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Molecular Phylogenetics and Evolution, 116, 182\u2013191. doi:10.1016/j.ympev.2017.09.005\n", "ot:studyYear": 2017, "studyID": "ot_2017", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Marki, 2017", "decision": "INCLUDED", "defaultSortOrder": 113, "name": "Fig. 1 BEAST (Marki, 2017)", "ot:focalCladeOTTTaxonName": "Passeriformes", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2016.12.021", "ot:studyPublicationReference": "Marki, Petter Z., Knud A. J\u00f8nsson, Martin Irestedt, Jacqueline M.T. Nguyen, Carsten Rahbek, Jon Fjelds\u00e5. 2017. Supermatrix phylogeny and biogeography of the Australasian Meliphagides radiation (Aves: Passeriformes). Molecular Phylogenetics and Evolution 107: 516-529", "ot:studyYear": 2017, "studyID": "ot_1043", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Liu, 2017", "decision": "INCLUDED", "defaultSortOrder": 114, "name": "TREE1 (Liu, 2017)", "ot:focalCladeOTTTaxonName": "Prunellidae", "ot:studyPublication": "http://dx.doi.org/10.1002/ece3.3136", "ot:studyPublicationReference": "Liu, B., Alstr\u00f6m, P., Olsson, U., Fjelds\u00e5, J., Quan, Q., Roselaar, K. C. S., Saitoh, T., Yao, C., Hao, Y., Wang, W., Qu, Y., & Lei, F. (2017). Explosive radiation and spatial expansion across the cold environments of the Old World in an avian family. Ecology and Evolution, 7(16), 6346\u20136357. Portico. https://doi.org/10.1002/ece3.3136\n", "ot:studyYear": 2017, "studyID": "ot_2148", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Shakya, 2017", "decision": "INCLUDED", "defaultSortOrder": 115, "name": "Fig. 2 (Bayesian, reduced matrix) (Shakya, 2017)", "ot:focalCladeOTTTaxonName": "Pycnonotidae", "ot:studyPublication": "http://dx.doi.org/10.1111/ibi.12464", "ot:studyPublicationReference": "Shakya, Subir B., Frederick H. Sheldon. 2017. The phylogeny of the world's bulbuls (Pycnonotidae) inferred using a supermatrix approach. Ibis 159 (3): 498-509", "ot:studyYear": 2017, "studyID": "ot_1170", "treeID": "tree2" }, { "SHA": "", "comments": "", "compactRefText": "Shakya, 2017", "decision": "INCLUDED", "defaultSortOrder": 116, "name": "Fig. 1 (Bayesian, complete matrix) (Shakya, 2017)", "ot:focalCladeOTTTaxonName": "Pycnonotidae", "ot:studyPublication": "http://dx.doi.org/10.1111/ibi.12464", "ot:studyPublicationReference": "Shakya, Subir B., Frederick H. Sheldon. 2017. The phylogeny of the world's bulbuls (Pycnonotidae) inferred using a supermatrix approach. Ibis 159 (3): 498-509", "ot:studyYear": 2017, "studyID": "ot_1170", "treeID": "tree3" }, { "SHA": "", "comments": "", "compactRefText": "Ferreira, 2016", "decision": "INCLUDED", "defaultSortOrder": 117, "name": "Untitled (tree1) (Ferreira, 2016)", "ot:focalCladeOTTTaxonName": "Malacoptila", "ot:studyPublication": "https://doi.org/10.1111/jbi.12888", "ot:studyPublicationReference": "Ferreira, M., Aleixo, A., Ribas, C. C., & Santos, M. P. D. (2016). Biogeography of the Neotropical genus Malacoptila (Aves: Bucconidae): the influence of the Andean orogeny, Amazonian drainage evolution and palaeoclimate. Journal of Biogeography, 44(4), 748\u2013759. Portico. https://doi.org/10.1111/jbi.12888\n", "ot:studyYear": 2017, "studyID": "ot_2373", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Grealy, 2017", "decision": "INCLUDED", "defaultSortOrder": 118, "name": "Fig. 3 (Bayesian chronogram) (Grealy, 2017)", "ot:focalCladeOTTTaxonName": "Palaeognathae", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2017.01.005", "ot:studyPublicationReference": "Grealy, Alicia, Matthew Phillips, Gifford Miller, M. Thomas P. Gilbert, Jean-Marie Rouillard, David Lambert, Michael Bunce, James Haile. 2017. Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell. Molecular Phylogenetics and Evolution 109: 151-163", "ot:studyYear": 2017, "studyID": "ot_1044", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Laura M. Zahn, 2017", "decision": "INCLUDED", "defaultSortOrder": 119, "name": "Galapagos cormorant (Laura M. Zahn, 2017)", "ot:studyPublication": "http://dx.doi.org/10.1126/science.356.6341.918-j", "ot:studyPublicationReference": "Laura M. Zahn, 2017, 'Loss of flight in the Galapagos cormorant', Science, vol. 356, no. 6341, pp. 918.10-919", "ot:studyYear": 2017, "studyID": "ot_1165", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Hooper, 2017", "decision": "INCLUDED", "defaultSortOrder": 120, "name": "Bayesian MCC tree (Hooper, 2017)", "ot:focalCladeOTTTaxonName": "Passeriformes", "ot:studyPublication": "http://dx.doi.org/10.1038/s41559-017-0284-6", "ot:studyPublicationReference": "Hooper, Daniel M., Trevor D. Price. 2017. Chromosomal inversion differences correlate with range overlap in passerine birds. 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The Auk 132 (2): 333-348.", "ot:studyYear": 2015, "studyID": "ot_770", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Selvatti, 2015", "decision": "INCLUDED", "defaultSortOrder": 156, "name": "Fig. 2 ML (Selvatti, 2015)", "ot:focalCladeOTTTaxonName": "Passeriformes", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2015.03.018", "ot:studyPublicationReference": "Selvatti, Alexandre Pedro, Luiz Pedreira Gonzaga, Claudia Augusta de Moraes Russo. 2015. A Paleogene origin for crown passerines and the diversification of the Oscines in the New World. Molecular Phylogenetics and Evolution 88: 1-15.", "ot:studyYear": 2015, "studyID": "ot_290", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Garcia-R., 2015", "decision": "INCLUDED", "defaultSortOrder": 157, "name": "Untitled (tree1) (Garcia-R., 2015)", "ot:focalCladeOTTTaxonName": "Porphyrio", "ot:studyPublication": "http://dx.doi.org/10.1642/auk-14-114.1", "ot:studyPublicationReference": "Garcia-R., J. C., & Trewick, S. A. (2015). Dispersal and speciation in purple swamphens (Rallidae:Porphyrio). The Auk, 132(1), 140\u2013155. https://doi.org/10.1642/auk-14-114.1\n", "ot:studyYear": 2015, "studyID": "ot_2268", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Prum, 2015", "decision": "INCLUDED", "defaultSortOrder": 158, "name": "BEAST (no Vegavis constraint) (Prum, 2015)", "ot:focalCladeOTTTaxonName": "Aves", "ot:studyPublication": "http://dx.doi.org/10.1038/nature15697", "ot:studyPublicationReference": "Prum, Richard O., Jacob S. Berv, Alex Dornburg, Daniel J. Field, Jeffrey P. Townsend, Emily Moriarty Lemmon, Alan R. Lemmon. 2015. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526, (7574): 569-573", "ot:studyYear": 2015, "studyID": "ot_500", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Claramunt, 2015", "decision": "INCLUDED", "defaultSortOrder": 159, "name": "Fig. 2b (RAG1 + RAG2) (Claramunt, 2015)", "ot:focalCladeOTTTaxonName": "Aves", "ot:studyPublication": "http://dx.doi.org/10.1126/sciadv.1501005", "ot:studyPublicationReference": "Claramunt, Santiago, Joel Cracraft. 2015. A new time tree reveals Earth historys imprint on the evolution of modern birds. Science Advances 1 (11): e1501005-e1501005", "ot:studyYear": 2015, "studyID": "ot_531", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Gibb, 2015", "decision": "INCLUDED", "defaultSortOrder": 160, "name": "Fig. 2 BEAST (Gibb, 2015)", "ot:focalCladeOTTTaxonName": "Passeriformes", "ot:studyPublication": "http://dx.doi.org/10.1093/gbe/evv196", "ot:studyPublicationReference": "Gibb, Gillian C., Ryan England, Gerrit Hartig, P.A. (Trish) McLenachan, Briar L. Taylor Smith, Bennet J. McComish, Alan Cooper, David Penny. 2015. New Zealand passerines help clarify the diversification of major songbird lineages during the Oligocene. Genome Biology and Evolution 7 (11): 2983-2995.", "ot:studyYear": 2015, "studyID": "ot_532", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Peter A. Hosner, 2015", "decision": "INCLUDED", "defaultSortOrder": 161, "name": "Untitled (tree1) (Peter A. Hosner, 2015)", "ot:focalCladeOTTTaxonName": "Odontophoridae", "ot:studyPublication": "http://dx.doi.org/10.1111/jbi.12555", "ot:studyPublicationReference": "Peter A. Hosner, Edward L. Braun, Rebecca T. Kimball, 2015, 'Land connectivity changes and global cooling shaped the colonization history and diversification of New World quail (Aves: Galliformes: Odontophoridae)', Journal of Biogeography, vol. 42, no. 10, pp. 1883-1895", "ot:studyYear": 2015, "studyID": "ot_1023", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Luke B. Klicka, 2015", "decision": "INCLUDED", "defaultSortOrder": 162, "name": "Fig 3. MCC tree (Luke B. Klicka, 2015)", "ot:studyPublication": "http://dx.doi.org/10.1007/s10592-015-0796-z", "ot:studyPublicationReference": "Luke B. Klicka, Barbara E. Kus, Pascal O. Title, Kevin J. Burns, 2015, 'Conservation genomics reveals multiple evolutionary units within Bell\u2019s Vireo (Vireo bellii)', Conservation Genetics, vol. 17, no. 2, pp. 455-471", "ot:studyYear": 2015, "studyID": "ot_1257", "treeID": "tree2" }, { "SHA": "", "comments": "", "compactRefText": "Taxonomy, [no year]", "decision": "INCLUDED", "defaultSortOrder": 163, "name": "Hand-crafted (Taxonomy, [no year])", "ot:focalCladeOTTTaxonName": "Cisticola", "ot:studyPublication": "https://open.uct.ac.za/items/d5644c7b-f4a8-4e30-a518-b6562c628ba3", "ot:studyPublicationReference": "Taxonomy, phylogeny and biogeography of cisticolas (Cisticola spp.)", "ot:studyYear": 2014, "studyID": "ot_2270", "treeID": "tree6" }, { "SHA": "", "comments": "Put back into correct place, down ranked Burleigh instead", "compactRefText": "Nagy, 2014", "decision": "INCLUDED", "defaultSortOrder": 164, "name": "TREE1 (Nagy, 2014)", "ot:focalCladeOTTTaxonName": "Accipitriformes", "ot:studyPublication": "http://dx.doi.org/10.2478/orhu-2014-0008", "ot:studyPublicationReference": "Nagy, J., & T\u00f6k\u00f6lyi, J. (2014). Phylogeny, Historical Biogeography and the Evolution of Migration in Accipitrid Birds of Prey (Aves: Accipitriformes). Ornis Hungarica, 22(1), 15\u201335. https://doi.org/10.2478/orhu-2014-0008\n", "ot:studyYear": 2014, "studyID": "ot_2186", "treeID": "tree1" }, { "SHA": "", "comments": "Put back into correct place, down ranked Burleigh instead", "compactRefText": "McGuire, 2014", "decision": "INCLUDED", "defaultSortOrder": 165, "name": "Fig. 1 Bayesian chronogram (McGuire, 2014)", "ot:focalCladeOTTTaxonName": "Trochilidae", "ot:studyPublication": "http://dx.doi.org/10.1016/j.cub.2014.03.016", "ot:studyPublicationReference": "McGuire, Jimmy A., Christopher C. Witt, J.V. Remsen, Ammon Corl, Daniel L. Rabosky, Douglas L. Altshuler, Robert Dudley. 2014. Molecular phylogenetics and the diversification of hummingbirds. 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Journal of Biogeography doi: 10.1111/jbi.12357", "ot:studyYear": 2014, "studyID": "ot_118", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Cibois, 2014", "decision": "INCLUDED", "defaultSortOrder": 169, "name": "Fig. 3 Bayesian chronogram (Cibois, 2014)", "ot:focalCladeOTTTaxonName": "Columbidae", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2013.08.019", "ot:studyPublicationReference": "Cibois, Alice, Jean-Claude Thibault, C\u00e9line Bonillo, Christopher E. Filardi, Dick Watling, Eric Pasquet. 2014. Phylogeny and biogeography of the fruit doves (Aves: Columbidae). 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A multi-locus inference of the evolutionary diversification of extant flamingos (Phoenicopteridae). BMC Evolutionary Biology 14 (1): 36.", "ot:studyYear": 2014, "studyID": "ot_122", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Slager, 2014", "decision": "INCLUDED", "defaultSortOrder": 173, "name": "starBEAST ND2 (Slager, 2014)", "ot:focalCladeOTTTaxonName": "Vireonidae", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2014.07.021", "ot:studyPublicationReference": "Slager, David L., C.J. Battey, Robert W. Bryson, Gary Voelker, John Klicka. 2014. A multilocus phylogeny of a major New World avian radiation: The Vireonidae. Molecular Phylogenetics and Evolution 80: 95-104", "ot:studyYear": 2014, "studyID": "ot_768", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Aggerbeck, 2014", "decision": "INCLUDED", "defaultSortOrder": 174, "name": "BEAST MCC tree (Aggerbeck, 2014)", "ot:focalCladeOTTTaxonName": "Corvoidea", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2013.09.027", "ot:studyPublicationReference": "Aggerbeck, Marie, Jon Fjelds\u00e5, Les Christidis, Pierre-Henri Fabre, Knud Andreas J\u00f8nsson. 2014. Resolving deep lineage divergences in core corvoid passerine birds supports a proto-Papuan island origin. 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Bryson, 2014)", "ot:focalCladeOTTTaxonName": "Cardinalidae", "ot:studyPublication": "http://dx.doi.org/10.1111/jbi.12218", "ot:studyPublicationReference": "Robert W. Bryson, Jaime Chaves, Brian Tilston Smith, Matthew J. Miller, Kevin Winker, Jorge L. P\u00e9rez-Em\u00e1n, John Klicka, 2014, 'Diversification across the New World within the \u2018blue\u2019 cardinalids (Aves: Cardinalidae)', Journal of Biogeography, vol. 41, no. 3, pp. 587-599", "ot:studyYear": 2014, "studyID": "ot_169", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Klicka, 2014", "decision": "INCLUDED", "defaultSortOrder": 180, "name": "Fig. 1 ML (mtDNA) (Klicka, 2014)", "ot:focalCladeOTTTaxonName": "Emberizinae", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2014.04.025", "ot:studyPublicationReference": "Klicka, John, F. Keith Barker, Kevin J. Burns, Scott M. Lanyon, Irby J. Lovette, Jaime A. Chaves, Robert W. Bryson. 2014. A comprehensive multilocus assessment of sparrow (Aves: Passerellidae) relationships. Molecular Phylogenetics and Evolution 77: 177\u2013182.", "ot:studyYear": 2014, "studyID": "pg_2924", "treeID": "tree6755" }, { "SHA": "", "comments": "", "compactRefText": "Harris, 2014", "decision": "INCLUDED", "defaultSortOrder": 181, "name": "Fig. 1 (Harris, 2014)", "ot:focalCladeOTTTaxonName": "Poecile", "ot:studyPublication": "http://dx.doi.org/10.1111/evo.12280", "ot:studyPublicationReference": "Harris, R.B., M.D. Carling, I.J. Lovette. 2014. The influence of sampling design on species tree inference: a new relationship for the New World chickadees (Aves: Poecile). Evolution 68 (2): 501-513.", "ot:studyYear": 2014, "studyID": "ot_173", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Price, 2014", "decision": "INCLUDED", "defaultSortOrder": 182, "name": "Bayesian chronogram (Passeriformes) (Price, 2014)", "ot:focalCladeOTTTaxonName": "Passeriformes", "ot:studyPublication": "http://dx.doi.org/10.1038/nature13272", "ot:studyPublicationReference": "Price, Trevor D., Daniel M. Hooper, Caitlyn D. Buchanan, Ulf S. Johansson, D. Thomas Tietze, Per Alstr\u00f6m, Urban Olsson, Mousumi Ghosh-Harihar, Farah Ishtiaq, Sandeep K. Gupta, Jochen Martens, Bettina Harr, Pratap Singh, Dhananjai Mohan. 2014. Niche filling slows the diversification of Himalayan songbirds. Nature 509: 222-225.", "ot:studyYear": 2014, "studyID": "pg_2913", "treeID": "tree6742" }, { "SHA": "", "comments": "", "compactRefText": "Alstrom, 2014", "decision": "INCLUDED", "defaultSortOrder": 183, "name": "Fig. S1 (Alstrom, 2014)", "ot:focalCladeOTTTaxonName": "Passeriformes", "ot:studyPublication": "http://dx.doi.org/10.1098/rsbl.2013.1067", "ot:studyPublicationReference": "Alstrom, P., D. M. Hooper, Y. Liu, U. Olsson, D. Mohan, M. Gelang, H. Le Manh, J. Zhao, F. Lei, T. D. Price. 2014. Discovery of a relict lineage and monotypic family of passerine birds. Biology Letters 10 (3): 20131067-20131067.", "ot:studyYear": 2014, "studyID": "ot_111", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Ericson, 2014", "decision": "INCLUDED", "defaultSortOrder": 184, "name": "Fig. 1 (IGR clock) (Ericson, 2014)", "ot:focalCladeOTTTaxonName": "Passeriformes", "ot:studyPublication": "http://dx.doi.org/10.1186/1471-2148-14-8", "ot:studyPublicationReference": "Ericson, Per GP, Seraina Klopfstein, Martin Irestedt, Jacqueline MT Nguyen and Johan AA Nylander. 2014. Dating the diversification of the major lineages of Passeriformes (Aves). BMC Evolutionary Biology, 14(8).", "ot:studyYear": 2014, "studyID": "ot_757", "treeID": "Tr70438" }, { "SHA": "", "comments": "", "compactRefText": "Barker, 2014", "decision": "INCLUDED", "defaultSortOrder": 185, "name": "pfinder AGY (Barker, 2014)", "ot:focalCladeOTTTaxonName": "Passeriformes", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2014.06.011", "ot:studyPublicationReference": "Barker, F.K. 2014. Mitogenomic data resolve basal relationships among passeriform and passeridan birds. Molecular Phylogenetics and Evolution 79: 313-324.", "ot:studyYear": 2014, "studyID": "ot_412", "treeID": "Tr77157" }, { "SHA": "", "comments": "", "compactRefText": "Price, 2014", "decision": "INCLUDED", "defaultSortOrder": 186, "name": "Bayesian chronogram (Non-Passeriformes) (Price, 2014)", "ot:focalCladeOTTTaxonName": "Passeriformes", "ot:studyPublication": "http://dx.doi.org/10.1038/nature13272", "ot:studyPublicationReference": "Price, Trevor D., Daniel M. Hooper, Caitlyn D. Buchanan, Ulf S. Johansson, D. Thomas Tietze, Per Alstr\u00f6m, Urban Olsson, Mousumi Ghosh-Harihar, Farah Ishtiaq, Sandeep K. Gupta, Jochen Martens, Bettina Harr, Pratap Singh, Dhananjai Mohan. 2014. Niche filling slows the diversification of Himalayan songbirds. Nature 509: 222-225.", "ot:studyYear": 2014, "studyID": "pg_2913", "treeID": "tree6741" }, { "SHA": "", "comments": "", "compactRefText": "Jarvis, 2014", "decision": "INCLUDED", "defaultSortOrder": 187, "name": "Fig.1 (dated TENT) (Jarvis, 2014)", "ot:focalCladeOTTTaxonName": "Aves", "ot:studyPublication": "http://dx.doi.org/10.1126/science.1253451", "ot:studyPublicationReference": "Jarvis, E. D., S. Mirarab, A. J. Aberer, B. Li, P. Houde, C. Li, S. Y. W. Ho, B. C. Faircloth, B. Nabholz, J. T. Howard, A. Suh, C. C. Weber, R. R. da Fonseca, J. Li, F. Zhang, H. Li, L. Zhou, N. Narula, L. Liu, G. Ganapathy, B. Boussau, M. S. Bayzid, V. Zavidovych, S. Subramanian, T. Gabaldon, S. Capella-Gutierrez, J. Huerta-Cepas, B. Rekepalli, K. Munch, M. Schierup, B. Lindow, W. C. Warren, D. Ray, R. E. Green, M. W. Bruford, X. Zhan, A. Dixon, S. Li, N. Li, Y. Huang, E. P. Derryberry, M. F. Bertelsen, F. H. Sheldon, R. T. Brumfield, C. V. Mello, P. V. Lovell, M. Wirthlin, M. P. C. Schneider, F. Prosdocimi, J. A. Samaniego, A. M. V. Velazquez, A. Alfaro-Nunez, P. F. Campos, B. Petersen, T. Sicheritz-Ponten, A. Pas, T. Bailey, P. Scofield, M. Bunce, D. M. Lambert, Q. Zhou, P. Perelman, A. C. Driskell, B. Shapiro, Z. Xiong, Y. Zeng, S. Liu, Z. Li, B. Liu, K. Wu, J. Xiao, X. Yinqi, Q. Zheng, Y. Zhang, H. Yang, J. Wang, L. Smeds, F. E. Rheindt, M. Braun, J. Fjeldsa, L. Orlando, F. K. Barker, K. A. Jonsson, W. Johnson, K.-P. Koepfli, S. O'Brien, D. Haussler, O. A. Ryder, C. Rahbek, E. Willerslev, G. R. Graves, T. C. Glenn, J. McCormack, D. Burt, H. Ellegren, P. Alstrom, S. V. Edwards, A. Stamatakis, D. P. Mindell, J. Cracraft, E. L. Braun, T. Warnow, W. Jun, M. T. P. Gilbert, G. Zhang. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346 (6215): 1320-1331.", "ot:studyYear": 2014, "studyID": "ot_214", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "den Tex, 2013", "decision": "INCLUDED", "defaultSortOrder": 188, "name": "Fig. 5 (den Tex, 2013)", "ot:focalCladeOTTTaxonName": "Megalaimidae", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2013.03.004", "ot:studyPublicationReference": "den Tex, Robert-Jan, Jennifer A. Leonard. 2013. A molecular phylogeny of Asian barbets: speciation and extinction in the tropics. 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Molecular Phylogenetics and Evolution 69 (3): 873-883.", "ot:studyYear": 2013, "studyID": "ot_154", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Corl, 2013", "decision": "INCLUDED", "defaultSortOrder": 190, "name": "Fig. 1 *BEAST (Corl, 2013)", "ot:focalCladeOTTTaxonName": "Scolopacidae", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2013.02.002", "ot:studyPublicationReference": "Corl, Ammon, Hans Ellegren. 2013. Sampling strategies for species trees: The effects on phylogenetic inference of the number of genes, number of individuals, and whether loci are mitochondrial, sex-linked, or autosomal. Molecular Phylogenetics and Evolution 67 (2): 358-366", "ot:studyYear": 2013, "studyID": "pg_2371", "treeID": "tree4985" }, { "SHA": "", "comments": "", "compactRefText": "Subramanian, 2013", "decision": "INCLUDED", "defaultSortOrder": 191, "name": "tree6497 (Subramanian, 2013)", "ot:focalCladeOTTTaxonName": "Sphenisciformes", "ot:studyPublication": "http://dx.doi.org/10.1098/rsbl.2013.0748", "ot:studyPublicationReference": "Subramanian, S., G. Beans-Picon, S. K. Swaminathan, C. D. Millar, D. M. Lambert. 2013. Evidence for a recent origin of penguins. Biology Letters 9 (6): 20130748-20130748.", "ot:studyYear": 2013, "studyID": "pg_2798", "treeID": "tree6497" }, { "SHA": "", "comments": "", "compactRefText": "Kennedy, 2013", "decision": "INCLUDED", "defaultSortOrder": 192, "name": "Fig.2 (Kennedy, 2013)", "ot:focalCladeOTTTaxonName": "Pelecanidae", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2012.09.034", "ot:studyPublicationReference": "Kennedy, M., S.A. Taylor, P. N\u00e1dvorn\u00edk, H. Spencer. 2013. The phylogenetic relationships of the extant pelicans inferred from DNA sequence data. Molecular Phylogenetics and Evolution 66 (1): 215-222.", "ot:studyYear": 2013, "studyID": "pg_1764", "treeID": "tree6299" }, { "SHA": "", "comments": "", "compactRefText": "Ramirez, 2013", "decision": "INCLUDED", "defaultSortOrder": 193, "name": "Fig. 3 (Ramirez, 2013)", "ot:focalCladeOTTTaxonName": "Threskiornithidae", "ot:studyPublication": "http://dx.doi.org/10.4238/2013.july.30.11", "ot:studyPublicationReference": "Ramirez, J.L., C.Y. Miyaki, S.N. Del Lama. 2013. Molecular phylogeny of Threskiornithidae (Aves: Pelecaniformes) based on nuclear and mitochondrial DNA. Genetics and Molecular Research 12 (3): 2740-2750.", "ot:studyYear": 2013, "studyID": "ot_139", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Gonzalez, 2013", "decision": "INCLUDED", "defaultSortOrder": 194, "name": "Fig. 3 (Gonzalez, 2013)", "ot:focalCladeOTTTaxonName": "Bucerotidae", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2013.02.012", "ot:studyPublicationReference": "Gonzalez, Juan-Carlos T., Ben C. Sheldon, Nigel J. Collar, Joseph A. Tobias. 2013. A comprehensive molecular phylogeny for the hornbills (Aves: Bucerotidae). 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Molecular Phylogenetics and Evolution 69 (3): 796-804.", "ot:studyYear": 2013, "studyID": "pg_2796", "treeID": "tree6491" }, { "SHA": "", "comments": "", "compactRefText": "Olsson, 2013", "decision": "INCLUDED", "defaultSortOrder": 196, "name": "con 50 majrule (Olsson, 2013)", "ot:focalCladeOTTTaxonName": "Cisticolidae", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2012.11.004", "ot:studyPublicationReference": "Olsson, U., Irestedt, M., Sangster, G., Ericson, P. G. P., & Alstr\u00f6m, P. (2013). Systematic revision of the avian family Cisticolidae based on a multi-locus phylogeny of all genera. Molecular Phylogenetics and Evolution, 66(3), 790\u2013799. https://doi.org/10.1016/j.ympev.2012.11.004\n", "ot:studyYear": 2013, "studyID": "ot_2169", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Alstr\u00f6m, 2013", "decision": "INCLUDED", "defaultSortOrder": 197, "name": "MrBayes consensus (Alstr\u00f6m, 2013)", "ot:focalCladeOTTTaxonName": "Alaudidae", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2013.06.005", "ot:studyPublicationReference": "Alstr\u00f6m, Per, Keith N. Barnes, Urban Olsson, F. Keith Barker, Paulette Bloomer, Aleem Ahmed Khan, Masood Ahmed Qureshi, Alban Guillaumet, Pierre-Andr\u00e9 Crochet, Peter G. Ryan. 2013. Multilocus phylogeny of the avian family Alaudidae (larks) reveals complex morphological evolution, non-monophyletic genera and hidden species diversity. Molecular Phylogenetics and Evolution 69 (3): 1043-1056.", "ot:studyYear": 2013, "studyID": "pg_2599", "treeID": "tree6021" }, { "SHA": "", "comments": "", "compactRefText": "Schweizer, 2013", "decision": "INCLUDED", "defaultSortOrder": 198, "name": "Fig. 4 (Schweizer, 2013)", "ot:focalCladeOTTTaxonName": "Oenanthe (genus in Opisthokonta)", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2013.08.010", "ot:studyPublicationReference": "Schweizer, Manuel, Hadoram Shirihai. 2013. Phylogeny of the Oenanthe lugens complex (Aves, Muscicapidae: Saxicolinae): paraphyly of a morphologically cohesive group within a recent radiation of open-habitat chats. Molecular Phylogenetics and Evolution 69 (3): 450-461.", "ot:studyYear": 2013, "studyID": "ot_110", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Tietze, 2013", "decision": "INCLUDED", "defaultSortOrder": 199, "name": "Fig. 1 (Tietze, 2013)", "ot:focalCladeOTTTaxonName": "Carpodacus", "ot:studyPublication": "http://dx.doi.org/10.1111/zoj.12057", "ot:studyPublicationReference": "Tietze, Dieter Thomas, Martin P\u00e4ckert, Jochen Martens, Henriette Lehmann, Yue-Hua Sun. 2013. Complete phylogeny and historical biogeography of true rosefinches (Aves: Carpodacus) . Zoological Journal of the Linnean Society 169 (1): 215-234.", "ot:studyYear": 2013, "studyID": "pg_2874", "treeID": "tree6667" }, { "SHA": "", "comments": "", "compactRefText": "Chaves, 2013", "decision": "INCLUDED", "defaultSortOrder": 200, "name": "Simplified topology (Chaves, 2013)", "ot:focalCladeOTTTaxonName": "Saltator (genus in tribe Cardinalini)", "ot:studyPublication": "http://dx.doi.org/10.1111/jbi.12150", "ot:studyPublicationReference": "Chaves, Jaime A., Jos\u00e9 R. Hidalgo, John Klicka. 2013. Biogeography and evolutionary history of the Neotropical genus Saltator (Aves: Thraupini). Journal of Biogeography 40 (11): 2180-2190.", "ot:studyYear": 2013, "studyID": "ot_101", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Pulgar\u00edn-R, 2013", "decision": "INCLUDED", "defaultSortOrder": 201, "name": "Fig. 3 topology (Pulgar\u00edn-R, 2013)", "ot:focalCladeOTTTaxonName": "Pheucticus", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2013.05.022", "ot:studyPublicationReference": "Pulgar\u00edn-R, Paulo C., Brian Tilston Smith, Robert W. Bryson, Garth M. Spellman, John Klicka. 2013. Multilocus phylogeny and biogeography of the New World Pheucticus grosbeaks (Aves: Cardinalidae). 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Molecular Phylogenetics and Evolution 69 (3): 852-860.", "ot:studyYear": 2013, "studyID": "pg_2600", "treeID": "tree6022" }, { "SHA": "", "comments": "", "compactRefText": "Barker, 2013", "decision": "INCLUDED", "defaultSortOrder": 203, "name": "MCC species tree chronogram (Barker, 2013)", "ot:focalCladeOTTTaxonName": "Passeriformes", "ot:studyPublication": "http://dx.doi.org/10.1093/sysbio/sys094", "ot:studyPublicationReference": "Barker, F. K., K. J. Burns, J. Klicka, S. M. Lanyon, I. J. Lovette. 2013. Going to extremes: contrasting rates of diversification in a recent radiation of New World passerine birds. Systematic Biology 62 (2): 298-320.", "ot:studyYear": 2013, "studyID": "pg_2575", "treeID": "tree5974" }, { "SHA": "", "comments": "", "compactRefText": "Fulton, 2012", "decision": "INCLUDED", "defaultSortOrder": 204, "name": "Fig. 3 (Fulton, 2012)", "ot:focalCladeOTTTaxonName": "Anatidae", "ot:studyPublication": "http://dx.doi.org/10.1098/rspb.2011.2599", "ot:studyPublicationReference": "Fulton, T. L., B. Letts, B. Shapiro. 2012. Multiple losses of flight and recent speciation in steamer ducks. Proceedings of the Royal Society B: Biological Sciences 279 (1737): 2339-2346.", "ot:studyYear": 2012, "studyID": "pg_2860", "treeID": "tree6646" }, { "SHA": "", "comments": "", "compactRefText": "Gibson, 2012", "decision": "INCLUDED", "defaultSortOrder": 205, "name": "Fig. 1 (Bayesian MCC) (Gibson, 2012)", "ot:focalCladeOTTTaxonName": "Charadriiformes", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2012.03.008", "ot:studyPublicationReference": "Gibson, Rosemary, Allan Baker. 2012. Multiple gene sequences resolve phylogenetic relationships in the shorebird suborder Scolopaci (Aves: Charadriiformes). Molecular Phylogenetics and Evolution 64 (1): 66-72", "ot:studyYear": 2012, "studyID": "ot_816", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Fuchs, 2012", "decision": "INCLUDED", "defaultSortOrder": 206, "name": "Fig. 3 species tree (Fuchs, 2012)", "ot:focalCladeOTTTaxonName": "Falconidae", "ot:studyPublication": "http://dx.doi.org/10.1111/j.1474-919X.2012.01222.x", "ot:studyPublicationReference": "Fuchs, J\u00e9r\u00f4me, Jeff A. Johnson, David P. Mindell. 2012. Molecular systematics of the caracaras and allies (Falconidae: Polyborinae) inferred from mitochondrial and nuclear sequence data. Ibis 154 (3): 520-532.", "ot:studyYear": 2012, "studyID": "pg_2871", "treeID": "tree6663" }, { "SHA": "", "comments": "", "compactRefText": " Quintero, 2012", "decision": "INCLUDED", "defaultSortOrder": 207, "name": "Fig. 4c ( Quintero, 2012)", "ot:focalCladeOTTTaxonName": "Psittacidae", "ot:studyPublication": "http://dx.doi.org/10.1111/j.1463-6409.2012.00567.x", "ot:studyPublicationReference": " Quintero, Esther, Camila C. Ribas, Joel Cracraft. 2012. The Andean Hapalopsittaca parrots (Psittacidae, Aves): an example of montane-tropical lowland vicariance. Zoologica Scripta 42 (1): 28-43.", "ot:studyYear": 2012, "studyID": "ot_166", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Schweizer, 2012", "decision": "INCLUDED", "defaultSortOrder": 208, "name": "Fig. 1 (Schweizer, 2012)", "ot:focalCladeOTTTaxonName": "Prioniturus", "ot:studyPublication": "http://dx.doi.org/10.1111/j.1439-0469.2012.00654.x", "ot:studyPublicationReference": "Schweizer, Manuel, Marcel G\u00fcntert, Stefan T. Hertwig. 2012. Phylogeny and biogeography of the parrot genus Prioniturus (Aves: Psittaciformes). Journal of Zoological Systematics and Evolutionary Research 50 (2): 145-156.", "ot:studyYear": 2012, "studyID": "ot_162", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Smith, 2012", "decision": "INCLUDED", "defaultSortOrder": 209, "name": "Fig. 3 (Smith, 2012)", "ot:focalCladeOTTTaxonName": "Forpus", "ot:studyPublication": "http://dx.doi.org/10.1111/mec.12118", "ot:studyPublicationReference": "Smith, Brian Tilston, Camila C. Ribas, Bret M. Whitney, Blanca E. Hern\u00c1ndez-ba\u00d1os, John Klicka. 2012. Identifying biases at different spatial and temporal scales of diversification: a case study in the Neotropical parrotlet genus Forpus. Molecular Ecology 22 (2): 483-494.", "ot:studyYear": 2012, "studyID": "ot_165", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Toon, 2012", "decision": "INCLUDED", "defaultSortOrder": 210, "name": "Untitled (tree1) (Toon, 2012)", "ot:studyPublication": "https://doi.org/10.1016/j.ympev.2011.09.026", "ot:studyPublicationReference": "Toon, A., Austin, J. J., Dolman, G., Pedler, L., & Joseph, L. (2012). Evolution of arid zone birds in Australia: Leapfrog distribution patterns and mesic-arid connections in quail-thrush (Cinclosoma, Cinclosomatidae). Molecular Phylogenetics and Evolution, 62(1), 286\u2013295. https://doi.org/10.1016/j.ympev.2011.09.026\n", "ot:studyYear": 2012, "studyID": "ot_2376", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "P\u00e4ckert, 2012", "decision": "INCLUDED", "defaultSortOrder": 211, "name": "Fig. 2 (P\u00e4ckert, 2012)", "ot:focalCladeOTTTaxonName": "Apodidae", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2012.02.002", "ot:studyPublicationReference": "P\u00e4ckert, Martin, Jochen Martens, Michael Wink, Anna Feigl, Dieter Thomas Tietze. 2012. Molecular phylogeny of Old World swifts (Aves: Apodiformes, Apodidae, Apus and Tachymarptis) based on mitochondrial and nuclear markers. 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Richardson, Barbara Helm, Juan Carlos Atienza, Brent C. Emerson, 2008, 'Phylogenetic relationships, biogeography and speciation in the avian genus Saxicola', Molecular Phylogenetics and Evolution, vol. 48, no. 3, pp. 1145-1154", "ot:studyYear": 2008, "studyID": "ot_856", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Irby J. Lovette, 2008", "decision": "INCLUDED", "defaultSortOrder": 273, "name": "lovette etal 2008 tree 1 (Irby J. Lovette, 2008)", "ot:focalCladeOTTTaxonName": "Sturnidae", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2008.01.020", "ot:studyPublicationReference": "Irby J. Lovette, Brynn V. McCleery, Amanda L. Talaba, Dustin R. 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Ericson, 2008, 'The systematic affinity of the enigmatic Lamprolia victoriae (Aves: Passeriformes)\u2014An example of avian dispersal between New Guinea and Fiji over Miocene intermittent land bridges?', Molecular Phylogenetics and Evolution, vol. 48, no. 3, pp. 1218-1222", "ot:studyYear": 2008, "studyID": "ot_855", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Simone Treplin, 2008", "decision": "INCLUDED", "defaultSortOrder": 280, "name": "treplin etal 2008 tree 1 (Simone Treplin, 2008)", "ot:focalCladeOTTTaxonName": "Passeriformes", "ot:studyPublication": "http://dx.doi.org/10.1111/j.1096-0031.2007.00178.x", "ot:studyPublicationReference": "Simone Treplin, Romy Siegert, Christoph Bleidorn, Hazell Shokellu Thompson, Roger Fotso, Ralph Tiedemann, 2008, 'Molecular phylogeny of songbirds (Aves: Passeriformes) and the relative utility of common nuclear marker loci', Cladistics, vol. 24, no. 3, pp. 328-349", "ot:studyYear": 2008, "studyID": "ot_841", "treeID": "tree1" }, { "SHA": "", "comments": "", "compactRefText": "Dumbacher, 2008", "decision": "INCLUDED", "defaultSortOrder": 281, "name": "Untitled (tree1) (Dumbacher, 2008)", "ot:focalCladeOTTTaxonName": "Passeriformes", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2008.09.018", "ot:studyPublicationReference": "Dumbacher, J. 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