD, McMahon AP, Koentges G, Neural crest origins of the neck and shoulder. Nature (2005)" "(...) the elusive cleithrum, the centralmost shoulder bone of all bony fish (osteichthyan) ancestors, which is absent from all extant land living vertebrates (tetrapods)(35) except frogs (36). The cleithrum is uniquely defined by its position and connectivity. In extant bony fish and frogs it serves as the sole attachment region for the trapezius/cucullaris muscles anteriorly (5, 36) and for fin, limb and trunk muscles at its posterior margin (light grey in box 1 in Figs 1 and 7) (35, 36). Two main historical hypotheses have been proposed to explain its absence from most living tetrapods: first, the cleithrum was lost in common tetrapod (stem-group) ancestors and re-acquired only in frogs; second, it was independently lost from the lineages leading to living salamanders, diapsids, turtles and mammals." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0004741 "cleithrum" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:16034409 "Matsuoka T, Ahlberg PE, Kessaris N, Iannarelli P, Dennehy U, Richardson WD, McMahon AP, Koentges G, Neural crest origins of the neck and shoulder. Nature (2005)" "(...) the elusive cleithrum, the centralmost shoulder bone of all bony fish (osteichthyan) ancestors, which is absent from all extant land living vertebrates (tetrapods)(35) except frogs (36). The cleithrum is uniquely defined by its position and connectivity. In extant bony fish and frogs it serves as the sole attachment region for the trapezius/cucullaris muscles anteriorly (5, 36) and for fin, limb and trunk muscles at its posterior margin (light grey in box 1 in Figs 1 and 7) (35, 36). Two main historical hypotheses have been proposed to explain its absence from most living tetrapods: first, the cleithrum was lost in common tetrapod (stem-group) ancestors and re-acquired only in frogs; second, it was independently lost from the lineages leading to living salamanders, diapsids, turtles and mammals." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0004741 "cleithrum" NOT 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:23155370 "Kague E, Gallagher M, Burke S, Parsons M, Franz-Odendaal T, Fisher S, Skeletogenic fate of zebrafish cranial and trunk neural crest. PLoS One (2012)" "the cleithrum is not directly homologous to any bone in mammals" bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0004742 "dentary" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:24067611 "Zhu M, Yu X, Ahlberg PE, Choo B, Lu J, Qiao T, Qu Q, Zhao W, Jia L, Blom H, Zhu Y, A Silurian placoderm with osteichthyan-like marginal jaw bones. Nature (2013)" "Here we describe a three-dimensionally preserved 419-million-year-old placoderm fish from the Silurian of China that represents the first stem gnathostome with dermal marginal jaw bones (premaxilla, maxilla and dentary), features previously restricted to Osteichthyes." bgee ANN 2013-10-09 HOM:0000007 "historical homology" UBERON:0004744 "articular/anguloarticular" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "The homologies of the malleus, incus and stapes to the articular, quadrate and columella, and tympanic ring and gonial to the angular and prearticular suggested by comparative anatomy 175 years ago have been recently confirmed by molecular and developmental biology." bgee ANN 2015-04-02 HOM:0000007 "historical homology" UBERON:0004747 "supraoccipital bone" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.237 Table 7.1" bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0004766 "cranial bone" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001474, negated: false, taxon ID: 7742 - entity: UBERON:0003128, negated: false, taxon ID: 89593" bgee HOM:0000007 "historical homology" UBERON:0004768 "bone of lower jaw" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001474, negated: false, taxon ID: 7742 - entity: UBERON:0001710, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0004771 "posterior nasal aperture" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001707, negated: false, taxon ID: 7742 - entity: UBERON:0001728, negated: false, taxon ID: 40674 - entity: UBERON:0010425, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0004798 "respiratory system basal lamina" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000482, negated: false, taxon ID: 33213 - entity: UBERON:0001004, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004798 "respiratory system basal lamina" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000482, negated: false, taxon ID: 33213 - entity: UBERON:0001004, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004800 "bronchus basal lamina" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000482, negated: false, taxon ID: 33213 - entity: UBERON:0002185, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0004801 "cervix epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000002, negated: false, taxon ID: 40674 - entity: UBERON:0000483, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0004802 "respiratory tract epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21669855 "Leys SP, Nichols SA, Adams ED, Epithelia and integration in sponges. Integrative and Comparative Biology (2009)" bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0004803 "penis epithelium" 8459 "Testudines" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000989, negated: false, taxon ID: 8459" bgee HOM:0000007 "historical homology" UBERON:0004803 "penis epithelium" 8492 "Archosauria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000989, negated: false, taxon ID: 8492" bgee HOM:0000007 "historical homology" UBERON:0004803 "penis epithelium" 8509 "Squamata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000989, negated: false, taxon ID: 8509" bgee HOM:0000007 "historical homology" UBERON:0004803 "penis epithelium" 32524 "Amniota" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000989, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0004803 "penis epithelium" NOT 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000989, negated: true, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0004803 "penis epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000989, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004804 "oviduct epithelium" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000993, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0004805 "seminal vesicle epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000998, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004806 "vas deferens epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001000, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004807 "respiratory system epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001004, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004807 "respiratory system epithelium" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001004, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004809 "salivary gland epithelium" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001044, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0004811 "endometrium epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001295, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004812 "male prepuce epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001332, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004813 "seminiferous tubule epithelium" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001343, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0004816 "larynx epithelium" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001737, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0004817 "lacrimal gland epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001817, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004819 "kidney epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002113, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004820 "bile duct epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002394, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004821 "pulmonary alveolus epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002299, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004829 "urethra skeletal muscle tissue" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000057, negated: false, taxon ID: 40674 - entity: UBERON:0001134, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004830 "respiratory system skeletal muscle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001004, negated: false, taxon ID: 7742 - entity: UBERON:0001134, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004830 "respiratory system skeletal muscle" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001004, negated: false, taxon ID: 33213 - entity: UBERON:0001134, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004831 "esophagus skeletal muscle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001043, negated: false, taxon ID: 7742 - entity: UBERON:0001134, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004831 "esophagus skeletal muscle" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001043, negated: false, taxon ID: 33213 - entity: UBERON:0001134, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0004833 "lip skeletal muscle" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001134, negated: false, taxon ID: 33213 - entity: UBERON:0001833, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004834 "hepatic duct smooth muscle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0005171, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004835 "epididymis smooth muscle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0001301, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004850 "lymph node endothelium" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000029, negated: false, taxon ID: 40674 - entity: UBERON:0001986, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004851 "aorta endothelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000947, negated: false, taxon ID: 7742 - entity: UBERON:0001986, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004852 "cardiovascular system endothelium" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23809110 "Monahan-Earley R, Dvorak AM, Aird WC, Evolutionary origins of the blood vascular system and endothelium. J Thromb Haemost (2013)" "The endothelium evolved in an ancestral vertebrate some 540-510 million years ago to optimize flow dynamics and barrier function, and/or to localize immune and coagulation functions." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0004854 "gastrointestinal system mesentery" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0521617147 "Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut." bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0004854 "gastrointestinal system mesentery" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:19303014 "McLin VA, Henning SJ, Jamrich M, The role of the visceral mesoderm in the development of the gastrointestinal tract. Gastroenterology (2009)" "Development of the vertebrate GI [gastrointestinal] tract, and of the VM [visceral mesoderm] in particular, is conserved across species. In very broad terms, it follows this sequence of events: gastrulation, formation of the primitive gut tube from the endoderm, and apposition of the inner leaflet of the lateral plate mesoderm against the endoderm." bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0004864 "vasculature of retina" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000966, negated: false, taxon ID: 7742 - entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0004865 "actinopterygian parietal bone" 117571 "Euteleostomi" CIO:0000003 "high confidence from single evidence" ECO:0000033 "traceable author statement" PMID:17599725 "Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, Westerfield M, Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zool B Mol Dev Evol (2007)" "The so-called parietal bone of actinopterygians is the homologue of the postparietal bone of piscine sarcopterygians and tetrapods (Jollie, '62; Schultze and Arsenault, '85)." bgee ANN 2013-08-27 HOM:0000007 "historical homology" UBERON:0004865 "actinopterygian parietal bone" 117571 "Euteleostomi" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-3899370805 "Arratia G, Schultze HP, Wilson MVH, Mesozoic Fishes 4 - Homology and Phylogeny (2008) p.23-48" "The homologization of cranial bones of actinopterygians with those of sarcopterygians based on the bone names established in human anatomy is favored in order to permit the building of phylogenetic relationship schemes beyond the taxonomic boundaries of osteichthyans (including tetrapods). (...) In actinopterygians, the terms parietal and postparietal bones have to replace the commonly used terms 'frontal' and 'parietal' bones for the two paired bones on the skull roof." bgee ANN 2013-08-27 HOM:0000007 "historical homology" UBERON:0004866 "actinopterygian frontal bone" 7898 "Actinopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:17599725 "Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, Westerfield M, Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zool B Mol Dev Evol (2007)" "There are several lines of evidence to suggest that the so-called frontal bone in actinopterygian fishes (including zebrafish) is the homologue of the parietal bone, and not the 'frontal' bone, in advanced 'piscine' sarcopterygians as well as in 'tetrapod' sarcopterygians such as frog, bird, mouse, or human. The so-called parietal bone of actinopterygians is the homologue of the postparietal bone of piscine sarcopterygians and tetrapods (Jollie, '62; Schultze and Arsenault, '85)." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0004872 "splanchnic layer of lateral plate mesoderm" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:19303014 "McLin VA, Henning SJ, Jamrich M, The role of the visceral mesoderm in the development of the gastrointestinal tract. Gastroenterology (2009)" "Development of the vertebrate GI [gastrointestinal] tract, and of the VM [visceral mesoderm] in particular, is conserved across species. In very broad terms, it follows this sequence of events: gastrulation, formation of the primitive gut tube from the endoderm, and apposition of the inner leaflet of the lateral plate mesoderm against the endoderm." bgee ANN 2013-10-18 HOM:0000007 "historical homology" UBERON:0004873 "splanchnopleure" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1073/pnas.97.9.4449 "Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) Figure 3" "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate." bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0004874 "somatopleure" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1073/pnas.97.9.4449 "Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) Figure 3" "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate." bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0004880 "chordamesoderm" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:25214631 "Lauri A, Brunet T, Handberg-Thorsager M, Fischer AH, Simakov O, Steinmetz PR, Tomer R, Keller PJ, Arendt D, Development of the annelid axochord: insights into notochord evolution. Science (2014)" "Our study of annelid development reveals a population of mesodermal cells that converge and extend along the ventral midline and express a combination of transcription factors, signaling molecules, and guidance factors that closely matches that of the vertebrate chordamesoderm. These comparative data suggest that a similar population of mesodermal midline cells already existed in urbilaterian ancestors but leave open its ancient developmental fate." bgee ANN 2014-04-27 HOM:0000007 "historical homology" UBERON:0004880|UBERON:0035148 "chordamesoderm|presumptive axochord" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" PMID:25214631 "Lauri A, Brunet T, Handberg-Thorsager M, Fischer AH, Simakov O, Steinmetz PR, Tomer R, Keller PJ, Arendt D, Development of the annelid axochord: insights into notochord evolution. Science (2014)" "Our study of annelid development reveals a population of mesodermal cells that converge and extend along the ventral midline and express a combination of transcription factors, signaling molecules, and guidance factors that closely matches that of the vertebrate chordamesoderm. These comparative data suggest that a similar population of mesodermal midline cells already existed in urbilaterian ancestors but leave open its ancient developmental fate." bgee ANN 2018-01-15 HOM:0000007 "historical homology" UBERON:0004880|UBERON:0035148 "chordamesoderm|presumptive axochord" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:25214631 "Lauri A, Brunet T, Handberg-Thorsager M, Fischer AH, Simakov O, Steinmetz PR, Tomer R, Keller PJ, Arendt D, Development of the annelid axochord: insights into notochord evolution. Science (2014)" "Our study of annelid development reveals a population of mesodermal cells that converge and extend along the ventral midline and express a combination of transcription factors, signaling molecules, and guidance factors that closely matches that of the vertebrate chordamesoderm. These comparative data suggest that a similar population of mesodermal midline cells already existed in urbilaterian ancestors but leave open its ancient developmental fate." bgee ANN 2018-01-15 HOM:0000007 "historical homology" UBERON:0004880|UBERON:0035148 "chordamesoderm|presumptive axochord" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:25214631 "Lauri A, Brunet T, Handberg-Thorsager M, Fischer AH, Simakov O, Steinmetz PR, Tomer R, Keller PJ, Arendt D, Development of the annelid axochord: insights into notochord evolution. Science (2014)" "Our study of annelid development reveals a population of mesodermal cells that converge and extend along the ventral midline and express a combination of transcription factors, signaling molecules, and guidance factors that closely matches that of the vertebrate chordamesoderm. These comparative data suggest that a similar population of mesodermal midline cells already existed in urbilaterian ancestors but leave open its ancient developmental fate." bgee ANN 2018-01-15 HOM:0000007 "historical homology" UBERON:0004883 "lung mesenchyme" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002048|UBERON:0006860, negated: false, taxon ID: 7776 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0004890 "right lung accessory lobe" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.596 and Figure 18-21" "The synapsid line of evolution culminating in mammals and the sauropsid line to reptiles and birds diverged millions of years ago, near the time of the origin of amniotes. Although mammals, too, evolved an efficient respiratory system, needed by endothermic animals, the mammalian system differs in many ways from that of birds because it evolved its complex design from the generalized amniote condition independently. The evolution of the secondary palate in mammals and their therapsid ancestors made possible a separation of food and respiratory passage." bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0004895 "alveolar smooth muscle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0002299, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0004896 "right lung accessory lobe lobar bronchus" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.596 and Figure 18-21" "The synapsid line of evolution culminating in mammals and the sauropsid line to reptiles and birds diverged millions of years ago, near the time of the origin of amniotes. Although mammals, too, evolved an efficient respiratory system, needed by endothermic animals, the mammalian system differs in many ways from that of birds because it evolved its complex design from the generalized amniote condition independently. The evolution of the secondary palate in mammals and their therapsid ancestors made possible a separation of food and respiratory passage." bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0004902 "urogenital sinus epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000164, negated: false, taxon ID: 40674 - entity: UBERON:0000483, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0004909 "epithelium of gonad" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000991, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004909 "epithelium of gonad" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000991, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0004909 "epithelium of gonad" NOT 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000991, negated: true, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0004910 "epithelium of male gonad" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000473, negated: false, taxon ID: 7742 - entity: UBERON:0000483, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0004910 "epithelium of male gonad" NOT 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000473, negated: true, taxon ID: 33208 - entity: UBERON:0000483, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0004910 "epithelium of male gonad" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000473, negated: false, taxon ID: 33213 - entity: UBERON:0000483, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0004911 "epithelium of female gonad" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000992, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0004911 "epithelium of female gonad" NOT 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000992, negated: true, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0004911 "epithelium of female gonad" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000992, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0005052 "gizzard" 8492 "Archosauria" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1073/pnas.1112694108 "Zheng X, Martin LD, Zhou Z, Burnham DA, Zhang F, Miao D, Fossil evidence of avian crops from the Early Cretaceous of China. PNAS (2011)" "The gizzard may be a more basal feature for birds, because it is widely distributed in sister groups, such as modern crocodilians. In recent birds the gizzard is posterior to the proventriculus or glandular part of the stomach. The practice of collecting large numbers of small stones in the gizzard is characteristic of seed eaters among modern birds and is often correlated with a well-developed crop." bgee ANN 2017-05-29 HOM:0000007 "historical homology" UBERON:0005052 "gizzard" 8782 "Aves" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1073/pnas.1112694108 "Zheng X, Martin LD, Zhou Z, Burnham DA, Zhang F, Miao D, Fossil evidence of avian crops from the Early Cretaceous of China. PNAS (2011)" "The gizzard may be a more basal feature for birds, because it is widely distributed in sister groups, such as modern crocodilians. In recent birds the gizzard is posterior to the proventriculus or glandular part of the stomach. The practice of collecting large numbers of small stones in the gizzard is characteristic of seed eaters among modern birds and is often correlated with a well-developed crop." bgee ANN 2017-05-29 HOM:0000007 "historical homology" UBERON:0005052 "gizzard" 117571 "Euteleostomi" CIO:0000005 "low confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.563" "Some vertebrates have unusual specializations of the stomach...A gizzard, which can grind up food, has evolved from all or much of the stomach in gizzard shad and certain other fishesÊ; some reptiles, including crocodilesÊ; and all birds." bgee ANN 2017-05-29 HOM:0000007 "historical homology" UBERON:0005053 "primary nerve cord" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:25903626 "Holland ND, Holland LZ, Holland PW, Scenarios for the making of vertebrates. Nature (2015)" "In the 1990s, advances in developmental genetics - again with arthropods leading the way - set the stage for the revival of the annelid theory. The fly dpp gene was found to be expressed dorsally and to have dorsalizing activity, whereas the homologous frog bmp4 was expressed ventrally and found to have ventralizing activity. Arendt and Nuebler-Jung interpreted this pattern as support for homology between arthropod and vertebrate nerve cords and indicative of a dorsoventral inversion of the body during the invertebrate-to-vertebrate transition. The proposed nerve-cord homology was strengthened by the discovery that the fly sog gene was expressed ventrally and had ventralizing activity, whereas the homologous frog chordin gene was expressed dorsally and had dorsalizing activity. In addition, sog/chordin and dpp/bmp4 antagonized one another to establish a dorsoventral axis that was reversed between flies and frogs. Additional support came from the finding that neural progenitor cells in the central nervous system (CNS) were organized in longitudinal bands each characterized by a distinctive suite of gene expression that was homologous between flies and vertebrates, and that gene expression in these bands was comparable mediolaterally in both organisms." bgee ANN 2015-04-30 HOM:0000007 "historical homology" UBERON:0005062 "neural fold" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0005062 "neural fold" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0005070 "anterior neuropore" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:20438724 "Veeman MT, Newman-Smith E, El-Nachef D, Smith WC, The ascidian mouth opening is derived from the anterior neuropore: reassessing the mouth/neural tube relationship in chordate evolution. Dev Biol (2010)" "The ascidian mouth opening is derived from the anterior neuropore (...) The relative positions of the brain and mouth are of central importance for models of chordate evolution. The dorsal hollow neural tube and the mouth have often been thought of as developmentally distinct structures that may have followed independent evolutionary paths. In most chordates however, including vertebrates and ascidians, the mouth primordia have been shown to fate to the anterior neural boundary. In ascidians such as Ciona there is a particularly intimate relationship between brain and mouth development, with a thin canal connecting the neural tube lumen to the mouth primordium at larval stages. This so-called neurohypophyseal canal was previously thought to be a secondary connection that formed relatively late, after the independent formation of the mouth primordium and the neural tube. Here we show that the Ciona neurohypophyseal canal is present from the end of neurulation and represents the anteriormost neural tube, and that the future mouth opening is actually derived from the anterior neuropore." bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0005071 "posterior neuropore" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0005078 "lamina terminalis of neural tube" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:8787764 "Holland ND, Panganiban G, Henyey EL, Holland LZ, Sequence and developmental expression of AmphiDll, an amphioxus Distal-less gene transcribed in the ectoderm, epidermis and nervous system: insights into evolution of craniate forebrain and neural crest. Development (1996)" "Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain." bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0005080 "metanephric ureteric bud" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000081, negated: false, taxon ID: 32524 - entity: UBERON:0000084, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0005081 "ureter ureteric bud" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000056, negated: false, taxon ID: 32524 - entity: UBERON:0000084, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0005091 "left horn of sinus venosus" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1152/physrev.00006.2003 "Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)" "Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0005092 "right horn of sinus venosus" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1152/physrev.00006.2003 "Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003" "Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0005103 "mesonephric epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000080, negated: false, taxon ID: 7742 - entity: UBERON:0000483, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0005106 "metanephric tubule" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543" "The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0005108 "metanephric epithelium" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000081, negated: false, taxon ID: 32524 - entity: UBERON:0000483, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0005109 "metanephric smooth muscle tissue" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000081, negated: false, taxon ID: 32524 - entity: UBERON:0001135, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0005110 "metanephric nephron" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639" "The ureteric bud itself forms the collecting tubules and the ureter that drain the adult kidney. This type of kidney, called the metanephros, occurs in all adult amniotes." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0005130 "metanephric loop of Henle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000081, negated: false, taxon ID: 32524 - entity: UBERON:0001288, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0005171 "hepatic duct" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.569-571 and Figures 17-9 and 17-10" "In the adults of all vertebrates, the liver is the largest organ in the body cavity, and it occupies most of the space in the abdomen. (...) Minute bile canaliculi lie between hepatic cells and drain bile, the secretion of the hepatic cells, into hepatic ducts that leave the liver and unite to form the common bile duct." bgee ANN 2013-09-06 HOM:0000007 "historical homology" UBERON:0005192 "deferent duct artery" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001000, negated: false, taxon ID: 40674 - entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0005195 "deferent duct vein" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001000, negated: false, taxon ID: 40674 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0005197 "segmental spinal nerve" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0005217 "midbrain subarachnoid space" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0005218 "diencephalon subarachnoid space" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000315, negated: false, taxon ID: 40674 - entity: UBERON:0001894, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0005219 "hindbrain subarachnoid space" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0005225 "upper leg epithelium" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000376, negated: false, taxon ID: 7776 - entity: UBERON:0000483, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0005226 "pedal digit epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21669855 "Leys SP, Nichols SA, Adams ED, Epithelia and integration in sponges. Integrative and Comparative Biology (2009)" bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0005227 "manual digit epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21669855 "Leys SP, Nichols SA, Adams ED, Epithelia and integration in sponges. Integrative and Comparative Biology (2009)" bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0005228 "upper arm epithelium" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0003822, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0005228 "upper arm epithelium" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0003822, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0005229 "lower leg epithelium" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0003823, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0005236 "osseus labyrinth vestibule" 32525 "Theria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:22404255 "Gunz P, Ramsier M, Kuhrig M, Hublin JJ, Spoor F, The mammalian bony labyrinth reconsidered, introducing a comprehensive geometric morphometric approach. J Anat (2012)" "The bony labyrinth inside the petrous portion of the temporal bone houses the sense organs of hearing and balance. Characterized in therian mammals by three semicircular canals and a coiled cochlea (Luo et al., 2011) its morphology is highly conserved. Nevertheless, the detailed morphology varies even among closely related taxa and carries valuable functional, developmental and phylogenetic information (e.g. Spoor & Zonneveld, 1998; Schmelzle et al., 2007; Lebrun et al., 2010)." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0005240 "basal plate medulla oblongata" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0005243 "interventricular septum endocardium" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.618" "Superficially, the mammalian heart resembles those of birds and crocodiles, but the interventricular septum evolved independently and develops embryonically in a slightly different way, so it is not homologous to the interventricular septum of these vertebrates." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0005243 "interventricular septum endocardium" NOT 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.618" "Superficially, the mammalian heart resembles those of birds and crocodiles, but the interventricular septum evolved independently and develops embryonically in a slightly different way, so it is not homologous to the interventricular septum of these vertebrates." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0005243 "interventricular septum endocardium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.618" "Superficially, the mammalian heart resembles those of birds and crocodiles, but the interventricular septum evolved independently and develops embryonically in a slightly different way, so it is not homologous to the interventricular septum of these vertebrates." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0005244 "lobar bronchus of right lung cranial lobe" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.596 and Figure 18-21" "The synapsid line of evolution culminating in mammals and the sauropsid line to reptiles and birds diverged millions of years ago, near the time of the origin of amniotes. Although mammals, too, evolved an efficient respiratory system, needed by endothermic animals, the mammalian system differs in many ways from that of birds because it evolved its complex design from the generalized amniote condition independently. The evolution of the secondary palate in mammals and their therapsid ancestors made possible a separation of food and respiratory passage." bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0005245 "lobar bronchus of right lung caudal lobe" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.596 and Figure 18-21" "The synapsid line of evolution culminating in mammals and the sauropsid line to reptiles and birds diverged millions of years ago, near the time of the origin of amniotes. Although mammals, too, evolved an efficient respiratory system, needed by endothermic animals, the mammalian system differs in many ways from that of birds because it evolved its complex design from the generalized amniote condition independently. The evolution of the secondary palate in mammals and their therapsid ancestors made possible a separation of food and respiratory passage." bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0005248 "bulbus cordis myocardium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450-451" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0005252 "lesser sac cavity" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1007/s00898-999-0002-1 "Brainerd EL, New perspectives on the evolution of lung ventilation mechanisms in vertebrates. Experimental Biology Online (1999)" "In green iguanas, as in most lepidosaurs, the body cavity is not divided into separate pleural and peritoneal spaces. Instead, the lungs and viscera are contained within a single, 'pleuroperitoneal' cavity. This condition is also seen in air-breathing fishes and amphibians, indicating that an undivided body cavity is the primitive condition for amniotes." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0005253 "head mesenchyme" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 33213 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0005253 "head mesenchyme" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 7742 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0005254 "upper leg mesenchyme" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000376, negated: false, taxon ID: 7776 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0005258 "upper arm mesenchyme" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0003104, negated: false, taxon ID: 7711 - entity: UBERON:0003822, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0005258 "upper arm mesenchyme" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0003104, negated: false, taxon ID: 7711 - entity: UBERON:0003822, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0005259 "lower leg mesenchyme" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0003104, negated: false, taxon ID: 7711 - entity: UBERON:0003823, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0005261 "atrium cardiac jelly" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:16675702 "Forouhar AS, Liebling M, Hickerson A, Nasiraei-Moghaddam A, Tsai HJ, Hove JR, Fraser SE, Dickinson ME, Gharib M, The embryonic vertebrate heart tube is a dynamic suction pump. Science (2006)" "The cardiovascular system is the first functional organ system to develop in vertebrate embryos. In its earliest stages, it consists of a primitive heart tube that drives blood through a simple vascular network. (...) The zebrafish offers a powerful vertebrate model for cardiogenetic studies (4-7) with multiple advantages for in vivo imaging: Eggs are externally fertilized; embryos are nearly transparent, providing optical access to the earliest stages of cardiogenesis; and many GFP (green fluorescent protein)-labeled transgenic strains have been derived. (...)The heart tube stems from the surface of the spherical yolk sac, acutely narrows to about 30 um, and becomes lined by an additional layer of cells (myocardium) and cardiac jelly that alters the elasticity of the heart tube at the inflow boundary." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0005262 "ventricle cardiac jelly" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:16675702 "Forouhar AS, Liebling M, Hickerson A, Nasiraei-Moghaddam A, Tsai HJ, Hove JR, Fraser SE, Dickinson ME, Gharib M, The embryonic vertebrate heart tube is a dynamic suction pump. Science (2006)" "The cardiovascular system is the first functional organ system to develop in vertebrate embryos. In its earliest stages, it consists of a primitive heart tube that drives blood through a simple vascular network. (...) The zebrafish offers a powerful vertebrate model for cardiogenetic studies (4-7) with multiple advantages for in vivo imaging: Eggs are externally fertilized; embryos are nearly transparent, providing optical access to the earliest stages of cardiogenesis; and many GFP (green fluorescent protein)-labeled transgenic strains have been derived. (...)The heart tube stems from the surface of the spherical yolk sac, acutely narrows to about 30 um, and becomes lined by an additional layer of cells (myocardium) and cardiac jelly that alters the elasticity of the heart tube at the inflow boundary." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0005263 "outflow tract cardiac jelly" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:16675702 "Forouhar AS, Liebling M, Hickerson A, Nasiraei-Moghaddam A, Tsai HJ, Hove JR, Fraser SE, Dickinson ME, Gharib M, The embryonic vertebrate heart tube is a dynamic suction pump. Science (2006)" "The cardiovascular system is the first functional organ system to develop in vertebrate embryos. In its earliest stages, it consists of a primitive heart tube that drives blood through a simple vascular network. (...) The zebrafish offers a powerful vertebrate model for cardiogenetic studies (4-7) with multiple advantages for in vivo imaging: Eggs are externally fertilized; embryos are nearly transparent, providing optical access to the earliest stages of cardiogenesis; and many GFP (green fluorescent protein)-labeled transgenic strains have been derived. (...)The heart tube stems from the surface of the spherical yolk sac, acutely narrows to about 30 um, and becomes lined by an additional layer of cells (myocardium) and cardiac jelly that alters the elasticity of the heart tube at the inflow boundary." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0005273 "nail bed" 9443 "Primates" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.225 and p.230-232" "Only primates have nails. In other vertebrates, the keratinizing system at the terminus of each digit produces claws or hooves." bgee ANN 2013-07-17 HOM:0000007 "historical homology" UBERON:0005278 "nail bed of finger" 9443 "Primates" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000024|UBERON:0002102, negated: false, taxon ID: 32524 - entity: UBERON:0005273, negated: false, taxon ID: 9443" bgee HOM:0000007 "historical homology" UBERON:0005279 "nail bed of toe" 9443 "Primates" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002103, negated: false, taxon ID: 32523 - entity: UBERON:0005273, negated: false, taxon ID: 9443" bgee HOM:0000007 "historical homology" UBERON:0005282 "ventricular system of brain" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19274662 "Lowery LA, Sive H, Totally tubular: the mystery behind function and origin of the brain ventricular system. Bioessays (2009)" "A unique feature of the vertebrate brain is the brain ventricular system, a series of connected cavities which are filled with cerebrospinal fluid (CSF) and surrounded by neuroepithelium." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0005290 "myelencephalon" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500" "The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0005296 "ovary sex cord" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1146/annurev.cellbio.042308.13350 "DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)" "Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0005297 "testis sex cord" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1146/annurev.cellbio.042308.13350 "DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)" "Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0005298 "skin of clitoris" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0001299|UBERON:0002411|UBERON:0004713, negated: false, taxon ID: 40674 - entity: UBERON:0002411, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0005305 "thyroid follicle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1007/s004270050309 "Ogasawara M, Overlapping expression of amphioxus homologs of the thyroid transcription factor-1 gene and thyroid peroxidase gene in the endostyle: insight into evolution of the thyroid gland. Dev Genes Evol (2000)" "The other function of the endostyle appears to be equivalent to that of the vertebrate thyroid gland follicle." bgee ANN 2018-03-27 HOM:0000007 "historical homology" UBERON:0005305|UBERON:0006870 "thyroid follicle|endostyle" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1007/s004270050309 "Ogasawara M, Overlapping expression of amphioxus homologs of the thyroid transcription factor-1 gene and thyroid peroxidase gene in the endostyle: insight into evolution of the thyroid gland. Dev Genes Evol (2000)" "To investigate the molecular mechanisms involved in the formation and function of the endostyle, with special reference to the evolution of the follicle of the thyroid gland, I isolated and characterized cDNA clones for the amphioxus homologs of the TTF-1 gene (BbTTF-1) and TPO gene (BbTPO) from Branchiostoma belcheri. Reverse transcriptase-polymerase chain reaction/Southern blotting revealed that both amphioxus TTF-1 and TPO genes are expressed mainly in the adult endostyle. Spatial and temporal expression patterns assessed by in situ hybridization revealed that BbTTF-1 is expressed in the endodermal cells during early embryogenesis and is maintained in all zones of the adult endostyle. On the other hand, expression of BbTPO is chiefly in zones 5 and 6 of the adult endostyle where it overlaps with that of BbTTF-1, and to a lesser extent in zones 1 and 3. This restriction of the expression of BbTTF-1 and BbTPO to the endostyle strongly suggests that the endostyle is homologous to the follicle of the thyroid gland. Moreover, the spatial and temporal expression patterns of these genes suggest that TTF-1 regulates TPO expression. The coexpression of these genes in amphioxus suggests that regulation of TPO by TTF-1 was present in the common ancestor of cephalochordates (acraniates) and craniates." bgee ANN 2017-05-01 HOM:0000007 "historical homology" UBERON:0005306 "blastema" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1016/j.ydbio.2008.04.004 "McClure KD, Sustar A, Schubiger G, Three genes control the timing, the site and the size of blastema formation in Drosophila. Dev Biol (2008)" "Our results indicate that rgn, alr and Mmp1 function in the timing, extent and position of the regeneration blastema, as well as in the regulation of regenerative plasticity. rgn, alr and Mmp1 homologs have all been implicated in the process of regeneration in vertebrates, and now, invertebrates, which suggests that they play a broadly conserved role in organ and tissue regeneration (Bai et al., 2005; Okamoto, 1999; Pawlowski and Jura, 2006). Such findings indicate that the function of Wg signaling in epimorphic regeneration can be investigated using Drosophila imaginal discs." bgee ANN 2017-10-10 HOM:0000007 "historical homology" UBERON:0005306 "blastema" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000205 "curator inference" DOI:10.15252/embr.201643795 "Slack JM, Animal regeneration: ancestral character or evolutionary novelty? EMBO Rep (2017)" "An old question about regeneration is whether it is an ancestral character which is a general property of living matter, or whether it represents a set of specific adaptations to the different circumstances faced by different types of animal. In this review, some recent results on regeneration are assessed to see if they can throw any new light on this question. Evidence in favour of an ancestral character comes from the role of Wnt and bone morphogenetic protein signalling in controlling the pattern of whole-body regeneration in acoels, which are a basal group of bilaterian animals. On the other hand, there is some evidence for adaptive acquisition or maintenance of the regeneration of appendages based on the occurrence of severe non-lethal predation, the existence of some novel genes in regenerating organisms, and differences at the molecular level between apparently similar forms of regeneration. It is tentatively concluded that whole-body regeneration is an ancestral character although has been lost from most animal lineages. Appendage regeneration is more likely to represent a derived character resulting from many specific adaptations." bgee ANN 2017-10-10 HOM:0000007 "historical homology" UBERON:0005309 "pronephric nephron" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001285, negated: false, taxon ID: 7742 - entity: UBERON:0002120, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0005316 "endocardial endothelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001986, negated: false, taxon ID: 7742 - entity: UBERON:0002165, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0005317 "pulmonary artery endothelium" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001986, negated: false, taxon ID: 7742 - entity: UBERON:0002012, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0005317 "pulmonary artery endothelium" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001986, negated: false, taxon ID: 7742 - entity: UBERON:0002012, negated: false, taxon ID: 117571" bgee HOM:0000007 "historical homology" UBERON:0005319 "mesonephric collecting duct" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000080, negated: false, taxon ID: 7742 - entity: UBERON:0001232, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0005321 "mesonephric smooth muscle tissue" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000080, negated: false, taxon ID: 7742 - entity: UBERON:0001135, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0005322 "mesonephric nephron" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000080, negated: false, taxon ID: 7742 - entity: UBERON:0001285, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0005323 "mesonephric mesenchyme" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639" "As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0005325 "mesonephric glomerulus" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0127224411 "Vize PD, Woolf AS, Bard JBL, The kidney: From normal development to congenital disease (2003) p.3" "In animals in which the mesonephros is the terminal kidney, such as amphibians and fish, the final organ is very complex, containing a large number of nephrons, most of which have an internal glomerulus." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0005337 "outflow tract of ventricle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002082, negated: false, taxon ID: 7742 - entity: UBERON:0004145, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0005338 "outflow tract aortic component" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1126/science.1190181 "Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010)" "The vertebrate heart is formed from diverse embryonic territories, including the first and second heart fields. The second heart field (SHF) gives rise to the right ventricle and outflow tract, yet its evolutionary origins are unclear. (...) SHF-like territories have been identified in frog, zebrafish, and lamprey, yet evidence for a deeper evolutionary origin remains obscured by the absence of a clear SHF in invertebrates." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0005339 "outflow tract pulmonary component" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1126/science.1190181 "Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010)" "The vertebrate heart is formed from diverse embryonic territories, including the first and second heart fields. The second heart field (SHF) gives rise to the right ventricle and outflow tract, yet its evolutionary origins are unclear. (...) SHF-like territories have been identified in frog, zebrafish, and lamprey, yet evidence for a deeper evolutionary origin remains obscured by the absence of a clear SHF in invertebrates." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0005356 "Rathke's pouch" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-4" "It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0005360 "inferior glossopharyngeal IX ganglion" 89593 "Craniata" CIO:0000005 "low confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...)" bgee ANN 2013-06-14 HOM:0000007 "historical homology" UBERON:0005361 "superior glossopharyngeal IX ganglion" 89593 "Craniata" CIO:0000005 "low confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...)" bgee ANN 2013-06-14 HOM:0000007 "historical homology" UBERON:0005362 "vagus X ganglion" 89593 "Craniata" CIO:0000005 "low confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625" "Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII)." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0005363 "inferior vagus X ganglion" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1046/j.1469-7580.2001.19910133.x "Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" "These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia." bgee ANN 2013-06-14 HOM:0000007 "historical homology" UBERON:0005364 "superior vagus X ganglion" 89593 "Craniata" CIO:0000005 "low confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625" "Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII)." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0005366 "olfactory lobe" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-3540237358 "Binder MD, Hirokawa N, Windhorst U (editors), Encyclopedia of Neuroscience (2009) p.1390-1400, Jarvis ED, Evolution of the Pallium in Birds and Reptiles" "pallial regions that are widely recognized to be homologous among birds, reptiles, mammals and other vertebrates: the hippocampus, olfactory cortex, and olfactory bulb" bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0005373 "spinal cord dorsal column" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0005374 "spinal cord lateral column" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:10867629 "Butler AB, Chordate evolution and the origin of craniates: an old brain in a new head. Anat Rec (2000)" "The lateral column expresses msh/Msx [in both Drosophila and vertebrates]. It gives rise to neural crest lineages, including the sensory bipolar neurons and glial cells, in vertebrates and to a variety of glial cells as well as to some motor neurons in Drosophila. The fates of the medial-, intermediate-, and lateral-column components, while not identical, thus have numerous and striking similarities in arthropods and craniates." bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0005375 "spinal cord ventral column" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0005384 "nasal cavity epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21669855 "Leys SP, Nichols SA, Adams ED, Epithelia and integration in sponges. Integrative and Comparative Biology (2009)" bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0005397 "brain arachnoid mater" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000955, negated: false, taxon ID: 33213 - entity: UBERON:0002362, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0005400 "telencephalon arachnoid mater" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001893, negated: false, taxon ID: 7742 - entity: UBERON:0002362, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0005401 "cerebral hemisphere gray matter" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001869, negated: false, taxon ID: 7742 - entity: UBERON:0002020, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0005402 "philtrum" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1242/dev.01705 "Helms JA, Cordero D, Tapadia MD, New insights into craniofacial morphogenesis. Development (2005) Figure 1" "[During development of the vertebrate craniofacial primordia] The frontonasal (or median nasal) prominence contributes to the forehead, the middle of the nose, the philtrum of the upper lip and the primary palate" bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0005407 "sublingual ganglion" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000045, negated: false, taxon ID: 33213 - entity: UBERON:0001832, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0005410 "cartilaginous otic capsule" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002418, negated: false, taxon ID: 7742 - entity: UBERON:0004637, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0005412 "optic fissure" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1038/nrn2283 "Lamb TD, Collin SP and Pugh EN, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)" "The folded arrangement of the vertebrate retina and RPE [retinal pigment epithelial] provides an evolutionary explanation for the occurrence of the choroid fissure, as proposed more than a century ago. Early in evolution, before the optic cup invaginated, the axons from retinal ganglion cells would simply have run over the surface of the structure. Hence, one can view the optic nerve as having acted rather like a rope in linking the retina to higher centres: the developing eye cup has simply wrapped around this 'rope', and the developing axons have thereby not needed to penetrate the retina." bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0005421 "pectoral appendage apical ectodermal ridge" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:17587327 "Mercader N, Early steps of paired fin development in zebrafish compared with tetrapod limb development. Development, growth and differentiation (2007)" "Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0005422 "pelvic appendage apical ectodermal ridge" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:17587327 "Mercader N, Early steps of paired fin development in zebrafish compared with tetrapod limb development. Development, growth and differentiation (2007)" "Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0005424 "presumptive retinal pigmented epithelium" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina." bgee ANN 2013-04-15 HOM:0000007 "historical homology" UBERON:0005425 "presumptive neural retina" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina." bgee ANN 2013-04-15 HOM:0000007 "historical homology" UBERON:0005426 "lens vesicle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens." bgee ANN 2013-04-15 HOM:0000007 "historical homology" UBERON:0005428 "vagal neural crest" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0005437 "conus medullaris" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0005439 "definitive endoderm" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:22742850 "Kraus MR, Grapin-Botton A, Patterning and shaping the endoderm in vivo and in culture. Curr Opin Genet Dev (2012)" "The definitive endoderm (DE) was first defined as the innermost germ layer found in all metazoan embryos. During development, it gives rise to a vast array of specialized epithelial cell types lining the respiratory and digestive systems, and contributes to associated organs such as thyroid, thymus, lungs, liver, and pancreas. In the adult, the DE provides a protective barrier against the environment and assumes many essential functions including digestion, nutrient absorption, and glucose homeostasis." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0005439 "definitive endoderm" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:22742850 "Kraus MR, Grapin-Botton A, Patterning and shaping the endoderm in vivo and in culture. Curr Opin Genet Dev (2012)" "The definitive endoderm (DE) was first defined as the innermost germ layer found in all metazoan embryos. During development, it gives rise to a vast array of specialized epithelial cell types lining the respiratory and digestive systems, and contributes to associated organs such as thyroid, thymus, lungs, liver, and pancreas. In the adult, the DE provides a protective barrier against the environment and assumes many essential functions including digestion, nutrient absorption, and glucose homeostasis." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0005440 "ductus arteriosus" 8287 "Sarcopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" "On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0005441 "external intercostal muscle" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0471090588 "Hildebrand M, Analysis of vertebrate structure (1983) p.193" "Behind the thorax, the lateral group (of muscles in reptiles and mammals) remains essentially as for amphibians. (It breaks into three sheet-like layers: external oblique muscle, the internal oblique, and the transversus). More anteriorly, however, the ribs, now enlarged, penetrate and alter this group of muscles. The transversus is excluded from the thorax and the external and internal obliques become, respectively, the external and internal intercostal muscles, which contribute to the new function of ventilation of the lungs." bgee ANN 2013-08-21 HOM:0000007 "historical homology" UBERON:0005442 "abdominal external oblique muscle" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0471090588 "Hildebrand M, Analysis of vertebrate structure (1983) p.193" "Behind the thorax, the lateral group (of muscles in reptiles and mammals) remains essentially as for amphibians. (It breaks into three sheet-like layers: external oblique muscle, the internal oblique, and the transversus). More anteriorly, however, the ribs, now enlarged, penetrate and alter this group of muscles. The transversus is excluded from the thorax and the external and internal obliques become, respectively, the external and internal intercostal muscles, which contribute to the new function of ventilation of the lungs." bgee ANN 2013-08-21 HOM:0000007 "historical homology" UBERON:0005443 "filum terminale" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0005446 "foramen rotundum" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" PMID:1018003 "Presley R, Steel FLD, On the homology of the alisphenoid. Journal of Anatomy (1976)" "It is suggested that the mammalian lamina ascendens arose from an upgrowth of the root of the quadrate ramus of the epipterygoid in cynodonts, separating foramen rotundum from foramen ovale." bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0005448 "greater omentum" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1007/s00898-999-0002-1 "Brainerd EL, New perspectives on the evolution of lung ventilation mechanisms in vertebrates. Experimental Biology Online (1999)" "In green iguanas, as in most lepidosaurs, the body cavity is not divided into separate pleural and peritoneal spaces. Instead, the lungs and viscera are contained within a single, 'pleuroperitoneal' cavity. This condition is also seen in air-breathing fishes and amphibians, indicating that an undivided body cavity is the primitive condition for amniotes." bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0005449 "greater sac" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1007/s00898-999-0002-1 "Brainerd EL, New perspectives on the evolution of lung ventilation mechanisms in vertebrates. Experimental Biology Online (1999)" "In green iguanas, as in most lepidosaurs, the body cavity is not divided into separate pleural and peritoneal spaces. Instead, the lungs and viscera are contained within a single, 'pleuroperitoneal' cavity. This condition is also seen in air-breathing fishes and amphibians, indicating that an undivided body cavity is the primitive condition for amniotes." bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0005450 "greater sac cavity" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1007/s00898-999-0002-1 "Brainerd EL, New perspectives on the evolution of lung ventilation mechanisms in vertebrates. Experimental Biology Online (1999)" "In green iguanas, as in most lepidosaurs, the body cavity is not divided into separate pleural and peritoneal spaces. Instead, the lungs and viscera are contained within a single, 'pleuroperitoneal' cavity. This condition is also seen in air-breathing fishes and amphibians, indicating that an undivided body cavity is the primitive condition for amniotes." bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0005454 "abdominal internal oblique muscle" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" ISBN:978-0471090588 "Hildebrand M, Analysis of vertebrate structure (1983) p.193" "Behind the thorax, the lateral group (of muscles in reptiles and mammals) remains essentially as for amphibians. (It breaks into three sheet-like layers: external oblique muscle, the internal oblique, and the transversus). More anteriorly, however, the ribs, now enlarged, penetrate and alter this group of muscles. The transversus is excluded from the thorax and the external and internal obliques become, respectively, the external and internal intercostal muscles, which contribute to the new function of ventilation of the lungs." bgee ANN 2013-08-21 HOM:0000007 "historical homology" UBERON:0005455 "interventricular groove" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1038/nature08324 "Koshiba-Takeuchi K, Mori AD, Kaynak BL, Cebra-Thomas J, Sukonnik T, Georges RO, Latham S, Beck L, Henkelman RM, Black BL, Olson EN, Wade J, Takeuchi JK, Nemer M, Gilbert SF, Bruneau BG, Reptilian heart development and the molecular basis of cardiac chamber evolution. Nature (2009)" "Amphibians have a three-chambered heart, whereas mammalian, crocodilian and avian hearts have four chambers, two each for pulmonary and systemic circulations. The acquisition of a fully septated ventricle has evolved independently in birds, mammals and crocodilians, and is an important example of convergent evolution." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0005455 "interventricular groove" NOT 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1038/nature08324 "Koshiba-Takeuchi K, Mori AD, Kaynak BL, Cebra-Thomas J, Sukonnik T, Georges RO, Latham S, Beck L, Henkelman RM, Black BL, Olson EN, Wade J, Takeuchi JK, Nemer M, Gilbert SF, Bruneau BG, Reptilian heart development and the molecular basis of cardiac chamber evolution. Nature (2009)" "Amphibians have a three-chambered heart, whereas mammalian, crocodilian and avian hearts have four chambers, two each for pulmonary and systemic circulations. The acquisition of a fully septated ventricle has evolved independently in birds, mammals and crocodilians, and is an important example of convergent evolution." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0005455 "interventricular groove" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1038/nature08324 "Koshiba-Takeuchi K, Mori AD, Kaynak BL, Cebra-Thomas J, Sukonnik T, Georges RO, Latham S, Beck L, Henkelman RM, Black BL, Olson EN, Wade J, Takeuchi JK, Nemer M, Gilbert SF, Bruneau BG, Reptilian heart development and the molecular basis of cardiac chamber evolution. Nature (2009)" "Amphibians have a three-chambered heart, whereas mammalian, crocodilian and avian hearts have four chambers, two each for pulmonary and systemic circulations. The acquisition of a fully septated ventricle has evolved independently in birds, mammals and crocodilians, and is an important example of convergent evolution." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0005455 "interventricular groove" 1294634 "Crocodylia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1038/nature08324 "Koshiba-Takeuchi K, Mori AD, Kaynak BL, Cebra-Thomas J, Sukonnik T, Georges RO, Latham S, Beck L, Henkelman RM, Black BL, Olson EN, Wade J, Takeuchi JK, Nemer M, Gilbert SF, Bruneau BG, Reptilian heart development and the molecular basis of cardiac chamber evolution. Nature (2009)" "Amphibians have a three-chambered heart, whereas mammalian, crocodilian and avian hearts have four chambers, two each for pulmonary and systemic circulations. The acquisition of a fully septated ventricle has evolved independently in birds, mammals and crocodilians, and is an important example of convergent evolution." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0005456 "jugular foramen" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1126/science.1058476 "Luo ZX, Crompton AW, Sun AL, A new mammaliaform from the early Jurassic and evolution of mammalian characteristics. Science (2001)" "Jugular foramen is one of the derived skull characteristics described in Hadrocodium, an early Jurassic mammaliaform. [curator]" bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0005458 "left umbilical artery" 9347 "Eutheria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1016/j.cbpa.2007.01.029 "Mess A, Carter AM, Evolution of the placenta during the early radiation of placental mammals. Comparative Biochemistry and Physiology - Part A: Molecular and Integrative Physiology (2007)" "Two umbilical arteries and one vein are characters of the common ancestor of living placental mammals. [curator]" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0005460 "left vitelline vein" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460" "Within each vertebrate group, the veins compose a few main functional systems that arise embryologically from what seems to be a common developmental pattern. (...) Early in development, three major sets of paired veins are present: the vitelline veins from the yolk sac, the cardinal veins from the body of the embryo itself, and the lateral abdominal veins from the pelvic region. The paired vitelline veins are among the first vessels to appear in the embryo. They arise over the yolk and follow the yolk stalk into the body. They then turn anteriorly, continue along the gut, and enter the sinus venosus." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0005467 "platysma" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.398" "One of these (facial muscles in mammals), the platysma, is an unspecialized muscle derived from the hyoid arch." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0005467 "platysma" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0521048712 "Edgeworth FH, The cranial muscles of vertebrates (1935) Chapter X p.120" "The platysma is present in all mammals except cetacea. It is variable in degree of development but generally extends through the neck and face." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0005470 "right umbilical artery" 9347 "Eutheria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1016/j.cbpa.2007.01.029 "Mess A, Carter AM, Evolution of the placenta during the early radiation of placental mammals. Comparative Biochemistry and Physiology - Part A: Molecular and Integrative Physiology (2007)" "Two umbilical arteries and one vein are characters of the common ancestor of living placental mammals. [curator]" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0005472 "right vitelline vein" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460" "Within each vertebrate group, the veins compose a few main functional systems that arise embryologically from what seems to be a common developmental pattern. (...) Early in development, three major sets of paired veins are present: the vitelline veins from the yolk sac, the cardinal veins from the body of the embryo itself, and the lateral abdominal veins from the pelvic region. The paired vitelline veins are among the first vessels to appear in the embryo. They arise over the yolk and follow the yolk stalk into the body. They then turn anteriorly, continue along the gut, and enter the sinus venosus." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0005477 "stomach fundus epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21669855 "Leys SP, Nichols SA, Adams ED, Epithelia and integration in sponges. Integrative and Comparative Biology (2009)" bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0005484 "tricuspid valve leaflet" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1161/CIRCRESAHA.109.201566 "Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009)" "The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0005487 "vitelline vein" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460" "Within each vertebrate group, the veins compose a few main functional systems that arise embryologically from what seems to be a common developmental pattern. (...) Early in development, three major sets of paired veins are present: the vitelline veins from the yolk sac, the cardinal veins from the body of the embryo itself, and the lateral abdominal veins from the pelvic region. The paired vitelline veins are among the first vessels to appear in the embryo. They arise over the yolk and follow the yolk stalk into the body. They then turn anteriorly, continue along the gut, and enter the sinus venosus." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0005493 "hyoid muscle" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" DOI:10.1186/1471-213X-8-24 "Diogo R, Hinits Y, Hughes SM, Development of mandibular, hyoid and hypobranchial muscles in the zebrafish: homologies and evolution of these muscles within bony fishes and tetrapods. BMC Developmental Biology (2008)" "Although the zebrafish occupies a rather derived phylogenetic position within actinopterygians and even within teleosts, with respect to the mandibular, hyoid and hypobranchial muscles it seems justified to consider it an appropriate representative of these two groups. Among these muscles, the three with clear homologues in tetrapods [the intermandibularis anterior, adductor mandibulae, and sternohyoideus] and the further three identified in sarcopterygian fish are particularly appropriate for comparisons of results between the actinopterygian zebrafish and the sarcopterygians." bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0005494 "intermediate mesenchyme" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1016/j.ydbio.2004.03.034 "Wilm B, James RG, Schultheiss TM, Hogan BL, The forkhead genes, Foxc1 and Foxc2, regulate paraxial versus intermediate mesoderm cell fate. Developmental biology (2004)" "During vertebrate embryogenesis, the newly formed mesoderm is allocated to the paraxial, intermediate, and lateral domains, each giving rise to different cell and tissue types. Here, we provide evidence that the forkhead genes, Foxc1 and Foxc2, play a role in the specification of mesoderm to paraxial versus intermediate fates." bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0005495 "midbrain lateral wall" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0005496 "neural tube lateral wall" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:19408244 "Garcia-Fernandez J, Benito-Gutierrez E, It's a long way from amphioxus: descendants of the earliest chordate. Bioessays (2009)" "[in amphioxus] Serial exiting of the nerve cord is not a rule for motoneurons, which never abandon the nerve cord and instead synapse in serially arranged synaptic zones located in the lateral walls of the neural tube." bgee ANN 2015-04-02 HOM:0000007 "historical homology" UBERON:0005497 "non-neural ectoderm" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/S0959-4388(99)00003-3 "Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)" "In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0005497 "non-neural ectoderm" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1016/S0959-4388(99)00003-3 "Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)" "In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0005501 "rhombomere lateral wall" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001892, negated: false, taxon ID: 7742 - entity: UBERON:0005496, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0005502 "rhombomere roof plate" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.6064/2012/475017 "Robertshaw E, Kiecker C, Phylogenetic Origins of Brain Organisers. Scientifica (2012)" "The signalling centres that regulate DV [dorso-ventral] patterning in vertebrates-notochord, prechordal plate, floor plate, MGE [medial ganglionic eminence], and roof plate-seem to have evolved more recently as they are only found in the chordate lineage." bgee ANN 2013-06-14 HOM:0000007 "historical homology" UBERON:0005563 "trigeminal neural crest" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0005565 "facio-acoustic neural crest" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0005600 "crus commune" 32525 "Theria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:22404255 "Gunz P, Ramsier M, Kuhrig M, Hublin JJ, Spoor F, The mammalian bony labyrinth reconsidered, introducing a comprehensive geometric morphometric approach. J Anat (2012)" "The bony labyrinth inside the petrous portion of the temporal bone houses the sense organs of hearing and balance. Characterized in therian mammals by three semicircular canals and a coiled cochlea (Luo et al., 2011) its morphology is highly conserved. Nevertheless, the detailed morphology varies even among closely related taxa and carries valuable functional, developmental and phylogenetic information (e.g. Spoor & Zonneveld, 1998; Schmelzle et al., 2007; Lebrun et al., 2010)." bgee ANN 2013-06-26 HOM:0000007 "historical homology" UBERON:0005601 "dorsal mesocardium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481" "While bird and mammal 4-chambered hearts arose independently from different groups of reptilian ancestor, the vertebrate chambered heart is commonly considered arising from fishes and then defined as an historical homology relationship. However uncertainty remains on the origin of the heart substructures and tissues. [curator]" bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0005602 "dorsal mesogastrium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) Development of the coelomic cavity and mesenteries, p.159-164" bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0005606 "hyaloid cavity" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1387/ijdb.041895ms "Saint-Geniez M, D'Amore PA, Development and pathology of the hyaloid, choroidal and retinal vasculature. International Journal of Developmental Biology (2004)" "The hyaloid cavity or hyaloid fossa is a reminiscence of the hyaloid vasculature, the transient embryonic vascular bed which is complete at birth in mammals and regresses contemporaneously with the formation of the retinal vasculature. [curator]" bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0005611 "inner canthus" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.430-431" "Vertebrate eyes have a median corner, where upper and lower movable lids (Tetrapoda) or stationary skin folds (Lampreys, Chondrichthyans, Actinopterygians), come together. [curator]" bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0005613 "left dorsal aorta" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0174480198 "Roberts MBV, Biology: a functional approach (1986) p.572" "A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0005614 "lens anterior epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000965, negated: false, taxon ID: 7742 - entity: UBERON:0001804, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0005615 "lens equatorial epithelium" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000205 "curator inference" PMID:18093866 "Andley UP, The lens epithelium: focus on the expression and function of the alpha-crystallin chaperones. Int J Biochem Cell Biol (2008) Fig. 1A" "Although all lens epithelial cells are capable of undergoing cell proliferation, in a mature lens, epithelial cell proliferation occurs mainly in a region above the lens equator called the germinative zone. Cells in the transitional zone have withdrawn from the cell cycle and are in transition to becoming secondary lens fiber cells. Formation of secondary lens fiber cells from epithelial cells occurs slightly posterior to the lens equator (horizontal dashed line)." bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0005616 "mesenteric artery" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000160, negated: false, taxon ID: 7742 - entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0005617 "mesenteric vein" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000160, negated: false, taxon ID: 7742 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0005619 "secondary palatal shelf" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.278 Figure 7.58 and p.498" "Early tetrapod possessed a primary palate that included the vomer, pterygoid, parasphenoid, palatine and ectopterygoid bones. Therapsid evolved a partial secondary palate formed by the medial extension of the premaxilla and maxilla. Mammals have a secondary palate that, in addition to extensions of the premaxilla and maxilla, includes part of the palatine bone." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0005620 "primary palate" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.278 Figure 7.58 and p.498" "Early tetrapod possessed a primary palate that included the vomer, pterygoid, parasphenoid, palatine and ectopterygoid bones. [curator]" bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0005621 "rhomboid" 8342 "Anura" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:20807270 "Abdala V, Diogo R, Comparative anatomy, homologies and evolution of the pectoral and forelimb musculature of tetrapods with special attention to extant limbed amphibians and reptiles. J Anat (2010)" "Our dissections and comparisons pointed out that the overall configuration and the proximal and distal attachments of the 'rhomboideus' of anurans, crocodylians and birds are similar to those of the rhomboideus of mammals. In all these taxa, the 'rhomboideus' is mainly horizontal, originating proximally from the axial skeleton and inserting distally onto the scapula. However, it should be noted that in view of the phylogenetic framework we are using in this paper, it is cladistically more parsimonious to consider that the 'rhomboideus' was independently acquired in anurans, archosaurs and mammals (three evolutionary steps) than to consider that it was present in the last common ancestor (LCA) of tetrapods and then secondarily lost in urodeles (considering that the 'subscapularis' of some authors does not correspond to the 'rhomboideus' of other tetrapods), turtles and lepidosaurs (four evolutionary steps; see Fig. 1). In this specific case, this cladistically most parsimonious hypothesis implies that anurans, archosaurians and mammals independently acquired a muscle with a similar origin, insertion, orientation and function." bgee ANN 2017-02-15 HOM:0000007 "historical homology" UBERON:0005621 "rhomboid" 8492 "Archosauria" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:20807270 "Abdala V, Diogo R, Comparative anatomy, homologies and evolution of the pectoral and forelimb musculature of tetrapods with special attention to extant limbed amphibians and reptiles. J Anat (2010)" "Our dissections and comparisons pointed out that the overall configuration and the proximal and distal attachments of the 'rhomboideus' of anurans, crocodylians and birds are similar to those of the rhomboideus of mammals. In all these taxa, the 'rhomboideus' is mainly horizontal, originating proximally from the axial skeleton and inserting distally onto the scapula. However, it should be noted that in view of the phylogenetic framework we are using in this paper, it is cladistically more parsimonious to consider that the 'rhomboideus' was independently acquired in anurans, archosaurs and mammals (three evolutionary steps) than to consider that it was present in the last common ancestor (LCA) of tetrapods and then secondarily lost in urodeles (considering that the 'subscapularis' of some authors does not correspond to the 'rhomboideus' of other tetrapods), turtles and lepidosaurs (four evolutionary steps; see Fig. 1). In this specific case, this cladistically most parsimonious hypothesis implies that anurans, archosaurians and mammals independently acquired a muscle with a similar origin, insertion, orientation and function." bgee ANN 2017-02-15 HOM:0000007 "historical homology" UBERON:0005621 "rhomboid" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19438764 "Diogo R, Abdala V, Aziz MA, Lonergan N, Wood BA, From fish to modern humans--comparative anatomy, homologies and evolution of the pectoral and forelimb musculature. J Anat (2009)" "Most textbooks state that the rhomboideus (Figs 4,5), a muscle derived from the postcranial axial musculature that also connects the axial skeleton to the pectoral girdle, is only consistently found in mammals (e.g. Walker 1954; Jouffroy 1971; Jouffroy & Lessertisseur 1971; Kardong & Zalisko 1998; Kardong 2002; Kisia & Onyango 2005). In the non-mammalian tetrapods dissected by us, the rhomboideus does seem to be absent as an independent muscle (Table 1). However, Dilkes (2000) stated that a 'rhomboideus' is found in numerous reptiles, and that what is not resolved is whether the plesiomorphic reptilian condition is to have one rhomboideus muscle or both a rhomboideus superficialis and a rhomboideus profundus. According to some authors, a 'rhomboideus' is also found in some anurans (e.g. Howell 1937b). Therefore, the hypothesis that the rhomboideus was originally present in the first amniotes and even in the first tetrapods, and that it was secondarily lost within these groups, cannot be rejected. A detailed phylogenetic study, including representatives of several extant tetrapod taxa but also taking into account the data available for fossils (e.g. Dilkes 2000), is needed to clarify this issue." bgee ANN 2017-02-15 HOM:0000007 "historical homology" UBERON:0005621 "rhomboid" NOT 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:20807270 "Abdala V, Diogo R, Comparative anatomy, homologies and evolution of the pectoral and forelimb musculature of tetrapods with special attention to extant limbed amphibians and reptiles. J Anat (2010)" "Our dissections and comparisons pointed out that the overall configuration and the proximal and distal attachments of the 'rhomboideus' of anurans, crocodylians and birds are similar to those of the rhomboideus of mammals. In all these taxa, the 'rhomboideus' is mainly horizontal, originating proximally from the axial skeleton and inserting distally onto the scapula. However, it should be noted that in view of the phylogenetic framework we are using in this paper, it is cladistically more parsimonious to consider that the 'rhomboideus' was independently acquired in anurans, archosaurs and mammals (three evolutionary steps) than to consider that it was present in the last common ancestor (LCA) of tetrapods and then secondarily lost in urodeles (considering that the 'subscapularis' of some authors does not correspond to the 'rhomboideus' of other tetrapods), turtles and lepidosaurs (four evolutionary steps; see Fig. 1). In this specific case, this cladistically most parsimonious hypothesis implies that anurans, archosaurians and mammals independently acquired a muscle with a similar origin, insertion, orientation and function." bgee ANN 2017-02-15 HOM:0000007 "historical homology" UBERON:0005621 "rhomboid" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19438764 "Diogo R, Abdala V, Aziz MA, Lonergan N, Wood BA, From fish to modern humans--comparative anatomy, homologies and evolution of the pectoral and forelimb musculature. J Anat (2009)" "Most textbooks state that the rhomboideus (Figs 4,5), a muscle derived from the postcranial axial musculature that also connects the axial skeleton to the pectoral girdle, is only consistently found in mammals (e.g. Walker 1954; Jouffroy 1971; Jouffroy & Lessertisseur 1971; Kardong & Zalisko 1998; Kardong 2002; Kisia & Onyango 2005). In the non-mammalian tetrapods dissected by us, the rhomboideus does seem to be absent as an independent muscle (Table 1). However, Dilkes (2000) stated that a 'rhomboideus' is found in numerous reptiles, and that what is not resolved is whether the plesiomorphic reptilian condition is to have one rhomboideus muscle or both a rhomboideus superficialis and a rhomboideus profundus. According to some authors, a 'rhomboideus' is also found in some anurans (e.g. Howell 1937b). Therefore, the hypothesis that the rhomboideus was originally present in the first amniotes and even in the first tetrapods, and that it was secondarily lost within these groups, cannot be rejected. A detailed phylogenetic study, including representatives of several extant tetrapod taxa but also taking into account the data available for fossils (e.g. Dilkes 2000), is needed to clarify this issue." bgee ANN 2017-02-15 HOM:0000007 "historical homology" UBERON:0005621 "rhomboid" NOT 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:20807270 "Abdala V, Diogo R, Comparative anatomy, homologies and evolution of the pectoral and forelimb musculature of tetrapods with special attention to extant limbed amphibians and reptiles. J Anat (2010)" "Our dissections and comparisons pointed out that the overall configuration and the proximal and distal attachments of the 'rhomboideus' of anurans, crocodylians and birds are similar to those of the rhomboideus of mammals. In all these taxa, the 'rhomboideus' is mainly horizontal, originating proximally from the axial skeleton and inserting distally onto the scapula. However, it should be noted that in view of the phylogenetic framework we are using in this paper, it is cladistically more parsimonious to consider that the 'rhomboideus' was independently acquired in anurans, archosaurs and mammals (three evolutionary steps) than to consider that it was present in the last common ancestor (LCA) of tetrapods and then secondarily lost in urodeles (considering that the 'subscapularis' of some authors does not correspond to the 'rhomboideus' of other tetrapods), turtles and lepidosaurs (four evolutionary steps; see Fig. 1). In this specific case, this cladistically most parsimonious hypothesis implies that anurans, archosaurians and mammals independently acquired a muscle with a similar origin, insertion, orientation and function." bgee ANN 2017-02-15 HOM:0000007 "historical homology" UBERON:0005621 "rhomboid" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19438764 "Diogo R, Abdala V, Aziz MA, Lonergan N, Wood BA, From fish to modern humans--comparative anatomy, homologies and evolution of the pectoral and forelimb musculature. J Anat (2009)" "Most textbooks state that the rhomboideus (Figs 4,5), a muscle derived from the postcranial axial musculature that also connects the axial skeleton to the pectoral girdle, is only consistently found in mammals (e.g. Walker 1954; Jouffroy 1971; Jouffroy & Lessertisseur 1971; Kardong & Zalisko 1998; Kardong 2002; Kisia & Onyango 2005)." bgee ANN 2017-02-15 HOM:0000007 "historical homology" UBERON:0005621 "rhomboid" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:20807270 "Abdala V, Diogo R, Comparative anatomy, homologies and evolution of the pectoral and forelimb musculature of tetrapods with special attention to extant limbed amphibians and reptiles. J Anat (2010)" "Our dissections and comparisons pointed out that the overall configuration and the proximal and distal attachments of the 'rhomboideus' of anurans, crocodylians and birds are similar to those of the rhomboideus of mammals. In all these taxa, the 'rhomboideus' is mainly horizontal, originating proximally from the axial skeleton and inserting distally onto the scapula. However, it should be noted that in view of the phylogenetic framework we are using in this paper, it is cladistically more parsimonious to consider that the 'rhomboideus' was independently acquired in anurans, archosaurs and mammals (three evolutionary steps) than to consider that it was present in the last common ancestor (LCA) of tetrapods and then secondarily lost in urodeles (considering that the 'subscapularis' of some authors does not correspond to the 'rhomboideus' of other tetrapods), turtles and lepidosaurs (four evolutionary steps; see Fig. 1). In this specific case, this cladistically most parsimonious hypothesis implies that anurans, archosaurians and mammals independently acquired a muscle with a similar origin, insertion, orientation and function." bgee ANN 2017-02-15 HOM:0000007 "historical homology" UBERON:0005621 "rhomboid" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.394 Table 10.2" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0005622 "right dorsal aorta" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0174480198 "Roberts MBV, Biology: a functional approach (1986) p.572" "A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0005623 "semi-lunar valve" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1161/CIRCRESAHA.109.201566 "Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009)" "The four-chambered vertebrate heart has aortic and pulmonic semilunar (SL) valves at the arterial pole as well as mitral and tricuspid valves separating the atria and ventricles. (...) Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0005624 "suprarenal artery" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0002369, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0005625 "tubotympanic recess lumen" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.417" "The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0005626 "ventral mesogastrium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) Development of the coelomic cavity and mesenteries, p.159-164" bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0005636 "caecum epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001153, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0005637 "pyloric region epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001166, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0005638 "anterior chamber epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001766, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0005639 "right lung cranial lobe epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002170, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0005640 "right lung caudal lobe epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002171, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0005642 "ultimobranchial body epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0003092, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0005655 "right lung accessory lobe epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0004890, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0005656 "lens vesicle epithelium" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:20691855 "Graw J, Eye development. Curr Top Dev Biol (2010)" "The vertebrate eye comprises tissues from different embryonic origins: the lens and the cornea are derived from the surface ectoderm (...) Once the lens vesicle has formed, the primary lens fibers elongate from the posterior epithelium of the lens vesicle and fill its entire lumen." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0005657 "crus commune epithelium" 32525 "Theria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:22404255 "Gunz P, Ramsier M, Kuhrig M, Hublin JJ, Spoor F, The mammalian bony labyrinth reconsidered, introducing a comprehensive geometric morphometric approach. J Anat (2012)" "The bony labyrinth inside the petrous portion of the temporal bone houses the sense organs of hearing and balance. Characterized in therian mammals by three semicircular canals and a coiled cochlea (Luo et al., 2011) its morphology is highly conserved. Nevertheless, the detailed morphology varies even among closely related taxa and carries valuable functional, developmental and phylogenetic information (e.g. Spoor & Zonneveld, 1998; Schmelzle et al., 2007; Lebrun et al., 2010)." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0005658 "secondary palatal shelf epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21669855 "Leys SP, Nichols SA, Adams ED, Epithelia and integration in sponges. Integrative and Comparative Biology (2009)" bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0005659 "primary palate epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21669855 "Leys SP, Nichols SA, Adams ED, Epithelia and integration in sponges. Integrative and Comparative Biology (2009)" bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0005671 "greater sac mesothelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) Development of the coelomic cavity and mesenteries, p.159-164" bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0005674 "right lung cranial lobe endothelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001986, negated: false, taxon ID: 7742 - entity: UBERON:0002170, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0005675 "right lung caudal lobe endothelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001986, negated: false, taxon ID: 7742 - entity: UBERON:0002171, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0005676 "right lung accessory lobe endothelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001986, negated: false, taxon ID: 7742 - entity: UBERON:0004890, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0005678 "right lung cranial lobe segmental bronchus" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002170, negated: false, taxon ID: 40674 - entity: UBERON:0002184, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0005679 "right lung caudal lobe segmental bronchus" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002171, negated: false, taxon ID: 40674 - entity: UBERON:0002184, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0005680 "right lung accessory lobe segmental bronchus" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002184, negated: false, taxon ID: 40674 - entity: UBERON:0004890, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0005681 "right lung upper lobe bronchiole" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002170, negated: false, taxon ID: 40674 - entity: UBERON:0002186, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0005682 "right lung accessory lobe bronchiole" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002186, negated: false, taxon ID: 40674 - entity: UBERON:0004890, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0005688 "lens vesicle cavity" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1159/000076105 "Glass AS, Dahm R, The Zebrafish as a Model Organism for Eye Development. Ophthalmic Research (2004)" "In contrast to the situation in mammals and birds, the lens in zebrafish forms by delamination of cells from the lens placode. Therefore the lens is solid from its beginning, never passing through a stage as a hollow lens vesicle." bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0005704 "secondary palatal shelf mesenchyme" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0003104, negated: false, taxon ID: 7711 - entity: UBERON:0005619, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0005705 "primary palate mesenchyme" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0003104, negated: false, taxon ID: 7711 - entity: UBERON:0005620, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0005720 "hindbrain venous system" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-15 HOM:0000007 "historical homology" UBERON:0005721 "pronephric mesoderm" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:9806915 "Drummond IA, Majumdar A, Hentschel H, Elger M, Solnica-Krezel L, Schier AF, Neuhauss SCF, Stemple DL, Zwartkruis F, Rangini Z, Driever W, Fishman MC, Early development of the zebrafish pronephros and analysis of mutations affecting pronephric function. Development (1998)" "The teleost pronephros shares many essential features with the amphibian pronephros including its derivation from mesoderm associated with the coelom and the derivation of the glomerular blood supply from the medial dorsal aorta." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0005721 "pronephric mesoderm" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0127224411 "Vize PD, Woolf AS, Bard JBL, The kidney: From normal development to congenital disease (2003) p.23" "Pronephric mesoderm is a vertebrate feature. [curator]" bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0005728 "extraembryonic mesoderm" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:23050970 "Sheng G, Foley AC, Diversification and conservation of the extraembryonic tissues in mediating nutrient uptake during amniote development. Annals of the New York Academy of Sciences (2012)" "Although all amniotes start with a similar 'tool kit' of extraembryonic tissues, an enormous diversity of extraembryonic tissue formation has evolved to accommodate embryological and physiological constraints unique to their developmental programs. (...) All amniotes contain the following four extraembryonic components: the amnion, chorion, yolk sac, and allantois (Fig. 1C). Like the intraembryonic tissues, these extraembryonic tissues are composed of cells representing the three germ layers: ectoderm, mesoderm, and endoderm.(...) A comparative knowledge of these extraembryonic tissues and their role in nutrient uptake during development is required to fully appreciate the adaptive changes in placental mammals." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0005745 "optic foramen" 9347 "Eutheria" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:3127652 "Shoshani J, Mammalian phylogeny: comparison of morphological and molecular results. Molecular Biology and Evolution (1986) Table 3" "Optic foramen is a synapomorphic character in Eutheria. [curator]" bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0005760 "urorectal septum" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0721676678 "Romer AS, Vertebrate body (1970) p.388-89 and Figure 300" "In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below." bgee ANN 2013-08-28 HOM:0000007 "historical homology" UBERON:0005792 "nephric ridge" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:15376276 "Mobjerg N, Jespersen A, Wilkinson M, Morphology of the kidney in the West African caecilian, Geotrypetes seraphini (Amphibia, Gymnophiona, Caeciliidae). J Morphol (2004)" "The original vertebrate kidney, archinephros or holonephros, is believed to have covered the entire length of the coelom, consisting of paired segmental tubules with associated glomeruli, archinephrons (Price, 1897; Goodrich, 1958). Each tubule opened into the coelom through a ciliated nephrostome and was connected to the archinephric duct, which led to the exterior (Goodrich, 1958). Nephrons were present at some time in all body segments, but later were restricted to the trunk region of the animal. A tendency for the most anterior tubules to develop and function in early life, and for the more posterior tubules to develop and function later in life led to the differentiation into pro-, meso-, and metanephros (Goodrich, 1958)." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0005795 "embryonic uterus" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0000995" bgee HOM:0000007 "historical homology" UBERON:0005805 "dorsal aorta" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0005870 "olfactory pit" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:19590178 "Zeiske E, Bartsch P, Hansen A, Early ontogeny of the olfactory organ in a basal actinopterygian fish: polypterus. Brain Behav Evol (2009)" "Our results indicate the following features to be plesiomorphic actinopterygian character states: The primary olfactory pit (prospective olfactory cavity) is formed by invagination of the epidermal and the subepidermal layer (as in Acipenser and Xenopus). (...) We conclude that Acipenser and Xenopus exhibit the most widely distributed features among basal osteognathostomes and thus ancestral character states in the development of the olfactory organs." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0005870 "olfactory pit" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:19590178 "Zeiske E, Bartsch P, Hansen A, Early ontogeny of the olfactory organ in a basal actinopterygian fish: polypterus. Brain Behav Evol (2009)" "Our results indicate the following features to be plesiomorphic actinopterygian character states: The primary olfactory pit (prospective olfactory cavity) is formed by invagination of the epidermal and the subepidermal layer (as in Acipenser and Xenopus). (...) We conclude that Acipenser and Xenopus exhibit the most widely distributed features among basal osteognathostomes and thus ancestral character states in the development of the olfactory organs." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0005872 "1st arch pharyngeal cleft" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/j.semcdb.2010.01.022 "Grevellec A, Tucker AS, The pharyngeal pouches and clefts: development, evolution, structure and derivatives. Seminars in Cell and Developmental Biology (2010)" "In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0005876 "undifferentiated genital tubercle" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1242/dev.036830 "Seifert AW, Yamaguchi T, Cohn MJ, Functional and phylogenetic analysis shows that Fgf8 is a marker of genital induction in mammals but is not required for external genital development. Development (2009)" "In mammalian embryos, male and female external genitalia develop from the genital tubercle." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0005879 "pharyngeal cleft" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/j.semcdb.2010.01.022 "Grevellec A, Tucker AS, The pharyngeal pouches and clefts: development, evolution, structure and derivatives. Seminars in Cell and Developmental Biology (2010)" "In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0005882 "neural tube alar plate" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:10867629 "Butler AB, Chordate evolution and the origin of craniates: an old brain in a new head. Anat Rec (2000)" "During embryological development of the craniate brain, the hollow nerve tube comprises a ventrally situated basal plate and a dorsally situated alar plate (...) The alar plate constitutes the sensory-receptive part of the nervous system." bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0005893 "leg bone" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000978, negated: false, taxon ID: 32523 - entity: UBERON:0001474, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0005897 "manus bone" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001474, negated: false, taxon ID: 7742 - entity: UBERON:0002398, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0005899 "pes bone" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001474, negated: false, taxon ID: 7742 - entity: UBERON:0002387, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0005911 "endo-epithelium" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000925, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0005911|UBERON:0012275 "endo-epithelium|meso-epithelium" 6072 "Eumetazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000925|UBERON:0000926, negated: false, taxon ID: 6072" bgee HOM:0000007 "historical homology" UBERON:0005928 "external naris" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.257 and Figure 7.27" "In a tetrapod, the nasal sac has an external naris (homologous with the anterior naris of the fish) (...)." bgee ANN 2017-02-20 HOM:0000007 "historical homology" UBERON:0005928|UBERON:0013477 "external naris|blowhole" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1007/978-3-642-58612-5_1 "Klima M, Development of the Cetacean Nasal Skull. Advances in Anatomy, Embryology and Cell Biology (1999)" "The fact that the cetacean nose moved, in the course of evolution, from the tip of the rostrum up to the vertex of the head, is among the most perfect of adaptations to aquatic life. In this and many other special adaptations of their morphology and physiology, cetaceans surpass most primarily aquatic animals even though they themselves have developed from land mammals that breathe with lungs, and have only secondarily conquered the aquatic environment [...] Conclusive paleontological evidence shows the way in which the nasal openings were moved in the course of phylogeny (see Kellogg 1928; Slijper 1962; Gaskin 1976; Oelschlaeger 1978, 1987, 1990; Moore 1981). That this evolutionary process is repeated in a way during ontogeny became obvious through external observations on embryos and fetuses (Kuekenthal 1893). At the earliest embryonic stages the nasal openings are still situated at the rostral tip like those of land mammals; they are gradually shifted more and more towards the vertex of the head at the older stages." bgee ANN 2017-09-12 HOM:0000007 "historical homology" UBERON:0005928|UBERON:0013477 "external naris|blowhole" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1007/978-3-642-58612-5_1 "Klima M, Development of the Cetacean Nasal Skull. Advances in Anatomy, Embryology and Cell Biology (1999)" "The fact that the cetacean nose moved, in the course of evolution, from the tip of the rostrum up to the vertex of the head, is among the most perfect of adaptations to aquatic life. In this and many other special adaptations of their morphology and physiology, cetaceans surpass most primarily aquatic animals even though they themselves have developed from land mammals that breathe with lungs, and have only secondarily conquered the aquatic environment [...] Conclusive paleontological evidence shows the way in which the nasal openings were moved in the course of phylogeny (see Kellogg 1928; Slijper 1962; Gaskin 1976; Oelschlaeger 1978, 1987, 1990; Moore 1981). That this evolutionary process is repeated in a way during ontogeny became obvious through external observations on embryos and fetuses (Kuekenthal 1893). At the earliest embryonic stages the nasal openings are still situated at the rostral tip like those of land mammals; they are gradually shifted more and more towards the vertex of the head at the older stages." bgee ANN 2017-09-12 HOM:0000007 "historical homology" UBERON:0005928|UBERON:2001427 "external naris|anterior naris" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-00725283s05 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.257 and Figure 7.27" "In a tetrapod, the nasal sac has an external naris (homologous with the anterior naris of the fish) (...)." bgee ANN 2018-03-26 HOM:0000007 "historical homology" UBERON:0005946 "outflow tract of atrium" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002081, negated: false, taxon ID: 7742 - entity: UBERON:0004145, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0005967 "conotruncal ridge" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0878932504 "Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.478-482 and Figure 15.8" "The left and right bulbar ridges, together with the endocardial cushion, are structures involved in the formation of the chambers and valves of the heart. [curator]" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0005998 "tricuspid valve cusp" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23755108 "Jensen B, van den Berg G, van den Doel R, Oostra RJ, Wang T, Moorman AF, Development of the hearts of lizards and snakes and perspectives to cardiac evolution. PLoS One (2013)" "The mesenchyme of the atrioventricular canal is strikingly similar in amniotes with a large cushion dorsally and ventrally. This suggests that the fully formed left and right atrioventricular valve of the reptilian heart are homologous to the septal leaflet of the right-sided tricuspid valve and the aortic leaflet of the left-sided mitral valve of the mammalian heart." bgee ANN 2015-04-13 HOM:0000007 "historical homology" UBERON:0006002 "vitelline artery" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001040, negated: false, taxon ID: 32524 - entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0006067 "musculature of hindlimb zeugopod" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001015, negated: false, taxon ID: 7776 - entity: UBERON:0003823, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0006208 "auditory hillocks" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.420" "Mammals have a third type of tympanic ear. An external flap, the auricle or pinna, helps funnel sound waves down the external acoustic meatus to the tympanic membrane." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0006212 "bulbo-ventricular groove" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:17064678 "Stadtfeld M, Ye M, Graf T, Identification of interventricular septum precursor cells in the mouse embryo. Dev Biol (2007)" "The bulbo-ventricular groove contains a population of cardiomyocytes that migrate and contribute to the interventricular septum in mouse. Interventricular septum is a non-homologous amniote structure (birds and mammals) involved in the vertebrate 4-chambered heart formation. [curator]" bgee ANN 2013-10-09 HOM:0000007 "historical homology" UBERON:0006217 "cloacal membrane" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572" "A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0006220 "diencephalic part of interventricular foramen" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0006222 "future diencephalon" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001894 - UBERON:0001894 - UBERON:0001894" bgee HOM:0000007 "historical homology" UBERON:0006226 "endolymphatic appendage" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:12168621 "Jeffery JE, Bininda-Emonds OR, Coates MI, Richardson MK, Analyzing evolutionary patterns in amniote embryonic development. Evol Dev (2002)" "Endolymphatic appendage is one of the vertebrate developmental events. [curator]" bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0006233 "female genital tubercle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/j.ydbio.2008.03.017 "Seifert AW, Harfe BD, Cohn MJ, Cell lineage analysis demonstrates an endodermal origin of the distal urethra and perineum. Developmental Biology (2008)" "In both male and female mammalian embryos, development of the external genitalia begins with the emergence of the paired genital swellings immediately above the cloaca (see Perriton et al. 2002 for a detailed description of normal external genitalia development in mouse). These swellings fuse medially and give rise to the bipotential genital tubercle, which can be masculinized to form the penis or feminized to form the clitoris. As the genital tubercle grows out, the ventral side of the cloacal endoderm forms a bilaminar urethral plate that extends into the genital tubercle, and this structure later cavitates in a proximal to distal direction to form the urethral tube (Hynes and Fraher, 2004a; Perriton et al., 2002)." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0006235 "foregut-midgut junction" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0521617147 "Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut." bgee AUC 2013-05-15 HOM:0000007 "historical homology" UBERON:0006238 "future brain" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0008823" bgee HOM:0000007 "historical homology" UBERON:0006238 "future brain" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0000955 - UBERON:0000955" bgee HOM:0000007 "historical homology" UBERON:0006239 "future central tendon" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000043, negated: false, taxon ID: 7742 - entity: UBERON:0006670, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0006239 "future central tendon" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0006670" bgee HOM:0000007 "historical homology" UBERON:0006240 "future forebrain" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001890" bgee HOM:0000007 "historical homology" UBERON:0006253 "embryonic intraretinal space" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina." bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0006257 "laryngotracheal groove" 314146 "Euarchontoglires" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:15817505 "Warburton D, Bellusci S, De Langhe S, Del Moral PM, Fleury V, Mailleux A, Tefft D, Unbekandt M, Wang K, Shi W, Molecular mechanisms of early lung specification and branching morphogenesis. Pediatric Research (2005)" "Lung development begins with the appearance of the laryngotracheal groove, which is a small diverticulum that arises from the floor of the primitive pharynx at E9 in mouse and 4 wk in human." bgee ANN 2015-03-11 HOM:0000007 "historical homology" UBERON:0006259 "lens pit" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 Figure 12-27" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens. The lens pit is an intermediate stage between the lens placode and the lens vesicle." bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0006260 "lingual swellings" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1046/j.1469-7580.2002.00073.x "Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002)" "Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0006261 "male genital tubercle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/j.ydbio.2008.03.017 "Seifert AW, Harfe BD, Cohn MJ, Cell lineage analysis demonstrates an endodermal origin of the distal urethra and perineum. Developmental Biology (2008)" "In both male and female mammalian embryos, development of the external genitalia begins with the emergence of the paired genital swellings immediately above the cloaca (see Perriton et al. 2002 for a detailed description of normal external genitalia development in mouse). These swellings fuse medially and give rise to the bipotential genital tubercle, which can be masculinized to form the penis or feminized to form the clitoris. As the genital tubercle grows out, the ventral side of the cloacal endoderm forms a bilaminar urethral plate that extends into the genital tubercle, and this structure later cavitates in a proximal to distal direction to form the urethral tube (Hynes and Fraher, 2004a; Perriton et al., 2002)." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0006264 "mouth-foregut junction" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0521617147 "Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut." bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0006265 "mural trophectoderm" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0721676685 "Romer AS, Parsons T, Vertebrate body (1977) p.105-106" "(...) the trophoblast develops rapidly so that contact may be made with the maternal uterine tissues when conditions are appropriate. We have here an excellent example of an embryonic adaptation, the development of a structure never present in either adult or embryo of 'lower' vertebrates." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0006267 "notochordal plate" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...)." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0006268 "notochordal process" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...)." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0006270 "optic pit" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1146/annurev.cellbio.17.1.255 "Chow RL and Lang RA, Early eye development in vertebrates. Annual Review of Cell and Developmental Biology (2001)" "The first morphological sign of eye development in vertebrates is the bilateral evagination of diencephalon in the early neurula. In mammals, this is marked by the appearance of the optic pit, whereas in fish and amphibians a bulging of the optic primordia is observed. Continued evagination of the optic primordia leads to the formation of the optic vesicles." bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0006270 "optic pit" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles" bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0006272 "oronasal cavity" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1098/rstb.2001.0976 "Kuratani S, Nobusada Y, Horigome N, Shigetani Y, Embryology of the lamprey and evolution of the vertebrate jaw: insights from molecular and developmental perspectives. Philosophical transactions of the Royal Society of London, Series B, Biological sciences (2001) Figure 9" "Comparaison between lamprey and gnathostome embryos. (...) No direct homologies can be established in the oral parts between gnathostomes and lampreys." bgee ANN 2013-06-26 HOM:0000007 "historical homology" UBERON:0006273 "otic pit" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413 and Figure 12-14" "The inner ear develops embryonically in all vertebrates as an invagination of the ectodermal otic placode to form an otic vesicle. The otic pit is an intermediate stage between the otic placode and otic vesicle." bgee ANN 2013-06-25 HOM:0000007 "historical homology" UBERON:0006275 "pericardio-peritoneal canal" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) Development of the coelomic cavity and mesenteries, p.159-164 and Figure 4-32" bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0006277 "pleuropericardial canals" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) Development of the coelomic cavity and mesenteries, p.159-164" bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0006278 "pleuropericardial folds" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0471090588 "Hildebrand M, Analysis of vertebrate structure (1983) p.205-206" "The heart [of other tetrapods than amphibian] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes." bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0006279 "pleuroperitoneal canal" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) Development of the coelomic cavity and mesenteries, p.159-164 and Figure 4-32" bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0006280 "polar trophectoderm" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0721676685 "Romer AS, Parsons TS, Vertebrate body (1977) p.105-106" "(...) the trophoblast develops rapidly so that contact may be made with the maternal uterine tissues when conditions are appropriate. We have here an excellent example of an embryonic adaptation, the development of a structure never present in either adult or embryo of 'lower' vertebrates." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0006283 "future cardiac ventricle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0002082" bgee HOM:0000007 "historical homology" UBERON:0006284 "early prosencephalic vesicle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500" "The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0006301 "telencephalic part of interventricular foramen" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0006304 "future trigeminal ganglion" NOT 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001675" bgee HOM:0000007 "historical homology" UBERON:0006304 "future trigeminal ganglion" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001675 - UBERON:0003070 - UBERON:0003070" bgee HOM:0000007 "historical homology" UBERON:0006305 "tunica vasculosa lentis" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/j.semcdb.2007.08.014 "Beebe DC, Maintening transparency: A review of the developmental physiology and pathophysiology of two avascular tissues. Seminars in Cell and Developmental Biology (2008) Fig.1" "Soon after it forms, the mammalian lens becomes invested with a network of capillaries. (...) The capillary network on the posterior of the lens is the tunica vasculosa lentis (TVL). (...) the fetal vasculature plays only a minor role in lens development. This observation is consistent with the absence of capillaries around the lenses of most non-mammalian vertebrates. It also raises the question of why the fetal vasculature appeared in mammalian evolution." bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0006307 "urogenital membrane" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0878932504 "Gilbert SF, Developmental Biology (2006), The digestive tube and its derivatives, p.495-496" bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0006320 "inferior oblique extraocular muscle" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.331" "The ability to rotate the eyeball is common to all vertebrates with well-developed eyes, regardless of the habitat in which they live, so these [extrinsic ocular] muscles tend to be conservative. They change little during the course of evolution." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0006321 "superior oblique extraocular muscle" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.331" "The ability to rotate the eyeball is common to all vertebrates with well-developed eyes, regardless of the habitat in which they live, so these [extrinsic ocular] muscles tend to be conservative. They change little during the course of evolution." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0006322 "inferior rectus extraocular muscle" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.331" "The ability to rotate the eyeball is common to all vertebrates with well-developed eyes, regardless of the habitat in which they live, so these [extrinsic ocular] muscles tend to be conservative. They change little during the course of evolution." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0006323 "superior rectus extraocular muscle" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.331" "The ability to rotate the eyeball is common to all vertebrates with well-developed eyes, regardless of the habitat in which they live, so these [extrinsic ocular] muscles tend to be conservative. They change little during the course of evolution." bgee ANN 2013-09-23 HOM:0000007 "historical homology" UBERON:0006347 "communicating artery" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0006349 "epigastric artery" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0006635, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0006355 "superior vesical vein" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000056, negated: false, taxon ID: 32524 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0006356 "epigastric vein" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0006635, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0006435 "os penis" 32524 "Amniota" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000989, negated: false, taxon ID: 32524 - entity: UBERON:0001474, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0006435 "os penis" NOT 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000989, negated: true, taxon ID: 32524 - entity: UBERON:0001474, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0006435 "os penis" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000989, negated: false, taxon ID: 40674 - entity: UBERON:0001474, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0006440 "os clitoris" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001299|UBERON:0002411|UBERON:0004713, negated: false, taxon ID: 40674 - entity: UBERON:0001474, negated: false, taxon ID: 7742 - entity: UBERON:0002411, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0006544 "kidney vasculature" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208 - entity: UBERON:0002113, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0006562 "pharynx" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030259821 "Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.204" "Pharynx is cited as a common feature to Bilateria. [curator]" bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0006591 "transformed artery" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001637" bgee HOM:0000007 "historical homology" UBERON:0006592 "transformed vein" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001638" bgee HOM:0000007 "historical homology" UBERON:0006595 "presumptive endoderm" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0000925" bgee HOM:0000007 "historical homology" UBERON:0006595|UBERON:0006603 "presumptive endoderm|presumptive mesoderm" 6072 "Eumetazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0000925|UBERON:0000926 - UBERON:0000925|UBERON:0000926" bgee HOM:0000007 "historical homology" UBERON:0006596 "presumptive blood" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0000178 - UBERON:0000178" bgee HOM:0000007 "historical homology" UBERON:0006597 "quadrate bone" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1017/S0022215100009087 "Gerrie J, The phylogeny of the mammalian tympanic cavity and auditory ossicles. The Journal of Laryngology and Otology (1948)" "According to this theory [Reichert-Gaupp theory], the mammalian stapes is derived from the reptilian columella, the incus from the quadrate and the malleus from the articular (...)." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0006599 "presumptive hypochord" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0003058 - UBERON:0003058" bgee HOM:0000007 "historical homology" UBERON:0006601 "presumptive ectoderm" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0000924" bgee HOM:0000007 "historical homology" UBERON:0006603 "presumptive mesoderm" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0000926 - UBERON:0000926" bgee HOM:0000007 "historical homology" UBERON:0006603 "presumptive mesoderm" NOT 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0000926" bgee HOM:0000007 "historical homology" UBERON:0006616 "right external ear" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000468, negated: false, taxon ID: 33208 - entity: UBERON:0001691, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0006616 "right external ear" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000468, negated: false, taxon ID: 33208 - entity: UBERON:0001691, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0006617 "left external ear" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000468, negated: false, taxon ID: 33208 - entity: UBERON:0001691, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0006617 "left external ear" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000468, negated: false, taxon ID: 33208 - entity: UBERON:0001691, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0006635 "anterior abdominal wall" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1186/1742-9994-8-4 "Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011)" "The plesiomorphic segmental organization of the axial musculature underwent stepwise reorganization during the evolution of tetrapods.(...) The hypaxial musculature consists of the abdominal wall muscles and a subvertebral muscle mass, which is associated with the ventral aspect of the vertebrae and ribs." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0006643 "tunica albuginea of testis" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1387/ijdb.072470fc "Carmona FD, Lupianez DG, Martin JE, Burgos M, Jimenez R, Zurita F, The spatio-temporal pattern of testis organogenesis in mammals - insights from the mole. The International Journal of Developmental Biology (2009)" "The tunica albuginea testis is the major component of the capsule of mammalian testes. (...) Our results from studying the mole provide evidence that the spatio-temporal pattern of testis development is not perfectly conserved in mammals, since we found differences with respect to the mouse testis organogenesis. This fact is even more significant when we consider that, apart from the mouse, the mole is probably the one of the best-known mammalian species in terms of the genetic control of testis development, implying that more peculiarities would be found if more species were investigated." bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0006670 "central tendon of diaphragm" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1016/j.resp.2006.06.003 "Brainerd EL, Owerkowicz T, Functional morphology and evolution of aspiration breathing in tetrapods. Respiratory physiology and neurobiology (2006)" "In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm's apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs." bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0006678 "foramen secundum" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0006678 "foramen secundum" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21513818 "Dzialowski EM, Sirsat T, van der Sterren S, Villamor E, Prenatal cardiovascular shunts in amniotic vertebrates. Respir Physiol Neurobiol (2011)" "During amniotic vertebrate development, the embryo and fetus employ a number of cardiovascular shunts. These shunts provide a right-to-left shunt of blood and are essential components of embryonic life ensuring proper blood circulation to developing organs and fetal gas exchanger, as well as bypassing the pulmonary circuit and the unventilated, fluid filled lungs." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0006686 "spinal vein" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001130, negated: false, taxon ID: 7742 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0006686 "spinal vein" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001130, negated: false, taxon ID: 32523 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0006691 "tentorium cerebelli" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0006694 "cerebellum vasculature" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002037, negated: false, taxon ID: 7776 - entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0006699 "foramen cecum of tongue" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1210/er.2003-0028 "De Felice M, Di Lauro R, Thyroid development and its disorders: genetics and molecular mechanisms. Endocrine Reviews (2004)" "By E10, the thyroid primordium appears as a flask-like structure with a narrow neck that rapidly becomes a diverticulum. A small hole at the site of origin in the pharyngeal floor (the foramen cecum) is the remnant of the anlage, connected with the migrating thyroid primordium by a narrow channel (the thyroglossal duct)." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0006722 "manubrium of malleus" NOT 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "from classical comparative anatomy and fossil data it had been suggested that the retroarticular process was homologous to the manubrium of the malleus (Kermack & Musset, 1983; Allin & Hopson, 1992). The fate-mapping experiments, however, argue strongly against this and suggest that the manubrium is a novel mammalian structure without a homologue in birds and reptiles." bgee ANN 2015-04-02 HOM:0000007 "historical homology" UBERON:0006722 "manubrium of malleus" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "from classical comparative anatomy and fossil data it had been suggested that the retroarticular process was homologous to the manubrium of the malleus (Kermack & Musset, 1983; Allin & Hopson, 1992). The fate-mapping experiments, however, argue strongly against this and suggest that the manubrium is a novel mammalian structure without a homologue in birds and reptiles." bgee ANN 2015-04-02 HOM:0000007 "historical homology" UBERON:0006726 "outer canthus" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.430-431" "Balancing the inner canthus (medial canthus), a lateral canthus (outer canthus) should be present in the eye of vertebrates. [curator]" bgee ANN 2013-06-24 HOM:0000007 "historical homology" UBERON:0006756 "median lingual swelling" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1046/j.1469-7580.2002.00073.x "Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002)" "Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0006757 "lateral lingual swelling" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1046/j.1469-7580.2002.00073.x "Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002)" "Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle." bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0006849 "scapula" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.330-333 and Figure 9.18" bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0006858 "adrenal/interrenal gland" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:9405124 "Grassi Milano E, Basari F, Chimenti C, Adrenocortical and adrenomedullary homologs in eight species of adult and developing teleosts: morphology, histology, and immunohistochemistry. Gen Comp Endocrinol (1997)" "Teleost fish have functional equivalents of the adrenal gland of tetrapod vertebrates, frequently called the adrenal homolog (Chester Jones and Mosley, 1980) or adrenal gland for short (Nandi, 1962; Butler, 1973; Hanke and Kloas, 1995). This organ, however, unlike that of tetrapods, is not a discrete organ, nor is it located on the renal surface or in the peritoneal cavity; rather it resides within the kidney. The adrenal gland of teleosts, however, is homologous to that of tetrapods and is composed of the same two tissues, which differ in embryological origin and secrete different hormones (Hanke and Kloas, 1995)." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0006860 "swim bladder" 7898 "Actinopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210" "In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ." bgee ANN 2015-03-11 HOM:0000007 "historical homology" UBERON:0006866 "terminal part of digestive tract" NOT 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1038/nature07309 "Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)" "A through gut could have been present in the last common ancestor of all bilaterians and the anus could have been lost independently in both Acoela and Nemertodermatida lineages. The expression of hindgut markers at the posterior pole in C. longifissura would therefore be remnants of a posterior anal opening. The more parsimonious explanation, however, is to assume that the metazoan mouth evolved first and the anal opening arose independently through co-option of hindgut genes in posterior domains at the ectodermal-endodermal interface." bgee ANN 2013-07-09 HOM:0000007 "historical homology" UBERON:0006870 "endostyle" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:15592682 "Kluge B, Renault N, Rohr KB, Anatomical and molecular reinvestigation of lamprey endostyle development provides new insight into thyroid gland evolution. Development genes and evolution (2005)" "The thyroid gland of vertebrates is considered to be homologous to the endostyle of non-vertebrate chordates (cephalochordates, urochordates), a key character for understanding the origin and evolution of the chordate body plan." bgee ANN 2018-03-27 HOM:0000007 "historical homology" UBERON:0006877 "vasculature of liver" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208 - entity: UBERON:0002107, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0006913 "lip epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001833, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0006937 "inner ear epithelium" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001846, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0006937 "inner ear epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001846, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0006937 "inner ear epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001846, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0006938 "pinna surface epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001757, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0006955 "uterine epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000995, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0006964 "pars distalis of adenohypophysis" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5" "Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. The adenohypophysis forms a thick pars distalis and, in most vertebrates, a pars intermedia, which lies between the pars distalis and the neurohypophysis." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0006966 "coronary capillary" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 7742 - entity: UBERON:0000948|UBERON:0002376, negated: false, taxon ID: 7742 - entity: UBERON:0001982, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0006966 "coronary capillary" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 8782 - entity: UBERON:0001982, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0006966 "coronary capillary" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 40674 - entity: UBERON:0001982, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0006973 "protonephridium" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000033 "traceable author statement" PMID:22973977 "Baeumler N, Haszprunar G, Ruthensteiner B, Development of the excretory system in a polyplacophoran mollusc: stages in metanephridial system development. Front Zool (2012)" "Two types of excretory systems, protonephridia and metanephridial systems are common among bilaterians. The homology of protonephridia of lophotrochozoan taxa has been widely accepted." bgee ANN 2015-01-28 HOM:0000007 "historical homology" UBERON:0007005 "cardiogenic splanchnic mesoderm" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481" "While bird and mammal 4-chambered hearts arose independently from different groups of reptilian ancestor, the vertebrate chambered heart is commonly considered arising from fishes and then defined as an historical homology relationship. However uncertainty remains on the origin of the heart substructures and tissues. [curator]" bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0007010 "cleaving embryo" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000107, negated: false, taxon ID: 33213 - entity: UBERON:0000468, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0007026 "presumptive gut" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001555" bgee HOM:0000007 "historical homology" UBERON:0007026 "presumptive gut" NOT 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001555 - UBERON:0001555 - UBERON:0001555" bgee HOM:0000007 "historical homology" UBERON:0007097 "chordo neural hinge" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" DOI:10.1002/dvdy.20017 "Liu C, Knezevic V, Mackem S, Ventral tail bud mesenchyme is a signaling for tail paraxial mesoderm induction. Developmental Dynamics (2004)" "Although there is mounting evidence showing the comparability of events and formation of different nascent tissue types during gastrulation and tail development, recent work also suggests the presence of an ongoing stem cell population capable of contributing to multiple tissue types in the tail of several different vertebrates, situated in the chordoneural hinge region of the tail bud. It would seem likely that secondary signaling centers regulate the fate to be adopted by such pluripotent progenitors." bgee ANN 2013-06-07 HOM:0000007 "historical homology" UBERON:0007097 "chordo neural hinge" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1002/dvdy.20017 "Liu C, Knezevic V, Mackem S, Ventral tail bud mesenchyme is a signaling for tail paraxial mesoderm induction. Developmental Dynamics (2004)" "Although there is mounting evidence showing the comparability of events and formation of different nascent tissue types during gastrulation and tail development, recent work also suggests the presence of an ongoing stem cell population capable of contributing to multiple tissue types in the tail of several different vertebrates, situated in the chordoneural hinge region of the tail bud. It would seem likely that secondary signaling centers regulate the fate to be adopted by such pluripotent progenitors." bgee ANN 2013-06-07 HOM:0000007 "historical homology" UBERON:0007097 "chordo neural hinge" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1002/dvdy.20017 "Liu C, Knezevic V, Mackem S, Ventral tail bud mesenchyme is a signaling for tail paraxial mesoderm induction. Developmental Dynamics (2004)" "Although there is mounting evidence showing the comparability of events and formation of different nascent tissue types during gastrulation and tail development, recent work also suggests the presence of an ongoing stem cell population capable of contributing to multiple tissue types in the tail of several different vertebrates, situated in the chordoneural hinge region of the tail bud. It would seem likely that secondary signaling centers regulate the fate to be adopted by such pluripotent progenitors." bgee ANN 2013-06-07 HOM:0000007 "historical homology" UBERON:0007100 "primary circulatory organ" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:17223594 "Davidson B, Ciona intestinalis as a model for cardiac development. Ciona intestinalis as a model for cardiac development. Semin Cell Dev Biol (2007)" "In older juveniles (approximately 2 weeks after metamorphosis) the Ciona heart tube begins to fold into its characteristic V-shape (BD, personal observations). This shape change may be caused by the growth of the heart tube in length while the two ends remain at a relatively fixed distance [28]. It is possible that the bending is also influenced by the spiral orientation of the cardiac myofibers. Whether this event bears any homology to cardiac looping in vertebrates remains purely speculative. A detailed characterization of the mechanistic and genetic basis for heart bending in Ciona is required to resolve this issue." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0007100 "primary circulatory organ" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:23809110 "Monahan-Earley R, Dvorak AM, Aird WC, Evolutionary origins of the blood vascular system and endothelium. J Thromb Haemost (2013)" "There is an interesting body of the literature debating the degree to which the drosophila and vertebrate hearts are homologous [7, 12, 64, 65]. An important concept is that homology can apply to different levels of organization (e.g. genetic, molecular, cellular, tissue structure, function) [3, 7].30 For example, the drosophila and vertebrate hearts are hardly homologous in three-dimensional structure (at least in the adult stages)." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0007122 "pharyngeal pouch 1" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/j.semcdb.2010.01.022 "Grevellec A, Tucker AS, The pharyngeal pouches and clefts: development, evolution, structure and derivatives. Seminars in Cell and Developmental Biology (2010)" "In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft." bgee AUC 2013-03-27 HOM:0000007 "historical homology" UBERON:0007144 "embryonic post-anal tail" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0002533" bgee HOM:0000007 "historical homology" UBERON:0007145 "dome of diaphragm" NOT 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1016/j.resp.2006.06.003 "Brainerd EL, Owerkowicz T, Functional morphology and evolution of aspiration breathing in tetrapods. Respiratory physiology and neurobiology (2006)" "Crocodylians, mammals and turtles have all evolved accessory respiratory muscles that reduce or eliminate their reliance on costal aspiration. These are all sometimes called diaphragm muscles, presumably by analogy with the mammalian diaphragm muscle, but they are not homologous structures." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0007145 "dome of diaphragm" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0471384618 "Colbert EH, Evolution of the vertebrates: a history of the backboned animals through time (2001) p.278" "The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...)." bgee ANN 2015-03-30 HOM:0000007 "historical homology" UBERON:0007151 "mitral valve leaflet" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1161/CIRCRESAHA.109.201566 "Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009)" "The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0007174 "medial border of scapula" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:20136669 "Valasek P, Theis S, Krejci E, Grim M, Maina F, Shwartz Y, Otto A, Huang R, Patel K, Somitic origin of the medial border of the mammalian scapula and its homology to the avian scapula blade. J Anat (2010)" "The scapula is the main skeletal element of the pectoral girdle allowing muscular fixation of the forelimb to the axial skeleton. The vertebrate limb skeleton has traditionally been considered to develop from the lateral plate mesoderm, whereas the musculature originates from the axial somites. However, in birds, the scapular blade has been shown to develop from the somites. We investigated whether a somitic contribution was also present in the mammalian scapula. Using genetic lineage-tracing techniques, we show that the medial border of the mammalian scapula develops from somitic cells. (...) Our results establish the avian scapular blade and medial border of the mammalian scapula as homologous structures as they share the same developmental origin." bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0007174|UBERON:1500000 "medial border of scapula|scapular blade" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:20136669 "Valasek P, Theis S, Krejci E, Grim M, Maina F, Shwartz Y, Otto A, Huang R, Patel K, Somitic origin of the medial border of the mammalian scapula and its homology to the avian scapula blade. J Anat (2010)" "The scapula is the main skeletal element of the pectoral girdle allowing muscular fixation of the forelimb to the axial skeleton. The vertebrate limb skeleton has traditionally been considered to develop from the lateral plate mesoderm, whereas the musculature originates from the axial somites. However, in birds, the scapular blade has been shown to develop from the somites. We investigated whether a somitic contribution was also present in the mammalian scapula. Using genetic lineage-tracing techniques, we show that the medial border of the mammalian scapula develops from somitic cells. (...) Our results establish the avian scapular blade and medial border of the mammalian scapula as homologous structures as they share the same developmental origin." bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:0007185 "pericardio-peritoneal canal mesothelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) Development of the coelomic cavity and mesenteries, p.159-164 and Figure 4-32" bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0007186 "pericardial visceral mesothelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1152/ajpheart.00967.2007 "Joebsis PD, Ashikaga H, Wen H, Rothstein EC, Horvath KA, McVeigh ER, Balaban RS, The visceral pericardium: macromolecular structure and contribution to passive mechanical properties of the left ventricle. American journal of physiology, Heart and circulatory physiology (2007)" "Found in all vertebrates, the VP (visceral pericardium) is also known as the cardiac epimysium. This outermost layer of the epicardium consists of a thin layer of mesothelial cells over a dense network of collagen and elastin fibers." bgee ANN 2013-06-21 HOM:0000007 "historical homology" UBERON:0007213 "mesenchyme derived from head neural crest" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0003099, negated: false, taxon ID: 89593 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0007214 "mesenchyme derived from trunk neural crest" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0003083, negated: false, taxon ID: 89593 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0007237 "1st arch mandibular component" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1046/j.1469-7580.2001.19910133.x "Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0007238 "1st arch maxillary component" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1046/j.1469-7580.2001.19910133.x "Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0007269 "pectoral appendage musculature" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001015, negated: false, taxon ID: 7776 - entity: UBERON:0004710, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0007269 "pectoral appendage musculature" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001015, negated: false, taxon ID: 7776 - entity: UBERON:0004710, negated: false, taxon ID: 117571" bgee HOM:0000007 "historical homology" UBERON:0007277 "presumptive hindbrain" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0002028 - UBERON:0002028 - UBERON:0002028" bgee HOM:0000007 "historical homology" UBERON:0007278 "presumptive sinus venosus" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0002063 - UBERON:0002063" bgee HOM:0000007 "historical homology" UBERON:0007279 "presumptive atrioventricular canal" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0002087" bgee HOM:0000007 "historical homology" UBERON:0007280 "presumptive endocardium" NOT 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0002165" bgee HOM:0000007 "historical homology" UBERON:0007280 "presumptive endocardium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0002165" bgee HOM:0000007 "historical homology" UBERON:0007281 "presumptive midbrain hindbrain boundary" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0003052" bgee HOM:0000007 "historical homology" UBERON:0007282 "presumptive segmental plate" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0003059" bgee HOM:0000007 "historical homology" UBERON:0007283 "presumptive shield" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0003062" bgee HOM:0000007 "historical homology" UBERON:0007283 "presumptive shield" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0003062" bgee HOM:0000007 "historical homology" UBERON:0007284 "presumptive neural plate" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0003075 - UBERON:0003075" bgee HOM:0000007 "historical homology" UBERON:0007285 "presumptive paraxial mesoderm" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0003077" bgee HOM:0000007 "historical homology" UBERON:0007286 "presumptive floor plate" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0003079" bgee HOM:0000007 "historical homology" UBERON:0007297 "presumptive pronephric mesoderm" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0005721 - UBERON:0005721" bgee HOM:0000007 "historical homology" UBERON:0007299 "choroid plexus of tectal ventricle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001886, negated: false, taxon ID: 7711 - entity: UBERON:0002289, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0007300 "pectoral appendage blood vessel" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0004710, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0007300 "pectoral appendage blood vessel" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0004710, negated: false, taxon ID: 117571" bgee HOM:0000007 "historical homology" UBERON:0007302 "pectoral appendage vasculature" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208 - entity: UBERON:0004710, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0007302 "pectoral appendage vasculature" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208 - entity: UBERON:0004710, negated: false, taxon ID: 117571" bgee HOM:0000007 "historical homology" UBERON:0007303 "pharyngeal vasculature" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001042, negated: false, taxon ID: 7711 - entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0007303 "pharyngeal vasculature" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001042, negated: false, taxon ID: 7742 - entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0007329 "pancreatic duct" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1016/j.ydbio.2005.04.035 "Yee NS, Lorent K, Pack M, Exocrine pancreas development in zebrafish. Developmental Biology (2005)" "These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium." bgee ANN 2013-08-12 HOM:0000007 "historical homology" UBERON:0007350 "arcopallium" 8782 "Aves" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" DOI:10.1098/rstb.2015.0060 "Karten HJ, Vertebrate brains and evolutionary connectomics: on the origins of the mammalian 'neocortex'. Philos Trans R Soc Lond B Biol Sci (2015)" "As noted in Zeier & Karten [14], the region of the arcopallium in birds resembles an isolated zone of cells corresponding to those of layers 5 and 6 of mammalian cortex. These cells are clearly connected to the populations of cells of layers 2, 3 and 4, but rely on axonal recurrence over moderately lengthy distances, with only scant prospects of the complex dendrodendritic connections of the mammalian cortex. While this might imply a longer time delay in feedback loops owing to axonal conduction times, there is no evidence that it results in laggardly behavioural performance within the auditory or visual systems of birds when compared with comparable pathways in mammals." bgee ANN 2017-05-16 HOM:0000007 "historical homology" UBERON:0007350 "arcopallium" 8782 "Aves" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1098/rstb.2015.0060 "Karten HJ, Vertebrate brains and evolutionary connectomics: on the origins of the mammalian 'neocortex'. Philos Trans R Soc Lond B Biol Sci (2015)" "As noted in Zeier & Karten [14], the region of the arcopallium in birds resembles an isolated zone of cells corresponding to those of layers 5 and 6 of mammalian cortex. These cells are clearly connected to the populations of cells of layers 2, 3 and 4, but rely on axonal recurrence over moderately lengthy distances, with only scant prospects of the complex dendrodendritic connections of the mammalian cortex. While this might imply a longer time delay in feedback loops owing to axonal conduction times, there is no evidence that it results in laggardly behavioural performance within the auditory or visual systems of birds when compared with comparable pathways in mammals." bgee ANN 2017-05-16 HOM:0000007 "historical homology" UBERON:0007350 "arcopallium" 8782 "Aves" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1098/rstb.2015.0060 "Karten HJ, Vertebrate brains and evolutionary connectomics: on the origins of the mammalian 'neocortex'. Philos Trans R Soc Lond B Biol Sci (2015)" "As noted in Zeier & Karten [14], the region of the arcopallium in birds resembles an isolated zone of cells corresponding to those of layers 5 and 6 of mammalian cortex. These cells are clearly connected to the populations of cells of layers 2, 3 and 4, but rely on axonal recurrence over moderately lengthy distances, with only scant prospects of the complex dendrodendritic connections of the mammalian cortex. While this might imply a longer time delay in feedback loops owing to axonal conduction times, there is no evidence that it results in laggardly behavioural performance within the auditory or visual systems of birds when compared with comparable pathways in mammals." bgee ANN 2017-05-16 HOM:0000007 "historical homology" UBERON:0007376 "outer epithelium" 33208 "Metazoa" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72" "(...) outer epithelia in all metazoan animals are homologous." bgee ANN 2013-07-17 HOM:0000007 "historical homology" UBERON:0007385 "pectoral appendage lymph vessel" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001473, negated: false, taxon ID: 32523 - entity: UBERON:0004710, negated: false, taxon ID: 117571" bgee HOM:0000007 "historical homology" UBERON:0007390 "pectoral appendage cartilage tissue" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002418, negated: false, taxon ID: 7742 - entity: UBERON:0004710, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0007390 "pectoral appendage cartilage tissue" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002418, negated: false, taxon ID: 7742 - entity: UBERON:0004710, negated: false, taxon ID: 117571" bgee HOM:0000007 "historical homology" UBERON:0007645 "future meninx" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0002360" bgee HOM:0000007 "historical homology" UBERON:0007647 "ectomeninx" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0002363" bgee HOM:0000007 "historical homology" UBERON:0007681 "facial neural crest" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0007689 "thyroid diverticulum" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0002046 - UBERON:0002046" bgee HOM:0000007 "historical homology" UBERON:0007689 "thyroid diverticulum" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0002046" bgee HOM:0000007 "historical homology" UBERON:0007690 "early pharyngeal endoderm" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1046/j.1469-7580.2001.19910133.x "Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0007778 "umbilical artery endothelium" 9347 "Eutheria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001310, negated: false, taxon ID: 9347 - entity: UBERON:0001986, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0007812 "post-anal tail" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0002533" bgee HOM:0000007 "historical homology" UBERON:0007830 "pelvic girdle bone/zone" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001474, negated: false, taxon ID: 7742 - entity: UBERON:0007832, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0007831 "pectoral girdle skeleton" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" PMID:19324642 "Zhu M, Yu X, Stem sarcopterygians have primitive polybasal fin articulation. Biology letters (2009)" "Here we describe three-dimensionally preserved shoulder girdles of two stem sarcopterygians (Psarolepis and Achoania) from the Lower Devonian of Yunnan, which demonstrate that stem sarcopterygians have polybasal pectoral fin articulation as in basal actinopterygians. (...) The finding demonstrates that stem sarcopterygians have polybasal pectoral fin articulation as in chondrichthyans and basal actinopterygians such as Mimia, paddlefish and bowfins (figure 2). Consequently, the origin of the monobasal sarcopterygian fin must have occurred at a point crownward to Psarolepis and Achoania, instead of that at the split between sarcopterygians and actinopterygians." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0007832 "pelvic girdle skeleton" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333" "The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin." bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0007997 "sesamoid bone of manus" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001479, negated: false, taxon ID: 117571 - entity: UBERON:0002398, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0008000 "sesamoid bone of pes" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001479, negated: false, taxon ID: 117571 - entity: UBERON:0002387, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0008188 "tendon of biceps brachii" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000043, negated: false, taxon ID: 7742 - entity: UBERON:0001507, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0008192 "tendon of triceps brachii" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000043, negated: false, taxon ID: 7742 - entity: UBERON:0001509, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0008201 "scute" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1111/j.1469-7580.2008.01043.x "Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)" "Available evidence clearly supports osteoderms as plesiomorphic for tetrapods, evolving from the ancestral cosmoid scale following the loss of odontogenic tissues and the ramifying pore-canal system." bgee ANN 2013-07-17 HOM:0000007 "historical homology" UBERON:0008255 "right clavicle" 32440 "Chondrostei" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001105, negated: false, taxon ID: 32440 - entity: UBERON:0002091, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0008255 "right clavicle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001105, negated: false, taxon ID: 40674 - entity: UBERON:0002091, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0008256 "left clavicle" 32440 "Chondrostei" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001105, negated: false, taxon ID: 32440 - entity: UBERON:0002091, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0008256 "left clavicle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001105, negated: false, taxon ID: 40674 - entity: UBERON:0002091, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0008266 "periodontal ligament" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:24023957 "Leblanc AR, Reisz RR, Periodontal ligament, cementum, and alveolar bone in the oldest herbivorous tetrapods, and their evolutionary significance. PLoS One (2013)" "The presence of a tripartite periodontium in diadectids supports the hypothesis that the dental follicle and its derivatives (cementum, alveolar bone, and periodontal ligament) were present in these stem amniotes. We provide the earliest record of a tripartite periodontium in a tetrapod by demonstrating its presence in the Diadectidae, a group that persisted from the Late Pennsylvanian into the Early Permian [27]. The presence of a tripartite periodontium in diadectids and several amniote taxa [2], [3], [8], [11] provides an increasing amount of evidence that all amniotes share the ability to produce the periodontal tissues that have historically been associated with mammalian and crocodilian thecodonty." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0008281 "tooth bud" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001091" bgee HOM:0000007 "historical homology" UBERON:0008281 "tooth bud" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001091" bgee HOM:0000007 "historical homology" UBERON:0008307 "heart endothelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 7742 - entity: UBERON:0000948|UBERON:0002376, negated: false, taxon ID: 7742 - entity: UBERON:0001986, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0008307 "heart endothelium" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 8782 - entity: UBERON:0001986, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0008307 "heart endothelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 40674 - entity: UBERON:0001986, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0008331 "clitoral smooth muscle" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0001299|UBERON:0002411|UBERON:0004713, negated: false, taxon ID: 40674 - entity: UBERON:0002411, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0008345 "ileal epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002116, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0008346 "duodenal epithelium" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002114, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0008447 "intertarsal joint" 32523 "Tetrapoda" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0001447, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0008447 "intertarsal joint" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0001447, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0008523 "infrahyoid muscle" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001685, negated: false, taxon ID: 7742 - entity: UBERON:0005493, negated: false, taxon ID: 117571" bgee HOM:0000007 "historical homology" UBERON:0008571 "suprahyoid muscle" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001685, negated: false, taxon ID: 7742 - entity: UBERON:0005493, negated: false, taxon ID: 117571" bgee HOM:0000007 "historical homology" UBERON:0008588 "procerus" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1111/j.1469-7580.2009.01111.x "Diogo R, Wood BA, Aziz MA, Burrows A, On the origin, homologies and evolution of primate facial muscles, with a particular focus on hominoids and a suggested unifying nomenclature for the facial muscles of the Mammalia. J Anat (2009)" "Rodents such as rats (Fig. 1) have up to 20 distinct facial muscles (Diogo et al. 2008; see Table 1). There is still some controversy regarding certain homologies between the facial muscles of monotremes and of other mammals. However, there is strong supporting evidence for the hypothesis that the occipitalis + auricularis posterior, procerus and dilatator nasi + maxillo-naso-labialis + levator anguli oris facialis of rats correspond to part of the platysma cervicale, naso-labialis and orbicularis oris of monotremes, respectively (Diogo et al. 2008; Table 1)." bgee ANN 2017-05-29 HOM:0000007 "historical homology" UBERON:0008588 "procerus" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1111/j.1469-7580.2009.01111.x "Diogo R, Wood BA, Aziz MA, Burrows A, On the origin, homologies and evolution of primate facial muscles, with a particular focus on hominoids and a suggested unifying nomenclature for the facial muscles of the Mammalia. J Anat (2009)" "Rodents such as rats (Fig. 1) have up to 20 distinct facial muscles (Diogo et al. 2008; see Table 1). There is still some controversy regarding certain homologies between the facial muscles of monotremes and of other mammals. However, there is strong supporting evidence for the hypothesis that the occipitalis + auricularis posterior, procerus and dilatator nasi + maxillo-naso-labialis + levator anguli oris facialis of rats correspond to part of the platysma cervicale, naso-labialis and orbicularis oris of monotremes, respectively (Diogo et al. 2008; Table 1)." bgee ANN 2017-05-29 HOM:0000007 "historical homology" UBERON:0008588 "procerus" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1111/j.1469-7580.2009.01111.x "Diogo R, Wood BA, Aziz MA, Burrows A, On the origin, homologies and evolution of primate facial muscles, with a particular focus on hominoids and a suggested unifying nomenclature for the facial muscles of the Mammalia. J Anat (2009)" "Rodents such as rats (Fig. 1) have up to 20 distinct facial muscles (Diogo et al. 2008; see Table 1). There is still some controversy regarding certain homologies between the facial muscles of monotremes and of other mammals. However, there is strong supporting evidence for the hypothesis that the occipitalis + auricularis posterior, procerus and dilatator nasi + maxillo-naso-labialis + levator anguli oris facialis of rats correspond to part of the platysma cervicale, naso-labialis and orbicularis oris of monotremes, respectively (Diogo et al. 2008; Table 1)." bgee ANN 2017-05-29 HOM:0000007 "historical homology" UBERON:0008780 "inner cell mass derived epiblast" 9347 "Eutheria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000087, negated: false, taxon ID: 9347 - entity: UBERON:0002532, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0008814 "pharyngeal arch system" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:25664163 "Koop D, Chen J, Theodosiou M, Carvalho JE, Alvarez S, de Lera AR, Holland LZ, Schubert M, Roles of retinoic acid and Tbx1/10 in pharyngeal segmentation: amphioxus and the ancestral chordate condition. Evodevo (2014)" "Chordates generally possess a segmented pharynx, but even though anatomical evidence and gene expression analyses suggest homologies between the pharyngeal apparatus of invertebrate chordates, such as the cephalochordate amphioxus, and vertebrates, these homologies remain contested. We, therefore, decided to study the evolution of the chordate head by examining the molecular mechanisms underlying pharyngeal morphogenesis in amphioxus, an animal lacking definitive neural crest (...) These results indicate that the involvement of RA signaling and its interactions with Tbx1/10 in head segmentation preceded the evolution of neural crest and were thus likely present in the ancestral chordate. Furthermore, developmental comparisons between different deuterostome models suggest that the genetic mechanisms for pharyngeal segmentation are evolutionary ancient and very likely predate the origin of chordates." bgee ANN 2016-05-09 HOM:0000007 "historical homology" UBERON:0008814 "pharyngeal arch system" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:25664163 "Koop D, Chen J, Theodosiou M, Carvalho JE, Alvarez S, de Lera AR, Holland LZ, Schubert M, Roles of retinoic acid and Tbx1/10 in pharyngeal segmentation: amphioxus and the ancestral chordate condition. Evodevo (2014)" "Chordates generally possess a segmented pharynx, but even though anatomical evidence and gene expression analyses suggest homologies between the pharyngeal apparatus of invertebrate chordates, such as the cephalochordate amphioxus, and vertebrates, these homologies remain contested. We, therefore, decided to study the evolution of the chordate head by examining the molecular mechanisms underlying pharyngeal morphogenesis in amphioxus, an animal lacking definitive neural crest (...) These results indicate that the involvement of RA signaling and its interactions with Tbx1/10 in head segmentation preceded the evolution of neural crest and were thus likely present in the ancestral chordate. Furthermore, developmental comparisons between different deuterostome models suggest that the genetic mechanisms for pharyngeal segmentation are evolutionary ancient and very likely predate the origin of chordates." bgee ANN 2016-05-09 HOM:0000007 "historical homology" UBERON:0008814 "pharyngeal arch system" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/j.semcdb.2010.01.022 "Grevellec A, Tucker AS, The pharyngeal pouches and clefts: development, evolution, structure and derivatives. Seminars in Cell and Developmental Biology (2010)" "In vertebrates, the pharyngeal apparatus develops from a transient series of segmental structures appearing as bulges on the cranial lateral side of the embryo and named the pharyngeal, or branchial, arches. The pharyngeal arches form successively in a cranial to caudal way during ontogeny." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0008814 "pharyngeal arch system" 33511 "Deuterostomia" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:23020903 "Graham A, Richardson J, Developmental and evolutionary origins of the pharyngeal apparatus. Evodevo (2012)." "it has now been established that a key event in vertebrate pharyngeal development is the outpocketing of the endoderm to form the pharyngeal pouches. Significantly, outpocketing of the pharyngeal endoderm is a basal deuterostome character and the regulatory network that mediates this process is conserved. Thus, the framework around which the vertebrate pharyngeal apparatus is built is ancient." bgee ANN 2015-02-24 HOM:0000007 "historical homology" UBERON:0008814 "pharyngeal arch system" 33511 "Deuterostomia" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:23020903 "Graham A, Richardson J, Developmental and evolutionary origins of the pharyngeal apparatus. Evodevo (2012)." "it has now been established that a key event in vertebrate pharyngeal development is the outpocketing of the endoderm to form the pharyngeal pouches. Significantly, outpocketing of the pharyngeal endoderm is a basal deuterostome character and the regulatory network that mediates this process is conserved. Thus, the framework around which the vertebrate pharyngeal apparatus is built is ancient." bgee ANN 2015-02-24 HOM:0000007 "historical homology" UBERON:0008815 "pharyngeal slit" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23020903 "Graham A, Richardson J, Developmental and evolutionary origins of the pharyngeal apparatus. Evodevo (2012)." "Given that the presence of a series of pharyngeal slits is a defining chordate feature, homology between vertebrate pharyngeal pouches and amphioxus pharyngeal perforations is perhaps to be anticipated. However, it has also become clear that pharyngeal development built around endodermal outpocketing is more ancient and that it is probably a deuterostome characteristic" bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0008815 "pharyngeal slit" 33511 "Deuterostomia" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:10226012 "Ogasawara M, Wada H, Peters H, Satoh N, Developmental expression of Pax1/9 genes in urochordate and hemichordate gills: insight into function and evolution of the pharyngeal epithelium. Development (1999)" "the present study investigated a relationship between Pax1/9 genes and the gill formation during protochordate later embryogenesis. Our results provide evidence for that pharyngeal gill slits are homologous between hemichordates and chordates, and therefore strongly support William Bateson's proposal for a close link between enteropneusts and chordates." bgee ANN 2015-04-30 HOM:0000007 "historical homology" UBERON:0008816 "embryonic head" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 7742 - entity: UBERON:0000922, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0008816 "embryonic head" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 33213 - entity: UBERON:0000922, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0008823 "neural tube derived brain" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.164-165" "Although the pattern of gastrulation varies considerably among the chordate groups, it is usually based on a few methods of cell movement in various combination (...) The most common method of neurulation is primary neurulation wherein the neural tube is formed through folding of the dorsal ectoderm (...) The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system))." bgee ANN 2013-10-04 HOM:0000007 "historical homology" UBERON:0008895 "splanchnocranium" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.235" "Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates." bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0008909 "perichordal bone" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001474, negated: false, taxon ID: 7742 - entity: UBERON:0002328, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0008969 "dental follicle" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:24023957 "Leblanc AR, Reisz RR, Periodontal ligament, cementum, and alveolar bone in the oldest herbivorous tetrapods, and their evolutionary significance. PLoS One (2013)" "The presence of a tripartite periodontium in diadectids supports the hypothesis that the dental follicle and its derivatives (cementum, alveolar bone, and periodontal ligament) were present in these stem amniotes. We provide the earliest record of a tripartite periodontium in a tetrapod by demonstrating its presence in the Diadectidae, a group that persisted from the Late Pennsylvanian into the Early Permian [27]. The presence of a tripartite periodontium in diadectids and several amniote taxa [2], [3], [8], [11] provides an increasing amount of evidence that all amniotes share the ability to produce the periodontal tissues that have historically been associated with mammalian and crocodilian thecodonty." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0008975 "oviduct shell gland" 8457 "Sauropsida" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" http://en.wikipedia.org/wiki/Uterus "uterus on Wikipedia" "the shell gland of birds and reptiles, with which the uterus is homologous" bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0009027 "vesical artery" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001255, negated: false, taxon ID: 32523 - entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009027 "vesical artery" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001255, negated: false, taxon ID: 32524 - entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009074 "syrinx organ" 8782 "Aves" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1126/science.1157632 "Bass AH, Gilland EH, Baker R, Evolutionary origins for social vocalization in a vertebrate hindbrain-spinal compartment. Science (2008)" "The most parsimonious interpretation of a cladistic analysis (10) is that a vocal hindbrain-spinal compartment originated in a common ancestor of the two major groups of living fishes, the Actinopterygii, which includes the teleosts studied here, and the Sarcopterygii, which includes lobe-finned fishes (lungfish and coelacanth) and tetrapods (Fig. 1A). The vocal muscles of fish and tetrapods also share origins from occipital somites (Fig. 1A) (7, 26, 27), although the innervation of the vocal muscle associated with the sound-generating organ evolved at least three times (Fig. 1A): occipital nerve and swim bladder of fish (Actinopterygii) (4) (fig. S1); vagal nerve and larynx of nonavian tetrapods (17–19, 22–25); and hypoglossal nerve and syrinx of birds (20). We conclude that our results reveal the ancestral origins of neural pattern generators for vocal-acoustic behaviors that mediate social signaling among all the major vertebrate lineages (Fig. 1A)." bgee ANN 2017-11-20 HOM:0000007 "historical homology" UBERON:0009074 "syrinx organ" 8782 "Aves" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1126/science.1157632 "Bass AH, Gilland EH, Baker R, Evolutionary origins for social vocalization in a vertebrate hindbrain-spinal compartment. Science (2008)" "The most parsimonious interpretation of a cladistic analysis (10) is that a vocal hindbrain-spinal compartment originated in a common ancestor of the two major groups of living fishes, the Actinopterygii, which includes the teleosts studied here, and the Sarcopterygii, which includes lobe-finned fishes (lungfish and coelacanth) and tetrapods (Fig. 1A). The vocal muscles of fish and tetrapods also share origins from occipital somites (Fig. 1A) (7, 26, 27), although the innervation of the vocal muscle associated with the sound-generating organ evolved at least three times (Fig. 1A): occipital nerve and swim bladder of fish (Actinopterygii) (4) (fig. S1); vagal nerve and larynx of nonavian tetrapods (17–19, 22–25); and hypoglossal nerve and syrinx of birds (20). We conclude that our results reveal the ancestral origins of neural pattern generators for vocal-acoustic behaviors that mediate social signaling among all the major vertebrate lineages (Fig. 1A)." bgee ANN 2017-11-20 HOM:0000007 "historical homology" UBERON:0009078 "pessulus" 8825 "Neognathae" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1038/nature19852 "Clarke JA, Chatterjee S, Li Z, Riede T, Agnolin F, Goller F, Isasi MP, Martinioni DR, Mussel FJ, Novas FE, Fossil evidence of the avian vocal organ from the Mesozoic. Nature (2016)" "Many basally divergent Aves lack a pessulus, thought by some to be key to anchoring larger vocal membranes or labia5. A well mineralized pessulus, present in both fossils is here found to be ancestral to Neognathae with several subsequent losses of this trait (for example in Columbiformes and some Passeri)." bgee ANN 2017-05-29 HOM:0000007 "historical homology" UBERON:0009078 "pessulus" 9126 "Passeriformes" CIO:0000005 "low confidence from single evidence" ECO:0000060 "positional similarity evidence" http://www.jstor.org/stable/4088558 "Prum RO, Phylogeny, biogeography, and evolution of the broadbills (Eurylaimidae) and asities (Philepittidae) based on morphology. The Auk (1993) p.304-324" "Any dorsoventrally oriented supporting element at the tracheobronchial junction has been called a pessulus; however, given the variation in shape, connection, and composition of these structures, there is little evidence to support their homology in all passerine lineages. It is equally parsimonious to hypothesize four independent origins for the pessulus in passerines or a single origin with three secondary losses or redevelopments." bgee ANN 2017-12-18 HOM:0000007 "historical homology" UBERON:0009078 "pessulus" 9126 "Passeriformes" CIO:0000005 "low confidence from single evidence" ECO:0000063 "compositional similarity evidence" http://www.jstor.org/stable/4088558 "Prum RO, Phylogeny, biogeography, and evolution of the broadbills (Eurylaimidae) and asities (Philepittidae) based on morphology. The Auk (1993) p.304-324" "Any dorsoventrally oriented supporting element at the tracheobronchial junction has been called a pessulus; however, given the variation in shape, connection, and composition of these structures, there is little evidence to support their homology in all passerine lineages. It is equally parsimonious to hypothesize four independent origins for the pessulus in passerines or a single origin with three secondary losses or redevelopments." bgee ANN 2017-12-18 HOM:0000007 "historical homology" UBERON:0009078 "pessulus" 9126 "Passeriformes" CIO:0000005 "low confidence from single evidence" ECO:0000071 "morphological similarity evidence" http://www.jstor.org/stable/4088558 "Prum RO, Phylogeny, biogeography, and evolution of the broadbills (Eurylaimidae) and asities (Philepittidae) based on morphology. The Auk (1993) p.304-324" "Any dorsoventrally oriented supporting element at the tracheobronchial junction has been called a pessulus; however, given the variation in shape, connection, and composition of these structures, there is little evidence to support their homology in all passerine lineages. It is equally parsimonious to hypothesize four independent origins for the pessulus in passerines or a single origin with three secondary losses or redevelopments." bgee ANN 2017-12-18 HOM:0000007 "historical homology" UBERON:0009078 "pessulus" NOT 9126 "Passeriformes" CIO:0000005 "low confidence from single evidence" ECO:0000060 "positional similarity evidence" http://www.jstor.org/stable/4088558 "Prum RO, Phylogeny, biogeography, and evolution of the broadbills (Eurylaimidae) and asities (Philepittidae) based on morphology. The Auk (1993) p.304-324" "Any dorsoventrally oriented supporting element at the tracheobronchial junction has been called a pessulus; however, given the variation in shape, connection, and composition of these structures, there is little evidence to support their homology in all passerine lineages. It is equally parsimonious to hypothesize four independent origins for the pessulus in passerines or a single origin with three secondary losses or redevelopments." bgee ANN 2017-05-29 HOM:0000007 "historical homology" UBERON:0009078 "pessulus" NOT 9126 "Passeriformes" CIO:0000005 "low confidence from single evidence" ECO:0000060 "positional similarity evidence" https://prumlab.yale.edu/publications "Prum, RO, Phylogeny, biogeography, and evolution of the broadbills (Eurylaimidae) and asities (Philepittidae) based on morphology. The Auk (1993) 110: 304–324" "The homology of the pessulus at these highest levels within passerines has not been assessed. Any dorsoventrally oriented supporting element at the tracheobronchial junction has been called a pessulus; however, given the variation in shape, connection, and composition of these structures, there is little evidence to support their homology in all passerine lineages. It is equally parsimonious to hypothesize four independent origins for the pessulus in passerines or a single origin with three secondary losses or redevelopments. Here, the pessulus in eurylamids and philepittids is hypothesized to be derived independently from that in other passerines." bgee ANN 2017-11-20 HOM:0000007 "historical homology" UBERON:0009078 "pessulus" NOT 9126 "Passeriformes" CIO:0000005 "low confidence from single evidence" ECO:0000063 "compositional similarity evidence" http://www.jstor.org/stable/4088558 "Prum RO, Phylogeny, biogeography, and evolution of the broadbills (Eurylaimidae) and asities (Philepittidae) based on morphology. The Auk (1993) p.304-324" "Any dorsoventrally oriented supporting element at the tracheobronchial junction has been called a pessulus; however, given the variation in shape, connection, and composition of these structures, there is little evidence to support their homology in all passerine lineages. It is equally parsimonious to hypothesize four independent origins for the pessulus in passerines or a single origin with three secondary losses or redevelopments." bgee ANN 2017-05-29 HOM:0000007 "historical homology" UBERON:0009078 "pessulus" NOT 9126 "Passeriformes" CIO:0000005 "low confidence from single evidence" ECO:0000063 "compositional similarity evidence" https://prumlab.yale.edu/publications "Prum, RO, Phylogeny, biogeography, and evolution of the broadbills (Eurylaimidae) and asities (Philepittidae) based on morphology. The Auk (1993) 110: 304–324" "The homology of the pessulus at these highest levels within passerines has not been assessed. Any dorsoventrally oriented supporting element at the tracheobronchial junction has been called a pessulus; however, given the variation in shape, connection, and composition of these structures, there is little evidence to support their homology in all passerine lineages. It is equally parsimonious to hypothesize four independent origins for the pessulus in passerines or a single origin with three secondary losses or redevelopments. Here, the pessulus in eurylamids and philepittids is hypothesized to be derived independently from that in other passerines." bgee ANN 2017-11-20 HOM:0000007 "historical homology" UBERON:0009078 "pessulus" NOT 9126 "Passeriformes" CIO:0000005 "low confidence from single evidence" ECO:0000071 "morphological similarity evidence" http://www.jstor.org/stable/4088558 "Prum RO, Phylogeny, biogeography, and evolution of the broadbills (Eurylaimidae) and asities (Philepittidae) based on morphology. The Auk (1993) p.304-324" "Any dorsoventrally oriented supporting element at the tracheobronchial junction has been called a pessulus; however, given the variation in shape, connection, and composition of these structures, there is little evidence to support their homology in all passerine lineages. It is equally parsimonious to hypothesize four independent origins for the pessulus in passerines or a single origin with three secondary losses or redevelopments." bgee ANN 2017-05-29 HOM:0000007 "historical homology" UBERON:0009078 "pessulus" NOT 9126 "Passeriformes" CIO:0000005 "low confidence from single evidence" ECO:0000071 "morphological similarity evidence" https://prumlab.yale.edu/publications "Prum, RO, Phylogeny, biogeography, and evolution of the broadbills (Eurylaimidae) and asities (Philepittidae) based on morphology. The Auk (1993) 110: 304–324" "The homology of the pessulus at these highest levels within passerines has not been assessed. Any dorsoventrally oriented supporting element at the tracheobronchial junction has been called a pessulus; however, given the variation in shape, connection, and composition of these structures, there is little evidence to support their homology in all passerine lineages. It is equally parsimonious to hypothesize four independent origins for the pessulus in passerines or a single origin with three secondary losses or redevelopments. Here, the pessulus in eurylamids and philepittids is hypothesized to be derived independently from that in other passerines." bgee ANN 2017-11-20 HOM:0000007 "historical homology" UBERON:0009078 "pessulus" NOT 9126 "Passeriformes" CIO:0000005 "low confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" https://prumlab.yale.edu/publications "Prum, RO, Phylogeny, biogeography, and evolution of the broadbills (Eurylaimidae) and asities (Philepittidae) based on morphology. The Auk (1993) 110: 304–324" "The homology of the pessulus at these highest levels within passerines has not been assessed. Any dorsoventrally oriented supporting element at the tracheobronchial junction has been called a pessulus; however, given the variation in shape, connection, and composition of these structures, there is little evidence to support their homology in all passerine lineages. It is equally parsimonious to hypothesize four independent origins for the pessulus in passerines or a single origin with three secondary losses or redevelopments. Here, the pessulus in eurylamids and philepittids is hypothesized to be derived independently from that in other passerines." bgee ANN 2017-11-20 HOM:0000007 "historical homology" UBERON:0009078 "pessulus" 81928 "Eurylaimidae" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" https://prumlab.yale.edu/publications "Prum, RO, Phylogeny, biogeography, and evolution of the broadbills (Eurylaimidae) and asities (Philepittidae) based on morphology. The Auk (1993) 110: 304–324" "The homology of the pessulus at these highest levels within passerines has not been assessed. Any dorsoventrally oriented supporting element at the tracheobronchial junction has been called a pessulus; however, given the variation in shape, connection, and composition of these structures, there is little evidence to support their homology in all passerine lineages. It is equally parsimonious to hypothesize four independent origins for the pessulus in passerines or a single origin with three secondary losses or redevelopments. Here, the pessulus in eurylamids and philepittids is hypothesized to be derived independently from that in other passerines." bgee ANN 2017-12-18 HOM:0000007 "historical homology" UBERON:0009078 "pessulus" 81928 "Eurylaimidae" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" https://prumlab.yale.edu/publications "Prum, RO, Phylogeny, biogeography, and evolution of the broadbills (Eurylaimidae) and asities (Philepittidae) based on morphology. The Auk (1993) 110: 304–324" "The homology of the pessulus at these highest levels within passerines has not been assessed. Any dorsoventrally oriented supporting element at the tracheobronchial junction has been called a pessulus; however, given the variation in shape, connection, and composition of these structures, there is little evidence to support their homology in all passerine lineages. It is equally parsimonious to hypothesize four independent origins for the pessulus in passerines or a single origin with three secondary losses or redevelopments. Here, the pessulus in eurylamids and philepittids is hypothesized to be derived independently from that in other passerines." bgee ANN 2017-12-18 HOM:0000007 "historical homology" UBERON:0009078 "pessulus" 81928 "Eurylaimidae" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" https://prumlab.yale.edu/publications "Prum, RO, Phylogeny, biogeography, and evolution of the broadbills (Eurylaimidae) and asities (Philepittidae) based on morphology. The Auk (1993) 110: 304–324" "The homology of the pessulus at these highest levels within passerines has not been assessed. Any dorsoventrally oriented supporting element at the tracheobronchial junction has been called a pessulus; however, given the variation in shape, connection, and composition of these structures, there is little evidence to support their homology in all passerine lineages. It is equally parsimonious to hypothesize four independent origins for the pessulus in passerines or a single origin with three secondary losses or redevelopments. Here, the pessulus in eurylamids and philepittids is hypothesized to be derived independently from that in other passerines." bgee ANN 2017-12-18 HOM:0000007 "historical homology" UBERON:0009078 "pessulus" 81928 "Eurylaimidae" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" https://prumlab.yale.edu/publications "Prum, RO, Phylogeny, biogeography, and evolution of the broadbills (Eurylaimidae) and asities (Philepittidae) based on morphology. The Auk (1993) 110: 304–324" "The homology of the pessulus at these highest levels within passerines has not been assessed. Any dorsoventrally oriented supporting element at the tracheobronchial junction has been called a pessulus; however, given the variation in shape, connection, and composition of these structures, there is little evidence to support their homology in all passerine lineages. It is equally parsimonious to hypothesize four independent origins for the pessulus in passerines or a single origin with three secondary losses or redevelopments. Here, the pessulus in eurylamids and philepittids is hypothesized to be derived independently from that in other passerines." bgee ANN 2017-12-18 HOM:0000007 "historical homology" UBERON:0009078 "pessulus" 137529 "Philepittidae" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" https://prumlab.yale.edu/publications "Prum, RO, Phylogeny, biogeography, and evolution of the broadbills (Eurylaimidae) and asities (Philepittidae) based on morphology. The Auk (1993) 110: 304–324" "The homology of the pessulus at these highest levels within passerines has not been assessed. Any dorsoventrally oriented supporting element at the tracheobronchial junction has been called a pessulus; however, given the variation in shape, connection, and composition of these structures, there is little evidence to support their homology in all passerine lineages. It is equally parsimonious to hypothesize four independent origins for the pessulus in passerines or a single origin with three secondary losses or redevelopments. Here, the pessulus in eurylamids and philepittids is hypothesized to be derived independently from that in other passerines." bgee ANN 2017-12-18 HOM:0000007 "historical homology" UBERON:0009078 "pessulus" 137529 "Philepittidae" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" https://prumlab.yale.edu/publications "Prum, RO, Phylogeny, biogeography, and evolution of the broadbills (Eurylaimidae) and asities (Philepittidae) based on morphology. The Auk (1993) 110: 304–324" "The homology of the pessulus at these highest levels within passerines has not been assessed. Any dorsoventrally oriented supporting element at the tracheobronchial junction has been called a pessulus; however, given the variation in shape, connection, and composition of these structures, there is little evidence to support their homology in all passerine lineages. It is equally parsimonious to hypothesize four independent origins for the pessulus in passerines or a single origin with three secondary losses or redevelopments. Here, the pessulus in eurylamids and philepittids is hypothesized to be derived independently from that in other passerines." bgee ANN 2017-12-18 HOM:0000007 "historical homology" UBERON:0009078 "pessulus" 137529 "Philepittidae" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" https://prumlab.yale.edu/publications "Prum, RO, Phylogeny, biogeography, and evolution of the broadbills (Eurylaimidae) and asities (Philepittidae) based on morphology. The Auk (1993) 110: 304–324" "The homology of the pessulus at these highest levels within passerines has not been assessed. Any dorsoventrally oriented supporting element at the tracheobronchial junction has been called a pessulus; however, given the variation in shape, connection, and composition of these structures, there is little evidence to support their homology in all passerine lineages. It is equally parsimonious to hypothesize four independent origins for the pessulus in passerines or a single origin with three secondary losses or redevelopments. Here, the pessulus in eurylamids and philepittids is hypothesized to be derived independently from that in other passerines." bgee ANN 2017-12-18 HOM:0000007 "historical homology" UBERON:0009078 "pessulus" 137529 "Philepittidae" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" https://prumlab.yale.edu/publications "Prum, RO, Phylogeny, biogeography, and evolution of the broadbills (Eurylaimidae) and asities (Philepittidae) based on morphology. The Auk (1993) 110: 304–324" "The homology of the pessulus at these highest levels within passerines has not been assessed. Any dorsoventrally oriented supporting element at the tracheobronchial junction has been called a pessulus; however, given the variation in shape, connection, and composition of these structures, there is little evidence to support their homology in all passerine lineages. It is equally parsimonious to hypothesize four independent origins for the pessulus in passerines or a single origin with three secondary losses or redevelopments. Here, the pessulus in eurylamids and philepittids is hypothesized to be derived independently from that in other passerines." bgee ANN 2017-12-18 HOM:0000007 "historical homology" UBERON:0009098 "gravid uterus" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000922, negated: false, taxon ID: 33213 - entity: UBERON:0000995, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0009122 "adenohypophyseal placode" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:25903628 "Diogo R, Kelly RG, Christiaen L, Levine M, Ziermann JM, Molnar JL, Noden DM, Tzahor E, A new heart for a new head in vertebrate cardiopharyngeal evolution. Nature (2015)" "The pan-placodal regulatory gene Six1/2 is expressed in a crescent of cells straddling the anterior-most region of the developing neural tube in C. intestinalis embryos, comparable with the sites of origin of cranial placodes in the fate maps of vertebrates. Ectodermal thickenings derived from this domain express placodal regulatory genes, including Six3/6, Pitx and Eya. For example, the atrial siphon placode shares extensive similarities with the vertebrate otic placode (Fig. 4), whereas the stomodeum (the oral siphon primordium) expresses regulatory genes implicated in the specification of the vertebrate olfactory and adenohypophyseal placodes, including Six, Eya and the anterior placode markers Pitx and Dlx. These new findings argue for homologies between urochordate siphon primordia and vertebrate placodes and suggest that; although certain placodes (profundal, maxillomandibular, epibranchial and lens) evolved by diversification within the vertebrate lineage, others (adenohypophyseal, olfactory and otic) appeared before the separation of vertebrates and urochordates (Figs 3, 4)." bgee ANN 2016-09-05 HOM:0000007 "historical homology" UBERON:0009127 "epibranchial ganglion" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001714, negated: false, taxon ID: 89593 - entity: UBERON:0003078, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0009129 "right atrium endocardium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450-451" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0009133 "pleuroperitoneal membrane" 8457 "Sauropsida" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.162-163" "In most living diapsids (some lizards, snakes, crocodiles, and birds) as well as all mammals, additional folds of coelomic epithelium separate de paired pleural recesses from the rest of the pleuroperitoneal cavity. The coelom of these animals thus consists of four compartments: the pericardial cavity, two pleural cavities, and the peritoneal cavity. [...] In reptiles and birds, the folds separating the pleural cavities from the peritoneal cavity form the oblique septum. In mammals, the separation between the two pleural cavities and the peritoneal cavity develops by the pleuroperitoneal membranes, which push in from the dorsolateral body wall, and by other folds that extend laterally from the mesenteries and medially from the body wall to meet the pleuroperitoneal membranes." bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0009133 "pleuroperitoneal membrane" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0471090588 "Hildebrand M, Analysis of vertebrate structure (1983) p.205-206" "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes." bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0009139 "right posterior cardinal vein" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000468, negated: false, taxon ID: 33208 - entity: UBERON:0002065, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0009149 "foramen primum" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0009149 "foramen primum" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:21513818 "Dzialowski EM, Sirsat T, van der Sterren S, Villamor E, Prenatal cardiovascular shunts in amniotic vertebrates. Respir Physiol Neurobiol (2011)" "During amniotic vertebrate development, the embryo and fetus employ a number of cardiovascular shunts. These shunts provide a right-to-left shunt of blood and are essential components of embryonic life ensuring proper blood circulation to developing organs and fetal gas exchanger, as well as bypassing the pulmonary circuit and the unventilated, fluid filled lungs." bgee ANN 2013-07-19 HOM:0000007 "historical homology" UBERON:0009200 "limb epidermis" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001003, negated: false, taxon ID: 33208 - entity: UBERON:0002101, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0009210 "pharyngeal membrane" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0124020603 "Kaufman MH, Bard JBL, The anatomical basis of mouse development (1999) p.72" "In all vertebrates, the endodermal epithelium lining each pouch contacts the surface ectoderm of the clefts to form a series of bilayered branchial membranes, that break down in fish to form the gill openings." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0009292 "embryonic nasal process" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0878932504 "Gilbert SF, Developmental Biology (2006) p.421 and Figure 13.13" "Frontal nasal process is present during mammal development. [curator]" bgee ANN 2013-06-26 HOM:0000007 "historical homology" UBERON:0009292 "embryonic nasal process" 89593 "Craniata" CIO:0000005 "low confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.41 and Figure 2-11 p.42" "Nose is one of the characteristics of craniates. [curator]" bgee ANN 2013-06-26 HOM:0000007 "historical homology" UBERON:0009293 "embryonic frontal process" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0009477 "associated mesenchyme of otic placode" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0003069, negated: false, taxon ID: 7711 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009477 "associated mesenchyme of otic placode" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0003069, negated: false, taxon ID: 7742 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009477 "associated mesenchyme of otic placode" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0003069, negated: false, taxon ID: 89593 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009481 "cavity of pericardio-peritoneal canal" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) Development of the coelomic cavity and mesenteries, p.159-164 and Figure 4-32" bgee ANN 2013-07-16 HOM:0000007 "historical homology" UBERON:0009482 "associated mesenchyme of foregut-midgut junction" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0003104, negated: false, taxon ID: 7711 - entity: UBERON:0006235, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0009483 "mesentery of foregut-midgut junction" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0521617147 "Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut." bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0009494 "pharyngeal arch mesenchymal region" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1046/j.1469-7580.2001.19910133.x "Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0009497 "epithelium of foregut-midgut junction" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0521617147 "Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut." bgee ANN 2013-07-18 HOM:0000007 "historical homology" UBERON:0009500 "periotic mesenchyme" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0003051, negated: false, taxon ID: 7742 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009503 "mesenchyme of hindgut" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001046, negated: false, taxon ID: 7742 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009504 "mesenchyme of main bronchus" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002182, negated: false, taxon ID: 32523 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009505 "mesenchyme of trachea" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0003104, negated: false, taxon ID: 7711 - entity: UBERON:0003126, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0009506 "mesenchyme of middle ear" 8292 "Amphibia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001756, negated: false, taxon ID: 8292 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009506 "mesenchyme of middle ear" 8457 "Sauropsida" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001756, negated: false, taxon ID: 8457 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009506 "mesenchyme of middle ear" 8459 "Testudines" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001756, negated: false, taxon ID: 8459 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009506 "mesenchyme of middle ear" 8492 "Archosauria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001756, negated: false, taxon ID: 8492 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009506 "mesenchyme of middle ear" 8504 "Lepidosauria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001756, negated: false, taxon ID: 8504 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009506 "mesenchyme of middle ear" 9255 "Monotremata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001756, negated: false, taxon ID: 9255 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009506 "mesenchyme of middle ear" NOT 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001756, negated: true, taxon ID: 32524 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009506 "mesenchyme of middle ear" 32525 "Theria" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001756, negated: false, taxon ID: 32525 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009506 "mesenchyme of middle ear" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001756, negated: false, taxon ID: 40674 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009506 "mesenchyme of middle ear" NOT 40674 "Mammalia" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001756, negated: true, taxon ID: 40674 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009522 "lateral lingual swelling epithelium" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0006757, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0009537 "vascular element of right lung" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.596 and Figure 18-21" "The synapsid line of evolution culminating in mammals and the sauropsid line to reptiles and birds diverged millions of years ago, near the time of the origin of amniotes. Although mammals, too, evolved an efficient respiratory system, needed by endothermic animals, the mammalian system differs in many ways from that of birds because it evolved its complex design from the generalized amniote condition independently. The evolution of the secondary palate in mammals and their therapsid ancestors made possible a separation of food and respiratory passage." bgee ANN 2013-06-28 HOM:0000007 "historical homology" UBERON:0009550 "endoderm of foregut-midgut junction" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000925, negated: false, taxon ID: 33213 - entity: UBERON:0006235, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0009564 "distal limb integumentary appendage" 8292 "Amphibia" CIO:0000004 "medium confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:17262827 "Maddin HC, Musat-Marcu S, Reisz RR, Histological microstructure of the claws of the African clawed frog, Xenopus laevis (Anura: Pipidae): implications for the evolution of claws in tetrapods. J Exp Zool B Mol Dev Evol (2007)" "The histology of the amphibian claw sheath differs significantly from that of amniotes in its microstructure and the pattern of claw growth. These differences, in addition to the relative rarity of claws in lissamphibians, lead us to conclude that claws were probably independently acquired in these two groups. However, we are unable to refute the possibility that the claws of amphibians and amniotes were derived from an ancestral keratinization process and common ancestral proteins." bgee ANN 2013-07-17 HOM:0000007 "historical homology" UBERON:0009564 "distal limb integumentary appendage" NOT 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:17262827 "Maddin HC, Musat-Marcu S, Reisz RR, Histological microstructure of the claws of the African clawed frog, Xenopus laevis (Anura: Pipidae): implications for the evolution of claws in tetrapods. J Exp Zool B Mol Dev Evol (2007)" "The microstructure of the frog claw differs from that of amniotes in several respects, including the lack of a specified zone of growth near the base of the claw. Amphibians and amniotes, therefore, have very different patterns of claw sheath growth. Observations do not support homology of claws on a structural level in these two groups; however, further experimental work may confirm a conserved pattern of cornification in these structures in tetrapods." bgee ANN 2013-07-17 HOM:0000007 "historical homology" UBERON:0009564 "distal limb integumentary appendage" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:17262827 "Maddin HC, Musat-Marcu S, Reisz RR, Histological microstructure of the claws of the African clawed frog, Xenopus laevis (Anura: Pipidae): implications for the evolution of claws in tetrapods. J Exp Zool B Mol Dev Evol (2007)" "The histology of the amphibian claw sheath differs significantly from that of amniotes in its microstructure and the pattern of claw growth. These differences, in addition to the relative rarity of claws in lissamphibians, lead us to conclude that claws were probably independently acquired in these two groups. However, we are unable to refute the possibility that the claws of amphibians and amniotes were derived from an ancestral keratinization process and common ancestral proteins." bgee ANN 2013-07-17 HOM:0000007 "historical homology" UBERON:0009564 "distal limb integumentary appendage" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:11710767 "Hamrick MW, Development and evolution of the mammalian limb: adaptive diversification of nails, hooves, and claws. Evolution and development (2001)" "Very little has been known, however, about the developmental mechanisms involved in patterning distal limb appendages until recently. Although it was well established (e.g., Dhouailly 1973 that epidermal (epithelial) differentiation is regulated by signals from the underlying mesenchyme, the sequence of cellular events and the molecular cues involved in organizing the various forms of nails, claws, and hooves was not well understood. The purpose of this paper is to present new evidence pertaining to the morphogenesis of mammalian distal limb appendages to highlight the developmental mechanisms important in the evolution and adaptive diversification of these integumentary structures.....The prevalence of convergences and parallelisms in nail and claw structure among mammals underscores the existence of multiple morphogenetic pathways for evolutionary change in distal limb appendages." bgee ANN 2013-07-17 HOM:0000007 "historical homology" UBERON:0009570 "spinal cord sulcus limitans" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0009572 "lumen of central canal of spinal cord" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0003842 - UBERON:0003842" bgee HOM:0000007 "historical homology" UBERON:0009581 "midbrain mantle layer" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0009582 "spinal cord lateral wall" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0009583 "spinal cord mantle layer" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-27 HOM:0000007 "historical homology" UBERON:0009584 "1st arch mandibular mesenchyme" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0003104, negated: false, taxon ID: 7711 - entity: UBERON:0007237, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0009615 "midbrain hindbrain boundary neural plate" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0003052" bgee HOM:0000007 "historical homology" UBERON:0009616 "presumptive midbrain" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001891 - UBERON:0001891 - UBERON:0001891" bgee HOM:0000007 "historical homology" UBERON:0009647 "tympanic membrane epithelium" 8292 "Amphibia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002364, negated: false, taxon ID: 8292" bgee HOM:0000007 "historical homology" UBERON:0009647 "tympanic membrane epithelium" 8457 "Sauropsida" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002364, negated: false, taxon ID: 8457" bgee HOM:0000007 "historical homology" UBERON:0009647 "tympanic membrane epithelium" NOT 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002364, negated: true, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0009647 "tympanic membrane epithelium" 32524 "Amniota" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002364, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0009647 "tympanic membrane epithelium" NOT 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002364, negated: true, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0009647 "tympanic membrane epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0002364, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0009655 "auricular artery" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0001690, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0009655 "auricular artery" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0001690, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0009657 "artery of lip" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0001833, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0009675 "chorda tympani branch of facial nerve" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625" "Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII)." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0009676 "early telencephalic vesicle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0002285" bgee HOM:0000007 "historical homology" UBERON:0009695 "epithelium of laryngopharynx" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001051, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0009697 "epithelium of appendix" 38609 "Diprotodontia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001154, negated: false, taxon ID: 38609" bgee HOM:0000007 "historical homology" UBERON:0009697 "epithelium of appendix" NOT 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001154, negated: true, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0009697 "epithelium of appendix" 314146 "Euarchontoglires" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001154, negated: false, taxon ID: 314146" bgee HOM:0000007 "historical homology" UBERON:0009712 "endocardium of right ventricle" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450-451" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0009713 "endocardium of left ventricle" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450-451" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0009718 "neurohypophyseal duct" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:20438724 "Veeman MT, Newman-Smith E, El-Nachef D, Smith WC, The ascidian mouth opening is derived from the anterior neuropore: reassessing the mouth/neural tube relationship in chordate evolution. Dev Biol (2010)" "The relative positions of the brain and mouth are of central importance for models of chordate evolution. The dorsal hollow neural tube and the mouth have often been thought of as developmentally distinct structures that may have followed independent evolutionary paths. In most chordates however, including vertebrates and ascidians, the mouth primordia have been shown to fate to the anterior neural boundary. In ascidians such as Ciona there is a particularly intimate relationship between brain and mouth development, with a thin canal connecting the neural tube lumen to the mouth primordium at larval stages. This so-called neurohypophyseal canal was previously thought to be a secondary connection that formed relatively late, after the independent formation of the mouth primordium and the neural tube. Here we show that the Ciona neurohypophyseal canal is present from the end of neurulation and represents the anteriormost neural tube, and that the future mouth opening is actually derived from the anterior neuropore." bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0009749 "limb mesenchyme" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002101, negated: false, taxon ID: 32523 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009751 "cardiac mesenchyme" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 7742 - entity: UBERON:0000948|UBERON:0002376, negated: false, taxon ID: 7742 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009751 "cardiac mesenchyme" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 8782 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009751 "cardiac mesenchyme" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 40674 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009752 "pancreas mesenchyme" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001264, negated: false, taxon ID: 89593 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009771 "left anterior cardinal vein" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000468, negated: false, taxon ID: 33208 - entity: UBERON:0003087, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0009772 "right anterior cardinal vein" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000468, negated: false, taxon ID: 33208 - entity: UBERON:0003087, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0009779 "cardiac muscle tissue of right auricle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450-451" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0009780 "cardiac muscle tissue of left auricle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450-451" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0009845 "urogenital sinus mesenchyme" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000164, negated: false, taxon ID: 40674 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009878 "mesopodial skeleton" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" DOI:10.1002/jez.1100 "Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001)" "The three main outgroup taxa of tetrapods, panderichthyids, osteolepiforms, and rhizodontids, have endoskeletal elements corresponding to the stylo- and zeugopodial elements in a tetrapod limb. In addition, there are elements that share the position and possibly the developmental derivation of the ulnare and the intermedium. From these observations, most authors have concluded that the stylo- and zeugopodial elements as well as the proximal mesopodial elements have counterparts in the fins of tetrapod ancestors, but there are no indications of wrist or ankle joints.""" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0009879 "tarsal skeleton" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" DOI:10.1002/jez.1100 "Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001)" "The three main outgroup taxa of tetrapods, panderichthyids, osteolepiforms, and rhizodontids, have endoskeletal elements corresponding to the stylo- and zeugopodial elements in a tetrapod limb. In addition, there are elements that share the position and possibly the developmental derivation of the ulnare and the intermedium. From these observations, most authors have concluded that the stylo- and zeugopodial elements as well as the proximal mesopodial elements have counterparts in the fins of tetrapod ancestors, but there are no indications of wrist or ankle joints.""" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0009880 "carpal skeleton" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:17849442 "Johanson Z, Joss J, Boisvert CA, Ericsson R, Sutija M, Ahlberg PE, Fish fingers: digit homologues in sarcopterygian fish fins. J Exp Zool B Mol Dev Evol (2007)" "the autopod evolved before the origin of tetrapods, represented by the more distal region of the sarcopterygian fin, with the 'origin of digits' simply representing a modest repatterning of this region rather than the origin of a new structure." bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0009880 "carpal skeleton" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" DOI:10.1002/jez.1100 "Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001)" "The three main outgroup taxa of tetrapods, panderichthyids, osteolepiforms, and rhizodontids, have endoskeletal elements corresponding to the stylo- and zeugopodial elements in a tetrapod limb. In addition, there are elements that share the position and possibly the developmental derivation of the ulnare and the intermedium. From these observations, most authors have concluded that the stylo- and zeugopodial elements as well as the proximal mesopodial elements have counterparts in the fins of tetrapod ancestors, but there are no indications of wrist or ankle joints.""" bgee ANN 2013-08-22 HOM:0000007 "historical homology" UBERON:0009891 "facial mesenchyme" 7742 "Vertebrata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001456, negated: false, taxon ID: 7742 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0009894 "siphon primordium" 7712 "Tunicata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:25903628 "Diogo R, Kelly RG, Christiaen L, Levine M, Ziermann JM, Molnar JL, Noden DM, Tzahor E, A new heart for a new head in vertebrate cardiopharyngeal evolution. Nature (2015)" "The pan-placodal regulatory gene Six1/2 is expressed in a crescent of cells straddling the anterior-most region of the developing neural tube in C. intestinalis embryos, comparable with the sites of origin of cranial placodes in the fate maps of vertebrates. Ectodermal thickenings derived from this domain express placodal regulatory genes, including Six3/6, Pitx and Eya. For example, the atrial siphon placode shares extensive similarities with the vertebrate otic placode (Fig. 4), whereas the stomodeum (the oral siphon primordium) expresses regulatory genes implicated in the specification of the vertebrate olfactory and adenohypophyseal placodes, including Six, Eya and the anterior placode markers Pitx and Dlx. These new findings argue for homologies between urochordate siphon primordia and vertebrate placodes and suggest that; although certain placodes (profundal, maxillomandibular, epibranchial and lens) evolved by diversification within the vertebrate lineage, others (adenohypophyseal, olfactory and otic) appeared before the separation of vertebrates and urochordates (Figs 3, 4)." bgee ANN 2015-05-01 HOM:0000007 "historical homology" UBERON:0009919 "ureter smooth muscle" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000056, negated: false, taxon ID: 32524 - entity: UBERON:0001135, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0009920 "optic neural crest" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0009955 "neurogenic placode" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...)." bgee ANN 2013-07-02 HOM:0000007 "historical homology" UBERON:0009970 "epithelium of pancreatic duct" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0007329, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0010011 "collection of basal ganglia" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1016/j.cub.2011.05.001 "Stephenson-Jones M, Samuelsson E, Ericsson J, Robertson B, Grillner S, Evolutionary conservation of the basal ganglia as a common vertebrate mechanism for action selection. Current Biology (2011)" "All nuclei of the mammalian basal ganglia are also present in the oldest vertebrates." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0010019 "spiracle (sensu Vertebrata)" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:24451680 "Graham JB, Wegner NC, Miller LA, Jew CJ, Lai NC, Berquist RM, Frank LR, Long JA, Spiracular air breathing in polypterid fishes and its implications for aerial respiration in stem tetrapods. Nat Commun (2014)" "The polypterids (bichirs and ropefish) are extant basal actinopterygian (ray-finned) fishes that breathe air and share similarities with extant lobe-finned sarcopterygians (lungfishes and tetrapods) in lung structure. They are also similar to some fossil sarcopterygians, including stem tetrapods, in having large paired openings (spiracles) on top of their head." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:0010045 "1st arch maxillary mesenchyme" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0003104, negated: false, taxon ID: 7711 - entity: UBERON:0007238, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0010046 "entire pharyngeal arch associated mesenchyme" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1046/j.1469-7580.2001.19910133.x "Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0010047 "oral gland" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:19835108 "Venturi S, Venturi M, Iodine in evolution of salivary glands and in oral health. Nutrition and health (2009)" "About 350 M/y/a the dry diet of terrestrial environment, firstly in anuran amphibians and after in reptiles (Shaham and Lewitus, 1971) (Figure 1 ), favoured the development of the primitive tongue and of the primitive salivary glands, which embryologically derived from primitive [iodine] I-concentrating oral cells, and which maintain I-concentrating ability. In amphibian metamorphosis iodides and thyroxine are the most important factors inducing the spectacular apoptosis of cells of tail, gills and fins." bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0010056 "future tongue" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001723" bgee HOM:0000007 "historical homology" UBERON:0010075 "sacral neural crest" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0010081 "future common hepatic duct" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001175" bgee HOM:0000007 "historical homology" UBERON:0010083 "future dermis" 7711 "Chordata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002067, negated: false, taxon ID: 7711 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0010083 "future dermis" 7711 "Chordata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0002067" bgee HOM:0000007 "historical homology" UBERON:0010083 "future dermis" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002067, negated: false, taxon ID: 7776 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0010083 "future dermis" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0002067" bgee HOM:0000007 "historical homology" UBERON:0010084 "future diaphragm" NOT 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001103" bgee HOM:0000007 "historical homology" UBERON:0010084 "future diaphragm" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001103" bgee HOM:0000007 "historical homology" UBERON:0010092 "future metencephalon" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001895" bgee HOM:0000007 "historical homology" UBERON:0010096 "future myelencephalon" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0005290" bgee HOM:0000007 "historical homology" UBERON:0010126 "future nucleus ambiguus" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001719, negated: false, taxon ID: 40674 - entity: UBERON:0002020, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0010126 "future nucleus ambiguus" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001719" bgee HOM:0000007 "historical homology" UBERON:0010141 "primitive sex cord of indifferent gonad" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0005297" bgee HOM:0000007 "historical homology" UBERON:0010207 "nictitating membrane" NOT 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.431" "The nictitating membrane of amniotes is not homologous to the nictitating membrane of sharks." bgee ANN 2013-09-05 HOM:0000007 "historical homology" UBERON:0010207 "nictitating membrane" 7778 "Elasmobranchii" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.431" "The nictitating membrane of amniotes is not homologous to the nictitating membrane of sharks." bgee ANN 2013-09-05 HOM:0000007 "historical homology" UBERON:0010207 "nictitating membrane" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.431" "The nictitating membrane of amniotes is not homologous to the nictitating membrane of sharks." bgee ANN 2013-09-05 HOM:0000007 "historical homology" UBERON:0010227 "future cardiac atrium" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0002081" bgee HOM:0000007 "historical homology" UBERON:0010230 "eyeball of camera-type eye" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.426-427 and Figure 12-28" "The eyeball is a common structure to the representative vertebrates, teleost, frog, lizard and owl. [curator]" bgee ANN 2013-09-06 HOM:0000007 "historical homology" UBERON:0010258 "mesenchyme from rhombencephalic neural crest" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0003104, negated: false, taxon ID: 7711 - entity: UBERON:0003852, negated: false, taxon ID: 89593" bgee HOM:0000007 "historical homology" UBERON:0010294 "scleral endothelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001773, negated: false, taxon ID: 7742 - entity: UBERON:0001986, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0010299 "scleral mesenchyme" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001773, negated: false, taxon ID: 7742 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0010303 "extraembryonic epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000478, negated: false, taxon ID: 40674 - entity: UBERON:0000483, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0010309 "palpebral bone" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001474, negated: false, taxon ID: 7742 - entity: UBERON:0001712, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0010359 "pharyngeal arch mesenchyme from neural crest" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1046/j.1469-7580.2001.19910133.x "Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0010360 "pharyngeal arch mesenchyme from head mesenchyme" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1046/j.1469-7580.2001.19910133.x "Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0010371 "ecto-epithelium" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000924, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0010377 "mesenchyme from somatopleure" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000922, negated: false, taxon ID: 33213 - entity: UBERON:0003104, negated: false, taxon ID: 7711 - entity: UBERON:0004874, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0010378 "mesenchyme from splanchnopleure" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000922, negated: false, taxon ID: 33213 - entity: UBERON:0003104, negated: false, taxon ID: 7711 - entity: UBERON:0004873, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0010425 "internal naris" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1038/nature02843 "Zhu M, Ahlberg PE, The origin of the internal nostril in tetrapodes. Nature (2004)" "The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla." bgee ANN 2017-02-20 HOM:0000007 "historical homology" UBERON:0010425 "internal naris" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1038/nature02843 "Zhu M, Ahlberg PE, The origin of the internal nostril in tetrapodes. Nature (2004)" "The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla." bgee ANN 2017-02-20 HOM:0000007 "historical homology" UBERON:0010425 "internal naris" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1038/nature02843 "Zhu M, Ahlberg PE, The origin of the internal nostril in tetrapodes. Nature (2004)" "The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla." bgee ANN 2013-06-26 HOM:0000007 "historical homology" UBERON:0010425 "internal naris" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1038/nature02843 "Zhu M, Ahlberg PE, The origin of the internal nostril in tetrapodes. Nature (2004)" "The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla." bgee ANN 2013-06-26 HOM:0000007 "historical homology" UBERON:0010532 "primitive nephron" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001285" bgee HOM:0000007 "historical homology" UBERON:0010533 "metanephros cortex" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543" "The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes." bgee ANN 2013-08-29 HOM:0000007 "historical homology" UBERON:0010535 "primitive metanephric nephron" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0005110" bgee HOM:0000007 "historical homology" UBERON:0010702 "digit mesenchyme" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002544, negated: false, taxon ID: 8782 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0010702 "digit mesenchyme" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002544, negated: false, taxon ID: 32523 - entity: UBERON:0002544|UBERON:4000172, negated: false, taxon ID: 32523 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0010702 "digit mesenchyme" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002544, negated: false, taxon ID: 32524 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0010702 "digit mesenchyme" NOT 32524 "Amniota" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002544, negated: true, taxon ID: 32524 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0010702 "digit mesenchyme" NOT 1338369 "Dipnotetrapodomorpha" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002544|UBERON:2000271, negated: true, taxon ID: 1338369 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0010704 "parenchyma of quadrate lobe of liver" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001116, negated: false, taxon ID: 7742 - entity: UBERON:0001280, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0010706 "parenchyma of caudate lobe of liver" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001117, negated: false, taxon ID: 7742 - entity: UBERON:0001280, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0010743 "meningeal cluster" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm." bgee ANN 2013-07-03 HOM:0000007 "historical homology" UBERON:0010855 "skin of forelimb wing" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0000024, negated: false, taxon ID: 32524 - entity: UBERON:0000024|UBERON:0002102, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0010893 "median external naris" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 7742 - entity: UBERON:0005928, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0010893 "median external naris" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 7742 - entity: UBERON:0005928|UBERON:0013477, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0010899 "synchronous hermaphroditic organism" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000468, negated: false, taxon ID: 33208 - entity: UBERON:0000473, negated: false, taxon ID: 7742 - entity: UBERON:0000992, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0010899 "synchronous hermaphroditic organism" NOT 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000468, negated: false, taxon ID: 33208 - entity: UBERON:0000473, negated: true, taxon ID: 33208 - entity: UBERON:0000992, negated: true, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0010899 "synchronous hermaphroditic organism" 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000468, negated: false, taxon ID: 33208 - entity: UBERON:0000473, negated: false, taxon ID: 33213 - entity: UBERON:0000992, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0010975 "external oblique pre-muscle mass" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0005442" bgee HOM:0000007 "historical homology" UBERON:0011006 "endocardium of left auricle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450-451" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0011007 "endocardium of right auricle" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450-451" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0011079 "angular bone" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "Developmental biology can also help identify the homologous elements for the associated membranous bones of the ear. The tympanic ring and gonial, for example have been suggested to be homologous to the angular bone and prearticular, respectively. Again, by following the position and relative timing of these bones as they develop, clear homologies can be identified (Fig. 2). Bapx1 is also expressed around these membraneous bones in both chick and mouse (Tucker et al. 2004)." bgee ANN 2015-04-02 HOM:0000007 "historical homology" UBERON:0011085 "palatoquadrate arch" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1046/j.1469-7580.2001.19910133.x "Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0011088 "ligament of knee joint" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000211, negated: false, taxon ID: 40674 - entity: UBERON:0001485, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0011096 "lacrimal nerve" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0001817, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0011120 "laryngeal joint" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0001739, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0011121 "cricothyroid joint" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0001738, negated: false, taxon ID: 40674 - entity: UBERON:0002375, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0011150 "pharyngeal arch derived gill" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.2174/1874196701104010035 "Carvalho O, Goncalves C, Comparative Physiology of the Respiratory System in the Animal Kingdom. The Open Biology Journal (2011)" "The development of the respiratory organs of vertebrates is closely related to the primitive pharynx, since the gills of aquatic vertebrates and the lungs of terrestrial vertebrates and aquatic mammals have pharyngeal embryology origin." bgee ANN 2013-06-27 HOM:0000007 "historical homology" UBERON:0011150 "pharyngeal arch derived gill" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.209" "Gill slits in the pharyngeal region of the intestine, which are also present in (at least) tunicates and acranians, are taken over to the craniote ancestor. But while the role of the gill slits in respiration is probably minor in tunicates and acranians, it becomes more pronounced in craniotes." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0011150 "pharyngeal arch derived gill" 33511 "Deuterostomia" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" PMID:23031503 "Smith AB, Cambrian problematica and the diversification of deuterostomes. BMC Biol (2012)" "one generally accepted model is that the latest common ancestor of deuterostomes was a worm-like creature with pharyngeal gill slits, a terminal anus, a simple nerve plexus without regionalization, and well-developed circular and longitudinal muscles." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0011150 "pharyngeal arch derived gill" 33511 "Deuterostomia" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1139/z04-158 "Ruppert EE, Key characters uniting hemichordates and chordates: homologies or homoplasies? Canadian journal of zoology (2005)" "(...) set of genes that is specific to the pharyngeal epithelium has been localized in hemichordates and urochordates and suggests homology of hemichordate and chordate gills. In P. flava [hemichordate] these six genes are designated PfG1-PfG6 (Okai et al. 2000)." bgee ANN 2013-09-19 HOM:0000007 "historical homology" UBERON:0011150 "pharyngeal arch derived gill" 33511 "Deuterostomia" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0198566694 "Schmidt-Rhaesa A, The evolution of organ systems (2007) p.211" "It appears plausible that the gill slits in the anterior region of the intestine are comparable between craniotes, acranians, tunicates, enteropneusts, and at least the cephalodiscid pterobranchs (...) but it is debated when exactly such gill slits evolved." bgee ANN 2013-07-04 HOM:0000007 "historical homology" UBERON:0011151 "jaw depressor muscle" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000033 "traceable author statement" DOI:10.1186/1471-213X-8-24 "Diogo R, Hinits Y, Hughes SM, Development of mandibular, hyoid and hypobranchial muscles in the zebrafish: homologies and evolution of these muscles within bony fishes and tetrapods. BMC Developmental Biology (2008)" "according to e.g. Edgeworth [12] the genioglossus of salamanders such as Ambystoma is derived from the coracomandibularis [Probable plesiomorphic osteichthyan condition]" bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0011170 "quadrate-articular joint" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0001688|UBERON:0006597, negated: false, taxon ID: 32523 - entity: UBERON:0001689|UBERON:0004744, negated: false, taxon ID: 32523 - entity: UBERON:0004744, negated: false, taxon ID: 32523 - entity: UBERON:0006597, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0011171 "joint connecting upper and lower jaws" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0003277, negated: false, taxon ID: 40674 - entity: UBERON:0003278, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0011197 "parathyroid epithelium" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000206|UBERON:0001132, negated: false, taxon ID: 32523 - entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001132, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0011288 "stomochord" 10219 "Hemichordata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:25303744 "Satoh N, Tagawa K, Lowe CJ, Yu JK, Kawashima T, Takahashi H, Ogasawara M, Kirschner M, Hisata K, Su YH, Gerhart J, On a possible evolutionary link of the stomochord of hemichordates to pharyngeal organs of chordates. Genesis (2014)" "The stomochord of acorn worms is an anterior outgrowth of the pharynx endoderm into the proboscis. In 1886 Bateson proposed homology of this organ to the chordate notochord, crowning this animal group ""hemichordates."" Although this proposal has been debated for over a century, the question still remains unresolved." bgee ANN 2018-03-26 HOM:0000007 "historical homology" UBERON:0011299 "white matter of telencephalon" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001893, negated: false, taxon ID: 7742 - entity: UBERON:0002316, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0011300 "gray matter of telencephalon" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001893, negated: false, taxon ID: 7742 - entity: UBERON:0002020, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0011321 "masseteric nerve" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0001597, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0011332 "extrinsic tongue pre-muscle mass" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001575" bgee HOM:0000007 "historical homology" UBERON:0011363 "cranial lymph vasculature" 32443 "Teleostei" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 7742 - entity: UBERON:0004536, negated: false, taxon ID: 32443" bgee HOM:0000007 "historical homology" UBERON:0011363 "cranial lymph vasculature" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 7742 - entity: UBERON:0004536, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0011587 "pre-dentine" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001751" bgee HOM:0000007 "historical homology" UBERON:0011587 "pre-dentine" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001751" bgee HOM:0000007 "historical homology" UBERON:0011592 "future upper lip" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001834" bgee HOM:0000007 "historical homology" UBERON:0011593 "maxillary tooth" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001091, negated: false, taxon ID: 7776 - entity: UBERON:0002397, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0011594 "dentary tooth" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001091, negated: false, taxon ID: 7776 - entity: UBERON:0004742, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0011597 "bone of upper jaw" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001474, negated: false, taxon ID: 7742 - entity: UBERON:0001709, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0011601 "gingiva of upper jaw" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001709, negated: false, taxon ID: 7776 - entity: UBERON:0001828, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0011602 "gingiva of lower jaw" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001710, negated: false, taxon ID: 7776 - entity: UBERON:0001828, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0011606 "hyomandibular bone" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1017/S0022215100009087 "Gerrie J, The phylogeny of the mammalian tympanic cavity and auditory ossicles. The Journal of Laryngology and Otology (1948)" "This structure [the hyomandibular], on ontogenic grounds alone, can be considered homologous with the amphibian and reptilian columella and the mammalian stapes." bgee ANN 2015-04-02 HOM:0000007 "historical homology" UBERON:0011628 "early premaxilla" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0002244" bgee HOM:0000007 "historical homology" UBERON:0011637 "prearticular bone" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:22686855 "Anthwal N, Joshi L, Tucker AS, Evolution of the mammalian middle ear and jaw: adaptations and novel structures. J Anat (2013)" "Developmental biology can also help identify the homologous elements for the associated membranous bones of the ear. The tympanic ring and gonial, for example have been suggested to be homologous to the angular bone and prearticular, respectively. Again, by following the position and relative timing of these bones as they develop, clear homologies can be identified (Fig. 2). Bapx1 is also expressed around these membraneous bones in both chick and mouse (Tucker et al. 2004)." bgee ANN 2015-04-02 HOM:0000007 "historical homology" UBERON:0011647 "depressor mandibulae muscle" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.398" "The depressor mandibulae of tetrapods, which opens the jaws, is the homologue of the levator operculi and epihyoidean. In mammals, the depressor mandibulae evolves into the stapedius (...)." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0011648 "jaw muscle" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:25903628 "Diogo R, Kelly RG, Christiaen L, Levine M, Ziermann JM, Molnar JL, Noden DM, Tzahor E, A new heart for a new head in vertebrate cardiopharyngeal evolution. Nature (2015)" "This evolutionary scenario implies that the amphioxus orovelar muscles and urochordate oral siphon muscles may be homologous to the cyclostome orovelar muscles and gnathostome mandibular muscles, which could potentially explain why these muscles are derived from the CPF only in vertebrates." bgee ANN 2016-09-05 HOM:0000007 "historical homology" UBERON:0011648 "jaw muscle" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" DOI:10.1186/1471-213X-8-24 "Diogo R, Hinits Y, Hughes SM, Development of mandibular, hyoid and hypobranchial muscles in the zebrafish: homologies and evolution of these muscles within bony fishes and tetrapods. BMC Developmental Biology (2008)" "Although the zebrafish occupies a rather derived phylogenetic position within actinopterygians and even within teleosts, with respect to the mandibular, hyoid and hypobranchial muscles it seems justified to consider it an appropriate representative of these two groups. Among these muscles, the three with clear homologues in tetrapods [the intermandibularis anterior, adductor mandibulae, and sternohyoideus] and the further three identified in sarcopterygian fish are particularly appropriate for comparisons of results between the actinopterygian zebrafish and the sarcopterygians." bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0011649 "levator operculi" 7894 "Coelacanthiformes" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1186/1471-213X-8-24 "Diogo R, Hinits Y, Hughes SM, Development of mandibular, hyoid and hypobranchial muscles in the zebrafish: homologies and evolution of these muscles within bony fishes and tetrapods. BMC Developmental Biology (2008)" "the zebrafish, as most extant teleosts and the halecomorph Amia, has a muscle levator operculi (Figs.2, 3, 4, and 5A). Millot and Anthony [24] stated that Latimeria has a 'levator operculi'. However, whether this muscle is homologous to the levator operculi of zebrafish is doubtful for two main reasons. First, the muscles have distinct function: contrary to the zebrafish and other teleosts and to Amia, Latimeria does not have an interoperculo-mandibular ligament and, therefore, does not have an opercular mechanism mediating mandible depression [36]. Second, and more importantly, it is cladistically more parsimonious to consider that these muscles were independently acquired in actinistians and halecostomes (2 steps) than to have one acquisition (in the node leading to osteichthyans) and various independent losses (at least in non-actinistian sarcopterygians, in cladistians, in chondrosteans and in ginglymodians) (see Fig. 1). On balance, our view is that the 'levator operculi' of Latimeria is unlikely to be homologous with the levator operculi of the zebrafish and other teleosts and of Amia (see Tables 4, 5)." bgee ANN 2017-11-20 HOM:0000007 "historical homology" UBERON:0011649 "levator operculi" 41665 "Neopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1186/1471-213X-8-24 "Diogo R, Hinits Y, Hughes SM, Development of mandibular, hyoid and hypobranchial muscles in the zebrafish: homologies and evolution of these muscles within bony fishes and tetrapods. BMC Developmental Biology (2008)" "the zebrafish, as most extant teleosts and the halecomorph Amia, has a muscle levator operculi (Figs.2, 3, 4, and 5A). Millot and Anthony [24] stated that Latimeria has a 'levator operculi'. However, whether this muscle is homologous to the levator operculi of zebrafish is doubtful for two main reasons. First, the muscles have distinct function: contrary to the zebrafish and other teleosts and to Amia, Latimeria does not have an interoperculo-mandibular ligament and, therefore, does not have an opercular mechanism mediating mandible depression [36]. Second, and more importantly, it is cladistically more parsimonious to consider that these muscles were independently acquired in actinistians and halecostomes (2 steps) than to have one acquisition (in the node leading to osteichthyans) and various independent losses (at least in non-actinistian sarcopterygians, in cladistians, in chondrosteans and in ginglymodians) (see Fig. 1). On balance, our view is that the 'levator operculi' of Latimeria is unlikely to be homologous with the levator operculi of the zebrafish and other teleosts and of Amia (see Tables 4, 5)." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0011649 "levator operculi" 41665 "Neopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1186/1471-213X-8-24 "Diogo R, Hinits Y, Hughes SM, Development of mandibular, hyoid and hypobranchial muscles in the zebrafish: homologies and evolution of these muscles within bony fishes and tetrapods. BMC Developmental Biology (2008)" "the zebrafish, as most extant teleosts and the halecomorph Amia, has a muscle levator operculi (Figs.2, 3, 4, and 5A). Millot and Anthony [24] stated that Latimeria has a 'levator operculi'. However, whether this muscle is homologous to the levator operculi of zebrafish is doubtful for two main reasons. First, the muscles have distinct function: contrary to the zebrafish and other teleosts and to Amia, Latimeria does not have an interoperculo-mandibular ligament and, therefore, does not have an opercular mechanism mediating mandible depression [36]. Second, and more importantly, it is cladistically more parsimonious to consider that these muscles were independently acquired in actinistians and halecostomes (2 steps) than to have one acquisition (in the node leading to osteichthyans) and various independent losses (at least in non-actinistian sarcopterygians, in cladistians, in chondrosteans and in ginglymodians) (see Fig. 1). On balance, our view is that the 'levator operculi' of Latimeria is unlikely to be homologous with the levator operculi of the zebrafish and other teleosts and of Amia (see Tables 4, 5)." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0011649 "levator operculi" 117571 "Euteleostomi" CIO:0000005 "low confidence from single evidence" ECO:0000071 "morphological similarity evidence" DOI:10.1186/1471-213X-8-24 "Diogo R, Hinits Y, Hughes SM, Development of mandibular, hyoid and hypobranchial muscles in the zebrafish: homologies and evolution of these muscles within bony fishes and tetrapods. BMC Developmental Biology (2008)" "the zebrafish, as most extant teleosts and the halecomorph Amia, has a muscle levator operculi (Figs.2, 3, 4, and 5A). Millot and Anthony [24] stated that Latimeria has a 'levator operculi'. However, whether this muscle is homologous to the levator operculi of zebrafish is doubtful for two main reasons. First, the muscles have distinct function: contrary to the zebrafish and other teleosts and to Amia, Latimeria does not have an interoperculo-mandibular ligament and, therefore, does not have an opercular mechanism mediating mandible depression [36]. Second, and more importantly, it is cladistically more parsimonious to consider that these muscles were independently acquired in actinistians and halecostomes (2 steps) than to have one acquisition (in the node leading to osteichthyans) and various independent losses (at least in non-actinistian sarcopterygians, in cladistians, in chondrosteans and in ginglymodians) (see Fig. 1). On balance, our view is that the 'levator operculi' of Latimeria is unlikely to be homologous with the levator operculi of the zebrafish and other teleosts and of Amia (see Tables 4, 5)." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0011649 "levator operculi" NOT 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1186/1471-213X-8-24 "Diogo R, Hinits Y, Hughes SM, Development of mandibular, hyoid and hypobranchial muscles in the zebrafish: homologies and evolution of these muscles within bony fishes and tetrapods. BMC Developmental Biology (2008)" "the zebrafish, as most extant teleosts and the halecomorph Amia, has a muscle levator operculi (Figs.2, 3, 4, and 5A). Millot and Anthony [24] stated that Latimeria has a 'levator operculi'. However, whether this muscle is homologous to the levator operculi of zebrafish is doubtful for two main reasons. First, the muscles have distinct function: contrary to the zebrafish and other teleosts and to Amia, Latimeria does not have an interoperculo-mandibular ligament and, therefore, does not have an opercular mechanism mediating mandible depression [36]. Second, and more importantly, it is cladistically more parsimonious to consider that these muscles were independently acquired in actinistians and halecostomes (2 steps) than to have one acquisition (in the node leading to osteichthyans) and various independent losses (at least in non-actinistian sarcopterygians, in cladistians, in chondrosteans and in ginglymodians) (see Fig. 1). On balance, our view is that the 'levator operculi' of Latimeria is unlikely to be homologous with the levator operculi of the zebrafish and other teleosts and of Amia (see Tables 4, 5)." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0011649 "levator operculi" NOT 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1186/1471-213X-8-24 "Diogo R, Hinits Y, Hughes SM, Development of mandibular, hyoid and hypobranchial muscles in the zebrafish: homologies and evolution of these muscles within bony fishes and tetrapods. BMC Developmental Biology (2008)" "the zebrafish, as most extant teleosts and the halecomorph Amia, has a muscle levator operculi (Figs.2, 3, 4, and 5A). Millot and Anthony [24] stated that Latimeria has a 'levator operculi'. However, whether this muscle is homologous to the levator operculi of zebrafish is doubtful for two main reasons. First, the muscles have distinct function: contrary to the zebrafish and other teleosts and to Amia, Latimeria does not have an interoperculo-mandibular ligament and, therefore, does not have an opercular mechanism mediating mandible depression [36]. Second, and more importantly, it is cladistically more parsimonious to consider that these muscles were independently acquired in actinistians and halecostomes (2 steps) than to have one acquisition (in the node leading to osteichthyans) and various independent losses (at least in non-actinistian sarcopterygians, in cladistians, in chondrosteans and in ginglymodians) (see Fig. 1). On balance, our view is that the 'levator operculi' of Latimeria is unlikely to be homologous with the levator operculi of the zebrafish and other teleosts and of Amia (see Tables 4, 5)." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0011650 "epihyoidean" 119203 "Selachii" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.398" "The depressor mandibulae of tetrapods, which opens the jaws, is the homologue of the levator operculi and epihyoidean. In mammals, the depressor mandibulae evolves into the stapedius (...)." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0011692 "enameloid" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1002/jez.b.21090 "Donoghue PCJ, Sansom IJ, Downs JP, Early evolution of vertebrate skeletal tissues and cellular interactions, and the canalization of skeletal development. Journal of Experimental Zoology (Mol Dev Evol) (2006) Figure 1" "Origin of enamel predates the evolution of gnathostomes. [curator]" bgee ANN 2013-07-08 HOM:0000007 "historical homology" UBERON:0011693 "extraembryonic portion of umbilical artery" 9347 "Eutheria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1016/j.cbpa.2007.01.029 "Mess A, Carter AM, Evolution of the placenta during the early radiation of placental mammals. Comparative Biochemistry and Physiology - Part A: Molecular and Integrative Physiology (2007)" "Two umbilical arteries and one vein are characters of the common ancestor of living placental mammals. [curator]" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0011694 "embryo portion of umbilical artery" 9347 "Eutheria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1016/j.cbpa.2007.01.029 "Mess A, Carter AM, Evolution of the placenta during the early radiation of placental mammals. Comparative Biochemistry and Physiology - Part A: Molecular and Integrative Physiology (2007)" "Two umbilical arteries and one vein are characters of the common ancestor of living placental mammals. [curator]" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0011696 "left extraembryonic umbilical artery" 9347 "Eutheria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1016/j.cbpa.2007.01.029 "Mess A, Carter AM, Evolution of the placenta during the early radiation of placental mammals. Comparative Biochemistry and Physiology - Part A: Molecular and Integrative Physiology (2007)" "Two umbilical arteries and one vein are characters of the common ancestor of living placental mammals. [curator]" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0011697 "right extraembryonic umbilical artery" 9347 "Eutheria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1016/j.cbpa.2007.01.029 "Mess A, Carter AM, Evolution of the placenta during the early radiation of placental mammals. Comparative Biochemistry and Physiology - Part A: Molecular and Integrative Physiology (2007)" "Two umbilical arteries and one vein are characters of the common ancestor of living placental mammals. [curator]" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0011698 "midgut loop" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0521617147 "Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut." bgee ANN 2013-07-05 HOM:0000007 "historical homology" UBERON:0011737 "caudate lobe hepatic sinusoid" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001117, negated: false, taxon ID: 7742 - entity: UBERON:0001281, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0011738 "quadrate lobe hepatic sinusoid" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001116, negated: false, taxon ID: 7742 - entity: UBERON:0001281, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0011742 "aortic valve leaflet" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1161/CIRCRESAHA.109.201566 "Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009)" "The four-chambered vertebrate heart has aortic and pulmonic semilunar (SL) valves at the arterial pole as well as mitral and tricuspid valves separating the atria and ventricles. (...) Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0011745 "pulmonary valve leaflets" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1161/CIRCRESAHA.109.201566 "Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009)" "The four-chambered vertebrate heart has aortic and pulmonic semilunar (SL) valves at the arterial pole as well as mitral and tricuspid valves separating the atria and ventricles. (...) Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human." bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0011754 "genital swelling" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" ISBN:978-0813815541 "Schatten H, Constantinescu G, Comparative Reproductive Biology (2007) p.1-4" "Genital labioscrotal swellings are the mammal embryonic structures that generate the male scrotum or the female labia majora. [curator]" bgee ANN 2013-08-30 HOM:0000007 "historical homology" UBERON:0011755 "female labial swelling" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000474, negated: false, taxon ID: 7742 - entity: UBERON:0011754, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0011765 "jugular lymph sac" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1016/j.ydbio.2010.01.002 "Peyrot SM, Martin BL, Harland RM, Lymph heart musculature is under distinct developmental control from lymphatic endothelium. Developmental Biology (2010)" "Lymph hearts are pulsatile organs, present in lower vertebrates, that function to propel lymph into the venous system. Although they are absent in mammals, the initial veno-lymphatic plexus that forms during mammalian jugular lymph sac development has been described as the vestigial homologue of the nascent stage of ancestral anterior lymph hearts." bgee ANN 2013-07-01 HOM:0000007 "historical homology" UBERON:0011765|UBERON:0015202 "jugular lymph sac|lymph heart" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1016/j.ydbio.2010.01.002 "Peyrot SM, Martin BL, Harland RM, Lymph heart musculature is under distinct developmental control from lymphatic endothelium. Developmental Biology (2010)" "Lymph hearts are pulsatile organs, present in lower vertebrates, that function to propel lymph into the venous system. Although they are absent in mammals, the initial veno-lymphatic plexus that forms during mammalian jugular lymph sac development has been described as the vestigial homologue of the nascent stage of ancestral anterior lymph hearts." bgee ANN 2013-07-01 HOM:0000007 "historical homology" UBERON:0011768 "pineal gland stalk" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" ISBN:978-0471210054 "Butler AB, Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.66" "The epithalamus contains the epiphysis (pineal gland and related structures), which is located at the end of a stalk, the epiphyseal stalk." bgee ANN 2013-06-11 HOM:0000007 "historical homology" UBERON:0011779 "nerve of head region" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 33213 - entity: UBERON:0001021, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0011779 "nerve of head region" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 7742 - entity: UBERON:0001021, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0011817 "skin appendage placode" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:25963196 "Musser JM, Wagner GP, Prum RO, Nuclear beta-catenin localization supports homology of feathers, avian scutate scales, and alligator scales in early development. Evol Dev (2015)" "Nuclear beta-catenin localization supports homology of feathers, avian scutate scales, and alligator scales in early development...To investigate the homology of feathers and archosaur scales we examined patterns of nuclear beta-catenin localization during early development of feathers and different bird and alligator scales. In birds, nuclear beta-catenin is first localized to the feather placode, and then exhibits a dynamic pattern of localization in both epidermis and dermis of the feather bud. We found that asymmetric avian scutate scales and alligator scales share similar patterns of nuclear beta-catenin localization with feathers. This supports the hypothesis that feathers, scutate scales, and alligator scales are homologous during early developmental stages, and are derived from early developmental stages of an asymmetric scale present in the archosaur ancestor. Furthermore, given that the earliest stage of beta-catenin localization in feathers and archosaur scales is also found in placodes of several mammalian skin appendages, including hair and mammary glands, we hypothesize that a common skin appendage placode originated in the common ancestor of all amniotes. We suggest a skin placode should not be defined by anatomical features, but as a local, organized molecular signaling center from which an epidermal appendage develops." bgee ANN 2016-10-03 HOM:0000007 "historical homology" UBERON:0011817 "skin appendage placode" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:25963196 "Musser JM, Wagner GP, Prum RO, Nuclear beta-catenin localization supports homology of feathers, avian scutate scales, and alligator scales in early development. Evol Dev (2015)" "Nuclear beta-catenin localization supports homology of feathers, avian scutate scales, and alligator scales in early development...To investigate the homology of feathers and archosaur scales we examined patterns of nuclear beta-catenin localization during early development of feathers and different bird and alligator scales. In birds, nuclear beta-catenin is first localized to the feather placode, and then exhibits a dynamic pattern of localization in both epidermis and dermis of the feather bud. We found that asymmetric avian scutate scales and alligator scales share similar patterns of nuclear beta-catenin localization with feathers. This supports the hypothesis that feathers, scutate scales, and alligator scales are homologous during early developmental stages, and are derived from early developmental stages of an asymmetric scale present in the archosaur ancestor. Furthermore, given that the earliest stage of beta-catenin localization in feathers and archosaur scales is also found in placodes of several mammalian skin appendages, including hair and mammary glands, we hypothesize that a common skin appendage placode originated in the common ancestor of all amniotes. We suggest a skin placode should not be defined by anatomical features, but as a local, organized molecular signaling center from which an epidermal appendage develops." bgee ANN 2016-10-03 HOM:0000007 "historical homology" UBERON:0011903 "gizzard smooth muscle" 8492 "Archosauria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0005052, negated: false, taxon ID: 8492" bgee HOM:0000007 "historical homology" UBERON:0011903 "gizzard smooth muscle" 8782 "Aves" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0005052, negated: false, taxon ID: 8782" bgee HOM:0000007 "historical homology" UBERON:0011903 "gizzard smooth muscle" 117571 "Euteleostomi" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001135, negated: false, taxon ID: 33213 - entity: UBERON:0005052, negated: false, taxon ID: 117571" bgee HOM:0000007 "historical homology" UBERON:0011997 "coelom" 33213 "Bilateria" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" PMID:24010725 "Kaul-Strehlow S, Stach T, A detailed description of the development of the hemichordate Saccoglossus kowalevskii using SEM, TEM, Histology and 3D-reconstructions. Front Zool (2013)" "By comparing our results with those reported from other deuterostomes such as echinoderms, pterobranchs, and cephalochordates, we argue that instead of an echinoid-type coelom formation, it is more likely that coelom formation in the last common ancestor of Deuterostomia was by a single anterior protocoel and paired meso- and metacoela evaginating from the middle and posterior regions of the endoderm, respectively. Consequently, the aforementioned echinoid-type of coelom formation has to be regarded as a derived condition that evolved within echinoderms." bgee ANN 2013-09-24 HOM:0000007 "historical homology" UBERON:0012054 "myocoele" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1038/sj.embor.embor920 "Hollway GE, Currie PD, Myotome meanderings. Cellular morphogenesis and the making of muscle. EMBO Rep.(2003)" "In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome." bgee ANN 2013-07-11 HOM:0000007 "historical homology" UBERON:0012059 "right lung lower lobe bronchiole" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002171, negated: false, taxon ID: 40674 - entity: UBERON:0002186, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0012118 "infraspinatus tendon" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000043, negated: false, taxon ID: 7742 - entity: UBERON:0001477, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0012168 "umbilical cord blood" 9347 "Eutheria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000178, negated: false, taxon ID: 33208 - entity: UBERON:0001310, negated: false, taxon ID: 9347" bgee HOM:0000007 "historical homology" UBERON:0012175 "acoustico-facial VII-VIII ganglion complex" 89593 "Craniata" CIO:0000005 "low confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...)" bgee ANN 2013-06-14 HOM:0000007 "historical homology" UBERON:0012193 "phrenic vein" NOT 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001103, negated: true, taxon ID: 32524 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0012193 "phrenic vein" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001103, negated: false, taxon ID: 40674 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0012239 "urinary bladder vasculature" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001255, negated: false, taxon ID: 32523 - entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0012239 "urinary bladder vasculature" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001255, negated: false, taxon ID: 32524 - entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0012275 "meso-epithelium" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000926, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0012275 "meso-epithelium" NOT 33213 "Bilateria" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0000926, negated: true, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0012363 "thyroid follicle epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0005305, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0012466 "extraembryonic cavity" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1387/ijdb.092935md "Dobreva MP, Pereira PN, Deprest J, Zwijsen A, On the origin of amniotic stem cells: of mice and men. The International Journal of Developmental Biology (2010)" "The profound differences in the development of the extraembryonic membranes and cavities between primates and rodents may result in comparing cell types of different developmental origins, eventually leading to missinterpretations." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0012466 "extraembryonic cavity" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:23050970 "Sheng G, Foley AC, Diversification and conservation of the extraembryonic tissues in mediating nutrient uptake during amniote development. Annals of the New York Academy of Sciences (2012)" "Although all amniotes start with a similar 'tool kit' of extraembryonic tissues, an enormous diversity of extraembryonic tissue formation has evolved to accommodate embryological and physiological constraints unique to their developmental programs. (...) All amniotes contain the following four extraembryonic components: the amnion, chorion, yolk sac, and allantois (Fig. 1C). Like the intraembryonic tissues, these extraembryonic tissues are composed of cells representing the three germ layers: ectoderm, mesoderm, and endoderm.(...) A comparative knowledge of these extraembryonic tissues and their role in nutrient uptake during development is required to fully appreciate the adaptive changes in placental mammals. (...) The chorion marks the external boundary of the embryo. The space between the amnion and the chorion is the extraembryonic coelomic (body) cavity." bgee ANN 2013-07-10 HOM:0000007 "historical homology" UBERON:0012474 "hepatic cecum" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:21052758 "Wang Y, Zhang S, Identification and expression of liver-specific genes after LPS challenge in amphioxus: the hepatic cecum as liver-like organ and (pre-hepatic) acute phase response. Functional and integrative genomics (2011)" "Liver is present in all vertebrates and central to many physiological processes including processing of nutrients from ingested food, plasma protein synthesis, hormone production, and detoxification. However, its evolutionary origin remains open to date. Liver is also the principal organ of acute phase response (APR) but when the vertebrate-like APR regulatory network emerges during the chordate evolution is unknown. (...) These similarities in liver/hepatic cecum-specific genes, APR, and regulatory networks between amphioxus and zebrafish supports the idea that hepatic cecum in amphioxus is the ""pre-hepatic"" organ homologous to vertebrate liver and acts as an immunological organ, playing an important role in APR. (...) In this study, by combining global genome survey and qRT-PCR data sets, we clearly demonstrate the presence of 58 vertebrate (zebrafish) liver-specific genes in amphioxus (hepatic cecum-specific genes), including genes encoding metabolic or catabolic enzymes and blood components, which are expressed in atissue-specific manner in the hepatic cecum." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0012481 "cloacal epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000162, negated: false, taxon ID: 7742 - entity: UBERON:0000483, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0013124 "left posterior cardinal vein" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000468, negated: false, taxon ID: 33208 - entity: UBERON:0002065, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0013136 "vein of lip" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0001833, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0013143 "gastrocnemius vein" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001388, negated: false, taxon ID: 40674 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0013146 "venous system of brain" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000034 "non-traceable author statement" no:id "Holland LZ, October 7th 2010 in Lausanne (zholland@ucsd.edu)" bgee AUC 2013-05-15 HOM:0000007 "historical homology" UBERON:0013151 "choroidal artery" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0001886, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0013161 "left lateral ventricle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001893, negated: false, taxon ID: 7742 - entity: UBERON:0002285, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0013162 "right lateral ventricle" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001893, negated: false, taxon ID: 7742 - entity: UBERON:0002285, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0013239 "future glans penis" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001299" bgee HOM:0000007 "historical homology" UBERON:0013477 "blowhole" 9722 "Odontoceti" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:25440939 "Buono MR, Fernandez MS, Fordyce RE, Reidenberg JS, Anatomy of nasal complex in the southern right whale, Eubalaena australis (Cetacea, Mysticeti). J Anat (2015)" "The two groups of modern cetaceans, toothed whales, dolphins and porpoises (Odontoceti) and baleen whales (Mysticeti), exhibit quite different configurations of the epicranial narial passages in response to different functions. Mysticetes retain two separate nostrils as paired blowholes in mysticetes, but odontocetes have a single blowhole. Major differences also exist in the internal nasal anatomy between the two cetacean groups." bgee ANN 2018-03-26 HOM:0000007 "historical homology" UBERON:0013477 "blowhole" 9761 "Mysticeti" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:25440939 "Buono MR, Fernandez MS, Fordyce RE, Reidenberg JS, Anatomy of nasal complex in the southern right whale, Eubalaena australis (Cetacea, Mysticeti). J Anat (2015)" "The two groups of modern cetaceans, toothed whales, dolphins and porpoises (Odontoceti) and baleen whales (Mysticeti), exhibit quite different configurations of the epicranial narial passages in response to different functions. Mysticetes retain two separate nostrils as paired blowholes in mysticetes, but odontocetes have a single blowhole. Major differences also exist in the internal nasal anatomy between the two cetacean groups." bgee ANN 2018-03-26 HOM:0000007 "historical homology" UBERON:0013498 "vestibulo-cochlear VIII ganglion complex" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001648, negated: false, taxon ID: 89593 - entity: UBERON:0001714, negated: false, taxon ID: 89593" bgee HOM:0000007 "historical homology" UBERON:0013511 "ambiens muscle" 8457 "Sauropsida" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.391" "The ambiens of reptiles and the iliotibialis of amphibians are likely homologues of the sartorius." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0013648 "masseteric artery" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001597, negated: false, taxon ID: 40674 - entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0013694 "brain endothelium" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000955, negated: false, taxon ID: 33213 - entity: UBERON:0001986, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0013695 "colon endothelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001155, negated: false, taxon ID: 7742 - entity: UBERON:0001986, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0013697 "exocrine pancreas epithelium" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000017, negated: false, taxon ID: 7776 - entity: UBERON:0000483, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0013701 "main body axis" 6072 "Eumetazoa" CIO:0000005 "low confidence from single evidence" ECO:0000067 "developmental similarity evidence" DOI:10.1242/dev.141507 "Genikhovich G, Technau U, On the evolution of bilaterality. Development (2017)" "Comparative embryology data show that a cnidarian is, in essence, a 'stretched gastrula', where the main body axis corresponds exactly to the animal-vegetal axis of the egg. The body plan of the bilaterian early gastrulae is very comparable. Therefore, we argue below that the body plan of the bilaterally symmetric early planula of Nematostella can be used as a proxy for the body plan of the hypothetical bilaterally symmetric cnidarian-bilaterian ancestor, considering the ‘blind gut’ and the ‘through gut’ urbilaterian hypotheses separately." bgee ANN 2017-10-10 HOM:0000007 "historical homology" UBERON:0013701 "main body axis" 6072 "Eumetazoa" CIO:0000005 "low confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.1242/dev.141507 "Genikhovich G, Technau U, On the evolution of bilaterality. Development (2017)" "The emergence of bilaterality was a major evolutionary transition, as it allowed animals to evolve more complex body plans. Therefore, how bilaterality evolved and whether it evolved once or several times independently is a fundamental issue in evolutionary developmental biology. Recent findings from non-bilaterian animals, in particular from Cnidaria, the sister group to Bilateria, have shed new light into the evolutionary origin of bilaterality. Here, we compare the molecular control of body axes in radially and bilaterally symmetric cnidarians and bilaterians, identify the minimal set of traits common for Bilateria, and evaluate whether bilaterality arose once or more than once during evolution." bgee ANN 2017-10-10 HOM:0000007 "historical homology" UBERON:0013731 "basilar papilla" 8457 "Sauropsida" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1007/s10162-016-0579-3 "Manley GA, Comparative Auditory Neuroscience: Understanding the Evolution and Function of Ears. J Assoc Res Otolaryngol (2017)" "Where the basilar papilla of non-mammalian amniotes (and its later relative, the mammalian organ of Corti) came from and when it originated is still an open question. One of the reasons the present discussion does not deal with the (fascinating!) group of amphibians is that neither of their one or two hearing organs is clearly homologous to the amniote basilar papilla (Smothermann and Narins 2004). Thus, the modern amphibians, that are placed in their own group (Lissamphibia) and differ in many respects from the ancestral amphibians from which the amniotes arose, are no help in deciding on the origin of the basilar papilla. The amniote basilar papilla is defined as a patch of sensory hair cells that is supported on a free basilar membrane and lies (at least originally) between the saccular and lagenar maculae." bgee ANN 2018-03-26 HOM:0000007 "historical homology" UBERON:0013755 "arterial blood" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000178, negated: false, taxon ID: 33208 - entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0013756 "venous blood" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000178, negated: false, taxon ID: 33208 - entity: UBERON:0001638, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0013757 "capillary blood" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000178, negated: false, taxon ID: 33208 - entity: UBERON:0001982, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0014371 "future telencephalon" NOT 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001893" bgee HOM:0000007 "historical homology" UBERON:0014371 "future telencephalon" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001893" bgee HOM:0000007 "historical homology" UBERON:0014387 "mesenchyme derived from neural crest" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002342, negated: false, taxon ID: 89593 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0014388 "kidney collecting duct epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001232, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0014451 "tongue taste bud" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001723, negated: false, taxon ID: 32523 - entity: UBERON:0001727, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0014475 "endostylar duct" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1007/s00427-004-0450-0 "Kluge B, Renault N, Rohr KB, Anatomical and molecular reinvestigation of lamprey endostyle development provides new insight into thyroid gland evolution. Development genes and evolution (2005)" "Analysing lamprey endostyle development using semi-thin histological sections, immunohistochemical detection of thyroid hormone, and the molecular marker thyroid transcription factor1 (Ttf1) refines our current view of the homology between endostyle and thyroid gland. In contrast to earlier literature, we find that a duct always persists to connect the endostyle lumen to the pharynx, a structure that resembles the thyroglossal duct in thyroid development and could further support the homology between endostyle and thyroid." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0014644 "cerebrocerebellum" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" ISBN:978-0471210054 "Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.242" "Descriptions of the cerebella of mammals sometimes include terms such as paleocerebellum, archicerebellum, and neocerebellum to refer to the relative ages or stages of evolutionary development of the major components of these structure...In particular, the term 'neocerebellum' was applied to large lateral extensions of the cerebellum in mammals. A number of investigators of the comparative anatomy of the cerebellum now regard avian and mammalian cerebella as having a very similar organization; therefore, if the term 'neocerebellum' has any utility at all, it should be appied both to birds and mammals." bgee ANN 2017-09-26 HOM:0000007 "historical homology" UBERON:0014644 "cerebrocerebellum" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471210054 "Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.246" "In mammals, a foliated corpus cerebelli also is present as the midline vermis. In addition, the mammalian cerebellum shows a large, highly foliated, lateral expansion known as the neocerebellum. Similar patterns may be seen in the cerebella of cartilaginous fishes, amphibians, and reptiles. In birds, the corpus cerebelli becomes foliated into 10 folia. Whether the lateral expansion in mammals is in fact 'new' or is merely a variation on the same foliated plan as seen in birds is a matter now being debated. Evidence does exist, however, to suggest that, rather than being a new addition to the cerebellum, the neocerebellum is, in fact, merely a lateral expansion of the corpus cerebelli." bgee ANN 2017-09-26 HOM:0000007 "historical homology" UBERON:0014649 "white matter of medulla oblongata" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001896, negated: false, taxon ID: 7742 - entity: UBERON:0002316, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0014705 "median lingual swelling epithelium" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0006756, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0014756 "Wulst" 8782 "Aves" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:26554047 "Karten HJ, Vertebrate brains and evolutionary connectomics: on the origins of the mammalian 'neocortex'. Philos Trans R Soc Lond B Biol Sci (2015)" "In birds, a separate pallial region, the dorsomedial 'wulst' or 'bump' shares many properties with the mammalian striate cortex, though with the output layer lying most externally...Wulst, 'bump' homologous to mammalian striate cortex" bgee ANN 2018-03-27 HOM:0000007 "historical homology" UBERON:0014783 "cloacal muscle" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000162, negated: false, taxon ID: 7742 - entity: UBERON:0001630, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0014786 "extraembryonic umbilical vein" 9347 "Eutheria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" DOI:10.1016/j.cbpa.2007.01.029 "Mess A, Carter AM, Evolution of the placenta during the early radiation of placental mammals. Comparative Biochemistry and Physiology - Part A: Molecular and Integrative Physiology (2007)" "Two umbilical arteries and one vein are characters of the common ancestor of living placental mammals. [curator]" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0014787 "left extraembryonic umbilical vein" 9347 "Eutheria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.608 and Figure 19-4, D" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0014788 "right extraembryonic umbilical vein" 9347 "Eutheria" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.608 and Figure 19-4, D" bgee ANN 2013-09-09 HOM:0000007 "historical homology" UBERON:0014791 "musculature of forelimb stylopod" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001015, negated: false, taxon ID: 7776 - entity: UBERON:0003822, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0014791 "musculature of forelimb stylopod" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001015, negated: false, taxon ID: 7776 - entity: UBERON:0003822, negated: false, taxon ID: 8287" bgee HOM:0000007 "historical homology" UBERON:0014840 "supracoracoideus muscle" 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:20807270 "Abdala V, Diogo R, Comparative anatomy, homologies and evolution of the pectoral and forelimb musculature of tetrapods with special attention to extant limbed amphibians and reptiles. J Anat (2010)" "It is now accepted that the mammalian supraspinatus and infraspinatus, which usually connect the dorsal region of the pectoral girdle to the proximal region of the arm, derive from the supracoracoideus (Tables 1 and 2), a muscle that lies ventral, not dorsal, to the pectoral girdle in most other extant tetrapods (e.g. Kardong, 2002; Diogo et al. 2009a)." bgee ANN 2017-02-15 HOM:0000007 "historical homology" UBERON:0014854 "anterior leaflet of mitral valve" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23755108 "Jensen B, van den Berg G, van den Doel R, Oostra RJ, Wang T, Moorman AF, Development of the hearts of lizards and snakes and perspectives to cardiac evolution. PLoS One (2013)" "The mesenchyme of the atrioventricular canal is strikingly similar in amniotes with a large cushion dorsally and ventrally. This suggests that the fully formed left and right atrioventricular valve of the reptilian heart are homologous to the septal leaflet of the right-sided tricuspid valve and the aortic leaflet of the left-sided mitral valve of the mammalian heart." bgee ANN 2015-04-13 HOM:0000007 "historical homology" UBERON:0014888 "iliotibialis muscle" 8292 "Amphibia" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.391" "The ambiens of reptiles and the iliotibialis of amphibians are likely homologues of the sartorius." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:0014891 "brainstem white matter" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002298, negated: false, taxon ID: 7711 - entity: UBERON:0002316, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0015117 "lamina terminalis of cerebral hemisphere" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0005078" bgee HOM:0000007 "historical homology" UBERON:0015120 "right outer canthus" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 7742 - entity: UBERON:0006726, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0015121 "left outer canthus" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 7742 - entity: UBERON:0006726, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0015129 "epicardial fat" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 7742 - entity: UBERON:0000948|UBERON:0002376, negated: false, taxon ID: 7742 - entity: UBERON:0001013, negated: false, taxon ID: 7742 - entity: UBERON:0002348, negated: false, taxon ID: 7742 - entity: UBERON:0002425, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0015129 "epicardial fat" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 8782 - entity: UBERON:0001013, negated: false, taxon ID: 7742 - entity: UBERON:0002348, negated: false, taxon ID: 7742 - entity: UBERON:0002425, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0015129 "epicardial fat" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 40674 - entity: UBERON:0001013, negated: false, taxon ID: 7742 - entity: UBERON:0002348, negated: false, taxon ID: 7742 - entity: UBERON:0002425, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0015161 "inferior branch of oculomotor nerve" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0001643, negated: false, taxon ID: 89593 - entity: UBERON:0006322, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0015162 "superior branch of oculomotor nerve" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0001643, negated: false, taxon ID: 89593 - entity: UBERON:0006323, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0015172 "endometrial blood vessel" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001295, negated: false, taxon ID: 40674 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0015202 "lymph heart" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1016/j.ydbio.2010.01.002 "Peyrot SM, Martin BL, Harland RM, Lymph heart musculature is under distinct developmental control from lymphatic endothelium. Developmental Biology (2010)" "Lymph hearts are pulsatile organs, present in lower vertebrates, that function to propel lymph into the venous system. Although they are absent in mammals, the initial veno-lymphatic plexus that forms during mammalian jugular lymph sac development has been described as the vestigial homologue of the nascent stage of ancestral anterior lymph hearts." bgee ANN 2018-03-26 HOM:0000007 "historical homology" UBERON:0015214 "arcuate ligament" NOT 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000211, negated: false, taxon ID: 7742 - entity: UBERON:0001103, negated: true, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0015214 "arcuate ligament" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000211, negated: false, taxon ID: 40674 - entity: UBERON:0001103, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0015249 "digit skin" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0002544, negated: false, taxon ID: 8782" bgee HOM:0000007 "historical homology" UBERON:0015249 "digit skin" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0002544, negated: false, taxon ID: 32523 - entity: UBERON:0002544|UBERON:4000172, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0015249 "digit skin" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0002544, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0015249 "digit skin" NOT 32524 "Amniota" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0002544, negated: true, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0015249 "digit skin" NOT 1338369 "Dipnotetrapodomorpha" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0002544|UBERON:2000271, negated: true, taxon ID: 1338369" bgee HOM:0000007 "historical homology" UBERON:0015418 "urethra mesenchymal layer" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000057, negated: false, taxon ID: 40674 - entity: UBERON:0003104, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0015790 "autopod skin" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0002470, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0015790 "autopod skin" NOT 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0002470, negated: true, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0015790 "autopod skin" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0002470, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0015796 "liver blood vessel" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0002107, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0015807 "ear epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001690, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0015807 "ear epithelium" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001690, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0015808 "eye epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000019, negated: false, taxon ID: 7742 - entity: UBERON:0000483, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0015813 "middle ear epithelium" 8292 "Amphibia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001756, negated: false, taxon ID: 8292" bgee HOM:0000007 "historical homology" UBERON:0015813 "middle ear epithelium" 8457 "Sauropsida" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001756, negated: false, taxon ID: 8457" bgee HOM:0000007 "historical homology" UBERON:0015813 "middle ear epithelium" 8459 "Testudines" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001756, negated: false, taxon ID: 8459" bgee HOM:0000007 "historical homology" UBERON:0015813 "middle ear epithelium" 8492 "Archosauria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001756, negated: false, taxon ID: 8492" bgee HOM:0000007 "historical homology" UBERON:0015813 "middle ear epithelium" 8504 "Lepidosauria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001756, negated: false, taxon ID: 8504" bgee HOM:0000007 "historical homology" UBERON:0015813 "middle ear epithelium" 9255 "Monotremata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001756, negated: false, taxon ID: 9255" bgee HOM:0000007 "historical homology" UBERON:0015813 "middle ear epithelium" NOT 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001756, negated: true, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0015813 "middle ear epithelium" 32525 "Theria" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001756, negated: false, taxon ID: 32525" bgee HOM:0000007 "historical homology" UBERON:0015813 "middle ear epithelium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001756, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0015813 "middle ear epithelium" NOT 40674 "Mammalia" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001756, negated: true, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0015814 "outer ear epithelium" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001691, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0015814 "outer ear epithelium" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001691, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0015833 "foregut epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001041, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0015833 "foregut epithelium" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0001041, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0015870 "lymph node of head" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000029, negated: false, taxon ID: 40674 - entity: UBERON:0000033, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0015871 "facial lymph node" 40674 "Mammalia" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000029, negated: false, taxon ID: 40674 - entity: UBERON:0001456, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0016398 "lymph node of lower limb" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000029, negated: false, taxon ID: 40674 - entity: UBERON:0002103, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0016399 "lymph node of upper limb" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000024|UBERON:0002102, negated: false, taxon ID: 32524 - entity: UBERON:0000029, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0016405 "pulmonary capillary" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001982, negated: false, taxon ID: 7711 - entity: UBERON:0002048|UBERON:0006860, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0016481 "bronchial lymph node" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000029, negated: false, taxon ID: 40674 - entity: UBERON:0002185, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0016554 "white matter of midbrain" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001891, negated: false, taxon ID: 7711 - entity: UBERON:0002316, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0016565 "cerebral blood vessel" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0002037, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0016879 "future central nervous system" 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001017 - UBERON:0001017 - UBERON:0001017 - UBERON:0001017" bgee HOM:0000007 "historical homology" UBERON:0016880 "future nervous system" 6072 "Eumetazoa" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001016" bgee HOM:0000007 "historical homology" UBERON:0016884 "shoulder joint" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0001467, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0016885 "epithelium of terminal part of digestive tract" NOT 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000483, negated: false, taxon ID: 33208 - entity: UBERON:0006866, negated: true, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0018112 "rectum smooth muscle tissue" NOT 33213 "Bilateria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001052, negated: true, taxon ID: 33213 - entity: UBERON:0001135, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0018151 "skin of upper lip" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0001834, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0018154 "ligament of middle ear" 8292 "Amphibia" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000211, negated: false, taxon ID: 7742 - entity: UBERON:0001756, negated: false, taxon ID: 8292" bgee HOM:0000007 "historical homology" UBERON:0018154 "ligament of middle ear" 8457 "Sauropsida" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000211, negated: false, taxon ID: 7742 - entity: UBERON:0001756, negated: false, taxon ID: 8457" bgee HOM:0000007 "historical homology" UBERON:0018154 "ligament of middle ear" 8459 "Testudines" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000211, negated: false, taxon ID: 7742 - entity: UBERON:0001756, negated: false, taxon ID: 8459" bgee HOM:0000007 "historical homology" UBERON:0018154 "ligament of middle ear" 8492 "Archosauria" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000211, negated: false, taxon ID: 7742 - entity: UBERON:0001756, negated: false, taxon ID: 8492" bgee HOM:0000007 "historical homology" UBERON:0018154 "ligament of middle ear" 8504 "Lepidosauria" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000211, negated: false, taxon ID: 7742 - entity: UBERON:0001756, negated: false, taxon ID: 8504" bgee HOM:0000007 "historical homology" UBERON:0018154 "ligament of middle ear" 9255 "Monotremata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000211, negated: false, taxon ID: 40674 - entity: UBERON:0001756, negated: false, taxon ID: 9255" bgee HOM:0000007 "historical homology" UBERON:0018154 "ligament of middle ear" NOT 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000211, negated: false, taxon ID: 7742 - entity: UBERON:0001756, negated: true, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0018154 "ligament of middle ear" 32525 "Theria" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000211, negated: false, taxon ID: 40674 - entity: UBERON:0001756, negated: false, taxon ID: 32525" bgee HOM:0000007 "historical homology" UBERON:0018154 "ligament of middle ear" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000211, negated: false, taxon ID: 40674 - entity: UBERON:0001756, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0018154 "ligament of middle ear" NOT 40674 "Mammalia" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000211, negated: false, taxon ID: 40674 - entity: UBERON:0001756, negated: true, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0018227 "pulmonary lymphatic vessel" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001473, negated: false, taxon ID: 32523 - entity: UBERON:0002048|UBERON:0006860, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0018243 "thymic artery" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0002370, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0018246 "thyroid vein" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0002046, negated: false, taxon ID: 7711 - entity: UBERON:0002046|UBERON:0006870, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0018246 "thyroid vein" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0002046, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0018251 "meningeal vein" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0002360, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0018256 "lacrimal vein" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0001817, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0018544 "trigeminal nerve muscle" 89593 "Craniata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001630, negated: false, taxon ID: 33208 - entity: UBERON:0001645, negated: false, taxon ID: 89593" bgee HOM:0000007 "historical homology" UBERON:0018674 "heart vasculature" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 7742 - entity: UBERON:0000948|UBERON:0002376, negated: false, taxon ID: 7742 - entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0018674 "heart vasculature" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 8782 - entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0018674 "heart vasculature" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 40674 - entity: UBERON:0002049|UBERON:0007798, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0019204 "skin epithelium" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0000483, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0019258 "white matter of hindbrain" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002028, negated: false, taxon ID: 7711 - entity: UBERON:0002316, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0019261 "white matter of forebrain" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001890, negated: false, taxon ID: 7711 - entity: UBERON:0002316, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0019262 "white matter of myelencephalon" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002316, negated: false, taxon ID: 7742 - entity: UBERON:0005290, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0019263 "gray matter of hindbrain" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002020, negated: false, taxon ID: 7742 - entity: UBERON:0002028, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0019264 "gray matter of forebrain" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001890, negated: false, taxon ID: 7711 - entity: UBERON:0002020, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0019267 "gray matter of midbrain" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001891, negated: false, taxon ID: 7711 - entity: UBERON:0002020, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0019269 "gray matter of diencephalon" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001894, negated: false, taxon ID: 7711 - entity: UBERON:0002020, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0019291 "white matter of metencephalon" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001895, negated: false, taxon ID: 7742 - entity: UBERON:0002316, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0019292 "white matter of pons" 8782 "Aves" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000988, negated: false, taxon ID: 8782 - entity: UBERON:0002316, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0019292 "white matter of pons" NOT 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000988, negated: true, taxon ID: 32524 - entity: UBERON:0002316, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0019292 "white matter of pons" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000988, negated: false, taxon ID: 40674 - entity: UBERON:0002316, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0019304 "sensory organ epithelium" 33208 "Metazoa" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000020, negated: false, taxon ID: 33208 - entity: UBERON:0000483, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0020550 "auricular blood vessel" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001690, negated: false, taxon ID: 7742 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0020550 "auricular blood vessel" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001690, negated: false, taxon ID: 32523 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0022292 "splenic arteriole" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001980, negated: false, taxon ID: 7742 - entity: UBERON:0002106, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0022298 "lower eyelid nerve" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0001713, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0022299 "upper eyelid nerve" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0001712, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0022358 "placenta blood vessel" 9347 "Eutheria" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0001987, negated: false, taxon ID: 9347" bgee HOM:0000007 "historical homology" UBERON:0022358 "placenta blood vessel" 32525 "Theria" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001981, negated: false, taxon ID: 7711 - entity: UBERON:0001987, negated: false, taxon ID: 32525" bgee HOM:0000007 "historical homology" UBERON:0024045 "white matter of the cerebellar cortex" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002129, negated: false, taxon ID: 7711 - entity: UBERON:0002316, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0034708 "cerebellum marginal layer" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002037, negated: false, taxon ID: 7776 - entity: UBERON:0004062, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0034709 "hindbrain marginal layer" 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002028, negated: false, taxon ID: 7711 - entity: UBERON:0004062, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0034717 "integumental taste bud" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001727, negated: false, taxon ID: 7742 - entity: UBERON:0002416, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:0034719 "lip taste bud" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001727, negated: false, taxon ID: 7742 - entity: UBERON:0001833, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0034721 "pharyngeal taste bud" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001042|UBERON:0006562, negated: false, taxon ID: 33213 - entity: UBERON:0001727, negated: false, taxon ID: 7742 - entity: UBERON:0006562, negated: false, taxon ID: 33213" bgee HOM:0000007 "historical homology" UBERON:0034724 "esophageal taste bud" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001043, negated: false, taxon ID: 7742 - entity: UBERON:0001727, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0034729 "sympathetic nerve" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000013, negated: false, taxon ID: 7742 - entity: UBERON:0001021, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0034729 "sympathetic nerve" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000013, negated: false, taxon ID: 32523 - entity: UBERON:0001021, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0034764 "remnant of cardiac valve" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0000946" bgee HOM:0000007 "historical homology" UBERON:0034875 "future pituitary gland" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0000007" bgee HOM:0000007 "historical homology" UBERON:0034878 "prechordal mesoderm" NOT 7711 "Chordata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0003063" bgee HOM:0000007 "historical homology" UBERON:0034878 "prechordal mesoderm" 7742 "Vertebrata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0003063" bgee HOM:0000007 "historical homology" UBERON:0034898 "alveolar ridge of premaxilla" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002244, negated: false, taxon ID: 7776 - entity: UBERON:0004103, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0034903 "left atrium endocardium" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450-451" bgee ANN 2015-02-16 HOM:0000007 "historical homology" UBERON:0034950 "lymph sac of lymph heart" 8342 "Anura" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1152/japplphysiol.00201.2013 "Hedrick MS, Hillman SS, Drewes RC, Withers PC, Lymphatic regulation in nonmammalian vertebrates. Journal of applied physiology (2013)" "The lymphatic system of anuran amphibians is characterized by large lymphatic sacs and two pairs of lymph hearts that return lymph into the venous circulation but no lymph vessels per se." bgee ANN 2017-10-24 HOM:0000007 "historical homology" UBERON:0034959 "right lymph heart" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000468, negated: false, taxon ID: 33208 - entity: UBERON:0011765|UBERON:0015202, negated: false, taxon ID: 7742 - entity: UBERON:0015202, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0034960 "left lymph heart" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000468, negated: false, taxon ID: 33208 - entity: UBERON:0011765|UBERON:0015202, negated: false, taxon ID: 7742 - entity: UBERON:0015202, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0034961 "embryonic lymph heart" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000922, negated: false, taxon ID: 33213 - entity: UBERON:0011765|UBERON:0015202, negated: false, taxon ID: 7742 - entity: UBERON:0015202, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0035005 "preputial swelling of male" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001332" bgee HOM:0000007 "historical homology" UBERON:0035020 "left vagus X nerve trunk" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001016, negated: false, taxon ID: 6072 - entity: UBERON:0003535, negated: false, taxon ID: 89593" bgee HOM:0000007 "historical homology" UBERON:0035021 "right vagus X nerve trunk" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001016, negated: false, taxon ID: 6072 - entity: UBERON:0003535, negated: false, taxon ID: 89593" bgee HOM:0000007 "historical homology" UBERON:0035036 "naris epithelium" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000003, negated: false, taxon ID: 32523 - entity: UBERON:0000483, negated: false, taxon ID: 33208" bgee HOM:0000007 "historical homology" UBERON:0035147 "axochord" 6340 "Annelida" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:25214631 "Lauri A, Brunet T, Handberg-Thorsager M, Fischer AH, Simakov O, Steinmetz PR, Tomer R, Keller PJ, Arendt D, Development of the annelid axochord: insights into notochord evolution. Science (2014)" "We identify a population of mesodermal cells in a developing invertebrate, the marine annelid Platynereis dumerilii, that converges and extends toward the midline and expresses a notochord-specific combination of genes. These cells differentiate into a longitudinal muscle, the axochord, that is positioned between central nervous system and axial blood vessel and secretes a strong collagenous extracellular matrix." bgee ANN 2017-11-21 HOM:0000007 "historical homology" UBERON:0035148 "presumptive axochord" 6340 "Annelida" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:25214631 "Lauri A, Brunet T, Handberg-Thorsager M, Fischer AH, Simakov O, Steinmetz PR, Tomer R, Keller PJ, Arendt D, Development of the annelid axochord: insights into notochord evolution. Science (2014)" "We identify a population of mesodermal cells in a developing invertebrate, the marine annelid Platynereis dumerilii, that converges and extends toward the midline and expresses a notochord-specific combination of genes. These cells differentiate into a longitudinal muscle, the axochord, that is positioned between central nervous system and axial blood vessel and secretes a strong collagenous extracellular matrix." bgee ANN 2017-11-21 HOM:0000007 "historical homology" UBERON:0035174 "right ear" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 7742 - entity: UBERON:0001690, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0035174 "right ear" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 7742 - entity: UBERON:0001690, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0035295 "left ear" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 7742 - entity: UBERON:0001690, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0035295 "left ear" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000033, negated: false, taxon ID: 7742 - entity: UBERON:0001690, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0035403 "hypophysial artery" 89593 "Craniata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000007, negated: false, taxon ID: 89593 - entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0035489 "branch of basilar artery" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001633, negated: false, taxon ID: 7742 - entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0035539 "esophageal artery" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001043, negated: false, taxon ID: 33213 - entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0035539 "esophageal artery" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001043, negated: false, taxon ID: 7742 - entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0035548 "colic artery" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001155, negated: false, taxon ID: 7742 - entity: UBERON:0001637, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0035602 "collar nerve cord" 10220 "Enteropneusta" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:24177053 "Miyamoto N, Wada H, Hemichordate neurulation and the origin of the neural tube. Nat Commun (2013)" "To investigate the potential homology between the collar cord and neural tube, we here examine the development of the collar cord in the enteropneust Balanoglossus simodensis, focusing on the expression patterns of genes known to be critical for the early patterning and formation of the chordate neural tube. We find conserved gene expression patterns between neurulations of hemichordates and chordates. The present results suggest that the origin of genetic mechanisms to form and pattern a tubular nervous system predates the diversification of hemichordates and chordates." bgee ANN 2018-03-27 HOM:0000007 "historical homology" UBERON:0035608 "dura mater lymph vessel" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001473, negated: false, taxon ID: 32523 - entity: UBERON:0002363, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0035642 "laryngeal nerve" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0001737, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0035648 "nerve innervating pinna" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0001757, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0035649 "nerve of penis" 8459 "Testudines" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000989, negated: false, taxon ID: 8459 - entity: UBERON:0001021, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0035649 "nerve of penis" 8492 "Archosauria" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000989, negated: false, taxon ID: 8492 - entity: UBERON:0001021, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0035649 "nerve of penis" 8509 "Squamata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000989, negated: false, taxon ID: 8509 - entity: UBERON:0001021, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0035649 "nerve of penis" 32524 "Amniota" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000989, negated: false, taxon ID: 32524 - entity: UBERON:0001021, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0035649 "nerve of penis" NOT 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000989, negated: true, taxon ID: 32524 - entity: UBERON:0001021, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0035649 "nerve of penis" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000989, negated: false, taxon ID: 40674 - entity: UBERON:0001021, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0035650 "nerve of clitoris" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001021, negated: false, taxon ID: 7711 - entity: UBERON:0001299|UBERON:0002411|UBERON:0004713, negated: false, taxon ID: 40674 - entity: UBERON:0002411, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0035662 "parotid vein" 32524 "Amniota" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001638, negated: false, taxon ID: 7711 - entity: UBERON:0001831, negated: false, taxon ID: 32524" bgee HOM:0000007 "historical homology" UBERON:0035767 "intrapulmonary bronchus" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002048|UBERON:0006860, negated: false, taxon ID: 7776 - entity: UBERON:0002185, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:0035814 "pericardial fat" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 7742 - entity: UBERON:0000948|UBERON:0002376, negated: false, taxon ID: 7742 - entity: UBERON:0001013, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0035814 "pericardial fat" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 8782 - entity: UBERON:0001013, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0035814 "pericardial fat" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 40674 - entity: UBERON:0001013, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0035815 "paracardial fat" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 7742 - entity: UBERON:0000948|UBERON:0002376, negated: false, taxon ID: 7742 - entity: UBERON:0001013, negated: false, taxon ID: 7742 - entity: UBERON:0002408, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0035815 "paracardial fat" 8782 "Aves" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 8782 - entity: UBERON:0001013, negated: false, taxon ID: 7742 - entity: UBERON:0002408, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0035815 "paracardial fat" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000948, negated: false, taxon ID: 40674 - entity: UBERON:0001013, negated: false, taxon ID: 7742 - entity: UBERON:0002408, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:0036071 "diaphragmaticus muscle" 8493 "Crocodylidae" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" DOI:10.1016/j.resp.2006.06.003 "Brainerd EL, Owerkowicz T, Functional morphology and evolution of aspiration breathing in tetrapods. Respiratory physiology and neurobiology (2006)" "Crocodylians, mammals and turtles have all evolved accessory respiratory muscles that reduce or eliminate their reliance on costal aspiration. These are all sometimes called diaphragm muscles, presumably by analogy with the mammalian diaphragm muscle, but they are not homologous structures." bgee ANN 2018-01-16 HOM:0000007 "historical homology" UBERON:0036146 "cardiopharyngeal field" 7711 "Chordata" CIO:0000005 "low confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:25903628 "Diogo R, Kelly RG, Christiaen L, Levine M, Ziermann JM, Molnar JL, Noden DM, Tzahor E, A new heart for a new head in vertebrate cardiopharyngeal evolution. Nature (2015)" "Molecular studies suggest that the amphioxus homologues of Tbx1, Nkx2-5 and Isl1 are expressed in overlapping mesodermal domains in the pharyngeal region101_103. This domain includes cells that also express the vertebrate cardiac markers Hand and Tbx20 (refs 59, 104) and is thought to produce the branchial artery, a possible - but controversial - homo-logue of the heart with diffuse contractility105. These observations raise the possibility that the LCA of extant chordates had a CPF." bgee ANN 2016-09-26 HOM:0000007 "historical homology" UBERON:0036146 "cardiopharyngeal field" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:25903628 "Diogo R, Kelly RG, Christiaen L, Levine M, Ziermann JM, Molnar JL, Noden DM, Tzahor E, A new heart for a new head in vertebrate cardiopharyngeal evolution. Nature (2015)" "lamprey embryos express homologues of Isl1, Nkx2-5 and Tbx1 in seemingly overlapping anterior and ventral mesodermal domains (58, 59, 60, 61), comparable with the patterns of their homologues in the amniote CPF [cardiopharyngeal field]. Interestingly, the emergence of heterogeneous head-muscle groups at the base of vertebrates coincided with the emergence of chambered hearts (62, 63) (Fig. 3). This intriguing correlation suggests that the two innovations are linked by their common developmental origin in the CPF." bgee ANN 2016-09-26 HOM:0000007 "historical homology" UBERON:0036218 "secondary prosencephalon" 7742 "Vertebrata" CIO:0000005 "low confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1111/dgd.12348 "Yamamoto K, Bloch S, Vernier P, New perspective on the regionalization of the anterior forebrain in Osteichthyes. Dev Growth Differ (2017)" "Our comparative analyses suggest that the presence of the three regions (telencephalon, ORR, hypothalamus) in the secondary prosencephalon is conserved in vertebrates. However, the organization of each subregion is highly diversified. Current models of the brain organization is based on a mammalian-centric view, but recent studies in teleost brains, in comparison with tetrapod brains, have allowed a better understanding of general organization of the brains of Osteichthyes. More data are needed for a concrete scenario of the regional homology of the vertebrate brain, and it is important to take into account a large range of species." bgee ANN 2017-08-31 HOM:0000007 "historical homology" UBERON:0036218 "secondary prosencephalon" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" DOI:10.3389/fnana.2011.00012 "Moreno N, Gonzalez A, The non-evaginated secondary prosencephalon of vertebrates. Front Neuroanat (2011)" "the evolutionary analysis of transcription factors involved in the patterning of the non-evaginated secondary prosencephalon in key vertebrate groups would be of special interest for understanding its evolution (Figures 2 and 3). In recent years, cell groups and regions that were characterized according to gene expression patterns in the prosencephalon of mammals have been similarly analyzed in the brains of multiple vertebrates.These cell groups and regions in the secondary prosencephalon, and many of their neurochemical and connectional features, appear to be highly conserved in the evolution of tetrapods, since these features show similarities from amphibians through mammals (for review see Reiner et al., 1998; Mar’n et al., 1998; ten Donkelar, 1998; Moreno et al., 2009). Nevertheless, although many characteristics are shared, the degree of complexity increases during evolution from the common ancestor of tetrapods to birds and mammals." bgee ANN 2017-08-31 HOM:0000007 "historical homology" UBERON:0036218 "secondary prosencephalon" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" DOI:10.3389/fnana.2011.00012 "Moreno N, Gonzalez A, The non-evaginated secondary prosencephalon of vertebrates. Front Neuroanat (2011)" "the evolutionary analysis of transcription factors involved in the patterning of the non-evaginated secondary prosencephalon in key vertebrate groups would be of special interest for understanding its evolution (Figures 2 and 3). In recent years, cell groups and regions that were characterized according to gene expression patterns in the prosencephalon of mammals have been similarly analyzed in the brains of multiple vertebrates.These cell groups and regions in the secondary prosencephalon, and many of their neurochemical and connectional features, appear to be highly conserved in the evolution of tetrapods, since these features show similarities from amphibians through mammals (for review see Reiner et al., 1998; Mar’n et al., 1998; ten Donkelar, 1998; Moreno et al., 2009). Nevertheless, although many characteristics are shared, the degree of complexity increases during evolution from the common ancestor of tetrapods to birds and mammals." bgee ANN 2017-08-31 HOM:0000007 "historical homology" UBERON:0036262 "uterine ligament" 40674 "Mammalia" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000002, negated: false, taxon ID: 40674 - entity: UBERON:0000211, negated: false, taxon ID: 40674" bgee HOM:0000007 "historical homology" UBERON:0036269 "penis blood vessel" 8459 "Testudines" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000989, negated: false, taxon ID: 8459 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0036269 "penis blood vessel" 8492 "Archosauria" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000989, negated: false, taxon ID: 8492 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0036269 "penis blood vessel" 8509 "Squamata" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000989, negated: false, taxon ID: 8509 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0036269 "penis blood vessel" 32524 "Amniota" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000989, negated: false, taxon ID: 32524 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0036269 "penis blood vessel" NOT 32524 "Amniota" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000989, negated: true, taxon ID: 32524 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:0036269 "penis blood vessel" 40674 "Mammalia" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000989, negated: false, taxon ID: 40674 - entity: UBERON:0001981, negated: false, taxon ID: 7711" bgee HOM:0000007 "historical homology" UBERON:1000021 "skin of face" 7742 "Vertebrata" CIO:0000005 "low confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000014|UBERON:0002097, negated: false, taxon ID: 7742 - entity: UBERON:0001456, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:1500000 "scapular blade" 8782 "Aves" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:20136669 "Valasek P, Theis S, Krejci E, Grim M, Maina F, Shwartz Y, Otto A, Huang R, Patel K, Somitic origin of the medial border of the mammalian scapula and its homology to the avian scapula blade. J Anat (2010)" "The scapula is the main skeletal element of the pectoral girdle allowing muscular fixation of the forelimb to the axial skeleton. The vertebrate limb skeleton has traditionally been considered to develop from the lateral plate mesoderm, whereas the musculature originates from the axial somites. However, in birds, the scapular blade has been shown to develop from the somites. We investigated whether a somitic contribution was also present in the mammalian scapula. Using genetic lineage-tracing techniques, we show that the medial border of the mammalian scapula develops from somitic cells. (...) Our results establish the avian scapular blade and medial border of the mammalian scapula as homologous structures as they share the same developmental origin." bgee ANN 2013-09-10 HOM:0000007 "historical homology" UBERON:2000040 "median fin fold" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:16878142 "Freitas R, Zhang G, Cohn MJ, Evidence that mechanisms of fin development evolved in the midline of early vertebrates. Nature (2006)" "Conservation of the embryonic origin and the patterns of Hox and Tbx gene expression in shark and lamprey median fins suggests that the molecular mechanisms of fin development evolved in the midline before the origin of paired fins. Our finding that median fin mesenchyme arises predominantly from somites suggests that these cells may acquire their positional identities, in the form of Hox and Tbx expression, during regionalization of paraxial mesoderm. We suggest that the origin of paired appendages from lateral plate mesoderm involved re-deployment of mechanisms that were originally restricted to paraxial mesoderm, where they regulated development of cartilage (Hox9-Hox13, Tbx18), muscle (Pax7, Paraxis) and tendon (Scleraxis) in the axial skeleton and median fins. Reports of Msx and Dlx expression in paired and median fins of zebrafish (28, 29) may reflect additional evolutionary signatures of this co-option. It is possible that the mechanisms of fin and limb development were established in median finfolds even before the origin of vertebrates. Analysis of median finfold development in cephalochordates will further test the hypothesis that these mechanisms emerged early in chordate evolution." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:2000089 "actinotrichium" 7898 "Actinopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:20574421 "Zhang J, Wagh P, Guay D, Sanchez-Pulido L, Padhi BK, Korzh V, Andrade-Navarro MA, Akimenko M, Loss of fish actinotrichia proteins and the fin-to-limb transition. Nature (2010)" "Actinotrichia are found in the fins of developing and adult Actinopterygii (ray-finned fishes including the teleostei) and in the developing fins of the lobe-finned fishes. They are homologous to the ceratotrichia of Chondrichthyes (cartilaginous fishes)" bgee ANN 2018-03-26 HOM:0000007 "historical homology" UBERON:2000089|UBERON:4400001 "actinotrichium|ceratotrichium" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:20574421 "Zhang J, Wagh P, Guay D, Sanchez-Pulido L, Padhi BK, Korzh V, Andrade-Navarro MA, Akimenko M, Loss of fish actinotrichia proteins and the fin-to-limb transition. Nature (2010)" "Actinotrichia are found in the fins of developing and adult Actinopterygii (ray-finned fishes including the teleostei) and in the developing fins of the lobe-finned fishes. They are homologous to the ceratotrichia of Chondrichthyes (cartilaginous fishes)" bgee ANN 2018-03-26 HOM:0000007 "historical homology" UBERON:2000188 "corpus cerebelli" 7742 "Vertebrata" CIO:0000005 "low confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0471210054 "Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.241" "The main divisions of the cerebellum that are common to most vertebrates are the corpus cerebelli (body of the cerebellum) and a cerebellar auricle (little ear). These are formed of an outer layer, the cerebellar cortex, and sometimes a distinct layer of white matter below." bgee ANN 2017-10-03 HOM:0000007 "historical homology" UBERON:2000202 "efferent portion of pharyngeal arch artery" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0004363, negated: false, taxon ID: 7742 - entity: UBERON:0011150, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:2000223 "infraorbital 1" 7898 "Actinopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-3899370805 "Arratia G, Schultze HP, Wilson MVH, Mesozoic Fishes 4 - Homology and Phylogeny (2008) p.23-48" "The infraorbital bone 1 of actinopterygians is homologous with the lacrimal bone (...)." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:2000271 "radial bone" 7878 "Dipnoi" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23434323 "Schneider I, Shubin NH, The origin of the tetrapod limb: from expeditions to enhancers. Trends Genet (2013)" "bony radials of lungfish fins have been compared to digits, but these notions have been controversial" bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:2000315 "asteriscus" 32523 "Tetrapoda" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001844, negated: false, taxon ID: 32523 - entity: UBERON:0002280, negated: false, taxon ID: 117571" bgee HOM:0000007 "historical homology" UBERON:2000315 "asteriscus" 32525 "Theria" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001844, negated: false, taxon ID: 32525 - entity: UBERON:0002280, negated: false, taxon ID: 117571" bgee HOM:0000007 "historical homology" UBERON:2000442 "supraneural bone" 7898 "Actinopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:11746457 "Arratia G, Schultze HP, Casciotta J, Vertebral column and associated elements in dipnoans and comparison with other fishes: development and homology. J Morphol (2001)" "The so-called supraneural bones form in different ways in both lineages [sarcopterygians and actinopterygians]: The 'supraneurals' develop from one single cartilage that also forms the neural spine and the radial in sarcopterygians. The three elements articulate with each other. In contrast, the supraneural develops independently from both the neural spine and the radial in actinopterygians. Primitively, the three series (radials _ supraneurals _ neural spines) develop from three different series of cartilages in actinopterygians. Because we do not know the supraneural condition in the most primitive members of both lineages (Fig. 48) and, in addition, the condition is unknown in acanthodians, it is more parsimonious to interpret the supraneurals of actinopterygians and of sarcopterygians as independently acquired in both lineages. Consequently, the supraneural bones of actinopterygians are not homologs with the 'supraneural' bones of sarcopterygians." bgee ANN 2017-02-14 HOM:0000007 "historical homology" UBERON:2000442 "supraneural bone" 7898 "Actinopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:11746457 "Arratia G, Schultze HP, Casciotta J, Vertebral column and associated elements in dipnoans and comparison with other fishes: development and homology. J Morphol (2001)" "The so-called supraneural bones form in different ways in both lineages [sarcopterygians and actinopterygians]: The 'supraneurals' develop from one single cartilage that also forms the neural spine and the radial in sarcopterygians. The three elements articulate with each other. In contrast, the supraneural develops independently from both the neural spine and the radial in actinopterygians. Primitively, the three series (radials _ supraneurals _ neural spines) develop from three different series of cartilages in actinopterygians. Because we do not know the supraneural condition in the most primitive members of both lineages (Fig. 48) and, in addition, the condition is unknown in acanthodians, it is more parsimonious to interpret the supraneurals of actinopterygians and of sarcopterygians as independently acquired in both lineages. Consequently, the supraneural bones of actinopterygians are not homologs with the 'supraneural' bones of sarcopterygians." bgee ANN 2017-02-14 HOM:0000007 "historical homology" UBERON:2000442 "supraneural bone" 8287 "Sarcopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:11746457 "Arratia G, Schultze HP, Casciotta J, Vertebral column and associated elements in dipnoans and comparison with other fishes: development and homology. J Morphol (2001)" "The so-called supraneural bones form in different ways in both lineages [sarcopterygians and actinopterygians]: The 'supraneurals' develop from one single cartilage that also forms the neural spine and the radial in sarcopterygians. The three elements articulate with each other. In contrast, the supraneural develops independently from both the neural spine and the radial in actinopterygians. Primitively, the three series (radials _ supraneurals _ neural spines) develop from three different series of cartilages in actinopterygians. Because we do not know the supraneural condition in the most primitive members of both lineages (Fig. 48) and, in addition, the condition is unknown in acanthodians, it is more parsimonious to interpret the supraneurals of actinopterygians and of sarcopterygians as independently acquired in both lineages. Consequently, the supraneural bones of actinopterygians are not homologs with the 'supraneural' bones of sarcopterygians." bgee ANN 2017-02-14 HOM:0000007 "historical homology" UBERON:2000442 "supraneural bone" 8287 "Sarcopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:11746457 "Arratia G, Schultze HP, Casciotta J, Vertebral column and associated elements in dipnoans and comparison with other fishes: development and homology. J Morphol (2001)" "The so-called supraneural bones form in different ways in both lineages [sarcopterygians and actinopterygians]: The 'supraneurals' develop from one single cartilage that also forms the neural spine and the radial in sarcopterygians. The three elements articulate with each other. In contrast, the supraneural develops independently from both the neural spine and the radial in actinopterygians. Primitively, the three series (radials _ supraneurals _ neural spines) develop from three different series of cartilages in actinopterygians. Because we do not know the supraneural condition in the most primitive members of both lineages (Fig. 48) and, in addition, the condition is unknown in acanthodians, it is more parsimonious to interpret the supraneurals of actinopterygians and of sarcopterygians as independently acquired in both lineages. Consequently, the supraneural bones of actinopterygians are not homologs with the 'supraneural' bones of sarcopterygians." bgee ANN 2017-02-14 HOM:0000007 "historical homology" UBERON:2000442 "supraneural bone" NOT 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000063 "compositional similarity evidence" PMID:11746457 "Arratia G, Schultze HP, Casciotta J, Vertebral column and associated elements in dipnoans and comparison with other fishes: development and homology. J Morphol (2001)" "The so-called supraneural bones form in different ways in both lineages [sarcopterygians and actinopterygians]: The 'supraneurals' develop from one single cartilage that also forms the neural spine and the radial in sarcopterygians. The three elements articulate with each other. In contrast, the supraneural develops independently from both the neural spine and the radial in actinopterygians. Primitively, the three series (radials _ supraneurals _ neural spines) develop from three different series of cartilages in actinopterygians. Because we do not know the supraneural condition in the most primitive members of both lineages (Fig. 48) and, in addition, the condition is unknown in acanthodians, it is more parsimonious to interpret the supraneurals of actinopterygians and of sarcopterygians as independently acquired in both lineages. Consequently, the supraneural bones of actinopterygians are not homologs with the 'supraneural' bones of sarcopterygians." bgee ANN 2017-02-14 HOM:0000007 "historical homology" UBERON:2000442 "supraneural bone" NOT 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000067 "developmental similarity evidence" PMID:11746457 "Arratia G, Schultze HP, Casciotta J, Vertebral column and associated elements in dipnoans and comparison with other fishes: development and homology. J Morphol (2001)" "The so-called supraneural bones form in different ways in both lineages [sarcopterygians and actinopterygians]: The 'supraneurals' develop from one single cartilage that also forms the neural spine and the radial in sarcopterygians. The three elements articulate with each other. In contrast, the supraneural develops independently from both the neural spine and the radial in actinopterygians. Primitively, the three series (radials _ supraneurals _ neural spines) develop from three different series of cartilages in actinopterygians. Because we do not know the supraneural condition in the most primitive members of both lineages (Fig. 48) and, in addition, the condition is unknown in acanthodians, it is more parsimonious to interpret the supraneurals of actinopterygians and of sarcopterygians as independently acquired in both lineages. Consequently, the supraneural bones of actinopterygians are not homologs with the 'supraneural' bones of sarcopterygians." bgee ANN 2017-02-14 HOM:0000007 "historical homology" UBERON:2000508 "pelvic fin radial bone" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000205 "curator inference" PMID:17849442 "Johanson Z, Joss J, Boisvert CA, Ericsson R, Sutija M, Ahlberg PE, Fish fingers: digit homologues in sarcopterygian fish fins. J Exp Zool B Mol Dev Evol (2007)" "the autopod evolved before the origin of tetrapods, represented by the more distal region of the sarcopterygian fin, with the 'origin of digits' simply representing a modest repatterning of this region rather than the origin of a new structure." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:2000544 "pectoral fin actinotrichium" 7898 "Actinopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000151, negated: false, taxon ID: 7776 - entity: UBERON:2000089, negated: false, taxon ID: 7898" bgee HOM:0000007 "historical homology" UBERON:2000596 "pelvic fin actinotrichium" 7898 "Actinopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000152, negated: false, taxon ID: 7776 - entity: UBERON:2000089, negated: false, taxon ID: 7898" bgee HOM:0000007 "historical homology" UBERON:2000633 "caudal tuberculum" 32443 "Teleostei" CIO:0000004 "medium confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:19439422 "Flinn L, Mortiboys H, Volkmann K, Koster RW, Ingham PW, Bandmann O, Complex I deficiency and dopaminergic neuronal cell loss in parkin-deficient zebrafish (Danio rerio). Brain (2009)" "The zebrafish Parkin protein is 62% identical to its human counterpart with 78% identity in functionally relevant regions. The parkin gene is expressed throughout zebrafish development and ubiquitously in adult zebrafish tissue. Abrogation of Parkin activity leads to a significant decrease in the number of ascending dopaminergic neurons in the posterior tuberculum (homologous to the substantia nigra in humans), an effect enhanced by exposure to MPP+." bgee ANN 2018-03-19 HOM:0000007 "historical homology" UBERON:2000716 "afferent portion of pharyngeal arch artery" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001637, negated: false, taxon ID: 7711 - entity: UBERON:0004363, negated: false, taxon ID: 7742 - entity: UBERON:0011150, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:2001089 "myoseptum" 7711 "Chordata" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1016/S1095-6433(02)00241-6 "Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002)" "Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:2001408 "infraorbital 3" 7898 "Actinopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000034 "non-traceable author statement" ISBN:978-3899370805 "Arratia G, Schultze HP, Wilson MVH, Mesozoic Fishes 4 - Homology and Phylogeny (2008) p.23-48" "(...) and the infraorbital bone 3 of advanced actinopterygians (is homologous) with the jugal bone of sarcopterygians." bgee ANN 2015-03-31 HOM:0000007 "historical homology" UBERON:2001426 "posterior naris" 7898 "Actinopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0072528305 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.256" "The nasolacrimal duct is probably homologous to the posterior (excurrent) naris of actinopterygian fishes." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:2001427 "anterior naris" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-00725283s05 "Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.257 and Figure 7.27" "In a tetrapod, the nasal sac has an external naris (homologous with the anterior naris of the fish) (...)." bgee ANN 2018-03-26 HOM:0000007 "historical homology" UBERON:2001431 "primitive olfactory epithelium" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from transformation_of relations using annotations to same HOM ID, same NCBI taxon ID, same qualifier, and Entity IDs equal to: UBERON:0001997" bgee HOM:0000007 "historical homology" UBERON:2001586 "pectoral fin radial bone" 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:17849442 "Johanson Z, Joss J, Boisvert CA, Ericsson R, Sutija M, Ahlberg PE, Fish fingers: digit homologues in sarcopterygian fish fins. J Exp Zool B Mol Dev Evol (2007)" "the autopod evolved before the origin of tetrapods, represented by the more distal region of the sarcopterygian fin, with the 'origin of digits' simply representing a modest repatterning of this region rather than the origin of a new structure." bgee ANN 2015-04-01 HOM:0000007 "historical homology" UBERON:2001626 "premaxillary tooth" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0001091, negated: false, taxon ID: 7776 - entity: UBERON:0002244, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:2001749 "dentary-anguloarticular joint" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0001689|UBERON:0004744, negated: false, taxon ID: 32523 - entity: UBERON:0004742, negated: false, taxon ID: 7776 - entity: UBERON:0004744, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:2001801 "quadrate-hyomandibula joint" 32523 "Tetrapoda" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0001687|UBERON:0011606, negated: false, taxon ID: 32523 - entity: UBERON:0001688|UBERON:0006597, negated: false, taxon ID: 32523 - entity: UBERON:0006597, negated: false, taxon ID: 32523 - entity: UBERON:0011606, negated: false, taxon ID: 32523" bgee HOM:0000007 "historical homology" UBERON:2001950 "inter-premaxillary joint" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0002244, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:2002038 "basioccipital-exoccipital joint" 7742 "Vertebrata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0001692, negated: false, taxon ID: 7742 - entity: UBERON:0001693, negated: false, taxon ID: 7742" bgee HOM:0000007 "historical homology" UBERON:2002260 "premaxillary-maxillary joint" 7776 "Gnathostomata" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0002244, negated: false, taxon ID: 7776 - entity: UBERON:0002397, negated: false, taxon ID: 7776" bgee HOM:0000007 "historical homology" UBERON:2005264 "supraoccipital-parietal joint" 117571 "Euteleostomi" CIO:0000004 "medium confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000982, negated: false, taxon ID: 7742 - entity: UBERON:0004747, negated: false, taxon ID: 7742 - entity: UBERON:0004865, negated: false, taxon ID: 117571" bgee HOM:0000007 "historical homology" UBERON:3010692 "m. cucullaris" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" PMID:23765280 "Trinajstic K, Sanchez S, Dupret V, Tafforeau P, Long J, Young G, Senden T, Boisvert C, Power N, Ahlberg PE, Fossil musculature of the most primitive jawed vertebrates. Science (2013)" "Lateral to the articulation of the neck joint [in placoderms] (Figs. 1, B and C; 2A; and 3J), an oblique muscle that originates on the inner face of the dermal shoulder girdle and inserts in a hollow on the inner face of the skull roof is identified as the cucullaris muscle (see supplementary text and fig. S1F). It represents the phylogenetically deepest record of this characteristic gnathostome muscle. In mammals, the cucullaris reaches the dorsal midline of the neck, whereas in sharks it is narrower and bounded dorsally by somitic epaxial muscles. The latter morphology is often viewed as primitive for gnathostomes (11), but both differ from the placoderm condition in forming part of a flexible neck region rather than operating a constrained pivoting joint." bgee ANN 2016-09-26 HOM:0000007 "historical homology" UBERON:3010692 "m. cucullaris" 7776 "Gnathostomata" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:23765280 "Trinajstic K, Sanchez S, Dupret V, Tafforeau P, Long J, Young G, Senden T, Boisvert C, Power N, Ahlberg PE, Fossil musculature of the most primitive jawed vertebrates. Science (2013)" "Lateral to the articulation of the neck joint [in placoderms] (Figs. 1, B and C; 2A; and 3J), an oblique muscle that originates on the inner face of the dermal shoulder girdle and inserts in a hollow on the inner face of the skull roof is identified as the cucullaris muscle (see supplementary text and fig. S1F). It represents the phylogenetically deepest record of this characteristic gnathostome muscle. In mammals, the cucullaris reaches the dorsal midline of the neck, whereas in sharks it is narrower and bounded dorsally by somitic epaxial muscles. The latter morphology is often viewed as primitive for gnathostomes (11), but both differ from the placoderm condition in forming part of a flexible neck region rather than operating a constrained pivoting joint." bgee ANN 2016-09-26 HOM:0000007 "historical homology" UBERON:4000160 "anocleithrum" 7878 "Dipnoi" CIO:0000003 "high confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1007/BF03043636 "Campbell KSW, Barwick RE, den Blaauwen JL, Structure and Function of the Shoulder Girdle in Dipnoans: New Material from Dipterus valenciennesi. Senckenbergiana lethaea (2006)" "We do not accept that the ""anocleithrum"" in dipnoans is homologous with those of the sarcopterygians, and this point is discussed later in the text. For this reason we use the word ""anocleithrum"" in quotes for the dipnoan structure...We have suggested that the ""anocleithrum"" was buried in the epaxial muscles and this and the unique restricted gill structure in dipnoans are intimately related; and together they make a feature that is characteristic of dipnoans... We now consider that the major changes in the gill apparatus and the development of an ""anocleithrum"" were also part of the changes brought about by gene regulation. Any attempts to discuss relationships between the dipnoans and other sarcopterygians must take into account the separation of these evolutionary lineages. In so doing they must indicate that similarities between the lineages after their separation will be the result of convergences." bgee ANN 2017-05-23 HOM:0000007 "historical homology" UBERON:4000160 "anocleithrum" 7878 "Dipnoi" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0801424977 "Schultze HP, Trueb L, Origins of the Higher Groups of Tetrapods: Controversy and Consensus (1992) p.22" "The anocleithrum is present in the dermal shoulder girdle of coelacanths, porolepiforms, and dipnoans, but the element is absent in tetrapods. It is simpler to consider the presence of an anocleithrum to be a synapomorphy of those groups possessing it than to argue for its loss in tetrapods." bgee ANN 2017-05-23 HOM:0000007 "historical homology" UBERON:4000160 "anocleithrum" 7894 "Coelacanthiformes" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0801424977 "Schultze HP, Trueb L, Origins of the Higher Groups of Tetrapods: Controversy and Consensus (1992) p.22" "The anocleithrum is present in the dermal shoulder girdle of coelacanths, porolepiforms, and dipnoans, but the element is absent in tetrapods. It is simpler to consider the presence of an anocleithrum to be a synapomorphy of those groups possessing it than to argue for its loss in tetrapods." bgee ANN 2017-05-23 HOM:0000007 "historical homology" UBERON:4000160 "anocleithrum" NOT 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000060 "positional similarity evidence" DOI:10.1007/BF03043636 "Campbell KSW, Barwick RE, den Blaauwen JL, Structure and Function of the Shoulder Girdle in Dipnoans: New Material from Dipterus valenciennesi. Senckenbergiana lethaea (2006)" "We do not accept that the ""anocleithrum"" in dipnoans is homologous with those of the sarcopterygians, and this point is discussed later in the text. For this reason we use the word ""anocleithrum"" in quotes for the dipnoan structure...We have suggested that the ""anocleithrum"" was buried in the epaxial muscles and this and the unique restricted gill structure in dipnoans are intimately related; and together they make a feature that is characteristic of dipnoans... We now consider that the major changes in the gill apparatus and the development of an ""anocleithrum"" were also part of the changes brought about by gene regulation. Any attempts to discuss relationships between the dipnoans and other sarcopterygians must take into account the separation of these evolutionary lineages. In so doing they must indicate that similarities between the lineages after their separation will be the result of convergences." bgee ANN 2017-05-23 HOM:0000007 "historical homology" UBERON:4000160 "anocleithrum" NOT 8287 "Sarcopterygii" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1007/BF03043636 "Campbell KSW, Barwick RE, den Blaauwen JL, Structure and Function of the Shoulder Girdle in Dipnoans: New Material from Dipterus valenciennesi. Senckenbergiana lethaea (2006)" "We do not accept that the ""anocleithrum"" in dipnoans is homologous with those of the sarcopterygians, and this point is discussed later in the text. For this reason we use the word ""anocleithrum"" in quotes for the dipnoan structure...We have suggested that the ""anocleithrum"" was buried in the epaxial muscles and this and the unique restricted gill structure in dipnoans are intimately related; and together they make a feature that is characteristic of dipnoans... We now consider that the major changes in the gill apparatus and the development of an ""anocleithrum"" were also part of the changes brought about by gene regulation. Any attempts to discuss relationships between the dipnoans and other sarcopterygians must take into account the separation of these evolutionary lineages. In so doing they must indicate that similarities between the lineages after their separation will be the result of convergences." bgee ANN 2017-05-23 HOM:0000007 "historical homology" UBERON:4000160 "anocleithrum" NOT 1338369 "Dipnotetrapodomorpha" CIO:0000004 "medium confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" ISBN:978-0801424977 "Schultze HP, Trueb L, Origins of the Higher Groups of Tetrapods: Controversy and Consensus (1992) p.22" "The anocleithrum is present in the dermal shoulder girdle of coelacanths, porolepiforms, and dipnoans, but the element is absent in tetrapods. It is simpler to consider the presence of an anocleithrum to be a synapomorphy of those groups possessing it than to argue for its loss in tetrapods." bgee ANN 2017-05-23 HOM:0000007 "historical homology" UBERON:4000172 "lepidotrichium" 7898 "Actinopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000075 "gene expression similarity evidence" PMID:20574421 "Zhang J, Wagh P, Guay D, Sanchez-Pulido L, Padhi BK, Korzh V, Andrade-Navarro MA, Akimenko M, Loss of fish actinotrichia proteins and the fin-to-limb transition. Nature (2010)" "The altered expression of genes involved in anteroposterior patterning of the limb following impaired function of and1 and and2 and actinotrichia formation allows us to propose hypotheses regarding appendage evolution. The reduced growth of morphant pectoral fins and their defective fold suggest that the resulting adult fins would be shorter and distally truncated. Notably, formation of the lepidotrichia, the dermal bony rays, seems to be compromised, as suggested by the absence of migration of mesenchymal cells (which include progenitors of lepidotrichia-forming cells) in the distal portion of the morphant pectoral fins (Fig. 3g, h). If our observations in zebrafish apply to an ancestral fish, it is tempting to propose that, during evolution, the loss of the actinotrichia in an ancestral fish may have contributed to the concurrent loss of the lepidotrichia. However, this consequence may apply uniquely to the pectoral fins as the effects of the loss of function of and1 and and2 in zebrafish seem to be less drastic in the tail, and lepidotrichia may develop normally (Fig. 3). This hypothesis fits with fossil records showing that the earliest primitive aquatic tetrapods of the late-Devonian period had lost lepidotrichia in paired appendages but still retained a ‘fish tail’ with lepidotrichia27." bgee ANN 2018-03-26 HOM:0000007 "historical homology" UBERON:4000173 "pelvic fin lepidotrichium" 7898 "Actinopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000152, negated: false, taxon ID: 7776 - entity: UBERON:4000172, negated: false, taxon ID: 7898" bgee HOM:0000007 "historical homology" UBERON:4000175 "pectoral fin lepidotrichium" 7898 "Actinopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0000151, negated: false, taxon ID: 7776 - entity: UBERON:4000172, negated: false, taxon ID: 7898" bgee HOM:0000007 "historical homology" UBERON:4400001 "ceratotrichium" 7777 "Chondrichthyes" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" PMID:20574421 "Zhang J, Wagh P, Guay D, Sanchez-Pulido L, Padhi BK, Korzh V, Andrade-Navarro MA, Akimenko M, Loss of fish actinotrichia proteins and the fin-to-limb transition. Nature (2010)" "Actinotrichia are found in the fins of developing and adult Actinopterygii (ray-finned fishes including the teleostei) and in the developing fins of the lobe-finned fishes. They are homologous to the ceratotrichia of Chondrichthyes (cartilaginous fishes)" bgee ANN 2018-03-26 HOM:0000007 "historical homology" UBERON:4440011 "paired fin lepidotrichium" 7898 "Actinopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000501 "evidence used in automatic assertion" "Annotation inferred from logical constraints using annotations to same HOM ID and: entity: UBERON:0002101|UBERON:0002534, negated: false, taxon ID: 7742 - entity: UBERON:0002534, negated: false, taxon ID: 7742 - entity: UBERON:0002534|UBERON:2000040, negated: false, taxon ID: 7742 - entity: UBERON:4000172, negated: false, taxon ID: 7898" bgee HOM:0000007 "historical homology" ZFA:0000302 "ventral habenular nucleus (Danio)" 7898 "Actinopterygii" CIO:0000003 "high confidence from single evidence" ECO:0000355 "phylogenetic distribution evidence" DOI:10.1523/JNEUROSCI.3690-09.2010 "Amo R, Aizawa H, Takahoko M, Kobayashi M, Takahashi R, Aoki T, Okamoto H, Identification of the Zebrafish ventral habenula as a homolog of the mammalian lateral habenula. The Journal of Neuroscience (2010)" "Identification of the Zebrafish ventral habenula as a homolog of the mammalian lateral habenula (...) Gene expression analyses revealed that the ventromedially positioned ventral habenula in the adult originated from the region of primordium lateral to the dorsal habenula during development. This suggested that zebrafish habenulae emerge during development with mediolateral orientation similar to that of the mammalian medial and lateral habenulae. These findings indicated that the lateral habenular pathways are evolutionarily conserved pathways and might control adaptive behaviors in vertebrates through the regulation of monoaminergic activities." bgee ANN 2015-04-14