{
"contributors": [
{
"login": "DMaddison",
"name": "David Maddison"
},
{
"login": "cdspecht",
"name": "cdspecht (None)"
},
{
"login": "mtholder",
"name": "Mark T. Holder"
},
{
"login": "plewis",
"name": "Paul O. Lewis"
},
{
"login": "josephwb",
"name": "Joseph W. Brown"
},
{
"login": "blackrim",
"name": "Stephen Smith"
}
],
"creator": {
"login": "kcranston",
"name": "Karen Cranston"
},
"decisions": [
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Fig. 2 ML (Selvatti, 2015)",
"studyID": "ot_290",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Zingiberales Sass et al PeerJ 2016 (Chodon Sass, 2016)",
"studyID": "ot_709",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Majority-Rule Consensus of 2000 trees from Trees stored in block \"7Genes MLBoot Trees (PartitionFinder)\" (David Maddison, 2014)",
"studyID": "ot_624",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree 3 (Shayla Salzman, 2015)",
"studyID": "ot_711",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Fig. 2 (Yang X., 2014)",
"studyID": "ot_44",
"treeID": "Tr64893"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Tr63070 (Lorch J.M., 2012)",
"studyID": "ot_19",
"treeID": "Tr63070"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Fig. 2b (Callejas R., 2008)",
"studyID": "pg_108",
"treeID": "tree4130"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Ericales (tree530) (S. A. Smith, 2008)",
"studyID": "pg_422",
"treeID": "tree530"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree1 (Tedford, 2009)",
"studyID": "ot_278",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree4 (Yoshiyuki Ishitani, 2011)",
"studyID": "ot_97",
"treeID": "tree4"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Tr77496 (K. M. Kozak, 2015)",
"studyID": "ot_488",
"treeID": "Tr77496"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree6388 (Barker F., 2004)",
"studyID": "pg_2404",
"treeID": "tree6388"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "con 50 majrule++ (Mariangeles Arce H., 2013)",
"studyID": "ot_623",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Fig. 24 (Marcelo R. Britto, 2003)",
"studyID": "ot_597",
"treeID": "Tr53543"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Figs. 36-38 (Armbruster J.W. , 2004)",
"studyID": "pg_2071",
"treeID": "tree4264"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Fig. 3 (BEAST) (Cushing, 2015)",
"studyID": "ot_509",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "best (Kaliszewska Z.A., 2015)",
"studyID": "ot_530",
"treeID": "Tr81397"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Fig. \uf732. Mid-point rooted maximum likelihood phylogeny (ITS, nLSU, nSSU, rpb2) of the Tricholomataceae s.str. Bootstrap values \u2265 70 and Bayesian posterior probabilities \u2265 0.95 are shown at branches. Types of generic names are indicated in bold. Taxa labels follow updated nomenclature presented in the Taxonomy section. (Sanchez-garcia M., 2014)",
"studyID": "ot_331",
"treeID": "Tr77751"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "FIG. 1. Phylogram based on ML analyses of ITS1-5.8S-ITS2 rDNA sequences, showing where fungal associates of pine bark beetles in Spain from the study of Romo\u00b4n et al. (2007) groups within the Ophiostomatales. (P. Romon, 2014)",
"studyID": "ot_340",
"treeID": "Tr52077"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Figure 1 (no edge lengths) (O'Leary, 2013)",
"studyID": "pg_2647",
"treeID": "tree6169"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Fig. 1 Maximum likelihood (ML) tree obtained from the combined LSU and ITS sequences of 61 representative taxa of Microascaceae and Graphiaceae. (Sandoval-denis M.P., 2016)",
"studyID": "ot_453",
"treeID": "Tr87992"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Fig 5 strict consensus (Sidlauskas B.L. , 2008)",
"studyID": "pg_1879",
"treeID": "tree3796"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Bayesian consensus (Ohlson, 2013)",
"studyID": "pg_2796",
"treeID": "tree6491"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree6130 (Sandra C. Craveiro, 2011)",
"studyID": "pg_2618",
"treeID": "tree6130"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree3743 (Mann, 2006)",
"studyID": "pg_1854",
"treeID": "tree3743"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Tr63300 (J. L. Alves, 2013)",
"studyID": "ot_389",
"treeID": "Tr63300"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree1 (K.Y. Ma, 2009)",
"studyID": "ot_115",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree1585 (Porter T.M., 2011)",
"studyID": "pg_827",
"treeID": "tree1585"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Tr3688 (Cooke D., 2000)",
"studyID": "ot_26",
"treeID": "Tr3688"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree6744 (P\u00e9rez-Losada M, 2012)",
"studyID": "pg_2916",
"treeID": "tree6744"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Tr53059 (T. Shirouzu, 2013)",
"studyID": "ot_317",
"treeID": "Tr53059"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Tr80994 (M. J. Trappe, 2015)",
"studyID": "ot_458",
"treeID": "Tr80994"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree6760 (Thiago da Silva Paiva, 2014)",
"studyID": "pg_2927",
"treeID": "tree6760"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Tr74361 (M. Gelardi, 2014)",
"studyID": "ot_443",
"treeID": "Tr74361"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree505 (Schroers, 2005)",
"studyID": "pg_404",
"treeID": "tree505"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree2 (dos Reis, 2015)",
"studyID": "ot_508",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree6545 (Lartillot, 2012)",
"studyID": "pg_2812",
"treeID": "tree6545"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree1 (Qi Kou, 2013)",
"studyID": "ot_131",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree4 (K.M. Hultgren, 2008)",
"studyID": "ot_657",
"treeID": "tree4"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree1 (Sun, 2016)",
"studyID": "ot_535",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree1 (Ksepka, 2015)",
"studyID": "ot_534",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Tr85942 (Frederik Leliaert, 2015)",
"studyID": "ot_546",
"treeID": "Tr85942"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree1 (Gao, 2014)",
"studyID": "ot_105",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree1 (Ka Yan Ma, 2011)",
"studyID": "ot_114",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree1 (Qi Kou, 2013)",
"studyID": "ot_132",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree4 (Dietrich, 1994)",
"studyID": "ot_218",
"treeID": "tree4"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Tr72273 (Thongklang N., 2014)",
"studyID": "ot_221",
"treeID": "Tr72273"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Tr3687 (Cooke D., 2000)",
"studyID": "ot_26",
"treeID": "Tr3687"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree1 (Dos Remedios, 2015)",
"studyID": "ot_289",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree1 (Oatley, 2015)",
"studyID": "ot_305",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Tr70597 (A. da Marcela Vasco-Palacios, 2014)",
"studyID": "ot_435",
"treeID": "Tr70597"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Tr75519 (P. Sandoval-Leiva, 2014)",
"studyID": "ot_445",
"treeID": "Tr75519"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree3798 (Sidlauskas B.L. , 2008)",
"studyID": "pg_1879",
"treeID": "tree3798"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Tr75532 (H. Urbina, 2012)",
"studyID": "ot_447",
"treeID": "Tr75532"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Tr92138 (Hisayoshi Nozaki, 2015)",
"studyID": "ot_555",
"treeID": "Tr92138"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Tr70451 (Ryo Matsuzaki, 2014)",
"studyID": "ot_559",
"treeID": "Tr70451"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree2 (Gibb, 2015)",
"studyID": "ot_647",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree856 (Thomas B. Patterson, 2002)",
"studyID": "pg_580",
"treeID": "tree856"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree2455 (Delsuc, 2008)",
"studyID": "pg_1217",
"treeID": "tree2455"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree3298 (Endo M., 2008)",
"studyID": "pg_1632",
"treeID": "tree3298"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree6271 (Floudas, 6089)",
"studyID": "pg_2701",
"treeID": "tree6271"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree6432 (Wyth L. Marshall, 2008)",
"studyID": "pg_2775",
"treeID": "tree6432"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree6705 (Shuhei Ota, 2012)",
"studyID": "pg_2793",
"treeID": "tree6705"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree6550 (Rota-Stabelli, 2011)",
"studyID": "pg_2813",
"treeID": "tree6550"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree6667 (Tietze, 2013)",
"studyID": "pg_2874",
"treeID": "tree6667"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree6698 (Bonnie R. Lei, 2014)",
"studyID": "pg_2889",
"treeID": "tree6698"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree6701 (Rice, 2005)",
"studyID": "pg_2890",
"treeID": "tree6701"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree6551 (Rota-Stabelli, 2013)",
"studyID": "pg_2814",
"treeID": "tree6551"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Bayesian 18S Chlorophyceae (S. Watanabe, 2016)",
"studyID": "ot_752",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "Figure 1 (Martin Malmstr\u00f8m, [no year])",
"studyID": "ot_771",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "ML majority-rule consensus (Betancur-R., 2013)",
"studyID": "pg_2651",
"treeID": "tree6177"
},
{
"SHA": "",
"comments": "",
"decision": "INCLUDED",
"name": "tree1 (Thornhill, 2015)",
"studyID": "ot_306",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from R. J. Machida, M. U. Miya, M. Nishida, S. Nishida, 2006, 'Molecular phylogeny and evolution of the pelagic copepod genus Neocalanus (Crustacea: Copepoda)', Marine Biology, vol. 148, no. 5, pp. 1071-1079",
"decision": "INCLUDED",
"name": "Machida_etal_2006",
"studyID": "ot_1016",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from A. Bucklin, B. Frost, J. Bradford-Grieve, L. Allen, N. Copley, 2003, 'Molecular systematic and phylogenetic assessment of 34 calanoid copepod species of the Calanidae and Clausocalanidae', Marine Biology, vol. 142, no. 2, pp. 333-343",
"decision": "INCLUDED",
"name": "Default Symmetrical Tree+",
"studyID": "ot_1019",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from A. Bucklin, B. Frost, J. Bradford-Grieve, L. Allen, N. Copley, 2003, 'Molecular systematic and phylogenetic assessment of 34 calanoid copepod species of the Calanidae and Clausocalanidae', Marine Biology, vol. 142, no. 2, pp. 333-343",
"decision": "INCLUDED",
"name": "Tree Fig. 2",
"studyID": "ot_1019",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from A. Bucklin, B. Frost, J. Bradford-Grieve, L. Allen, N. Copley, 2003, 'Molecular systematic and phylogenetic assessment of 34 calanoid copepod species of the Calanidae and Clausocalanidae', Marine Biology, vol. 142, no. 2, pp. 333-343",
"decision": "INCLUDED",
"name": "Tree Fig. 1",
"studyID": "ot_1019",
"treeID": "tree3"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from A. Bucklin, B. Frost, J. Bradford-Grieve, L. Allen, N. Copley, 2003, 'Molecular systematic and phylogenetic assessment of 34 calanoid copepod species of the Calanidae and Clausocalanidae', Marine Biology, vol. 142, no. 2, pp. 333-343",
"decision": "INCLUDED",
"name": "Tree Fig. 4",
"studyID": "ot_1019",
"treeID": "tree4"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Rony Huys, Julia Llewellyn-Hughes, Sophie Conroy-Dalton, Peter D. Olson, Jennifer N. Spinks, David A. Johnston, 2007, 'Extraordinary host switching in siphonostomatoid copepods and the demise of the Monstrilloida: Integrating molecular data, ontogeny and antennulary morphology', Molecular Phylogenetics and Evolution, vol. 43, no. 2, pp. 368-378",
"decision": "INCLUDED",
"name": "Default Symmetrical Tree+",
"studyID": "ot_1020",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from 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",
"decision": "INCLUDED",
"name": "Untitled (tree1)",
"studyID": "ot_1023",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Leocadio Blanco-Bercial, Janet Bradford-Grieve, Ann Bucklin, 2011, 'Molecular phylogeny of the Calanoida (Crustacea: Copepoda)', Molecular Phylogenetics and Evolution, vol. 59, no. 1, pp. 103-113",
"decision": "INCLUDED",
"name": "Blanco_Bercial_etal_2011_ML",
"studyID": "ot_1024",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from M. Taniguchi, 2004, 'Molecular phylogeny of Neocalanus copepods in the subarctic Pacific Ocean, with notes on non-geographical genetic variations for Neocalanus cristatus', Journal of Plankton Research, vol. 26, no. 10, pp. 1249-1255",
"decision": "INCLUDED",
"name": "Tree fig. 2",
"studyID": "ot_1025",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from M. Taniguchi, 2004, 'Molecular phylogeny of Neocalanus copepods in the subarctic Pacific Ocean, with notes on non-geographical genetic variations for Neocalanus cristatus', Journal of Plankton Research, vol. 26, no. 10, pp. 1249-1255",
"decision": "INCLUDED",
"name": "Tree fig. 3",
"studyID": "ot_1025",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from E. Braga, R. Zardoya, A. Meyer, J. Yen, 1999, 'Mitochondrial and nuclear rRNA based copepod phylogeny with emphasis on the Euchaetidae (Calanoida)', Marine Biology, vol. 133, no. 1, pp. 79-90",
"decision": "INCLUDED",
"name": "Fig 3",
"studyID": "ot_1027",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from E. Braga, R. Zardoya, A. Meyer, J. Yen, 1999, 'Mitochondrial and nuclear rRNA based copepod phylogeny with emphasis on the Euchaetidae (Calanoida)', Marine Biology, vol. 133, no. 1, pp. 79-90",
"decision": "INCLUDED",
"name": "Fig 6",
"studyID": "ot_1027",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from SARAH J. ADAMOWICZ, SILVINA MENU-MARQUE, PAUL D. N. HEBERT, ANDY PURVIS, 2007, 'Molecular systematics and patterns of morphological evolution in the Centropagidae (Copepoda: Calanoida) of Argentina', Biological Journal of the Linnean Society, vol. 90, no. 2, pp. 279-292",
"decision": "INCLUDED",
"name": "Fig. 3",
"studyID": "ot_1029",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Wang Minxiao, Sun Song, Li Chaolun, Shen Xin, 2011, 'Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies', BMC Genomics, vol. 12, no. 1",
"decision": "INCLUDED",
"name": "Fig 9",
"studyID": "ot_1030",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Astrid Cornils, Leocadio Blanco-Bercial, 2013, 'Phylogeny of the Paracalanidae Giesbrecht, 1888 (Crustacea: Copepoda: Calanoida)', Molecular Phylogenetics and Evolution, vol. 69, no. 3, pp. 861-872",
"decision": "INCLUDED",
"name": "Fig. 3 ML",
"studyID": "ot_1032",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Silke Laakmann, Holger Auel, Marc Kochzius, 2012, 'Evolution in the deep sea: Biological traits, ecology and phylogenetics of pelagic copepods', Molecular Phylogenetics and Evolution, vol. 65, no. 2, pp. 535-546",
"decision": "INCLUDED",
"name": "Fig. 2a",
"studyID": "ot_1034",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Robert Alexander Pyron, Sumaithangi Rajagopalan Ganesh, Amit Sayyed, Vivek Sharma, Van Wallach, Ruchira Somaweera, 2016, 'A catalogue and systematic overview of the shield-tailed snakes (Serpentes: Uropeltidae)', Zoosystema, vol. 38, no. 4, pp. 453-506",
"decision": "INCLUDED",
"name": "con all compat",
"studyID": "ot_1037",
"treeID": "tree3"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Laurin-Lemay, S., Brinkmann, H., & Philippe, H. (2012). Origin of land plants revisited in the light of sequence contamination and missing data. Current Biology, 22(15), R593-R594.",
"decision": "INCLUDED",
"name": "Untitled (tree2507)",
"studyID": "pg_1242",
"treeID": "tree2507"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Rony Huys, Jacqueline Mackenzie-Dodds, Julia Llewellyn-Hughes, 2009, 'Cancrincolidae (Copepoda, Harpacticoida) associated with land crabs: A semiterrestrial leaf of the ameirid tree', Molecular Phylogenetics and Evolution, vol. 51, no. 2, pp. 143-156",
"decision": "INCLUDED",
"name": "Fig. 1",
"studyID": "ot_1039",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Yuchi Zheng, John J. Wiens, 2016, 'Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species', Molecular Phylogenetics and Evolution, vol. 94, pp. 537-547",
"decision": "INCLUDED",
"name": "Fig 2. appendix S3 ML tree calibrated in BEAST",
"studyID": "ot_1041",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Sara Ruane, Christopher C. Austin, 2017, 'Phylogenomics using formalin-fixed and 100+ year old intractable natural history specimens', Molecular Ecology Resources",
"decision": "INCLUDED",
"name": "Untitled (tree1)",
"studyID": "ot_1042",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Benjamin Ollomo, Patrick Durand, Franck Prugnolle, Emmanuel Douzery, Celine Arnathau, Dieudonne Nkoghe, Eric Leroy, Francois Renaud, 2009, 'A New Malaria Agent in African Hominids', PLoS Pathogens, vol. 5, no. 5, p. e1000446",
"decision": "INCLUDED",
"name": "Untitled (tree6417)",
"studyID": "pg_2770",
"treeID": "tree6417"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Rony Huys, Farrah Fatih, Susumu Ohtsuka, Julia Llewellyn-Hughes, 2012, 'Evolution of the bomolochiform superfamily complex (Copepoda: Cyclopoida): New insights from ssrDNA and morphology, and origin of umazuracolids from polychaete-infesting ancestors rejected', International Journal for Parasitology, vol. 42, no. 1, pp. 71-92",
"decision": "INCLUDED",
"name": "Fig. 2",
"studyID": "ot_1045",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Seong-il Eyun, 2017, 'Phylogenomic analysis of Copepoda (Arthropoda, Crustacea) reveals unexpected similarities with earlier proposed morphological phylogenies', BMC Evolutionary Biology, vol. 17, no. 1",
"decision": "INCLUDED",
"name": "Fig. 3",
"studyID": "ot_1046",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from T. H. Oakley, J. M. Wolfe, A. R. Lindgren, A. K. Zaharoff, 2012, 'Phylotranscriptomics to Bring the Understudied into the Fold: Monophyletic Ostracoda, Fossil Placement, and Pancrustacean Phylogeny', Molecular Biology and Evolution, vol. 30, no. 1, pp. 215-233",
"decision": "INCLUDED",
"name": "Fig. 1",
"studyID": "ot_1047",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Che-Huang Tung, Yu-Rong Cheng, Ching-Yi Lin, Ju-Shey Ho, Chih-Horng Kuo, Jr-Kai Yu, Yi-Hsien Su, 2014, 'A New Copepod With Transformed Body Plan and Unique Phylogenetic Position Parasitic in the Acorn Worm Ptychodera flava', The Biological Bulletin, vol. 226, no. 1, pp. 69-80",
"decision": "INCLUDED",
"name": "Default Symmetrical Tree+",
"studyID": "ot_1048",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Ralph S. Peters, Lars Krogmann, Christoph Mayer, Alexander Donath, Simon Gunkel, Karen Meusemann, Alexey Kozlov, Lars Podsiadlowski, Malte Petersen, Robert Lanfear, Patricia A. Diez, John Heraty, Karl M. Kjer, Seraina Klopfstein, Rudolf Meier, Carlo Polidori, Thomas Schmitt, Shanlin Liu, Xin Zhou, Torsten Wappler, Jes Rust, Bernhard Misof, Oliver Niehuis, 2017, 'Evolutionary History of the Hymenoptera', Current Biology",
"decision": "INCLUDED",
"name": "Figure 1",
"studyID": "ot_1053",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Dahiana Arcila, Guillermo Ort\u00ed, Richard Vari, Jonathan W. Armbruster, Melanie L. J. Stiassny, Kyung D. Ko, Mark H. Sabaj, John Lundberg, Liam J. Revell, Ricardo Betancur-R., 2017, 'Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life', Nature Ecology & Evolution, vol. 1, p. 0020",
"decision": "INCLUDED",
"name": "Figure 3",
"studyID": "ot_1054",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Nyakatura, Katrin, Olaf RP Bininda-Emonds. 2012. Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates. BMC Biology 10 (1): 12",
"decision": "INCLUDED",
"name": "Figure 1: best dates",
"studyID": "ot_328",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Moreau C.S., & Bell C. 2013. Testing the museum versus cradle tropical biological diversity hypothesis: Phylogeny, diversification, and ancestral biogeographic range evolution of the ants. Evolution, 67(8): 2240-2257.",
"decision": "INCLUDED",
"name": "MLT",
"studyID": "ot_1056",
"treeID": "Tr66754"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Allison K. Miller, Alexander M. Kerr, Gustav Paulay, Mike Reich, Nerida G. Wilson, Jose I. Carvajal, Greg W. Rouse, 2017, 'Molecular phylogeny of extant Holothuroidea (Echinodermata)', Molecular Phylogenetics and Evolution, vol. 111, pp. 110-131",
"decision": "INCLUDED",
"name": "Figure 3 - first tree from supp. data 2",
"studyID": "ot_1058",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from William J.D. Iles, Chodon Sass, Laura Lagomarsino, Gracie Benson-Martin, Heather Driscoll, Chelsea D. Specht, 2016, 'The phylogeny of Heliconia (Heliconiaceae) and the evolution of floral presentation', Molecular Phylogenetics and Evolution",
"decision": "INCLUDED",
"name": "Heliconiaceae",
"studyID": "ot_1062",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from T. Yu. Mayor, N. G. Sheveleva, L. V. Sukhanova, O. A. Timoshkin, S. V. Kiril\u2019chik, 2010, 'Molecular-phylogenetic analysis of cyclopoids (Copepoda: Cyclopoida) from Lake Baikal and its water catchment basin', Russian Journal of Genetics, vol. 46, no. 11, pp. 1373-1380",
"decision": "INCLUDED",
"name": "Fig. 3",
"studyID": "ot_1064",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from R. W. Thacker, A. L. Hill, M. S. Hill, N. E. Redmond, A. G. Collins, C. C. Morrow, L. Spicer, C. A. Carmack, M. E. Zappe, D. Pohlmann, C. Hall, M. C. Diaz, P. V. Bangalore, 2013, 'Nearly Complete 28S rRNA Gene Sequences Confirm New Hypotheses of Sponge Evolution', Integrative and Comparative Biology, vol. 53, no. 3, pp. 373-387",
"decision": "INCLUDED",
"name": "Thacker et al. 2013 (tree1)",
"studyID": "ot_1067",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Martin Dohrmann, Christopher Kelley, Michelle Kelly, Andrzej Pisera, John N. A. Hooper, Henry M. Reiswig, 2017, 'An integrative systematic framework helps to reconstruct skeletal evolution of glass sponges (Porifera, Hexactinellida)', Frontiers in Zoology, vol. 14, no. 1",
"decision": "INCLUDED",
"name": "molecular supermatrix raxml",
"studyID": "ot_1068",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from E. Hajdu, T. S. de Paula, N. E. Redmond, B. Cosme, A. G. Collins, G. Lobo-Hajdu, 2013, 'Mycalina: Another Crack in the Poecilosclerida Framework', Integrative and Comparative Biology, vol. 53, no. 3, pp. 462-472",
"decision": "INCLUDED",
"name": "18S Hajdu 2013 (tree1)",
"studyID": "ot_1070",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Deng J., Drew B.T., Mavrodiev E.V., Gitzendanner M.A., Soltis P., & Soltis D. 2014. Saxifragaceae: Phylogeny, divergence times, and historical biogeography. Molecular Phylogentics and Evolution, .",
"decision": "INCLUDED",
"name": "cpDNA+nrDNA-ML",
"studyID": "ot_1072",
"treeID": "Tr77370"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Ryan A. Folk, Jennifer R. Mandel, John V. Freudenstein, 2016, 'Ancestral Gene Flow and Parallel Organellar Genome Capture Result in Extreme Phylogenomic Discord in a Lineage of Angiosperms', Systematic Biology, p. syw083",
"decision": "INCLUDED",
"name": "Unpartitioned concatenated",
"studyID": "ot_1075",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Brett R. Aiello, Mark W. Westneat, Melina E. Hale, 2017, 'Mechanosensation is evolutionarily tuned to locomotor mechanics', Proceedings of the National Academy of Sciences, vol. 114, no. 17, pp. 4459-4464",
"decision": "INCLUDED",
"name": "Imported tree 1",
"studyID": "ot_1078",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Jessica L. Ware, Christopher D. Beatty, Melissa S\u00e1nchez Herrera, Steve Valley, Jim Johnson, Cary Kerst, Michael L. May, Gunther Theischinger, 2014, 'The petaltail dragonflies (Odonata: Petaluridae): Mesozoic habitat specialists that survive to the modern day', Journal of Biogeography, vol. 41, no. 7, pp. 1291-1300",
"decision": "INCLUDED",
"name": "tree 1",
"studyID": "ot_1079",
"treeID": "tree3"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Gonz\u00e1lez D., Rodriguez-carres M., Boekhout T., Stalpers J.A., Kuramae E.E., Nakatani A.K., Vilgalys R., & Cubeta M.A. 2016. Phylogenetic Relationships of Rhizoctonia Fungi within the Cantharellales. Fungal Biology, 120(4): 603-619.",
"decision": "INCLUDED",
"name": "bootrep100",
"studyID": "ot_1088",
"treeID": "Tr102832"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Adam L. Bazinet, Michael P. Cummings, Kim T. Mitter, Charles W. Mitter, 2013, 'Can RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory Study', PLoS ONE, vol. 8, no. 12, p. e82615",
"decision": "INCLUDED",
"name": "bestREP1",
"studyID": "ot_1085",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Chen J., Cui B., & Dai Y.C. 2016. Global diversity and molecular systematics of Wrightoporia s.l. (Russulales, Basidiomycota). Persoonia, 37: 21-36.",
"decision": "INCLUDED",
"name": "Fig. 1",
"studyID": "ot_1090",
"treeID": "Tr99739"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Bazinet, A. L., Mitter, K. T., Davis, D. R., Van Nieukerken, E. J., Cummings, M. P., & Mitter, C. (2017). Phylotranscriptomics resolves ancient divergences in the Lepidoptera. Systematic Entomology, 42(2), 305-316",
"decision": "INCLUDED",
"name": " 0",
"studyID": "ot_1086",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Hwang, W. S. and Weirauch, C. 2012, 'Evolutionary History of Assassin Bugs (Insecta: Hemiptera: Reduviidae): Insights from Divergence Dating and Ancestral State Reconstruction', PLoS ONE, vol. 7, no. 9, p. e45523",
"decision": "INCLUDED",
"name": "tree 1",
"studyID": "ot_1073",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Syme A.E., & Oakley T.H. 2011. Dispersal between shallow and abyssal seas and evolutionary loss and re-gain of compound eyes in cylindroleberidid ostracods: conflicting conclusions from different comparative methods. Systematic Biology, .",
"decision": "INCLUDED",
"name": "Fig. 1",
"studyID": "ot_1092",
"treeID": "Tr29847"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Irisarri I., Eernisse D.J., & Zardoya R. 2014. Molecular phylogeny of Acanthochitonina (Mollusca: Polyplacophora: Chitonida): three new mitochondrial genomes, rearranged gene orders and systematics. Journal of Natural History, .",
"decision": "INCLUDED",
"name": "Bayesian MRC multilocus nt",
"studyID": "ot_1105",
"treeID": "Tr76755"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from M. Klautau, F. Azevedo, B. Condor-Lujan, H. T. Rapp, A. Collins, C. A. d. M. Russo, 2013, 'A Molecular Phylogeny for the Order Clathrinida Rekindles and Refines Haeckel's Taxonomic Proposal for Calcareous Sponges', Integrative and Comparative Biology, vol. 53, no. 3, pp. 447-461",
"decision": "INCLUDED",
"name": "Klautau 2013 Clathrinida ITS",
"studyID": "ot_1106",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Daniela Campanella, Lily C. Hughes, Peter J. Unmack, Devin D. Bloom, Kyle R. Piller, Guillermo Ort\u00ed, 2015, 'Multi-locus fossil-calibrated phylogeny of Atheriniformes (Teleostei, Ovalentaria)', Molecular Phylogenetics and Evolution, vol. 86, pp. 8-23",
"decision": "INCLUDED",
"name": "Atheriniformes (tree1)",
"studyID": "ot_1112",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Mario Hoenemann, William F. Humphreys, Difei Li, Marco T. Neiber, Stefan Koenemann, Thomas M. Iliffe, Frederick R. Schram, 2013, 'Phylogenetic analysis and systematic revision of Remipedia (Nectiopoda) from Bayesian analysis of molecular data', Journal of Crustacean Biology, vol. 33, no. 5, pp. 603-619",
"decision": "INCLUDED",
"name": "Fig3_Honemann_Bayesian",
"studyID": "ot_1101",
"treeID": "tree3"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Weimin Ye, Chow-Yang Lee, Rudolf H. Scheffrahn, Jody M. Aleong, Nan-Yao Su, Gary W. Bennett, Michael E. Scharf, 2004, 'Phylogenetic relationships of nearctic Reticulitermes species (Isoptera: Rhinotermitidae) with particular reference to Reticulitermes arenincola Goellner', Molecular Phylogenetics and Evolution, vol. 30, no. 3, pp. 815-822",
"decision": "INCLUDED",
"name": "Tree3009",
"studyID": "ot_1114",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Marisol S\u00e1nchez-Garc\u00eda, Patrick Brandon Matheny, 2016, 'Is the switch to an ectomycorrhizal state an evolutionary key innovation in mushroom-forming fungi? A case study in the Tricholomatineae (Agaricales)', Evolution, vol. 71, no. 1, pp. 51-65",
"decision": "INCLUDED",
"name": "TREE1",
"studyID": "ot_1100",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Kawahara AY, Mignault AA, Regier JC, Kitching IJ, Mitter C (2009) 'Phylogeny and Biogeography of Hawkmoths (Lepidoptera: Sphingidae): Evidence from Five Nuclear Genes., PLoS ONE, vol. 4, no. 5, p. e5719",
"decision": "INCLUDED",
"name": "best",
"studyID": "ot_1098",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Harald Letsch, Brigitte Gottsberger, Jessica L. Ware, 2016, 'Not going with the flow: a comprehensive time-calibrated phylogeny of dragonflies (Anisoptera: Odonata: Insecta) provides evidence for the role of lentic habitats on diversification', Molecular Ecology, vol. 25, no. 6, pp. 1340-1353",
"decision": "INCLUDED",
"name": "Best Tree",
"studyID": "ot_1117",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Eric R.L. Gordon, Christiane Weirauch, 2016, 'Efficient capture of natural history data reveals prey conservatism of cryptic termite predators', Molecular Phylogenetics and Evolution, vol. 94, pp. 65-73",
"decision": "INCLUDED",
"name": "tree 1",
"studyID": "ot_1118",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from K.M. Abrams, M.T. Guzik, S.J.B. Cooper, W.F. Humphreys, R.A. King, J.-L. Cho, A.D. Austin, 2012, 'What lies beneath: Molecular phylogenetics and ancestral state reconstruction of the ancient subterranean Australian Parabathynellidae (Syncarida, Crustacea)', Molecular Phylogenetics and Evolution, vol. 64, no. 1, pp. 130-144",
"decision": "INCLUDED",
"name": "Fig.1_bayesian",
"studyID": "ot_1120",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from David T. Drumm, 2010, 'Phylogenetic Relationships of Tanaidacea (Eumalacostraca: Peracarida) Inferred from Three Molecular Loci', Journal of Crustacean Biology, vol. 30, no. 4, pp. 692-698",
"decision": "INCLUDED",
"name": "Fig.3_cladogram",
"studyID": "ot_1124",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Eric Robert Lucien Gordon, Quinn McFrederick, Christiane Weirauch, 2016, 'Phylogenetic Evidence for Ancient and Persistent Environmental Symbiont Reacquisition in Largidae (Hemiptera: Heteroptera)', Applied and Environmental Microbiology, vol. 82, no. 24, pp. 7123-7133",
"decision": "INCLUDED",
"name": "Maximum likelihood Tree",
"studyID": "ot_1125",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from John M. Heraty, Roger A. Burks, Astrid Cruaud, Gary A. P. Gibson, Johan Liljeblad, James Munro, Jean-Yves Rasplus, Gerard Delvare, Peter Jan\u0161ta, Alex Gumovsky, John Huber, James B. Woolley, Lars Krogmann, Steve Heydon, Andrew Polaszek, Stefan Schmidt, D. Chris Darling, Michael W. Gates, Jason Mottern, Elizabeth Murray, Ana Dal Molin, Serguei Triapitsyn, Hannes Baur, John D. Pinto, Simon van Noort, Jeremiah George, Matthew Yoder, 2013, 'A phylogenetic analysis of the megadiverse Chalcidoidea (Hymenoptera)', Cladistics, vol. 29, no. 5, pp. 466-542",
"decision": "INCLUDED",
"name": " Fig. 10 \"Best RaxML'",
"studyID": "ot_1093",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Nhu H. Nguyen, Heather E. Driscoll, Chelsea D. Specht, 2008, 'A molecular phylogeny of the wild onions (Allium; Alliaceae) with a focus on the western North American center of diversity', Molecular Phylogenetics and Evolution, vol. 47, no. 3, pp. 1157-1172",
"decision": "INCLUDED",
"name": "con 50 majrule",
"studyID": "ot_1095",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Chuan Ma, Yeying Wang, Chao Wu, Le Kang, Chunxiang Liu, 2014, 'The compact mitochondrial genome of Zorotypus medoensis provides insights into phylogenetic position of Zoraptera', BMC Genomics, vol. 15, no. 1, p. 1156",
"decision": "INCLUDED",
"name": "PCG12RNA BI",
"studyID": "ot_1132",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Hiroki Hata, Atsushi Sogabe, Shinya Tada, Ryohei Nishimoto, Reina Nakano, Nobuhiko Kohya, Hirohiko Takeshima, Ryota Kawanishi, 2017, 'Molecular phylogeny of obligate fish parasites of the family Cymothoidae (Isopoda, Crustacea): evolution of the attachment mode to host fish and the habitat shift from saline water to freshwater', Marine Biology, vol. 164, no. 5",
"decision": "INCLUDED",
"name": "Fig. 1 (combined ML)",
"studyID": "ot_1130",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Annie R Lindgren, Molly S Pankey, Frederick G Hochberg, Todd H Oakley, 2012, 'A multi-gene phylogeny of Cephalopoda supports convergent morphological evolution in association with multiple habitat shifts in the marine environment', BMC Evolutionary Biology, vol. 12, no. 1, p. 129",
"decision": "INCLUDED",
"name": "Largest Tree from Supplement Fig S1",
"studyID": "ot_1134",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from JESSICA L. WARE, ERIK PILGRIM, MICHAEL L. MAY, THOMAS W. DONNELLY, KENNETH TENNESSEN, 2016, 'Phylogenetic relationships of North American Gomphidae and their close relatives', Systematic Entomology, vol. 42, no. 2, pp. 347-358",
"decision": "INCLUDED",
"name": "Best tree",
"studyID": "ot_1135",
"treeID": "tree4"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Coelho G., Silveira A.D., Antoniolli Z.I., & Yurchenko E. 2016. Tropicoporus stratificans sp. nov. (Hymenochaetales, Basidiomycota) from southern Brazil. Phytotaxa, 245(2): 144-152.",
"decision": "INCLUDED",
"name": "ML tree",
"studyID": "ot_1138",
"treeID": "Tr89262"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Latha K., & Manimohan P. 2016. Five new species of Inocybe (Agaricales) from tropical India based on morphological and molecular data. Mycologia, 108(1): 110-122.",
"decision": "INCLUDED",
"name": "PAUP_1",
"studyID": "ot_1139",
"treeID": "Tr97436"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Adamcik S., Slovak M., Eberhardt U., Ronikier A., Jairus T., Hampe F., & Verbeken A. 2016. Molecular inference, multivariate morphometrics and ecological assessment are applied in concert to delimit species in the Russula clavipes complex. Mycologia, 108(4): 716-730.",
"decision": "INCLUDED",
"name": "PAUP_1",
"studyID": "ot_1140",
"treeID": "Tr103257"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Orihara T., Ohmae M., & Yamamoto K. 2016. First report of Chamonixia caespitosa (Boletaceae, Boletales) from Japan and its phylogeographic significance. Mycoscience, 57(1): 58-63.",
"decision": "INCLUDED",
"name": "Fig. 1",
"studyID": "ot_1141",
"treeID": "Tr88900"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Wang X., Lombard L., Groenewald J.Z., Li J., Videira S.I., Samson R., Liu X., & Crous P.W. 2016. Phylogenetic reassessment of the Chaetomium globosum species complex. Persoonia: Molecular Phylogeny and Evolution of Fungi, 36: 83-133.",
"decision": "INCLUDED",
"name": "Fig. 1",
"studyID": "ot_1142",
"treeID": "Tr91759"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from S.J. Longo, B.C. Faircloth, A. Meyer, M.W. Westneat, M.E. Alfaro, P.C. Wainwright, 2017, 'Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements', Molecular Phylogenetics and Evolution, vol. 113, pp. 33-48",
"decision": "INCLUDED",
"name": "Untitled (tree1)",
"studyID": "ot_1147",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Michael G. Branstetter, Bryan N. Danforth, James P. Pitts, Brant C. Faircloth, Philip S. Ward, Matthew L. Buffington, Michael W. Gates, Robert R. Kula, Se\u00e1n G. Brady, 2017, 'Phylogenomic Insights into the Evolution of Stinging Wasps and the Origins of Ants and Bees', Current Biology, vol. 27, no. 7, pp. 1019-1025",
"decision": "INCLUDED",
"name": "Untitled (tree1)",
"studyID": "ot_1059",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Graham J. Slater, Jeremy A. Goldbogen, Nicholas D. Pyenson, 2017, 'Independent evolution of baleen whale gigantism linked to Plio-Pleistocene ocean dynamics', Proceedings of the Royal Society B: Biological Sciences, vol. 284, no. 1855, p. 20170546",
"decision": "INCLUDED",
"name": "TREE1",
"studyID": "ot_1150",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Sarah J. Adamowicz, Silvina Menu-Marque, Stuart A. Halse, Janet C. Topan, Tyler S. Zemlak, Paul D.N. Hebert, Jonathan D.S. Witt, 2010, 'The evolutionary diversification of the Centropagidae (Crustacea, Calanoida): A history of habitat shifts', Molecular Phylogenetics and Evolution, vol. 55, no. 2, pp. 418-430",
"decision": "INCLUDED",
"name": "Fig. 3",
"studyID": "ot_1159",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Janet M. Bradford-Grieve, Geoffrey A. Boxshall, Leocadio Blanco-Bercial, 2014, 'Revision of basal calanoid copepod families, with a description of a new species and genus of Pseudocyclopidae', Zoological Journal of the Linnean Society, vol. 171, no. 3, pp. 507-533",
"decision": "INCLUDED",
"name": "Fig 12",
"studyID": "ot_1161",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Iole Di Capua, Fulvio Maffucci, Raimondo Pannone, Maria Grazia Mazzocchi, Elio Biffali, Alberto Amato, 2017, 'Molecular phylogeny of Oncaeidae (Copepoda) using nuclear ribosomal internal transcribed spacer (ITS rDNA)', PLOS ONE, vol. 12, no. 4, p. e0175662",
"decision": "INCLUDED",
"name": "Fig 1",
"studyID": "ot_1162",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Brown, G. K., Murphy, D. J., Miller, J. T., & Ladiges, P. Y. (2008). Acacia ss. and its relationship among tropical legumes, Tribe Ingeae (Leguminosae: Mimosoideae). Systematic Botany, 33(4), 739-751.",
"decision": "INCLUDED",
"name": "Figure 4 ITS and ets combined",
"studyID": "pg_155",
"treeID": "tree780"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Yan-Jie Feng, David C. Blackburn, Dan Liang, David M. Hillis, David B. Wake, David C. Cannatella, Peng Zhang, 2017, 'Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous\u2013Paleogene boundary', Proceedings of the National Academy of Sciences, p. 201704632",
"decision": "INCLUDED",
"name": "Gondwanan frogs",
"studyID": "ot_1164",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Laura M. Zahn, 2017, 'Loss of flight in the Galapagos cormorant', Science, vol. 356, no. 6341, pp. 918.10-919",
"decision": "INCLUDED",
"name": "Galapagos cormorant",
"studyID": "ot_1165",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Julia J. Day, Antoine Fages, Katherine J. Brown, Emmanuel J. Vreven, Melanie L. J. Stiassny, Roger Bills, John P. Friel, Lukas R\u00fcber, 2017, 'Multiple independent colonizations into the Congo Basin during the continental radiation of African Mastacembelus\n spiny eels', Journal of Biogeography",
"decision": "INCLUDED",
"name": "African Mastacembelus spiny eels",
"studyID": "ot_1167",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Michael D. D'Emic, Roger B.J. Benson, 2013, 'Measurement, variation, and scaling of osteocyte lacunae: a case study in birds', Bone, vol. 57, no. 1, pp. 300-310",
"decision": "INCLUDED",
"name": "Untitled (tree3)",
"studyID": "ot_1174",
"treeID": "tree3"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Shannon C.K. Straub, Michael J. Moore, Pamela S. Soltis, Douglas E. Soltis, Aaron Liston, Tatyana Livshultz, 2014, 'Phylogenetic signal detection from an ancient rapid radiation: Effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae', Molecular Phylogenetics and Evolution, vol. 80, pp. 169-185",
"decision": "INCLUDED",
"name": "crown clade Apocynaceae",
"studyID": "ot_1175",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Steven B. Cannon, Michael R. McKain, Alex Harkess, Matthew N. Nelson, Sudhansu Dash, Michael K. Deyholos, Yanhui Peng, Blake Joyce, Charles N. Stewart, Megan Rolf, Toni Kutchan, Xuemei Tan, Cui Chen, Yong Zhang, Eric Carpenter, Gane Ka-Shu Wong, Jeff J. Doyle, Jim Leebens-Mack, 2014, 'Multiple Polyploidy Events in the Early Radiation of Nodulating and Nonnodulating Legumes', Molecular Biology and Evolution, vol. 32, no. 1, pp. 193-210",
"decision": "INCLUDED",
"name": "single copy trees",
"studyID": "ot_1176",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Kiontke K., Gavin N., Raynes Y., Roehrig C., Piano F., & Fitch D. 2004. Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss. Proceedings of the National Academy of Sciences of the United States of America 101 (24): 9003-9008.",
"decision": "INCLUDED",
"name": "Untitled (tree4326)",
"studyID": "pg_2089",
"treeID": "tree4326"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Nepal M.P., & Ferguson C.J. 2011. Phylogenetics of Morus (Moraceae) Inferred from ITS and trnL-trnF Sequence Data. Systematic Botany, .",
"decision": "INCLUDED",
"name": "Fig. 3 ML",
"studyID": "ot_1182",
"treeID": "Tr43256"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Yang EC, Boo SM, Bhattacharya D, Saunders GW, Knoll AH, Fredericq S, Graf L, Yoon HS. 2016. Divergence time estimates and the evolution of major lineages in the florideophyte red algae. Scientific Reports 6: 21361.",
"decision": "INCLUDED",
"name": "ml",
"studyID": "ot_1184",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Chris J. Law, Graham J. Slater, Rita S. Mehta, 2017, 'Lineage Diversity and Size Disparity in Musteloidea: Testing Patterns of Adaptive Radiation Using Molecular and Fossil-Based Methods', Systematic Biology",
"decision": "INCLUDED",
"name": "Musteloidea",
"studyID": "ot_1185",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Perrie L., Wilson R., Shepherd L., Ohlsen D., Batty E., Brownsey P., & Bayly M.J. 2014. Molecular phylogenetics and generic taxonomy of the Blechnaceae ferns. Taxon, 63(4): 745-758.",
"decision": "INCLUDED",
"name": "Fig. 1",
"studyID": "ot_1202",
"treeID": "Tr96307"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Gernandt D.S., Holman G., Campbell C., Parks M., Mathews S., Raubeson L., Liston A., Stockey R., & Rothwell G. 2016. Phylogenetics of extant and fossil Pinaceae: methods for increasing topological stability. Botany, .",
"decision": "INCLUDED",
"name": "Fig. 1C",
"studyID": "ot_1198",
"treeID": "Tr97555"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Gernandt D.S., Holman G., Campbell C., Parks M., Mathews S., Raubeson L., Liston A., Stockey R., & Rothwell G. 2016. Phylogenetics of extant and fossil Pinaceae: methods for increasing topological stability. Botany, .",
"decision": "INCLUDED",
"name": "Fig. 1B",
"studyID": "ot_1198",
"treeID": "Tr97554"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Perrie L., Wilson R., Shepherd L., Ohlsen D., Batty E., Brownsey P., & Bayly M.J. 2014. Molecular phylogenetics and generic taxonomy of the Blechnaceae ferns. Taxon, 63(4): 745-758.",
"decision": "INCLUDED",
"name": "Fig. 1",
"studyID": "ot_1209",
"treeID": "Tr96307"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Portnoy D., Willis S., Hunt E., Swift D., Gold J., & Conway K.W. 2016. Molecular phylogenetics of New World searobins (Triglidae; Prionotinae). Molecular Phylogenetics and Evolution, .",
"decision": "INCLUDED",
"name": "TREE1",
"studyID": "ot_1208",
"treeID": "Tr99854"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Pohl, M., Milvertz, F. C., Meyer, A., & Vences, M. (2015). Multigene phylogeny of cyprinodontiform fishes suggests continental radiations and a rogue taxon position of Pantanodon. Vertebrate Zoology, 65(1), 37-44.",
"decision": "INCLUDED",
"name": "Bayesian tree",
"studyID": "ot_1212",
"treeID": "tree12"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Sahar Khodami, J. Vaun McArthur, Leocadio Blanco-Bercial, Pedro Martinez Arbizu, 2017, 'Molecular Phylogeny and Revision of Copepod Orders (Crustacea: Copepoda)', Scientific Reports, vol. 7, no. 1",
"decision": "INCLUDED",
"name": "Default Symmetrical Tree+",
"studyID": "ot_1215",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Sahar Khodami, J. Vaun McArthur, Leocadio Blanco-Bercial, Pedro Martinez Arbizu, 2017, 'Molecular Phylogeny and Revision of Copepod Orders (Crustacea: Copepoda)', Scientific Reports, vol. 7, no. 1",
"decision": "INCLUDED",
"name": "Fig S6",
"studyID": "ot_1215",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from K. L. Haag, T. Y. James, J.-F. Pombert, R. Larsson, T. M. M. Schaer, D. Refardt, D. Ebert, 2014, 'Evolution of a morphological novelty occurred before genome compaction in a lineage of extreme parasites', Proceedings of the National Academy of Sciences, vol. 111, no. 43, pp. 15480-15485",
"decision": "INCLUDED",
"name": "Fig 2",
"studyID": "ot_1216",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Mishler B., Knerr N., Gonz?lez-orozco C.E., Thornhill A.H., Laffan S., & Miller J.T. 2014. Phylogenetic Measures of Biodiversity and Neo- and Paleo-Endemism in Australian Acacia. Nature Communications, 5(4473).",
"decision": "INCLUDED",
"name": "tree 1",
"studyID": "ot_303",
"treeID": "Tr62284"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Huang D.I., & Friar E. 2010. Relationships in the Lupinus albifrons species complex (Fabaceae) based on two highly variable chloroplast regions. Systematic Botany, .",
"decision": "INCLUDED",
"name": "Fig. 1",
"studyID": "ot_607",
"treeID": "Tr25497"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Miller, J. T. [et al. 2003], Grimes, J. W,, Murphy, D. J., Bayer, R. J., & Ladiges, P. Y. 2003. A phylogenetic analysis of the Acacieae and Ingeae (Mimosoideae: Fabaceae) based on trnK, matK, psbA-trnH, and trnL/trnF sequence data. Syst. Bot. 28: 558-566.",
"decision": "INCLUDED",
"name": "Fig 1 Maximum parsimony strict consensus",
"studyID": "pg_295",
"treeID": "tree203"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Azani, Nasim, et al. \"A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny The Legume Phylogeny Working Group (LPWG).\" Taxon 66.1 (2017): 44-77.",
"decision": "INCLUDED",
"name": "Bayesian Majority Rule Phylobayes Consensus Tree",
"studyID": "ot_1050",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from C. Bessega, and R. H. Fortunato. 2010. Section Mimadenia: its phylogenetic relationships within the genus Mimosa (Leguminosae, Mimosoideae) using plastid trnL\u2013F sequence data. Australian Systematic Botany. 24: 104\u2013110.",
"decision": "INCLUDED",
"name": "Fig 1 ML tree",
"studyID": "pg_1864",
"treeID": "tree3763"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Jobson, R. W., & Luckow, M. 2007. Phylogenetic study of the genus Piptadenia (Mimosoideae: Leguminosae) using plastid trnL-F and trnK/matK sequence data. Syst. Bot. 32: 569-575",
"decision": "INCLUDED",
"name": "Untitled (tree3879)",
"studyID": "pg_1902",
"treeID": "tree3879"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from McMahon, M. M., & Sanderson, M. J. 2006. Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes. Syst. Biol. 55: 818-836.",
"decision": "INCLUDED",
"name": "Untitled (tree1940)",
"studyID": "pg_999",
"treeID": "tree1940"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Brown, G. K., Murphy, D. J., & Ladiges, P. Y. (2011). Relationships of the Australo\u2010Malesian genus Paraserianthes (Mimosoideae: Leguminosae) identifies the sister group of Acacia sensu stricto and two biogeographical tracks. Cladistics, 27(4), 380-390.",
"decision": "INCLUDED",
"name": "Figure 1",
"studyID": "pg_154",
"treeID": "tree782"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Daegan J.G. Inward, Alfried P. Vogler, Paul Eggleton, 2007, 'A comprehensive phylogenetic analysis of termites (Isoptera) illuminates key aspects of their evolutionary biology', Molecular Phylogenetics and Evolution, vol. 44, no. 3, pp. 953-967",
"decision": "INCLUDED",
"name": "Inward2007",
"studyID": "ot_1233",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Fr\u00e9d\u00e9ric Legendre, Michael F. Whiting, Christian Bordereau, Eliana M. Cancello, Theodore A. Evans, Philippe Grandcolas, 2008, 'The phylogeny of termites (Dictyoptera: Isoptera) based on mitochondrial and nuclear markers: Implications for the evolution of the worker and pseudergate castes, and foraging behaviors', Molecular Phylogenetics and Evolution, vol. 48, no. 2, pp. 615-627",
"decision": "INCLUDED",
"name": "Legendre2008",
"studyID": "ot_1234",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Duur K. Aanen, Paul Eggleton, 2005, 'Fungus-Growing Termites Originated in African Rain Forest', Current Biology, vol. 15, no. 9, pp. 851-855",
"decision": "INCLUDED",
"name": "Aenen2005fig1",
"studyID": "ot_1235",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Steven Poe, Adri\u00e1n Nieto-montes de oca, Omar Torres-carvajal, Kevin De Queiroz, Juli\u00e1n A. Velasco, Brad Truett, Levi N. Gray, Mason J. Ryan, Gunther K\u00f6hler, Fernando Ayala-varela, Ian Latella, 2017, 'A Phylogenetic, Biogeographic, and Taxonomic study of all Extant Species of Anolis (Squamata; Iguanidae)', Systematic Biology, vol. 66, no. 5, pp. 663-697",
"decision": "INCLUDED",
"name": "TREE1",
"studyID": "ot_1236",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Joseph T. Miller, Vanessa Terra, Chance Riggins, John E. Ebinger, David S. Seigler, 2017, 'Molecular Phylogenetics of Parasenegalia and Pseudosenegalia (Fabaceae: Mimosoideae)', Systematic Botany, vol. 42, no. 3, pp. 465-469",
"decision": "INCLUDED",
"name": "Maximum likelihood topology tree based on the combined ITS and plastid dataset.",
"studyID": "ot_1229",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Fernando B. Matos, Alejandra Vasco, Robbin C. Moran, 2018, 'Elaphoglossum doanense and Elaphoglossum tonduzii: New Members of Elaphoglossum Sect. Squamipedia (Dryopteridaceae) and Their Significance for Inferring the Evolution of Rhizome Habit and Nest-Forming Leaves within the Genus', International Journal of Plant Sciences, pp. 000-000",
"decision": "INCLUDED",
"name": "Squamipedia MP",
"studyID": "ot_1239",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Chen C., Rothfels C.J., Mustapeng A.M., Gubilil M., Karger D.N., Kessler M., & Huang Y. 2017. End of an enigma: Aenigmopteris belongs in Tectaria (Tectariaceae: Polypodiopsida). Journal of Plant Research, .",
"decision": "INCLUDED",
"name": "bestREP10",
"studyID": "ot_1241",
"treeID": "Tr103639"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Kuo L., Chen C., Shinohara W., Ebihara A., Hiroshi K., Hirotoshi S., Huang Y., & Chiou W. 2017. Not only in the temperate zone: independent gametophytes of two vittarioid ferns (Pteridaceae, Polypodiales) in East Asian subtropics. Journal of Plant Research, 130: 407-416.",
"decision": "INCLUDED",
"name": "TREE1",
"studyID": "ot_1246",
"treeID": "Tr108958"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Guillaume Chomicki, Philip S. Ward, Susanne S. Renner, 2015, 'Macroevolutionary assembly of ant/plant symbioses:Pseudomyrmexants and their ant-housing plants in the Neotropics', Proceedings of the Royal Society B: Biological Sciences, vol. 282, no. 1819, p. 20152200",
"decision": "INCLUDED",
"name": "bestREP1",
"studyID": "ot_1245",
"treeID": "Tr87460"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Boudinot B.E., Probst R.S., Brand\u00e3o C.R.F., Feitosa R.M., & Ward P. 2016. Out of the Neotropics: newly discovered relictual species sheds light on the biogeographical history of spider ants (Leptomyrmex, Dolichoderinae, Formicidae). Syst Entomol, 41: 658-671. ",
"decision": "INCLUDED",
"name": "bestREP1",
"studyID": "ot_1248",
"treeID": "Tr92236"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from WARD, P. S. and FISHER, B. L. (2016), Tales of dracula ants: the evolutionary history of the ant subfamily Amblyoponinae (Hymenoptera: Formicidae). Syst Entomol, 41: 683-693. ",
"decision": "INCLUDED",
"name": "bestREP1",
"studyID": "ot_1249",
"treeID": "Tr93670"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Amy E. Zanne, David C. Tank, William K. Cornwell, Jonathan M. Eastman, Stephen A. Smith, Richard G. FitzJohn, Daniel J. McGlinn, Brian C. O\u2019Meara, Angela T. Moles, Peter B. Reich, Dana L. Royer, Douglas E. Soltis, Peter F. Stevens, Mark Westoby, Ian J. Wright, Lonnie Aarssen, Robert I. Bertin, Andre Calaminus, Rafa\u00ebl Govaerts, Frank Hemmings, Michelle R. Leishman, Jacek Oleksyn, Pamela S. Soltis, Nathan G. Swenson, Laura Warman, Jeremy M. Beaulieu, 2013, 'Three keys to the radiation of angiosperms into freezing environments', Nature, vol. 506, no. 7486, pp. 89-92",
"decision": "INCLUDED",
"name": "Fig. 1 time-calibrated ML estimate",
"studyID": "ot_311",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Ward P.S., Brady S.G., Fisher B.L, and Schultz, T.R. 2015. The evolution of myrmicine ants: phylogeny and biogeography of a hyperdiverse ant clade (Hymenoptera: Formicidae). Syst Entomol, 40: 61-81. ",
"decision": "INCLUDED",
"name": "bestREP1",
"studyID": "ot_1247",
"treeID": "Tr74849"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Benedict King, Tuo Qiao, Michael S. Y. Lee, Min Zhu, John A. Long, 2016, 'Bayesian Morphological Clock Methods Resurrect Placoderm Monophyly and Reveal Rapid Early Evolution in Jawed Vertebrates', Systematic Biology, p. syw107",
"decision": "INCLUDED",
"name": "Figure3. MCC BEAST2 time tree",
"studyID": "ot_1253",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Gregory F.M. Jongsma, Michael F. Barej, Christopher D. Barratt, Marius Burger, Werner Conradie, Raffael Ernst, Eli Greenbaum, Mareike Hirschfeld, Adam D. Leach\u00e9, Johannes Penner, Daniel M. Portik, Ange-Ghislain Zassi-Boulou, Mark-Oliver R\u00f6del, David C. Blackburn, 2018, 'Diversity and biogeography of frogs in the genus Amnirana (Anura: Ranidae) across sub-Saharan Africa', Molecular Phylogenetics and Evolution, vol. 120, pp. 274-285",
"decision": "INCLUDED",
"name": "Sub-saharan Amnirana tree",
"studyID": "ot_1261",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Fraija-fernandez N., Olson P., Crespo E., Raga J.A., Aznar F.J., & Fernandez M. 2015. Independence host switching events by digeneans parasites of cetaceans inferred from ribosomal DNA. International Journal for Parasitology, 45(2-3): 167-173.",
"decision": "INCLUDED",
"name": "con 50 majrule",
"studyID": "ot_1273",
"treeID": "Tr89136"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Fraija-fernandez N., Olson P., Crespo E., Raga J.A., Aznar F.J., & Fernandez M. 2015. Independence host switching events by digeneans parasites of cetaceans inferred from ribosomal DNA. International Journal for Parasitology, 45(2-3): 167-173.",
"decision": "INCLUDED",
"name": "con 50 majrule",
"studyID": "ot_1273",
"treeID": "Tr89135"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Fr\u00e9d\u00e9ric Delsuc, Melanie Kuch, Gillian C. Gibb, Jonathan Hughes, Paul Szpak, John Southon, Jacob Enk, Ana T. Duggan, Hendrik N. Poinar, 2018, ' Resolving the phylogenetic position of Darwin's extinct ground sloth ( Mylodon darwinii) using mitogenomic and nuclear exon data', Proceedings of the Royal Society B: Biological Sciences, vol. 285, no. 1878, p. 20180214",
"decision": "INCLUDED",
"name": "Bayesian Mitochondrial",
"studyID": "ot_1278",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Fr\u00e9d\u00e9ric Delsuc, Melanie Kuch, Gillian C. Gibb, Jonathan Hughes, Paul Szpak, John Southon, Jacob Enk, Ana T. Duggan, Hendrik N. Poinar, 2018, ' Resolving the phylogenetic position of Darwin's extinct ground sloth ( Mylodon darwinii) using mitogenomic and nuclear exon data', Proceedings of the Royal Society B: Biological Sciences, vol. 285, no. 1878, p. 20180214",
"decision": "INCLUDED",
"name": "Bayesian Nuclear",
"studyID": "ot_1278",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Balci Y., Balci S., Blair J., Park S., Kang S., & Macdonald W. 2007. Phytophthora quercetorum sp. nov., a novel species isolated from eastern and north-central US oak forest soils. Mycological Research, null.",
"decision": "INCLUDED",
"name": "MB MajRule",
"studyID": "ot_1280",
"treeID": "Tr2912"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Rokas A., Melika G., Abe Y., Nieves-aldrey J., Cook J., & Stone G. 2003. Lifecycle closure, lineage sorting and hybridization revealed in a phylogenetic analysis of European oak gallwasps (Hymenoptera: Cynipidae: Cynipini) using mitochondrial sequence data. Molecular Phylogenetics and Evolution, 26(1): 36-45.",
"decision": "INCLUDED",
"name": "Fig. 2",
"studyID": "ot_1281",
"treeID": "Tr788"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Brian Tilston Smith, Robert W. Bryson, William M. Mauck, Jaime Chaves, Mark B. Robbins, Alexandre Aleixo, John Klicka, 2018, 'Species delimitation and biogeography of the gnatcatchers and gnatwrens (Aves: Polioptilidae)', Molecular Phylogenetics and Evolution, vol. 126, pp. 45-57",
"decision": "INCLUDED",
"name": "*Beast_7locus",
"studyID": "ot_1286",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Li-E Yang, Ying Meng, De-Li Peng, Ze-Long Nie, Hang Sun, 2018, 'Molecular phylogeny of Galium L. of the tribe Rubieae (Rubiaceae) \u2013 Emphasis on Chinese species and recognition of a new genus Pseudogalium', Molecular Phylogenetics and Evolution, vol. 126, pp. 221-232",
"decision": "INCLUDED",
"name": "Fig1_BI",
"studyID": "ot_1313",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Rowan J. Schley, Manuel de la Estrella, Oscar Alejandro P\u00e9rez-Escobar, Anne Bruneau, Timothy Barraclough, F\u00e9lix Forest, Bente Klitg\u00e5rd, 2018, 'Is Amazonia a \u2018museum\u2019 for Neotropical trees? The evolution of the Brownea clade (Detarioideae, Leguminosae)', Molecular Phylogenetics and Evolution, vol. 126, pp. 279-292",
"decision": "INCLUDED",
"name": "Fig2_BI_fossil-calib",
"studyID": "ot_1318",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Michael Tessler, Danielle de Carle, Madeleine L. Voiklis, Olivia A. Gresham, Johannes S. Neumann, Stanis\u0142aw Cios, Mark E. Siddall, 2018, 'Worms that suck: Phylogenetic analysis of Hirudinea solidifies the position of Acanthobdellida and necessitates the dissolution of Rhynchobdellida', Molecular Phylogenetics and Evolution, vol. 127, pp. 129-134",
"decision": "INCLUDED",
"name": "Fig1_ML",
"studyID": "ot_1315",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Riebesehl J., Langer E.J., Ordynets A., Striegel M.M., & Witzany C. 2015. Hyphodontia borbonica, a new species from La Reunion. Mycol Progress, 14: 104.",
"decision": "INCLUDED",
"name": "Fig. 7",
"studyID": "ot_1325",
"treeID": "Tr87612"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Azevedo E., Barata M., Marques I.M., & Caeiro M.F. 2017. Lulworthia atlantica: a new species supported by molecular phylogeny and morphological analysis. Mycologia, 109(2): 287-295.",
"decision": "INCLUDED",
"name": "con 50 majrule",
"studyID": "ot_1326",
"treeID": "Tr90799"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Struck T., Purschke G., & Halanych K. 2005. A scaleless scale worm: Molecular evidence for the phylogenetic placement of Pisione remota (Pisionidae, Annelida). Marine Biology Research, 1.",
"decision": "INCLUDED",
"name": "Fig. 3",
"studyID": "ot_1334",
"treeID": "Tr2234"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Struck T., Purschke G., & Halanych K. 2005. A scaleless scale worm: Molecular evidence for the phylogenetic placement of Pisione remota (Pisionidae, Annelida). Marine Biology Research, 1.",
"decision": "INCLUDED",
"name": "Fig. 4A",
"studyID": "ot_1334",
"treeID": "Tr2235"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Struck T., Purschke G., & Halanych K. 2005. A scaleless scale worm: Molecular evidence for the phylogenetic placement of Pisione remota (Pisionidae, Annelida). Marine Biology Research, 1.",
"decision": "INCLUDED",
"name": "Fig. 4B",
"studyID": "ot_1334",
"treeID": "Tr2236"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Struck T., Purschke G., & Halanych K. 2005. A scaleless scale worm: Molecular evidence for the phylogenetic placement of Pisione remota (Pisionidae, Annelida). Marine Biology Research, 1.",
"decision": "INCLUDED",
"name": "Fig. 5",
"studyID": "ot_1334",
"treeID": "Tr2237"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Langer M.C., Bittencourt J.S., & Schultz C.L. 2011. A reassessment of the basal dinosaur Guaibasaurus candelariensis, from the Late Triassic Caturrita Formation of South Brazil. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, 101: 301-332.",
"decision": "INCLUDED",
"name": "Figure 19A",
"studyID": "ot_1335",
"treeID": "Tr55332"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Hubka V., Novakova A., Jurjevic Z., & Peterson S.W. 2014. Revision of Aspergillus section Flavipedes: seven new species and proposal of section Jani sect. nov. Mycologia, .",
"decision": "INCLUDED",
"name": "combined data Flavipedes",
"studyID": "ot_1338",
"treeID": "Tr76168"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Juan Moles, Conxita Avila, Manuel A E Malaquias, 2017, 'Systematic revision of the Antarctic gastropod family Newnesiidae (Heterobranchia: Cephalaspidea) with the description of a new genus and a new abyssal species', Zoological Journal of the Linnean Society",
"decision": "INCLUDED",
"name": "Fig. 3",
"studyID": "ot_1339",
"treeID": "Tr105276"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from R\u00e9blov\u00e1 M., Fournier J., & Stepanek V. 2016. Two new lineages of aquatic ascomycetes: Atractospora gen. nov. and Rubellisphaeria gen. et sp. nov., and a sexual morph of Myrmecridium montsegurinum sp. nov. Mycological Progress, 15: 21.",
"decision": "INCLUDED",
"name": "Fig. 1",
"studyID": "ot_1340",
"treeID": "Tr92106"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from R\u00e9blov\u00e1 M., Fournier J., & Stepanek V. 2016. Two new lineages of aquatic ascomycetes: Atractospora gen. nov. and Rubellisphaeria gen. et sp. nov., and a sexual morph of Myrmecridium montsegurinum sp. nov. Mycological Progress, 15: 21.",
"decision": "INCLUDED",
"name": "Fig. 2",
"studyID": "ot_1340",
"treeID": "Tr92107"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Prosanta Chakrabarty, Brant C. Faircloth, Fernando Alda, William B. Ludt, Caleb D. Mcmahan, Thomas J. Near, Alex Dornburg, James S. Albert, Jairo Arroyave, Melanie L. J. Stiassny, Laurie Sorenson, Michael E. Alfaro, 2017, 'Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes', Systematic Biology, vol. 66, no. 6, pp. 881-895",
"decision": "INCLUDED",
"name": "Chakrabarty et al. (2017) Characiformes",
"studyID": "ot_1342",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Bret M. Boyd, Julie M. Allen, Nam Nguyen, Andrew D. Sweet, Tandy Warnow, Michael D. Shapiro, Scott M. Villa, Sarah E. Bush, Dale H. Clayton, Kevin P. Johnson, 2017, '\n Phylogenomics using Target-restricted Assembly Resolves Intra-generic Relationships of Parasitic Lice (Phthiraptera:\n Columbicola\n )\n ', Systematic Biology, p. syx027",
"decision": "INCLUDED",
"name": "ConcatenationBootstrapTree",
"studyID": "ot_1343",
"treeID": "tree7"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Garfinkel A.R., Lorenzini M., Zapparoli G., & Chastagner G.A. 2017. Botrytis euroamericana, a new species from peony and grape in North America and Europe. Mycologia , .",
"decision": "INCLUDED",
"name": "Imported tree 1",
"studyID": "ot_1350",
"treeID": "Tr105258"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Arora D., & Frank J.L. 2014. Clarifying the Butter Boletes: a new genus, Butyriboletus, is established to accommodate Boletus sect. Appendiculati, and seven new species are described. Mycologia, 106(3): 464-480.",
"decision": "INCLUDED",
"name": "PAUP 1",
"studyID": "ot_1351",
"treeID": "Tr61887"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Zhou J., Zhu L., Chen H., & Cui B. 2016. Taxonomy and phylogeny of Polyporus group Melanopus (Polyporales, Basidiomycota) from China. PloS ONE, 11(8): e0159495.",
"decision": "INCLUDED",
"name": "PAUP 1",
"studyID": "ot_1353",
"treeID": "Tr111812"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Marc S. Appelhans, Niklas Reichelt, Milton Groppo, Claudia Paetzold, Jun Wen, 2018, 'Phylogeny and biogeography of the pantropical genus Zanthoxylum and its closest relatives in the proto-Rutaceae group (Rutaceae)', Molecular Phylogenetics and Evolution, vol. 126, pp. 31-44",
"decision": "INCLUDED",
"name": "Fig3_4marker-tree",
"studyID": "ot_1354",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Pascual B., El-azaz J., De la torre F., Canas R.A., Avila C., & Canovas F.M. 2016. Biosynthesis and metabolic fate of phenylalanine in conifers. Frontiers in Plant Science, 7: 1030.",
"decision": "INCLUDED",
"name": "Fig. 2",
"studyID": "ot_1360",
"treeID": "Tr93591"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Sessegolo C., Burlet N., & Haudry A.V. 2016. Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies. Biology Letters, 12(8).",
"decision": "INCLUDED",
"name": "ML tree ",
"studyID": "ot_1362",
"treeID": "Tr96006"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Videira S.I., Groenewald J.Z., Braun U., Shin H., & Crous P.W. 2016. All that glitters is not Ramularia. Studies in Mycology, 83: 49-163.",
"decision": "INCLUDED",
"name": "Fig. 1 Bayesian tree",
"studyID": "ot_1363",
"treeID": "Tr110586"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Videira S.I., Groenewald J.Z., Braun U., Shin H., & Crous P.W. 2016. All that glitters is not Ramularia. Studies in Mycology, 83: 49-163.",
"decision": "INCLUDED",
"name": "Fig. 2 Baysian tree",
"studyID": "ot_1363",
"treeID": "Tr110589"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Springer M.S., Emerling C.A., Meredith R.W., Janecka J., Eizirik E., & Murphy W. 2016. Waking the undead: implications of a soft explosive model for the timing of placental mammal diversification. Molecular Phylogentics and Evolution, .",
"decision": "INCLUDED",
"name": "MajRule",
"studyID": "ot_1366",
"treeID": "Tr98763"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Abasova L., Aghayeva D., & Takamatsu S. 2018. Notes on powdery mildews of the genus Erysiphe from Azerbaijan. Current Research in Environmental & Applied Mycology, 8(1): 50-53 .",
"decision": "INCLUDED",
"name": "PAUP_1",
"studyID": "ot_1368",
"treeID": "Tr111745"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from T\u00e1rcia Fernanda da Silva, Horacio Schneider, Iracilda Sampaio, Arturo Angulo, Marcelo Fulg\u00eancio Guedes Brito, Alexandre Clistenes de Alc\u00e2ntara Santos, Jonas de Andrade Santos, Alfredo Carvalho-Filho, Simoni Santos, 2018, 'Phylogeny of the subfamily Stelliferinae suggests speciation in Ophioscion Gill, 1863 (Sciaenidae: Perciformes) in the western South Atlantic', Molecular Phylogenetics and Evolution, vol. 125, pp. 51-61",
"decision": "INCLUDED",
"name": "Fig3_4loci(2mtDNA)_tree",
"studyID": "ot_1370",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from T\u00e1rcia Fernanda da Silva, Horacio Schneider, Iracilda Sampaio, Arturo Angulo, Marcelo Fulg\u00eancio Guedes Brito, Alexandre Clistenes de Alc\u00e2ntara Santos, Jonas de Andrade Santos, Alfredo Carvalho-Filho, Simoni Santos, 2018, 'Phylogeny of the subfamily Stelliferinae suggests speciation in Ophioscion Gill, 1863 (Sciaenidae: Perciformes) in the western South Atlantic', Molecular Phylogenetics and Evolution, vol. 125, pp. 51-61",
"decision": "INCLUDED",
"name": "Fig4_4loci(2mtDNA)_time-tree",
"studyID": "ot_1370",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Chirivi-salomon J.S., Danies G., Restrepo S., & Sanjuan T.I. 2015. Lecanicillium sabanense sp. nov. (Cordycipitaceae) a new fungal entomopathogen of coccids. Phytotaxa, 234(1): 063-074.",
"decision": "INCLUDED",
"name": "con 50 majrule",
"studyID": "ot_1375",
"treeID": "Tr86809"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Chirivi-salomon J.S., Danies G., Restrepo S., & Sanjuan T.I. 2015. Lecanicillium sabanense sp. nov. (Cordycipitaceae) a new fungal entomopathogen of coccids. Phytotaxa, 234(1): 063-074.",
"decision": "INCLUDED",
"name": "con 50 majrule",
"studyID": "ot_1375",
"treeID": "Tr86807"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Wei Wang, Rosa Del C. Ortiz, Fr\u00e9d\u00e9ric M.B. Jacques, Shih-Wen Chung, Yang Liu, Xiao-Guo Xiang, Zhi-Duan Chen, 2017, 'New insights into the phylogeny of Burasaieae (Menispermaceae) with the recognition of a new genus and emphasis on the southern Taiwanese and mainland Chinese disjunction', Molecular Phylogenetics and Evolution, vol. 109, pp. 11-20",
"decision": "INCLUDED",
"name": "Wang et al. 2017",
"studyID": "ot_1378",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Thais N.C. Vasconcelos, Carol E.B. Proen\u00e7a, Berhaman Ahmad, Daniel S. Aguilar, Reinaldo Aguilar, Bruno S. Amorim, Keron Campbell, Itayguara R. Costa, Plauto S. De-Carvalho, Jair E.Q. Faria, Augusto Giaretta, Pepijn W. Kooij, Duane F. Lima, Fiorella F. Mazine, Brigido Peguero, Gerhard Prenner, Matheus F. Santos, Julia Soewarto, Astrid Wingler, Eve J. Lucas, 2017, 'Myrteae phylogeny, calibration, biogeography and diversification patterns: Increased understanding in the most species rich tribe of Myrtaceae', Molecular Phylogenetics and Evolution, vol. 109, pp. 113-137",
"decision": "INCLUDED",
"name": "Vasconcelos et al. (2017), Myrtae",
"studyID": "ot_1380",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Jose Tavera, Arturo Acero P., Peter C. Wainwright, 2018, 'Multilocus phylogeny, divergence times, and a major role for the benthic-to-pelagic axis in the diversification of grunts (Haemulidae)', Molecular Phylogenetics and Evolution, vol. 121, pp. 212-223",
"decision": "INCLUDED",
"name": "UNTITLED",
"studyID": "ot_1384",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Antoine Simon, Bernard Goffinet, Nicolas Magain, Emmanu\u00ebl S\u00e9rusiaux, 2018, 'High diversity, high insular endemism and recent origin in the lichen genus Sticta (lichenized Ascomycota, Peltigerales) in Madagascar and the Mascarenes', Molecular Phylogenetics and Evolution, vol. 122, pp. 15-28",
"decision": "INCLUDED",
"name": "ML_tree",
"studyID": "ot_1386",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Worthy T., Mitri M., Handley W.D., Lee M.S., Anderson A., & Sand C. 2016. Osteology Supports a Stem-Galliform Affinity for the Giant Extinct Flightless Bird Sylviornis neocaledoniae (Sylviornithidae, Galloanseres). PLoS ONE, 11(3): e0150871.",
"decision": "INCLUDED",
"name": "Fig. 13",
"studyID": "ot_1345",
"treeID": "Tr109614"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Anna V. Williams, Joseph T. Miller, Ian Small, Paul G. Nevill, Laura M. Boykin, 2016, 'Integration of complete chloroplast genome sequences with small amplicon datasets improves phylogenetic resolution in Acacia', Molecular Phylogenetics and Evolution, vol. 96, pp. 1-8",
"decision": "INCLUDED",
"name": "Williams et al. (2016), Acacia",
"studyID": "ot_1390",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Andrew L. Hipp, Paul S. Manos, Antonio Gonz\u00e1lez-Rodr\u00edguez, Marlene Hahn, Matthew Kaproth, John D. McVay, Susana Valencia Avalos, Jeannine Cavender-Bares, 2017, 'Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity', New Phytologist, vol. 217, no. 1, pp. 439-452",
"decision": "INCLUDED",
"name": "TREE1",
"studyID": "ot_1393",
"treeID": "tree8"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Mirian Watts, Isaac S. Winkler, Christophe Daugeron, Claudio J.B. de Carvalho, Steven P. Turner, Brian M. Wiegmann, 2016, 'Where do the Neotropical Empidini lineages (Diptera: Empididae: Empidinae) fit in a worldwide context?', Molecular Phylogenetics and Evolution, vol. 95, pp. 67-78",
"decision": "INCLUDED",
"name": "Watts et al., 2016, Empidinae",
"studyID": "ot_1394",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Theriot E.C., Ashworth M., Nakov T., Ruck E.C., & Jansen R.K. 2015. Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling. Molecular Phylogenetics and Evolution, 89: 28-36.",
"decision": "INCLUDED",
"name": "tree 1",
"studyID": "ot_1395",
"treeID": "Tr96911"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from E. Guatimosim, P.B. Schwartsburd, R.W. Barreto, P.W. Crous, 2016, 'Novel fungi from an ancient niche: cercosporoid and related sexual morphs on ferns', Persoonia - Molecular Phylogeny and Evolution of Fungi, vol. 37, no. 1, pp. 106-141",
"decision": "INCLUDED",
"name": "Fig. 2",
"studyID": "ot_1421",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from E. Guatimosim, P.B. Schwartsburd, R.W. Barreto, P.W. Crous, 2016, 'Novel fungi from an ancient niche: cercosporoid and related sexual morphs on ferns', Persoonia - Molecular Phylogeny and Evolution of Fungi, vol. 37, no. 1, pp. 106-141",
"decision": "INCLUDED",
"name": "Fig. 3",
"studyID": "ot_1421",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from E. Guatimosim, P.B. Schwartsburd, R.W. Barreto, P.W. Crous, 2016, 'Novel fungi from an ancient niche: cercosporoid and related sexual morphs on ferns', Persoonia - Molecular Phylogeny and Evolution of Fungi, vol. 37, no. 1, pp. 106-141",
"decision": "INCLUDED",
"name": "Fig. 1",
"studyID": "ot_1421",
"treeID": "tree3"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Anil raj K., Deepna latha K., Rajan I., & Manimohan P. 2016. Rhodophana squamulosa \u0097a new species from India. Mycoscience, 57 (2): 90-95.",
"decision": "INCLUDED",
"name": "PAUP_1",
"studyID": "ot_1423",
"treeID": "Tr97439"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Brusatte S.L., Benson R.B., Chure D., Xing X., Sullivan C., & Hone D.W. 2010. The first definitive carcharodontosaurid (Dinosauria: Theropoda) from Asia and the delayed ascent of tyrannosaurids. Naturwissenschaften, 96: 1051-1058.",
"decision": "INCLUDED",
"name": "Figure 3",
"studyID": "ot_1429",
"treeID": "Tr55911"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Luque J., Christy J., Hendy A.J., Rosenberg M., Portell R.W., Kerr K.A., & Palmer A.R. 2017. Quaternary intertidal and supratidal crabs (Decapoda, Brachyura) from tropical America and the systematic affinities of fossil fiddler crabs. Journal of Systematic Palaeontology, 00(00): 00\u009600.",
"decision": "INCLUDED",
"name": "Fig. 8",
"studyID": "ot_1328",
"treeID": "Tr107194"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Katharina Dittmar, Megan L. Porter, Susan Murray, Michael F. Whiting, 2006, 'Molecular phylogenetic analysis of nycteribiid and streblid bat flies (Diptera: Brachycera, Calyptratae): Implications for host associations and phylogeographic origins', Molecular Phylogenetics and Evolution, vol. 38, no. 1, pp. 155-170",
"decision": "INCLUDED",
"name": "Fig. 3 - MAP",
"studyID": "ot_1432",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Elizabeth Christina Miller, Hsiu-Chin Lin, Philip A. Hastings, 2016, 'Improved resolution and a novel phylogeny for the Neotropical triplefin blennies (Teleostei: Tripterygiidae)', Molecular Phylogenetics and Evolution, vol. 96, pp. 70-78",
"decision": "INCLUDED",
"name": "Miller et al. (2015)",
"studyID": "ot_1442",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Gustavo Ramos, Haroldo Cavalcante de Lima, Gerhard Prenner, Luciano Paganucci de Queiroz, Charles E. Zartman, Domingos Cardoso, 2016, 'Molecular systematics of the Amazonian genus Aldina , a phylogenetically enigmatic ectomycorrhizal lineage of papilionoid legumes', Molecular Phylogenetics and Evolution, vol. 97, pp. 11-18",
"decision": "INCLUDED",
"name": "Ramos, 2016",
"studyID": "ot_1443",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Hannes Lerp, Sebastian Klaus, Stefanie Allg\u00f6wer, Torsten Wronski, Markus Pfenninger, Martin Plath, 2016, 'Phylogenetic analyses of gazelles reveal repeated transitions of key ecological traits and provide novel insights into the origin of the genus Gazella', Molecular Phylogenetics and Evolution, vol. 98, pp. 1-10",
"decision": "INCLUDED",
"name": "Lerp, 2016 Gazella",
"studyID": "ot_1444",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Matthew G. Johnson, Claire Malley, Bernard Goffinet, A. Jonathan Shaw, Norman J. Wickett, 2016, 'A phylotranscriptomic analysis of gene family expansion and evolution in the largest order of pleurocarpous mosses (Hypnales, Bryophyta)', Molecular Phylogenetics and Evolution, vol. 98, pp. 29-40",
"decision": "INCLUDED",
"name": "Johnson et al., 2016",
"studyID": "ot_1446",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from M. Helmkampf, I. Bruchhaus, B. Hausdorf, 2008, 'Phylogenomic analyses of lophophorates (brachiopods, phoronids and bryozoans) confirm the Lophotrochozoa concept', Proceedings of the Royal Society B: Biological Sciences, vol. 275, no. 1645, pp. 1927-1933",
"decision": "INCLUDED",
"name": "Fig. 1b",
"studyID": "ot_1314",
"treeID": "Tr5182"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Dongyu H., Lianhai H., Lijun Z., & Xing X. 2010. A pre-Archaeopteryx troodontid theropod from China with long feathers on the metatarsus. Nature, 461: 640-643.",
"decision": "INCLUDED",
"name": "Figure 4",
"studyID": "ot_1431",
"treeID": "Tr55921"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Sereno P.C. 2010. \"Taxonomy, cranial morphology, and relationships of parrot-beaked dinosaurs.\" In: , eds. New Perspectives on Horned Dinosaurs. pp. 21-58. Bloomington, University of Indiana Press.",
"decision": "INCLUDED",
"name": "Figure 2.23 E",
"studyID": "ot_1430",
"treeID": "Tr55885"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Sekimoto S., Rochon D., Long J.E., Dee J.M., & Berbee M. 2011. A multigene phylogeny of Olpidium and its implications for early fungal evolution. BMC Evolutionary Biology, .",
"decision": "INCLUDED",
"name": "Fig. 3",
"studyID": "ot_1301",
"treeID": "Tr27546"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Rubilar-rogers D., Otero R.A., Yury-y\u00e1\u00f1ez R.E., Vargas A.O., & Gutstein C.S. 2012. An overview of the dinosaur fossil record from Chile. Journal of South American Earth Sciences, : 1-14.",
"decision": "INCLUDED",
"name": "Fig. 4",
"studyID": "ot_1427",
"treeID": "Tr55249"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Mart\u00edn J. Ram\u00edrez, 2014, 'The Morphology And Phylogeny Of Dionychan Spiders (Araneae: Araneomorphae)', Bulletin of the American Museum of Natural History, vol. 390, pp. 1-374",
"decision": "INCLUDED",
"name": "Imported tree 1",
"studyID": "ot_1268",
"treeID": "tree5"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Jackson J.A., Linse K.T., Whittle R., & Griffiths H. 2015. The evolutionary origins of the Southern Ocean philobryid bivalves: hidden biodiversity, ancient persistence. PLoS One, .",
"decision": "INCLUDED",
"name": "Fig. 7",
"studyID": "ot_1445",
"treeID": "Tr80174"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Wilson G.D., Shaik S., & Ranga reddy Y. 2015. A new species of Andhracoides Wilson & Ranga Reddy, 2011 (Crustacea, Isopoda, Hypsimetopidae) from Belum Cave, Andhra Pradesh, India, with a phylogenetic review of the family. Journal of Crustacean Biology, 35(2): 216-240.",
"decision": "INCLUDED",
"name": "tnt 9+",
"studyID": "ot_1447",
"treeID": "Tr80255"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Rojas D., Warsi O., & Davalos L.M. 2016. Bats (Chiroptera: Noctilionoidea) challenge a recent origin of extant neotropical diversity. Systematic Biology, 65(3): 432-448.",
"decision": "INCLUDED",
"name": "Fig. 2",
"studyID": "ot_1409",
"treeID": "Tr87541"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Zhang X., Smith M.R., Yang J., & Hou J. 2016. Onychophoran-like musculature in a phosphatized Cambrian lobopodian. Biology Letters, .",
"decision": "INCLUDED",
"name": "Majority-Rule",
"studyID": "ot_1389",
"treeID": "Tr97256"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Satoshi Eguchi, Minoru N. Tamura, 2016, 'Evolutionary timescale of monocots determined by the fossilized birth-death model using a large number of fossil records', Evolution, vol. 70, no. 5, pp. 1136-1144",
"decision": "INCLUDED",
"name": "mrbayes",
"studyID": "ot_1391",
"treeID": "Tr96262"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Vitek N.S., Danilov I.G., Nakajima Y., & Hirayama R. 2017. Redescription of the skull of \u0093Trionyx\u0094 kyrgyzensis and improved phylogenetic taxon sampling of Cretaceous and Paleogene soft-shelled turtles (Trionychidae) of Asia, including the oldest crown trionychids. Journal of Systematic Palaeontology, .",
"decision": "INCLUDED",
"name": "con all compat+",
"studyID": "ot_1388",
"treeID": "Tr101831"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Toljagić O., Voje K.L., Matschiner M., Liow L., & Hansen T.F. 2017. Millions of Years Behind: Slow Adaptation of Ruminants to Grasslands. Systematic Biology, .",
"decision": "INCLUDED",
"name": "TREE1",
"studyID": "ot_1344",
"treeID": "Tr105486"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Miller A.K., Kerr A.M., Paulay G., Reich M., Wilson N.G., Carvajal J.I., & Rouse G.W. 2017. Molecular phylogeny of extant Holothuroidea (Echinodermata). Molecular Phylogenetics and Evolution, 111: 110-131.",
"decision": "INCLUDED",
"name": "tree 1",
"studyID": "ot_1336",
"treeID": "Tr103781"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Coppard S.E., & Lessios H.A. 2017. Phylogeography of the sand dollar genus Encope: implications regarding the Central American Isthmus and rates of molecular evolution. Scientific Reports, .",
"decision": "INCLUDED",
"name": "con 50 majrule",
"studyID": "ot_1327",
"treeID": "Tr106359"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Tavares V.D., Warsi O., Balseiro F., Mancina C., & Davalos L.M. 2018. Out of the Antilles: fossil phylogenies support reverse colonization of bats to South America. Journal of Biogeography, .",
"decision": "INCLUDED",
"name": "Fig. 1",
"studyID": "ot_1448",
"treeID": "Tr108836"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Shu-an J., Atterholt J., O'connor J.K., Lamanna M.C., Harris J.D., Da-qing L., Hai-lu Y., & Dodson P. 2011. A new, three-dimensionally preserved enantiornithine bird (Aves: Ornithothoraces) from Gansu Province, north-western China. Zoological Journal of the Linnean Society, 162(1): 201-219.",
"decision": "INCLUDED",
"name": "Figure 5",
"studyID": "ot_1449",
"treeID": "Tr55330"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Gang Yao, Bryan T. Drew, Ting-Shuang Yi, Hai-Fei Yan, Yong-Ming Yuan, Xue-Jun Ge, 2016, 'Phylogenetic relationships, character evolution and biogeographic diversification of Pogostemon s.l. (Lamiaceae)', Molecular Phylogenetics and Evolution, vol. 98, pp. 184-200",
"decision": "INCLUDED",
"name": "Yao et al., 2016",
"studyID": "ot_1452",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Lee Ann Galindo, Nicolas Puillandre, Jos\u00e9 Utge, Pierre Lozouet, Philippe Bouchet, 2016, 'The phylogeny and systematics of the Nassariidae revisited (Gastropoda, Buccinoidea)', Molecular Phylogenetics and Evolution, vol. 99, pp. 337-353",
"decision": "INCLUDED",
"name": "Galindo et al., 2016 Nassariidae",
"studyID": "ot_1454",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Darli Massardo, Rodrigo Fornel, Marcus Kronforst, Gislene Lopes Gon\u00e7alves, Gilson Rudinei Pires Moreira, 2015, 'Diversification of the silverspot butterflies (Nymphalidae) in the Neotropics inferred from multi-locus DNA sequences', Molecular Phylogenetics and Evolution, vol. 82, pp. 156-165",
"decision": "INCLUDED",
"name": "Massardo et al., 2016 Nymphalidae",
"studyID": "ot_1456",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Meeboon J., & Takamatsu S. 2014. Notes on the powdery mildews (Erysiphales) in Japan II. Erysiphe sect. Microsphaera. Mycoscience, 56(1): 230-236.",
"decision": "INCLUDED",
"name": "Fig. 2",
"studyID": "ot_1459",
"treeID": "Tr74507"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Jayawardena R.S., Zhang W., Liu M., Maharachchikumbura M.S., Zhou Y., Huang J., Nilthong S., Wang Z., Li X., Yan J., & Hyde K.D. 2014. Identification and characterization of Pestalotiopsis-like fungi related to grapevine diseases in China. Fungal Biology, .",
"decision": "INCLUDED",
"name": "PAUP 1",
"studyID": "ot_1461",
"treeID": "Tr79340"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Siahaan S., Sakamoto H., Shinoda T., & Takamatsu S. 2018. Morphophylogenetic study revealed that Erysiphe gracilis (powdery mildew of evergreen oaks, Erysiphales) is a species complex consisting of six true species. Mycoscience, 59(2): 124-136.",
"decision": "INCLUDED",
"name": "Fig. 1",
"studyID": "ot_1460",
"treeID": "Tr105194"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Siahaan S., Sakamoto H., Shinoda T., & Takamatsu S. 2018. Morphophylogenetic study revealed that Erysiphe gracilis (powdery mildew of evergreen oaks, Erysiphales) is a species complex consisting of six true species. Mycoscience, 59(2): 124-136.",
"decision": "INCLUDED",
"name": "Fig. 3",
"studyID": "ot_1460",
"treeID": "Tr105196"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Siahaan S., Sakamoto H., Shinoda T., & Takamatsu S. 2018. Morphophylogenetic study revealed that Erysiphe gracilis (powdery mildew of evergreen oaks, Erysiphales) is a species complex consisting of six true species. Mycoscience, 59(2): 124-136.",
"decision": "INCLUDED",
"name": "Fig. 2",
"studyID": "ot_1460",
"treeID": "Tr105195"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Stuart V. Nielsen, Paul M. Oliver, 2017, '\n Morphological and genetic evidence for a new karst specialist lizard from New Guinea (\n Cyrtodactylus\n : Gekkonidae)\n ', Royal Society Open Science, vol. 4, no. 11, p. 170781",
"decision": "INCLUDED",
"name": "TREE1",
"studyID": "ot_1291",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Sturaro M.J., Avila-pires T.C., & Rodrigues M.T. 2017. Molecular phylogenetic diversity in the widespread lizard Cercosaura ocellata (Reptilia: Gymnophthalmidae) in South America. Systematics and Biodiversity, .",
"decision": "INCLUDED",
"name": "ML tree",
"studyID": "ot_1401",
"treeID": "Tr102060"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from LIN ZHU, JIA-HUI XING, BAO-KAI CUI, 2017, 'Morphological characters and phylogenetic analysis reveal a new species of Sanghuangporus from China', Phytotaxa, vol. 311, no. 3, p. 270",
"decision": "INCLUDED",
"name": "MajRule",
"studyID": "ot_1397",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Korotkova N., Borsch T., & Arias S. 2017. A phylogenetic framework for the Hylocereeae (Cactaceae) and implications for the circumscription of the genera. Phytotaxa, 327(1): 1-46.",
"decision": "INCLUDED",
"name": "con 50 majrule",
"studyID": "ot_1405",
"treeID": "Tr110606"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Hertweck K.L., & Pires J.C. 2014. Systematics and evolution of inflorescence structure in the Tradescantia alliance (Commelinaceae). Systematic Botany, 39(1): 105-116.",
"decision": "INCLUDED",
"name": "unconstrained",
"studyID": "ot_1462",
"treeID": "Tr74579"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Abalde S., Tenorio M.J., Afonso C.M., Uribe J.E., Echeverry A.M., & Zardoya R. 2017. Phylogenetic relationships of cone snails endemic to Cabo Verde based on mitochondrial genomes. BMC Evolutionary Biology, 17: 231.",
"decision": "INCLUDED",
"name": "ML",
"studyID": "ot_1406",
"treeID": "Tr109588"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Meeboon J., & Takamatsu S. 2015. Erysiphe takamatsui, a powdery mildew of lotus: rediscovery of teleomorph after 40 years, morphology and phylogeny. Mycoscience, 56(1): 159-167.",
"decision": "INCLUDED",
"name": "Fig. 2",
"studyID": "ot_1463",
"treeID": "Tr71674"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Meeboon J., & Takamatsu S. 2015. Erysiphe takamatsui, a powdery mildew of lotus: rediscovery of teleomorph after 40 years, morphology and phylogeny. Mycoscience, 56(1): 159-167.",
"decision": "INCLUDED",
"name": "Fig. 1",
"studyID": "ot_1463",
"treeID": "Tr71670"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Sosa-calvo J., Jesovnik A., Vasconcelos H.L., Bacci jr M., & Schultz T.R. 2017. Rediscovery of the enigmatic fungus-farming ant \"Mycetosoritis\" asper Mayr (Hymenoptera: Formicidae): Implications for taxonomy, phylogeny, and the evolution of agriculture in ants. PLoS ONE, 12(5): e0176498.",
"decision": "INCLUDED",
"name": "con all compat",
"studyID": "ot_1464",
"treeID": "Tr103429"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Mossebo D.C., Essouman F.E., Machouart M.C., & Gueidan C. 2017. Phylogenetic relationships, taxonomic revision and new taxa of Termitomyces (Basidiomycota, Lyophyllaceae) inferred from combined nLSU- and mtSSU-rDNA sequences. Fungal Diversity, 321(1): 71-102.",
"decision": "INCLUDED",
"name": "PAUP",
"studyID": "ot_1407",
"treeID": "Tr110818"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Rengifo E.M., & Pacheco V. 2017. Phylogenetic position of the Ancash-eared mouse, Phyllotis definitus Osgood 1915 (Rodentia: Cricetidae). Mammalia, .",
"decision": "INCLUDED",
"name": "Fig. 2",
"studyID": "ot_1408",
"treeID": "Tr107089"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Rengifo E.M., & Pacheco V. 2017. Phylogenetic position of the Ancash-eared mouse, Phyllotis definitus Osgood 1915 (Rodentia: Cricetidae). Mammalia, .",
"decision": "INCLUDED",
"name": "Fig. 2",
"studyID": "ot_1408",
"treeID": "Tr106909"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Okane I., & Ono Y. 2017. Phylogenetic study of indigenous grapevine leaf rust fungi in North America and biological identity of an invasive grapevine leaf rust fungus in Brazil. Mycoscience, .",
"decision": "INCLUDED",
"name": "PHYLIP 1+",
"studyID": "ot_1411",
"treeID": "Tr105655"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from White N.D., Barrowclough G.F., Groth J.G., & Braun M. 2016. A Multi-Gene Estimate of Higher-Level Phylogenetic Relationships Among Nightjars (Aves: Caprimulgidae). Ornitologia Neotropical, 27: 223-236.",
"decision": "INCLUDED",
"name": "Soma PartFinder",
"studyID": "ot_1410",
"treeID": "Tr97099"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from De campos santana M., Amalfi M., Castillo G., & Decock C. 2016. Multilocus, DNA-based phylogenetic analysis reveal three new species lineages in the P. gabonensis - P. caribaeo-quercicola species complex, including Phellinus amazonicus sp. nov. Mycologia, .",
"decision": "INCLUDED",
"name": "amazonicus",
"studyID": "ot_1416",
"treeID": "Tr95511"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Barber N.A., Jones H.P., Duvall M.R., Wysocki W.P., Hansen M.J., & Gibson D.J. 2016. Phylogenetic diversity is maintained despite richness losses over time in restored tallgrass prairie plant communities. Journal of Applied Ecology, .",
"decision": "INCLUDED",
"name": "con 50 majrule",
"studyID": "ot_1417",
"treeID": "Tr94055"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Wei X., Mccune B., Lumbsch H.T., Li H., Leavitt S., Yamamoto Y., Tchabanenko S., & Wei J. 2016. Limitations of Species Delimitation Based on Phylogenetic Analyses: A Case Study in the Hypogymnia hypotrypa Group (Parmeliaceae, Ascomycota). PLoS ONE, 11(11): e0163664.",
"decision": "INCLUDED",
"name": "Fig. S4",
"studyID": "ot_1413",
"treeID": "Tr95891"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Adams N.F., Collinson M.E., Smith S.Y., Bamford M.K., Forest F., Malakasi P., Marone F., & Sykes D. 2016. X-rays and virtual taphonomy reveal the first fossil record of Cissus (Vitaceae) in Africa: phylogenetic, biogeographic and paleoenvironmental implications. American Journal of Botany, .",
"decision": "INCLUDED",
"name": "BEAST dated",
"studyID": "ot_1414",
"treeID": "Tr91920"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Economo E.P., Klimov P.B., Sarnat E.M., Gu\u00e9nard B., Weiser M.D., Lecroq B., & Knowles L.L. 2014. Global phylogenetic structure of the hyperdiverse ant genus Pheidole reveals the repeated evolution of macroecological patterns. Proceedings of the Royal Society B: Biological Sciences, 282: 1-10.",
"decision": "INCLUDED",
"name": "Mrbayes con tree rooted",
"studyID": "ot_1465",
"treeID": "Tr86888"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Barrett R., Bayly M.J., Duretto M., Forster P.I., Ladiges P.Y., & Cantrill D.J. 2018. Phylogenetic analysis of Zieria (Rutaceae) in Australia and New Caledonia based on nuclear ribosomal DNA shows species polyphyly, divergent paralogues and incongruence with chloroplast DNA. Australian Systematic Botany, 31: 16-47.",
"decision": "INCLUDED",
"name": "Bayes con 50 majrule",
"studyID": "ot_1433",
"treeID": "Tr106415"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Chen L., Grimm G., Wang Q., & Renner S.S. 2015. A phylogeny and biogeographic analysis for the Cape-Pondweed family Aponogetonaceae (Alismatales). Molecular Phylogenetics and Evolution, 82: 111\u00e2\u0080\u0093117.",
"decision": "INCLUDED",
"name": "MLT",
"studyID": "ot_1466",
"treeID": "Tr75272"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Lazarus K., Benny G., Ho H., & Smith M.E. 2016. Phylogenetic systematics of Syncephalis (Zoopagales, Zoopagomycotina), a genus of ubiquitous mycoparasites. Mycologia, .",
"decision": "INCLUDED",
"name": "tree 1",
"studyID": "ot_1467",
"treeID": "Tr101085"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Fan P., Liu Y., Zhang Z., Zhao C., Li C., Liu W., & Li M. 2016. Phylogenetic position of the white-cheeked macaque (Macaca leucogenys), a newly described primate from Southeastern Tibet. Molecular Phylogentics and Evolution, .",
"decision": "INCLUDED",
"name": "con 50 majrule",
"studyID": "ot_1468",
"treeID": "Tr100263"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Fan P., Liu Y., Zhang Z., Zhao C., Li C., Liu W., & Li M. 2016. Phylogenetic position of the white-cheeked macaque (Macaca leucogenys), a newly described primate from Southeastern Tibet. Molecular Phylogentics and Evolution, .",
"decision": "INCLUDED",
"name": "con 50 majrule",
"studyID": "ot_1468",
"treeID": "Tr100261"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Fan P., Liu Y., Zhang Z., Zhao C., Li C., Liu W., & Li M. 2016. Phylogenetic position of the white-cheeked macaque (Macaca leucogenys), a newly described primate from Southeastern Tibet. Molecular Phylogentics and Evolution, .",
"decision": "INCLUDED",
"name": "TREE1",
"studyID": "ot_1468",
"treeID": "Tr100262"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Videira S.I., Groenewald J.Z., Nakashima C., Braun U., Barreto R.W., De wit P.J., & Crous P.W. 2017. Mycosphaerellaceae - Chaos or clarity?. Studies in Mycology , 87: 257-421.",
"decision": "INCLUDED",
"name": "Fig. 1",
"studyID": "ot_1469",
"treeID": "Tr108340"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from P.W. Crous, J.Z. Groenewald, 2011, 'Why everlastings don't last', Persoonia - Molecular Phylogeny and Evolution of Fungi, vol. 26, no. 1, pp. 70-84",
"decision": "INCLUDED",
"name": "Fig. 3",
"studyID": "ot_1471",
"treeID": "Tr31125"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from P.W. Crous, J.Z. Groenewald, 2011, 'Why everlastings don't last', Persoonia - Molecular Phylogeny and Evolution of Fungi, vol. 26, no. 1, pp. 70-84",
"decision": "INCLUDED",
"name": "Fig. 2",
"studyID": "ot_1471",
"treeID": "Tr31127"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from P.W. Crous, J.Z. Groenewald, 2011, 'Why everlastings don't last', Persoonia - Molecular Phylogeny and Evolution of Fungi, vol. 26, no. 1, pp. 70-84",
"decision": "INCLUDED",
"name": "Fig. 1",
"studyID": "ot_1471",
"treeID": "Tr31126"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Hirooka Y., Tanney J.B., Nguyen H., Redhead S., & Seifert K. 2017. Xerotolerant fungi in house dust: taxonomy of Spiromastix, Pseudospiromastix and Sigleria gen. nov. in Spiromastigaceae (Onygenales, Eurotiomycetes). Mycologia, 108(6): 135-156.",
"decision": "INCLUDED",
"name": "SSU+LSU bayesian",
"studyID": "ot_1472",
"treeID": "Tr76233"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Hirooka Y., Tanney J.B., Nguyen H., Redhead S., & Seifert K. 2017. Xerotolerant fungi in house dust: taxonomy of Spiromastix, Pseudospiromastix and Sigleria gen. nov. in Spiromastigaceae (Onygenales, Eurotiomycetes). Mycologia, 108(6): 135-156.",
"decision": "INCLUDED",
"name": "ITS bayesian",
"studyID": "ot_1472",
"treeID": "Tr76232"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Videira S.I., Groenewald J.Z., Kolecka A., Van haren L., Boekhout T., & Crous P.W. 2015. Elucidating the Ramularia eucalypti species complex. Persoonia: Molecular Phylogeny and Evolution of Fungi, 34: 50-64.",
"decision": "INCLUDED",
"name": "Fig. 3",
"studyID": "ot_1476",
"treeID": "Tr79968"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Voglmayr H., Mayer V., Maschwitz U., Moog J., Djieto-lordon C., & Blatrix R. 2011. The diversity of ant-associated black yeasts: Insights into a newly discovered world of symbiotic interactions. Fungal Biology, 115(9): 1077-1091.",
"decision": "INCLUDED",
"name": "PAUP 13",
"studyID": "ot_1477",
"treeID": "Tr25846"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Ren C. 2016. Phylogenetic position and independent generic status of Indocypraea (Asteraceae-Heliantheae-Ecliptinae): evidence from chloroplast DNA sequences. Phytotaxa, .",
"decision": "INCLUDED",
"name": "BI tree with node support",
"studyID": "ot_1473",
"treeID": "Tr98329"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Sandoval-leiva P., Mcdonald J.V., & Thorn R. 2016. Gymnopanella nothofagi, a new genus and species of gymnopoid fungi (Omphalotaceae) from Chilean Nothofagus forest. Mycologia, 108.",
"decision": "INCLUDED",
"name": "PAUP 1",
"studyID": "ot_1478",
"treeID": "Tr100017"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Wilson G.D., & Edgecombe G. 2003. The Triassic isopod Protamphisopus wianamattensis (Chilton) and comparison with extant taxa (Crustacea, phreatoicidea). Journal of Paleontology, 77(3): 454-470.",
"decision": "INCLUDED",
"name": "Fig. 14",
"studyID": "ot_1483",
"treeID": "Tr797"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Miao Sun, Douglas E. Soltis, Pamela S. Soltis, Xinyu Zhu, J. Gordon Burleigh, Zhiduan Chen, 2015, 'Deep phylogenetic incongruence in the angiosperm clade Rosidae', Molecular Phylogenetics and Evolution, vol. 83, pp. 156-166",
"decision": "INCLUDED",
"name": "Chloroplast",
"studyID": "ot_1489",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Miao Sun, Douglas E. Soltis, Pamela S. Soltis, Xinyu Zhu, J. Gordon Burleigh, Zhiduan Chen, 2015, 'Deep phylogenetic incongruence in the angiosperm clade Rosidae', Molecular Phylogenetics and Evolution, vol. 83, pp. 156-166",
"decision": "INCLUDED",
"name": "Nuclear",
"studyID": "ot_1489",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Miao Sun, Douglas E. Soltis, Pamela S. Soltis, Xinyu Zhu, J. Gordon Burleigh, Zhiduan Chen, 2015, 'Deep phylogenetic incongruence in the angiosperm clade Rosidae', Molecular Phylogenetics and Evolution, vol. 83, pp. 156-166",
"decision": "INCLUDED",
"name": "Mitochondrial",
"studyID": "ot_1489",
"treeID": "tree4"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Nicholas G. Crawford, James F. Parham, Anna B. Sellas, Brant C. Faircloth, Travis C. Glenn, Theodore J. Papenfuss, James B. Henderson, Madison H. Hansen, W. Brian Simison, 2015, 'A phylogenomic analysis of turtles', Molecular Phylogenetics and Evolution, vol. 83, pp. 250-257",
"decision": "INCLUDED",
"name": "Raxml",
"studyID": "ot_1490",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Meng-Yun Chen, Rong-Li Mao, Dan Liang, Masaki Kuro-o, Xiao-Mao Zeng, Peng Zhang, 2015, 'A reinvestigation of phylogeny and divergence times of Hynobiidae (Amphibia, Caudata) based on 29 nuclear genes', Molecular Phylogenetics and Evolution, vol. 83, pp. 1-6",
"decision": "INCLUDED",
"name": "RAxML",
"studyID": "ot_1491",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Percy D., Cronk Q., & Page R. 2004. Plant-insect interactions: double-dating associated insect and plant lineages reveals asynchronous radiations. Systematic Biology, 53(1): 120-127.",
"decision": "INCLUDED",
"name": "psyllid 12S+CO",
"studyID": "ot_1493",
"treeID": "Tr5854"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Domingos Cardoso, Wallace M.B. S\u00e3o-Mateus, Daiane Trabuco da Cruz, Charles E. Zartman, Dirce L. Komura, Geoffrey Kite, Gerhard Prenner, Jan J. Wieringa, Alexandra Clark, Gwilym Lewis, R. Toby Pennington, Luciano Paganucci de Queiroz, 2015, 'Filling in the gaps of the papilionoid legume phylogeny: The enigmatic Amazonian genus Petaladenium is a new branch of the early-diverging Amburaneae clade', Molecular Phylogenetics and Evolution, vol. 84, pp. 112-124",
"decision": "INCLUDED",
"name": "matK",
"studyID": "ot_1495",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Bibi F. 2013. A multi-calibrated mitochondrial phylogeny of extant Bovidae (Artiodactyla, Ruminantia) and the importance of the fossil record to systematics. BMC Evolutionary Biology, .",
"decision": "INCLUDED",
"name": "All16Calibs",
"studyID": "ot_1497",
"treeID": "Tr62775"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Richard C. Harrington, Thomas J. Near, 2015, 'Phylogenetic relationships of Goneaperca and the evolution of parental care in darters (Teleostei: Percidae)', Molecular Phylogenetics and Evolution, vol. 84, pp. 158-165",
"decision": "INCLUDED",
"name": "Bayesian",
"studyID": "ot_1496",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from William B. Ludt, Luiz A. Rocha, Mark V. Erdmann, Prosanta Chakrabarty, 2015, 'Skipping across the tropics: The evolutionary history of sawtail surgeonfishes (Acanthuridae: Prionurus)', Molecular Phylogenetics and Evolution, vol. 84, pp. 166-172",
"decision": "INCLUDED",
"name": "Maximum Likelihood",
"studyID": "ot_1498",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Dupin J., & Smith S.D. 2018. Phylogenetics of Datureae (Solanaceae), including description of the new genus Trompettia and re-circumscription of the tribe. Taxon, 67(2): 359-375.",
"decision": "INCLUDED",
"name": "TREE1",
"studyID": "ot_1499",
"treeID": "Tr109204"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Hermione T. Beckett, Sam Giles, Zerina Johanson, Matt Friedman, 2018, 'Morphology and phylogenetic relationships of fossil snake mackerels and cutlassfishes (Trichiuroidea) from the Eocene (Ypresian) London Clay Formation', Papers in Palaeontology",
"decision": "INCLUDED",
"name": "con all compat",
"studyID": "ot_1501",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Thompson R.S., Parish J.C., Maidment S.C., & Barrett P.M. 2011. Phylogeny of the ankylosaurian dinosaurs (Ornithischia: Thyreophora). Journal of Systematic Palaeontology, : 301-312.",
"decision": "INCLUDED",
"name": "Imported tree 0",
"studyID": "ot_1503",
"treeID": "Tr55253"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Li J., Zheng X., Cai Y., Liu S., Zhang X., Yang M., Yue B., & Li J. 2014. DNA barcoding of Murinae (Rodentia: Muridae) and Arvicolinae (Rodentia: Cricetidae) distributed in China. Molecular Ecology Resources, .",
"decision": "INCLUDED",
"name": "BI",
"studyID": "ot_1504",
"treeID": "Tr74597"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Carrano M.T., Benson R.B., & Sampson S.D. 2012. The phylogeny of Tetanurae (Dinosauria: Theropoda). Journal of Systematic Palaeontology, 10(2): 211-300.",
"decision": "INCLUDED",
"name": "Figure 7A",
"studyID": "ot_1510",
"treeID": "Tr55267"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Andres B., & Ji Q. 2008. A new pterosaur from the Liaoning Province of China, the phylogeny of the Pterodactyloidea, and convergence in their cervical vertebrae. Palaeontology, 51(2): 453-469.",
"decision": "INCLUDED",
"name": "stored 2",
"studyID": "ot_1511",
"treeID": "Tr60093"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Brusatte S.L., Benton M.J., Desojo J.B., & Langer M.C. 2010. The higher-level phylogeny of Archosauria (Tetrapoda: Diapsida). Journal of Systematic Palaeontology, 8(1): 3-47.",
"decision": "INCLUDED",
"name": "Figure 8",
"studyID": "ot_1512",
"treeID": "Tr55545"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Zanno L.E. 2010. A taxonomic and phylogenetic re-evaluation of Therizinosauria (Dinosauria: Maniraptora). Journal of Systematic Palaeontology, 8(4): 37-41.",
"decision": "INCLUDED",
"name": "Figure 6",
"studyID": "ot_1513",
"treeID": "Tr55903"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Hu D., Xu X., Hou L., & Sullivan C. 2012. A new enantiornithine bird from the Lower Cretaceous of Western Liaoning, China, and its implications for early avian evolution. Journal of Vertebrate Paleontology, 32(3): 639-645.",
"decision": "INCLUDED",
"name": "Fig. 3A",
"studyID": "ot_1516",
"treeID": "Tr55113"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Andres B.B., Clark J.M., & Xu X. 2012. A new rhamphorhynchid pterosaur from the Upper Jurassic of Xinjiang, China, and the phylogenetic relationships of basal pterosaurs. Journal of Vertebrate Paleontology, 30(1): 163-187.",
"decision": "INCLUDED",
"name": "UNTITLED",
"studyID": "ot_1517",
"treeID": "Tr60095"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Margarita Metallinou, Edwin Nicholas Arnold, Pierre-Andr\u00e9 Crochet, Philippe Geniez, Jos\u00e9 Carlos Brito, Petros Lymberakis, Sherif Baha El Din, Roberto Sindaco, Michael Robinson, Salvador Carranza, 2012, 'Conquering the Sahara and Arabian deserts: systematics and biogeography of Stenodactylus geckos (Reptilia: Gekkonidae)', BMC Evolutionary Biology, vol. 12, no. 1, p. 258",
"decision": "INCLUDED",
"name": "con 50 majrule",
"studyID": "ot_1518",
"treeID": "Tr59010"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Spinks P., Thomson R.C., Lovely G., & Bradley shaffer H. 2009. Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from Emydid turtles. BMC Evolutionary Biology, 9(56): 56.",
"decision": "INCLUDED",
"name": "nuDNA",
"studyID": "ot_1524",
"treeID": "Tr6135"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Spinks P., Thomson R.C., Lovely G., & Bradley shaffer H. 2009. Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from Emydid turtles. BMC Evolutionary Biology, 9(56): 56.",
"decision": "INCLUDED",
"name": "cyt b",
"studyID": "ot_1524",
"treeID": "Tr6600"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Parks M., Cronn R., & Liston A. 2012. Separating the Wheat from the Chaff:: Mitigating the Effects of Noise in a Plastome Phylogenomic Data Set from Pinus L. (Pinaceae). BMC Evolutionary Biology, .",
"decision": "INCLUDED",
"name": "PHYLIP 1",
"studyID": "ot_1525",
"treeID": "Tr52468"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Jessica D. Stephens, Willie L. Rogers, Karolina Heyduk, Jennifer M. Cruse-Sanders, Ron O. Determann, Travis C. Glenn, Russell L. Malmberg, 2015, 'Resolving phylogenetic relationships of the recently radiated carnivorous plant genus Sarracenia using target enrichment', Molecular Phylogenetics and Evolution, vol. 85, pp. 76-87",
"decision": "INCLUDED",
"name": "Setephens et al., 2015 ML Species Tree",
"studyID": "ot_1527",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Long-Hai Zou, Jiu-Xiang Huang, Guo-Qiang Zhang, Zhong-Jian Liu, Xue-Ying Zhuang, 2015, 'A molecular phylogeny of Aeridinae (Orchidaceae: Epidendroideae) inferred from multiple nuclear and chloroplast regions', Molecular Phylogenetics and Evolution, vol. 85, pp. 247-254",
"decision": "INCLUDED",
"name": "Zou et al., 2015, Bayesian",
"studyID": "ot_1528",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Leuchtmann A., Bacon C.W., Schardl C.L., White J., & Tadych M. 2013. Nomenclatural realignment of Neotyphodium species with genus Epichloe. Mycologia , .",
"decision": "INCLUDED",
"name": "tree 1",
"studyID": "ot_1530",
"treeID": "Tr68066"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from N\u00fcrk N.M., Scheriau C., & Madri\u00f1\u00e1n S. 2013. Explosive radiation in p\u00e1ramo Hypericum \u0096 rates of diversification among New World lineages. Frontiers in Genetics \u0096 Evolutionary and Population Genetics. Special volume: Effects of mountain formation and uplift on biological diversity, 4(175).",
"decision": "INCLUDED",
"name": "Fig. 3 UCLN",
"studyID": "ot_1532",
"treeID": "Tr64115"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from N\u00fcrk N.M., Scheriau C., & Madri\u00f1\u00e1n S. 2013. Explosive radiation in p\u00e1ramo Hypericum \u0096 rates of diversification among New World lineages. Frontiers in Genetics \u0096 Evolutionary and Population Genetics. Special volume: Effects of mountain formation and uplift on biological diversity, 4(175).",
"decision": "INCLUDED",
"name": "Fig. 2 BI",
"studyID": "ot_1532",
"treeID": "Tr64117"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Victor A. Tagliacollo, Maxwell J. Bernt, Jack M. Craig, Claudio Oliveira, James S. Albert, 2016, 'Model-based total evidence phylogeny of Neotropical electric knifefishes (Teleostei, Gymnotiformes)', Molecular Phylogenetics and Evolution, vol. 95, pp. 20-33",
"decision": "INCLUDED",
"name": "Tagliacollo et al., 2016 Maximum Likelihood",
"studyID": "ot_1537",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Nicholas W. Persons, Peter A. Hosner, Kelly A. Meiklejohn, Edward L. Braun, Rebecca T. Kimball, 2016, 'Sorting out relationships among the grouse and ptarmigan using intron, mitochondrial, and ultra-conserved element sequences', Molecular Phylogenetics and Evolution, vol. 98, pp. 123-132",
"decision": "INCLUDED",
"name": "Persons et al. 2016, Maximum Likelihood",
"studyID": "ot_1543",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Juli\u00e1n Aguirre-Santoro, Fabi\u00e1n A. Michelangeli, Dennis W. Stevenson, 2016, 'Molecular phylogenetics of the Ronnbergia Alliance (Bromeliaceae, Bromelioideae) and insights into their morphological evolution', Molecular Phylogenetics and Evolution, vol. 100, pp. 1-20",
"decision": "INCLUDED",
"name": "Aguirre-Santoro et al. 2016, Bayesian",
"studyID": "ot_1544",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Ricardo Kriebel, Fabi\u00e1n A. Michelangeli, Lawrence M. Kelly, 2015, 'Discovery of unusual anatomical and continuous characters in the evolutionary history of Conostegia (Miconieae: Melastomataceae)', Molecular Phylogenetics and Evolution, vol. 82, pp. 289-313",
"decision": "INCLUDED",
"name": "Kriebel et al., 2015 Bayesian",
"studyID": "ot_1545",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Nathan K. Lujan, Jonathan W. Armbruster, Nathan R. Lovejoy, Hern\u00e1n L\u00f3pez-Fern\u00e1ndez, 2015, 'Multilocus molecular phylogeny of the suckermouth armored catfishes (Siluriformes: Loricariidae) with a focus on subfamily Hypostominae', Molecular Phylogenetics and Evolution, vol. 82, pp. 269-288",
"decision": "INCLUDED",
"name": "Lujan et al., 2015 Bayesian",
"studyID": "ot_1546",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Yombiyeni P., & Decock C. 2017. Hymenochaetaceae (Hymenochaetales) from the Guineo-Congolian phytochorion: Phylloporia littoralis sp. nov. from coastal vegetation in Gabon and an identification key to the local species. Plant Ecology and Evolution, 150(2): 160-172.",
"decision": "INCLUDED",
"name": "tree 1",
"studyID": "ot_1548",
"treeID": "Tr107329"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Rahman M.Z., Uematsu S., Coffey M.D., Uzuhashi S., Suga H., & Koji K. 2014. Re-evaluation of Japanese Phytophthora isolates based on molecular phylogenetic analyses. Mycoscience, 55(4): 314-327.",
"decision": "INCLUDED",
"name": "MajRule",
"studyID": "ot_1550",
"treeID": "Tr59565"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from L\u00e9veill\u00e9-bourret \u00c9., Gilmour C.N., Starr J.R., Naczi R.F., Daniel S., & Sytsma K.J. 2014. Searching for the sister to sedges (Carex): resolving relationships within the Cariceae-Dulichieae-Scirpeae clade (Cyperaceae). Botanical Journal of the Linnean Society, 176(1): 1-21.",
"decision": "INCLUDED",
"name": "TREE1",
"studyID": "ot_1551",
"treeID": "Tr78321"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Francesco Santini, Laurie Sorenson, Michael E. Alfaro, 2016, 'Phylogeny and biogeography of hogfishes and allies ( Bodianus , Labridae)', Molecular Phylogenetics and Evolution, vol. 99, pp. 1-6",
"decision": "INCLUDED",
"name": "Santini et al., 2016 Bayesian",
"studyID": "ot_1552",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Leandro Aristide, Alfred L. Rosenberger, Marcelo F. Tejedor, S. Ivan Perez, 2015, 'Modeling lineage and phenotypic diversification in the New World monkey (Platyrrhini, Primates) radiation', Molecular Phylogenetics and Evolution, vol. 82, pp. 375-385",
"decision": "INCLUDED",
"name": "Aristide et al., 2015 Bayesian",
"studyID": "ot_1553",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Ivan Prates, Miguel Trefaut Rodrigues, Paulo Roberto Melo-Sampaio, Ana Carolina Carnaval, 2015, 'Phylogenetic relationships of Amazonian anole lizards (Dactyloa): Taxonomic implications, new insights about phenotypic evolution and the timing of diversification', Molecular Phylogenetics and Evolution, vol. 82, pp. 258-268",
"decision": "INCLUDED",
"name": "Prates et al., 2015 Bayesian",
"studyID": "ot_1555",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Ishan Agarwal, K. Praveen Karanth, 2015, 'A phylogeny of the only ground-dwelling radiation of Cyrtodactylus (Squamata, Gekkonidae): diversification of Geckoella across peninsular India and Sri Lanka', Molecular Phylogenetics and Evolution, vol. 82, pp. 193-199",
"decision": "INCLUDED",
"name": "Agarwal & Karanth, 2015 Maximum Likelihood",
"studyID": "ot_1559",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Lei Yang, Tetsuya Sado, M. Vincent Hirt, Emmanuel Pasco-Viel, M. Arunachalam, Junbing Li, Xuzhen Wang, J\u00f6rg Freyhof, Kenji Saitoh, Andrew M. Simons, Masaki Miya, Shunping He, Richard L. Mayden, 2015, 'Phylogeny and polyploidy: Resolving the classification of cyprinine fishes (Teleostei: Cypriniformes)', Molecular Phylogenetics and Evolution, vol. 85, pp. 97-116",
"decision": "INCLUDED",
"name": "Yang et al., 2015 Maximum Likelihood",
"studyID": "ot_1560",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Pellegrini M.O., Hunt D.R., Forzza R.C., & Sakuragui C.M. 2017. Morphological phylogeny of Tradescantia L. (Commelinaceae) sheds light on a new infrageneric classification and taxonomic novelties in subtribe Tradescantiinae. Phytokeys, .",
"decision": "INCLUDED",
"name": "Adams",
"studyID": "ot_1562",
"treeID": "Tr105990"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Tain\u00e1 C. Rocha, Fernando Sequeira, Alexandre Aleixo, P\u00e9ricles S. R\u00eago, Iracilda Sampaio, Horacio Schneider, Marcelo Vallinoto, 2015, 'Molecular phylogeny and diversification of a widespread Neotropical rainforest bird group: The Buff-throated Woodcreeper complex, Xiphorhynchus guttatus/susurrans (Aves: Dendrocolaptidae)', Molecular Phylogenetics and Evolution, vol. 85, pp. 131-140",
"decision": "INCLUDED",
"name": "Rocha et al., 2015 Maximum Likelihood",
"studyID": "ot_1566",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from M\u00e1rcia Goetze, Katharina Schulte, Clarisse Palma-Silva, Camila M. Zanella, Miriam V. B\u00fcttow, Fernanda Capra, Fernanda Bered, 2016, 'Diversification of Bromelioideae (Bromeliaceae) in the Brazilian Atlantic rainforest: A case study in Aechmea subgenus Ortgiesia', Molecular Phylogenetics and Evolution, vol. 98, pp. 346-357",
"decision": "INCLUDED",
"name": "Goetze et al., 2015 Neighbor Joining",
"studyID": "ot_1554",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Joshua M. Hallas, W. Brian Simison, Terrence M. Gosliner, 2016, 'Dating and biogeographical patterns in the sea slug genus Acanthodoris Gray, 1850 (Mollusca, Gastropoda, Nudibranchia)', Molecular Phylogenetics and Evolution, vol. 97, pp. 19-31",
"decision": "INCLUDED",
"name": "Hallas et al., 2016 Beast",
"studyID": "ot_1568",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Ivan Fiala, Marie Hlavni\u010dkov\u00e1, Alena Kod\u00e1dkov\u00e1, Mark A. Freeman, Pavla Barto\u0161ov\u00e1-Sojkov\u00e1, Stephen D. Atkinson, 2015, 'Evolutionary origin of Ceratonova shasta and phylogeny of the marine myxosporean lineage', Molecular Phylogenetics and Evolution, vol. 86, pp. 75-89",
"decision": "INCLUDED",
"name": "Fiala et al., 2015 Bayesian",
"studyID": "ot_1571",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Anthony J. Geneva, Jared Hilton, Sabina Noll, Richard E. Glor, 2015, 'Multilocus phylogenetic analyses of Hispaniolan and Bahamian trunk anoles (distichus species group)', Molecular Phylogenetics and Evolution, vol. 87, pp. 105-117",
"decision": "INCLUDED",
"name": "Geneva et al., 2015 MCC Beast Concatenated",
"studyID": "ot_1575",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Hwalran Choi, Seunggwan Shin, Sunghoon Jung, Dave J. Clarke, Seunghwan Lee, 2018, 'Molecular phylogeny of Macrosiphini (Hemiptera: Aphididae): An evolutionary hypothesis for the Pterocomma -group habitat adaptation', Molecular Phylogenetics and Evolution, vol. 121, pp. 12-22",
"decision": "INCLUDED",
"name": "Fig_2",
"studyID": "ot_1507",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from M\u00e1rio H. Terra-Araujo, Aparecida D. de Faria, Alberto Vicentini, Stephan Nylinder, Ulf Swenson, 2015, 'Species tree phylogeny and biogeography of the Neotropical genus Pradosia (Sapotaceae, Chrysophylloideae)', Molecular Phylogenetics and Evolution, vol. 87, pp. 1-13",
"decision": "INCLUDED",
"name": "Terra-Ara\u00fajo et al., 2015 Bayesian",
"studyID": "ot_1574",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Jessica Ware, Michael May, Karl Kjer, 2007, 'Phylogeny of the higher Libelluloidea (Anisoptera: Odonata): An exploration of the most speciose superfamily of dragonflies', Molecular Phylogenetics and Evolution, vol. 45, no. 1, pp. 289-310",
"decision": "INCLUDED",
"name": "Libelluloidea",
"studyID": "ot_1104",
"treeID": "tree3"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Luciano Paganucci de Queiroz, Jos\u00e9 Floriano B. Pastore, Domingos Cardoso, Cristiane Snak, Ana Lu\u00edsa de C. Lima, Edeline Gagnon, Mohammad Vatanparast, Ailsa E. Holland, Ashley N. Egan, 2015, 'A multilocus phylogenetic analysis reveals the monophyly of a recircumscribed papilionoid legume tribe Diocleae with well-supported generic relationships', Molecular Phylogenetics and Evolution, vol. 90, pp. 1-19",
"decision": "INCLUDED",
"name": "de Queiroz et al., 2015 Concatenated Bayesian",
"studyID": "ot_1584",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Jin-Mei Feng, Chuan-Qi Jiang, Alan Warren, Miao Tian, Jun Cheng, Guang-Long Liu, Jie Xiong, Wei Miao, 2015, 'Phylogenomic analyses reveal subclass Scuticociliatia as the sister group of subclass Hymenostomatia within class Oligohymenophorea', Molecular Phylogenetics and Evolution, vol. 90, pp. 104-111",
"decision": "INCLUDED",
"name": "Knie et al., 2015 Concatenated Maximum Likelihood",
"studyID": "ot_1587",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from E. Viale, I. Martinez-Sa\u00f1udo, J.M. Brown, M. Simonato, V. Girolami, A. Squartini, A. Bressan, M. Faccoli, L. Mazzon, 2015, 'Pattern of association between endemic Hawaiian fruit flies (Diptera, Tephritidae) and their symbiotic bacteria: Evidence of cospeciation events and proposal of \u201cCandidatus Stammerula trupaneae\u201d', Molecular Phylogenetics and Evolution, vol. 90, pp. 67-79",
"decision": "INCLUDED",
"name": "Viale et al., 2015 Bayesian Concatenated",
"studyID": "ot_1588",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Jin-Mei Feng, Chuan-Qi Jiang, Alan Warren, Miao Tian, Jun Cheng, Guang-Long Liu, Jie Xiong, Wei Miao, 2015, 'Phylogenomic analyses reveal subclass Scuticociliatia as the sister group of subclass Hymenostomatia within class Oligohymenophorea', Molecular Phylogenetics and Evolution, vol. 90, pp. 104-111",
"decision": "INCLUDED",
"name": "Feng et al., 2015 Bayesian Concatenated",
"studyID": "ot_1589",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Nils Knie, Simon Fischer, Felix Grewe, Monika Polsakiewicz, Volker Knoop, 2015, 'Horsetails are the sister group to all other monilophytes and Marattiales are sister to leptosporangiate ferns', Molecular Phylogenetics and Evolution, vol. 90, pp. 140-149",
"decision": "INCLUDED",
"name": "Knie et al., 2015 Bayesian Concatenated",
"studyID": "ot_1590",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Paul Masonick, Amy Michael, Sarah Frankenberg, Wolfgang Rabitsch, Christiane Weirauch, 2017, 'Molecular phylogenetics and biogeography of the ambush bugs (Hemiptera: Reduviidae: Phymatinae)', Molecular Phylogenetics and Evolution, vol. 114, pp. 225-233",
"decision": "INCLUDED",
"name": "Phymatinae",
"studyID": "ot_1581",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Akito Y. Kawahara, Jesse W. Breinholt, Marianne Espeland, Caroline Storer, David Plotkin, Kelly M. Dexter, Emmanuel F.A. Toussaint, Ryan A. St Laurent, Gunnar Brehm, Sergio Vargas, Dimitri Forero, Naomi E. Pierce, David J. Lohman, 2018, 'Phylogenetics of moth-like butterflies (Papilionoidea: Hedylidae) based on a new 13-locus target capture probe set', Molecular Phylogenetics and Evolution, vol. 127, pp. 600-605",
"decision": "INCLUDED",
"name": "Hedylidae (Kawahara et al. 2018)",
"studyID": "ot_1572",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from MANPREET KAUR KOHLI, THOMAS SCHNEIDER, OLE M\u00dcLLER, JESSICA L. WARE, 2013, 'Counting the spots: a molecular and morphological phylogeny of the spotted darnerBoyeria(Odonata: Anisoptera: Aeshnidae) with an emphasis on European taxa', Systematic Entomology, vol. 39, no. 1, pp. 190-195",
"decision": "INCLUDED",
"name": "best",
"studyID": "ot_1579",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Peter V\u010fa\u010dn\u00fd, \u013dubom\u00edr Rajter, Shahed Uddin Ahmed Shazib, Seok Won Jang, Mann Kyoon Shin, 2017, 'Diversification dynamics of rhynchostomatian ciliates: the impact of seven intrinsic traits on speciation and extinction in a microbial group', Scientific Reports, vol. 7, no. 1",
"decision": "INCLUDED",
"name": "Vdacny et al., 2017 Bayesian Concatenated",
"studyID": "ot_1601",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Brandon T. Sinn, Dylan D. Sedmak, Lawrence M. Kelly, John V. Freudenstein, 2018, 'Total duplication of the small single copy region in the angiosperm plastome: Rearrangement and inverted repeat instability in Asarum\n ', American Journal of Botany, vol. 105, no. 1, pp. 71-84",
"decision": "INCLUDED",
"name": "Sinn et al., 2018 Maximum Likelihood Concatenated",
"studyID": "ot_1602",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Gael J. Kergoat, Bruno P. Le Ru, Seyed E. Sadeghi, Midori Tuda, Chris A.M. Reid, Zolt\u00e1n Gy\u00f6rgy, Gwena\u00eblle Genson, Cibele S. Ribeiro-Costa, Alex Delobel, 2015, 'Evolution of Spermophagus seed beetles (Coleoptera, Bruchinae, Amblycerini) indicates both synchronous and delayed colonizations of host plants', Molecular Phylogenetics and Evolution, vol. 89, pp. 91-103",
"decision": "INCLUDED",
"name": "Kergoat et al., 2015 Bayesian Concatenated",
"studyID": "ot_1603",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Nikolaos Psonis, Katerina Vardinoyannis, Moisis Mylonas, Nikos Poulakakis, 2015, 'Unraveling the evolutionary history of the Chilostoma Fitzinger, 1833 (Mollusca, Gastropoda, Pulmonata) lineages in Greece', Molecular Phylogenetics and Evolution, vol. 91, pp. 210-225",
"decision": "INCLUDED",
"name": "Psonis et al., 2015 Bayesian Concatenated",
"studyID": "ot_1604",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Daniel L. Rabosky, Jonathan Chang, Pascal O. Title, Peter F. Cowman, Lauren Sallan, Matt Friedman, Kristin Kaschner, Cristina Garilao, Thomas J. Near, Marta Coll, Michael E. Alfaro, 2018, 'An inverse latitudinal gradient in speciation rate for marine fishes', Nature, vol. 559, no. 7714, pp. 392-395",
"decision": "INCLUDED",
"name": "actinopt12KtreePL",
"studyID": "ot_1592",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Corrinne E. Grover, Joseph P. Gallagher, Josef J. Jareczek, Justin T. Page, Joshua A. Udall, Michael A. Gore, Jonathan F. Wendel, 2015, 'Re-evaluating the phylogeny of allopolyploid Gossypium L.', Molecular Phylogenetics and Evolution, vol. 92, pp. 45-52",
"decision": "INCLUDED",
"name": "Grover et al., 2015 Concatenated Maximum Likelihood",
"studyID": "ot_1605",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Nogueira j\u00fanior A.F., Fischer I.H., Bragan\u00e7a C.A., Massola j\u00fanior N.S., & Amorim L. 2014. Identification of Botryosphaeriaceae species and characterisation of the monocycle of stylar-end rot of guava. Postharvest Biology and Technology, .",
"decision": "INCLUDED",
"name": "con 50 majrule",
"studyID": "ot_1622",
"treeID": "Tr85362"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Pirie M.D., Litsios G., Bellstedt D., Salamin N., & Kissling J. 2015. Back to Gondwanaland: Can ancient vicariance explain (some) Indian Ocean disjunct plant distributions?. Biology Letters, .",
"decision": "INCLUDED",
"name": "TREES1",
"studyID": "ot_1623",
"treeID": "Tr87940"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Jin L.S., Cadotte M.W., & Fortin M. 2015. Phylogenetic turnover patterns consistent with niche conservatism in montane plant species. Journal of Ecology, .",
"decision": "INCLUDED",
"name": "PhyloBayes+",
"studyID": "ot_1624",
"treeID": "Tr85668"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Blonder B.W., Baldwin B.G., Enquist B.J., & Robichaux R.H. 2015. Variation and macroevolution in leaf functional traits in the Hawaiian silversword alliance (Asteraceae). Journal of Ecology, .",
"decision": "INCLUDED",
"name": "Fig. 2",
"studyID": "ot_1625",
"treeID": "Tr87128"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Vinther J., Sperling E.A., Briggs D.E., & Peterson K.J. 2011. A molecular paleobiological hypothesis to the origin of aplacophorans and their derivation from chiton-like ancestors. Proceedings of the Royal Society B, .",
"decision": "INCLUDED",
"name": "tree 1",
"studyID": "ot_1627",
"treeID": "Tr46103"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Toussaint E.F., Condamine F., Hawlitschek O., Watts C., Porch N., Hendrich L., & Balke M. 2014. Unveiling the Diversification Dynamics of Australasian Predaceous Diving Beetles in the Cenozoic. Systematic Biology, .",
"decision": "INCLUDED",
"name": "con all compat",
"studyID": "ot_1631",
"treeID": "Tr75792"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from D.R. Brookes, J.P. Hereward, L.I. Terry, G.H. Walter, 2015, 'Evolutionary dynamics of a cycad obligate pollination mutualism \u2013 Pattern and process in extant Macrozamia cycads and their specialist thrips pollinators', Molecular Phylogenetics and Evolution, vol. 93, pp. 83-93",
"decision": "INCLUDED",
"name": "Brookes et al., 2015 Concatenated Bayesian",
"studyID": "ot_1635",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Lauren A. Esposito, Trevor Bloom, Laura Caicedo-Quiroga, Angela M. Alicea-Serrano, Jose A. S\u00e1nchez-Ru\u00edz, Laura J. May-Collado, Greta J. Binford, Ingi Agnarsson, 2015, 'Islands within islands: Diversification of tailless whip spiders (Amblypygi, Phrynus) in Caribbean caves', Molecular Phylogenetics and Evolution, vol. 93, pp. 107-117",
"decision": "INCLUDED",
"name": "Esposito et al., 2015 Concatenated Bayesian",
"studyID": "ot_1636",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Bjarte H. Jordal, 2015, 'Molecular phylogeny and biogeography of the weevil subfamily Platypodinae reveals evolutionarily conserved range patterns', Molecular Phylogenetics and Evolution, vol. 92, pp. 294-307",
"decision": "INCLUDED",
"name": "Jordal et al., 2015 Bayesian Concatenated",
"studyID": "ot_1638",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Marcela G.M. Lima, Jos\u00e9 de Sousa e Silva-J\u00fanior, David \u010cern\u00fd, Janet C. Buckner, Alexandre Aleixo, Jonathan Chang, Jimmy Zheng, Michael E. Alfaro, Amely Martins, Anthony Di Fiore, Jean P. Boubli, Jessica W. Lynch Alfaro, 2018, 'A phylogenomic perspective on the robust capuchin monkey ( Sapajus ) radiation: First evidence for extensive population admixture across South America', Molecular Phylogenetics and Evolution, vol. 124, pp. 137-150",
"decision": "INCLUDED",
"name": "PAUP 1",
"studyID": "ot_1639",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Shang-Yin Vanson Liu, Bruno Fr\u00e9d\u00e9rich, S\u00e9bastien Lavou\u00e9, Jonathan Chang, Mark V. Erdmann, Gusti Ngurah Mahardika, Paul H. Barber, 2018, 'Buccal venom gland associates with increased of diversification rate in the fang blenny fish Meiacanthus (Blenniidae; Teleostei)', Molecular Phylogenetics and Evolution, vol. 125, pp. 138-146",
"decision": "INCLUDED",
"name": "tree",
"studyID": "ot_1640",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Michael E. Alfaro, Brant C. Faircloth, Richard C. Harrington, Laurie Sorenson, Matt Friedman, Christine E. Thacker, Carl H. Oliveros, David \u010cern\u00fd, Thomas J. Near, 2018, 'Explosive diversification of marine fishes at the Cretaceous\u2013Palaeogene boundary', Nature Ecology & Evolution, vol. 2, no. 4, pp. 688-696",
"decision": "INCLUDED",
"name": "1",
"studyID": "ot_1641",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Luz E. Ochoa, Fabio F. Roxo, Carlos DoNascimiento, Mark H. Sabaj, Al\u00e9ssio Datovo, Michael Alfaro, Claudio Oliveira, 2017, 'Multilocus analysis of the catfish family Trichomycteridae (Teleostei: Ostariophysi: Siluriformes) supporting a monophyletic Trichomycterinae', Molecular Phylogenetics and Evolution, vol. 115, pp. 71-81",
"decision": "INCLUDED",
"name": "mrbayes",
"studyID": "ot_1642",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Jenny K. Archibald, Susan R. Kephart, Kathryn E. Theiss, Anna L. Petrosky, Theresa M. Culley, 2015, 'Multilocus phylogenetic inference in subfamily Chlorogaloideae and related genera of Agavaceae \u2013 Informing questions in taxonomy at multiple ranks', Molecular Phylogenetics and Evolution, vol. 84, pp. 266-283",
"decision": "INCLUDED",
"name": "Archibald et al., 2015 Bayesian Concatenated",
"studyID": "ot_1647",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Neiber M.T., & Hausdorf B. 2015. Phylogeography of the land snail genus Circassina Hesse, 1921 (Gastropoda: Hygromiidae) implies multiple Pleistocene refugia in the western Caucasus region. Molecular Phylogentics and Evolution, 93: 129-142.",
"decision": "INCLUDED",
"name": "Neiber & Hausdorf, 2015 Maximum Likelihood AFLP",
"studyID": "ot_1649",
"treeID": "Tr88213"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Neiber M.T., & Hausdorf B. 2015. Molecular phylogeny reveals the polyphyly of the banded snail genus Cepaea (Gastropoda: Helicidae). Molecular Phylogentics and Evolution, 93: 143-149.",
"decision": "INCLUDED",
"name": "Neiber & Hausdorf, 2015 Maximum Likelihood Concatenated",
"studyID": "ot_1650",
"treeID": "Tr91045"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Saslis-Lagoudakis, C., Chase, M. W., Robinson, D. N., Russell, S. J., & Klitgaard, B. B. (2008). Phylogenetics of neotropical Platymiscium (Leguminosae: Dalbergieae): systematics, divergence times, and biogeography inferred from nuclear ribosomal and plastid DNA sequence data. American Journal of Botany, 95(10), 1270-1286.",
"decision": "INCLUDED",
"name": "Max Parsimony (tree3760)",
"studyID": "pg_1862",
"treeID": "tree3760"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Xiaolu Zhao, Shan Gao, Yangbo Fan, Michaela Strueder-Kypke, Jie Huang, 2015, 'Phylogenetic framework of the systematically confused Anteholosticha\u2013Holosticha complex (Ciliophora, Hypotrichia) based on multigene analysis', Molecular Phylogenetics and Evolution, vol. 91, pp. 238-247",
"decision": "INCLUDED",
"name": "Zhao et al., 2015 Maximum Likelihood Concatenated",
"studyID": "ot_1654",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Janet C. Buckner, Jessica W. Lynch Alfaro, Anthony B. Rylands, Michael E. Alfaro, 2015, 'Biogeography of the marmosets and tamarins (Callitrichidae)', Molecular Phylogenetics and Evolution, vol. 82, pp. 413-425",
"decision": "INCLUDED",
"name": "Buckner et al., 2015 Bayesian Concatenated",
"studyID": "ot_1655",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Omar Torres-Carvajal, Sim\u00f3n E. Lobos, Pablo J. Venegas, 2015, 'Phylogeny of Neotropical Cercosaura (Squamata: Gymnophthalmidae) lizards', Molecular Phylogenetics and Evolution, vol. 93, pp. 281-288",
"decision": "INCLUDED",
"name": "Torres-Carvajal et al., 2015 Bayesian Concatenated",
"studyID": "ot_1656",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Jorge L. Ramirez, Pedro M. Galetti, 2015, 'DNA barcode and evolutionary relationship within Laemolyta Cope 1872 (Characiformes: Anostomidae) through molecular analyses', Molecular Phylogenetics and Evolution, vol. 93, pp. 77-82",
"decision": "INCLUDED",
"name": "Ramirez & Galetti, 2015 Concatenated Bayesian",
"studyID": "ot_1660",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Hussam Zaher, Mario H. Y\u00e1nez-Mu\u00f1oz, Miguel T. Rodrigues, Roberta Graboski, Fabio A. Machado, Marco Altamirano-Benavides, Sandro L. Bonatto, Felipe G. Grazziotin, 2018, 'Origin and hidden diversity within the poorly known Gal\u00e1pagos snake radiation (Serpentes: Dipsadidae)', Systematics and Biodiversity, pp. 1-29",
"decision": "INCLUDED",
"name": "tree 1",
"studyID": "ot_1665",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Noor D. White, Charles Mitter, Michael J. Braun, 2017, 'Ultraconserved elements resolve the phylogeny of potoos (Aves: Nyctibiidae)', Journal of Avian Biology, vol. 48, no. 6, pp. 872-880",
"decision": "INCLUDED",
"name": "GARLI",
"studyID": "ot_1662",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Lawrence T.J., & Datwyler S. 2016. Testing the Hypothesis of Allopolyploidy in the Origin of Penstemon azureus (PLANTAGINACEAE). Frontiers in Ecology and Evolution, 4(60).",
"decision": "INCLUDED",
"name": "con 50 majrule",
"studyID": "ot_1696",
"treeID": "Tr94605"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Munoz-ramirez C.P., Bitton P., Doucet S.M., & Knowles L.L. 2016. Mimics here and there, but not everywhere: M\u00fcllerian mimicry in Ceroglossus ground beetles?. Biology Letters, 12(9).",
"decision": "INCLUDED",
"name": "TREE1",
"studyID": "ot_1697",
"treeID": "Tr98182"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Habibu Aliyu, Pedro Lebre, Jochen Blom, Don Cowan, Pieter De Maayer, 2016, 'Phylogenomic re-assessment of the thermophilic genus Geobacillus', Systematic and Applied Microbiology, vol. 39, no. 8, pp. 527-533",
"decision": "INCLUDED",
"name": "tree 1",
"studyID": "ot_1704",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Xia J.W., Ma Y.R., Gao J.M., Yang C.L., Wang J.Y., Li Z., & Zhang X.G. 2017. Acrodictys-like wood decay fungi from southern China, with two new families Acrodictyaceae and Junewangiaceae. Scientific Reports, 7: 7888.",
"decision": "INCLUDED",
"name": "Fig. 1",
"studyID": "ot_1782",
"treeID": "Tr111615"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Zhao R., Li G., S\ufffdnchez-ram\ufffdrez S., Stata M., Yang Z., Wu G., Dai Y.C., He S., Cui B., Zhou J., Wu F., He M., Moncalvo J., & Hyde K.D. 2017. A six-gene phylogenetic overview of Basidiomycota and allied phyla with estimated divergence times of higher taxa and a phyloproteomics perspective. Fungal Diversity, 84(1): 43-74.",
"decision": "INCLUDED",
"name": "Imported tree 1",
"studyID": "ot_1784",
"treeID": "Tr106951"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Heluta V., Takamatsu S., & Siahaan S. 2017. Erysiphe salmonii (Erysiphales, Ascomycota), another East Asian powdery mildew fungus introduced into Ukraine. Ukrainian Botanical Journal, 74(3): 212\u0096219.",
"decision": "INCLUDED",
"name": "Fig. 2",
"studyID": "ot_1785",
"treeID": "Tr103704"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Siahaan S., Sakamoto H., Shinoda T., & Takamatsu S. 2018. Geographic and temporal distributions of four genotypes found in Erysiphe gracilis, a powdery mildew of evergreen oak (Erysiphales). Mycoscience, 59(2): 110-118.",
"decision": "INCLUDED",
"name": "Fig. 2",
"studyID": "ot_1786",
"treeID": "Tr103879"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Adeljean L.F.C. Ho, Christin L. Pruett, Junda Lin, 2016, 'Phylogeny and biogeography of Poecilia (Cyprinodontiformes: Poeciliinae) across Central and South America based on mitochondrial and nuclear DNA markers', Molecular Phylogenetics and Evolution, vol. 101, pp. 32-45",
"decision": "INCLUDED",
"name": "con 50 majrule",
"studyID": "ot_1810",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Jiang J., Li J., Fu C., Li M., & Lou X. 2008. Phylogenetics and biogeography of Wisteria (Fabaceae) inferred from sequences of chloroplast and nuclear DNA regions. Systematic Botany, null.",
"decision": "INCLUDED",
"name": "Untitled (tree6204)",
"studyID": "pg_129",
"treeID": "tree6204"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from le Roux, M. M., & van Wyk, B. E. (2013). A Taxonomic Revision of Amphitrichae, a New Section of Crotalaria (Fabaceae). Systematic Botany, 38(3), 638-652.",
"decision": "INCLUDED",
"name": "tree",
"studyID": "pg_2051",
"treeID": "tree4226"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Farruggia, F. T., & Howard, J. H. 2011. Examination of five nuclear markers for phylogenetic study of Hologalegina (Leguminosae). Brittonia 63: 489-499.",
"decision": "INCLUDED",
"name": "Maximum Parsimony",
"studyID": "pg_590",
"treeID": "tree882"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Hu M., Lavin M., Wojciechowski M., & Sanderson M. 2002. Phylogenetic analysis of nuclear ribosomal ITS/5.8 S sequences in the tribe Millettieae (Fabaceae): Poecilanthe-Cyclolobium, the core Millettieae, and the Callerya group. Systematic Botany, 27: 722-733.",
"decision": "INCLUDED",
"name": "two equally parsimonious trees from ITS",
"studyID": "pg_592",
"treeID": "tree887"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Hu M., Lavin M., Wojciechowski M., & Sanderson M. 2002. Phylogenetic analysis of nuclear ribosomal ITS/5.8 S sequences in the tribe Millettieae (Fabaceae): Poecilanthe-Cyclolobium, the core Millettieae, and the Callerya group. Systematic Botany, 27: 722-733.",
"decision": "INCLUDED",
"name": "One equally parsimonious tree ITS",
"studyID": "pg_592",
"treeID": "tree888"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Hu M., Lavin M., Wojciechowski M., & Sanderson M. 2002. Phylogenetic analysis of nuclear ribosomal ITS/5.8 S sequences in the tribe Millettieae (Fabaceae): Poecilanthe-Cyclolobium, the core Millettieae, and the Callerya group. Systematic Botany, 27: 722-733.",
"decision": "INCLUDED",
"name": "Parsimony ",
"studyID": "pg_592",
"treeID": "tree889"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Wojciechowski M., Sanderson M., & Hu J. 1999. Evidence on the Monophyly of Astragalus (Fabaceae) and its Major Subgroups Based on Nuclear Ribosomal DNA ITS and Chloroplast DNA trnL Intron Data. Systematic Botany, 24: 409-437.",
"decision": "INCLUDED",
"name": "Bootstrap majority rule tree of 500 reps",
"studyID": "pg_608",
"treeID": "tree959"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Wojciechowski M., Sanderson M., Baldwin B.G., & Donoghue M. 1993. Monophyly of aneuploid Astragalus (Fabaceae): Evidence from nuclear ribosomal DNA internal transcribed spacer sequences. American Journal of Botany, 80: 711-722.",
"decision": "INCLUDED",
"name": "MP; Fig 3a",
"studyID": "pg_607",
"treeID": "tree956"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Wojciechowski M., Sanderson M., Baldwin B.G., & Donoghue M. 1993. Monophyly of aneuploid Astragalus (Fabaceae): Evidence from nuclear ribosomal DNA internal transcribed spacer sequences. American Journal of Botany, 80: 711-722.",
"decision": "INCLUDED",
"name": "\tMP; Fig 2",
"studyID": "pg_607",
"treeID": "tree957"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Wojciechowski M., Sanderson M., Baldwin B.G., & Donoghue M. 1993. Monophyly of aneuploid Astragalus (Fabaceae): Evidence from nuclear ribosomal DNA internal transcribed spacer sequences. American Journal of Botany, 80: 711-722.",
"decision": "INCLUDED",
"name": "\tMP; Fig 3b",
"studyID": "pg_607",
"treeID": "tree958"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Martin Stervander, Peter G. Ryan, Martim Melo, Bengt Hansson, 2019, 'The origin of the world\u2019s smallest flightless bird, the Inaccessible Island Rail Atlantisia rogersi (Aves: Rallidae)', Molecular Phylogenetics and Evolution, vol. 130, pp. 92-98",
"decision": "INCLUDED",
"name": "TREE1",
"studyID": "ot_1844",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Wayne Maddison, Daiqin Li, Melissa Bodner, Junxia Zhang, Xu Xin, Qinqing Liu, Fengxiang Liu, 2014, 'The deep phylogeny of jumping spiders (Araneae,\u00a0Salticidae)', ZooKeys, vol. 440, pp. 57-87",
"decision": "INCLUDED",
"name": "Complete Analysis best of 100+",
"studyID": "ot_1846",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Yan-Jie Feng, David C. Blackburn, Dan Liang, David M. Hillis, David B. Wake, David C. Cannatella, Peng Zhang, 2017, 'Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous\u2013Paleogene boundary', Proceedings of the National Academy of Sciences, p. 201704632",
"decision": "INCLUDED",
"name": "309 taxon chronogram",
"studyID": "ot_1164",
"treeID": "tree3"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Ryan A Folk, Clayton J Visger, Pamela S Soltis, Douglas E Soltis, Robert P Guralnick, 2017, 'Geographic range dynamics drove ancient hybridization in a lineage of angiosperms'",
"decision": "INCLUDED",
"name": "1",
"studyID": "ot_1858",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Shannon C.K. Straub, Michael J. Moore, Pamela S. Soltis, Douglas E. Soltis, Aaron Liston, Tatyana Livshultz, 2014, 'Phylogenetic signal detection from an ancient rapid radiation: Effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae', Molecular Phylogenetics and Evolution, vol. 80, pp. 169-185",
"decision": "INCLUDED",
"name": "Untitled (tree1)",
"studyID": "ot_1859",
"treeID": "tree1"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Y. Franchesco Molina-Henao, Adriana L. Guerrero-Chac\u00f3n, M. Alejandra Jaramillo, 2016, 'Ecological and Geographic Dimensions of Diversification in Piper subgenus Ottonia: A Lineage of Neotropical Rainforest Shrubs', Systematic Botany, vol. 41, no. 2, pp. 253-262",
"decision": "INCLUDED",
"name": "Untitled (tree6)",
"studyID": "ot_1861",
"treeID": "tree6"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Marianne Espeland, Jesse Breinholt, Keith R. Willmott, Andrew D. Warren, Roger Vila, Emmanuel F.A. Toussaint, Sarah C. Maunsell, Kwaku Aduse-Poku, Gerard Talavera, Rod Eastwood, Marta A. Jarzyna, Robert Guralnick, David J. Lohman, Naomi E. Pierce, Akito Y. Kawahara, 2018, 'A Comprehensive and Dated Phylogenomic Analysis of Butterflies', Current Biology, vol. 28, no. 5, pp. 770-778.e5",
"decision": "INCLUDED",
"name": "Untitled (tree2)",
"studyID": "ot_1862",
"treeID": "tree2"
},
{
"SHA": "",
"comments": "Added via API (include_tree_in_synth) from Kelly M. Harkins, Rachel S. Schwartz, Reed A. Cartwright, Anne C. Stone, 2016, 'Phylogenomic reconstruction supports supercontinent origins for Leishmania', Infection, Genetics and Evolution, vol. 38, pp. 101-109",
"decision": "INCLUDED",
"name": "Fig. 3",
"studyID": "ot_1873",
"treeID": "tree2"
}
],
"description": "Trees for synthesis, but ranked lower than other synthesis collections",
"name": "Inputs to synthesis (default)",
"queries": []
}