John Gatesy, PhD - Publications

Biology University of California, Riverside, Riverside, CA, United States 

63 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Gatesy J, Sloan DB, Warren JM, Baker RH, Simmons MP, Springer MS. Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts. Molecular Phylogenetics and Evolution. 106539. PMID 31226465 DOI: 10.1016/J.Ympev.2019.106539  1
2018 Zhang Y, Huang W, Hayashi C, Gatesy J, McKittrick J. Microstructure and mechanical properties of different keratinous horns. Journal of the Royal Society, Interface. 15. PMID 29875283 DOI: 10.1098/Rsif.2018.0093  1
2016 Simmons MP, Gatesy J. Biases of tree-independent-character-subsampling methods. Molecular Phylogenetics and Evolution. PMID 27103257 DOI: 10.1016/J.Ympev.2016.04.022  1
2016 Simmons MP, Sloan DB, Gatesy J. The effects of subsampling gene trees on coalescent methods applied to ancient divergences. Molecular Phylogenetics and Evolution. PMID 26768112 DOI: 10.1016/J.Ympev.2015.12.013  1
2015 Springer MS, Starrett J, Morin PA, Lanzetti A, Hayashi C, Gatesy J. Inactivation of C4orf26 in Toothless Placental Mammals. Molecular Phylogenetics and Evolution. PMID 26596502 DOI: 10.1016/J.Ympev.2015.11.002  1
2015 Springer MS, Gatesy J. The gene tree delusion. Molecular Phylogenetics and Evolution. 94: 1-33. PMID 26238460 DOI: 10.1016/J.Ympev.2015.07.018  1
2015 Springer MS, Signore AV, Paijmans JL, Vélez-Juarbe J, Domning DP, Bauer CE, He K, Crerar L, Campos PF, Murphy WJ, Meredith RW, Gatesy J, Willerslev E, MacPhee RD, Hofreiter M, et al. Interordinal gene capture, the phylogenetic position of Steller's sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia. Molecular Phylogenetics and Evolution. 91: 178-93. PMID 26050523 DOI: 10.1016/J.Ympev.2015.05.022  1
2015 Simmons MP, Gatesy J. Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms Molecular Phylogenetics and Evolution. 91: 98-122. DOI: 10.1016/j.ympev.2015.05.011  1
2014 Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, ... ... Gatesy J, et al. Comparative genomics reveals insights into avian genome evolution and adaptation. Science (New York, N.Y.). 346: 1311-20. PMID 25504712 DOI: 10.1126/Science.1251385  0.36
2014 Gatesy J, Springer MS. Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. Molecular Phylogenetics and Evolution. 80: 231-66. PMID 25152276 DOI: 10.1016/J.Ympev.2014.08.013  1
2014 McGowen MR, Gatesy J, Wildman DE. Molecular evolution tracks macroevolutionary transitions in Cetacea Trends in Ecology and Evolution. 29: 336-346. PMID 24794916 DOI: 10.1016/J.Tree.2014.04.001  1
2014 Springer MS, Gatesy J. Land plant origins and coalescence confusion. Trends in Plant Science. 19: 267-9. PMID 24641875 DOI: 10.1016/J.Tplants.2014.02.012  1
2013 Montgomery SH, Geisler JH, McGowen MR, Fox C, Marino L, Gatesy J. The evolutionary history of cetacean brain and body size. Evolution; International Journal of Organic Evolution. 67: 3339-53. PMID 24152011 DOI: 10.1111/Evo.12197  1
2013 Meredith RW, Gatesy J, Emerling CA, York VM, Springer MS. Rod monochromacy and the coevolution of cetacean retinal opsins. Plos Genetics. 9: e1003432. PMID 23637615 DOI: 10.1371/Journal.Pgen.1003432  1
2013 Gatesy J, Springer MS. Concatenation versus coalescence versus "concatalescence". Proceedings of the National Academy of Sciences of the United States of America. 110: E1179. PMID 23460702 DOI: 10.1073/Pnas.1221121110  1
2013 Meredith RW, Gatesy J, Springer MS. Molecular decay of enamel matrix protein genes in turtles and other edentulous amniotes. Bmc Evolutionary Biology. 13: 20. PMID 23342979 DOI: 10.1186/1471-2148-13-20  1
2013 Gatesy J, Geisler JH, Chang J, Buell C, Berta A, Meredith RW, Springer MS, McGowen MR. A phylogenetic blueprint for a modern whale. Molecular Phylogenetics and Evolution. 66: 479-506. PMID 23103570 DOI: 10.1016/J.Ympev.2012.10.012  1
2012 Springer MS, Meredith RW, Gatesy J, Emerling CA, Park J, Rabosky DL, Stadler T, Steiner C, Ryder OA, Janečka JE, Fisher CA, Murphy WJ. Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix. Plos One. 7: e49521. PMID 23166696 DOI: 10.1371/Journal.Pone.0049521  1
2012 Murphy WJ, Janecka JE, Stadler T, Eizirik E, Ryder OA, Gatesy J, Meredith RW, Springer MS. Response to comment on "Impacts of the cretaceous terrestrial revolution and KPg extinction on mammal diversification" Science. 336: 34b. DOI: 10.1126/Science.1220078  1
2011 Meredith RW, Janečka JE, Gatesy J, Ryder OA, Fisher CA, Teeling EC, Goodbla A, Eizirik E, Simão TL, Stadler T, Rabosky DL, Honeycutt RL, Flynn JJ, Ingram CM, Steiner C, et al. Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science (New York, N.Y.). 334: 521-4. PMID 21940861 DOI: 10.1126/Science.1211028  1
2011 Geisler JH, McGowen MR, Yang G, Gatesy J. A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea Bmc Evolutionary Biology. 11. PMID 21518443 DOI: 10.1186/1471-2148-11-112  1
2011 McGowen MR, Montgomery SH, Clark C, Gatesy J. Phylogeny and adaptive evolution of the brain-development gene microcephalin (MCPH1) in cetaceans. Bmc Evolutionary Biology. 11: 98. PMID 21492470 DOI: 10.1186/1471-2148-11-98  1
2011 Meredith RW, Hekkala ER, Amato G, Gatesy J. A phylogenetic hypothesis for Crocodylus (Crocodylia) based on mitochondrial DNA: evidence for a trans-Atlantic voyage from Africa to the New World. Molecular Phylogenetics and Evolution. 60: 183-91. PMID 21459152 DOI: 10.1016/J.Ympev.2011.03.026  1
2011 Meredith RW, Gatesy J, Cheng J, Springer MS. Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales. Proceedings. Biological Sciences / the Royal Society. 278: 993-1002. PMID 20861053 DOI: 10.1098/Rspb.2010.1280  1
2011 Baldo L, De Queiroz A, Hedin M, Hayashi CY, Gatesy J. Nuclear-mitochondrial sequences as witnesses of past interbreeding and population diversity in the jumping bristletail mesomachilis Molecular Biology and Evolution. 28: 195-210. PMID 20667982 DOI: 10.1093/Molbev/Msq193  1
2009 Spaulding M, O'Leary MA, Gatesy J. Relationships of Cetacea (Artiodactyla) among mammals: Increased taxon sampling alters interpretations of key fossils and character evolution Plos One. 4. PMID 19774069 DOI: 10.1371/Journal.Pone.0007062  1
2009 Meredith RW, Gatesy J, Murphy WJ, Ryder OA, Springer MS. Molecular decay of the tooth gene Enamelin (ENAM) mirrors the loss of enamel in the fossil record of placental mammals. Plos Genetics. 5: e1000634. PMID 19730686 DOI: 10.1371/Journal.Pgen.1000634  1
2009 McGowen MR, Spaulding M, Gatesy J. Divergence date estimation and a comprehensive molecular tree of extant cetaceans Molecular Phylogenetics and Evolution. 53: 891-906. PMID 19699809 DOI: 10.1016/J.Ympev.2009.08.018  1
2009 Ayoub NA, McGowen MR, Clark C, Springer MS, Gatesy J. Evolution and phylogenetic utility of the melanocortin-1 receptor gene (MC1R) in Cetartiodactyla. Molecular Phylogenetics and Evolution. 52: 550-7. PMID 19303453 DOI: 10.1016/J.Ympev.2009.03.008  1
2008 McGowen MR, Clark C, Gatesy J. The vestigial olfactory receptor subgenome of odontocete whales: phylogenetic congruence between gene-tree reconciliation and supermatrix methods. Systematic Biology. 57: 574-590. PMID 18686195 DOI: 10.1080/10635150802304787  1
2008 Gatesy J, Amato G. The rapid accumulation of consistent molecular support for intergeneric crocodylian relationships Molecular Phylogenetics and Evolution. 48: 1232-1237. PMID 18372192 DOI: 10.1016/J.Ympev.2008.02.009  1
2008 Deméré TA, McGowen MR, Berta A, Gatesy J. Morphological and molecular evidence for a stepwise evolutionary transition from teeth to baleen in mysticete whales Systematic Biology. 57: 15-37. PMID 18266181 DOI: 10.1080/10635150701884632  1
2008 O'Leary MA, Gatesy J. Impact of increased character sampling on the phylogeny of Cetartiodactyla (Mammalia): Combined analysis including fossils Cladistics. 24: 397-442. DOI: 10.1111/J.1096-0031.2007.00187.X  1
2007 Gatesy J. A tenth crucial question regarding model use in phylogenetics Trends in Ecology and Evolution. 22: 509-510. PMID 17804115 DOI: 10.1016/J.Tree.2007.08.002  1
2007 Gatesy J, DeSalle R, Wahlberg N. How many genes should a systematist sample? Conflicting insights from a phylogenomic matrix characterized by replicated incongruence. Systematic Biology. 56: 355-63. PMID 17464890 DOI: 10.1080/10635150701294733  1
2007 de Queiroz A, Gatesy J. The supermatrix approach to systematics Trends in Ecology and Evolution. 22: 34-41. PMID 17046100 DOI: 10.1016/J.Tree.2006.10.002  1
2007 Gatesy J, Swanson WJ. Adaptive evolution and phylogenetic utility of Acr (acrosin), a rapidly evolving mammalian fertilization gene Journal of Mammalogy. 88: 32-42. DOI: 10.1644/05-Mamm-S-345R1.1  1
2005 Gatesy J, Baker RH. Hidden likelihood support in genomic data: can forty-five wrongs make a right? Systematic Biology. 54: 483-92. PMID 16012113 DOI: 10.1080/10635150590945368  1
2004 Gatesy J, Baker RH, Hayashi C. Inconsistencies in arguments for the supertree approach: supermatrices versus supertrees of Crocodylia. Systematic Biology. 53: 342-55. PMID 15205058 DOI: 10.1080/10635150490423971  1
2003 O'Leary MA, Gatesy J, Novacek MJ. Are the Dental Data Really at Odds with the Molecular Data? Morphological Evidence for Whale Phylogeny (Re)Reexamined Systematic Biology. 52: 853-864. PMID 14668123 DOI: 10.1093/Sysbio/52.6.853  1
2003 DeSalle R, Branham MA, O'Grady P, Gatesy J. The evolution of HOM-C homeoboxes in the Dipteran family Drosophilidae. Insect Molecular Biology. 12: 345-51. PMID 12864914 DOI: 10.1046/J.1365-2583.2003.00417.X  1
2003 Gatesy J, Amato G, Norell M, DeSalle R, Hayashi C. Combined support for wholesale taxic atavism in gavialine crocodylians. Systematic Biology. 52: 403-22. PMID 12775528 DOI: 10.1080/10635150390197037  1
2002 Gatesy J, Matthee C, DeSalle R, Hayashi C. Resolution of a supertree/supermatrix paradox. Systematic Biology. 51: 652-64. PMID 12228007 DOI: 10.1080/10635150290102311  1
2002 Gatesy J. Relative quality of different systematic datasets for cetartiodactyl mammals: assessments within a combined analysis framework. Exs. 45-67. PMID 11924503  1
2002 Baker RH, Gatesy J. Is morphology still relevant? Exs. 163-74. PMID 11924494  1
2001 Gatesy J, Hayashi C, Motriuk D, Woods J, Lewis R. Extreme diversity, conservation, and convergence of spider silk fibroin sequences Science. 291: 2603-2605. PMID 11283372 DOI: 10.1126/Science.1057561  1
2001 Gatesy J, O'Leary MA. Deciphering whale origins with molecules and fossils Trends in Ecology and Evolution. 16: 562-570. DOI: 10.1016/S0169-5347(01)02236-4  1
2000 Gatesy J. Linked branch support and tree stability Systematic Biology. 49: 800-807. PMID 12116441 DOI: 10.1080/106351500750049842  1
2000 Gatesy J, Arctander P. Hidden morphological support for the phylogenetic placement of Pseudoryx nghetinhensis with bovine bovids: A combined analysis of gross anatomical evidence and DNA sequences from five genes Systematic Biology. 49: 515-538. PMID 12116425  1
1999 Gatesy J, Milinkovitch M, Waddell V, Stanhope M. Stability of cladistic relationships between Cetacea and higher-level artiodactyl taxa Systematic Biology. 48: 9-20. PMID 12078645 DOI: 10.1080/106351599260409  1
1999 Gatesy J, O'Grady P, Baker RH. Corroboration among data sets in simultaneous analysis: Hidden support for phylogenetic relationships among higher level artiodactyl taxa Cladistics. 15: 271-313. DOI: 10.1006/Clad.1999.0111  1
1997 Gatesy J, Amato G, Vrba E, Schaller G, DeSalle R. A cladistic analysis of mitochondrial ribosomal DNA from the Bovidae. Molecular Phylogenetics and Evolution. 7: 303-19. PMID 9187090 DOI: 10.1006/Mpev.1997.0402  1
1997 Gatesy J. More DNA support for a cetacea/hippopotamidae clade: The blood-clotting protein gene γ-fibrinogen Molecular Biology and Evolution. 14: 537-543. PMID 9159931 DOI: 10.1093/Oxfordjournals.Molbev.A025790  1
1996 Gatesy J, Hayashi C, Cronin MA, Arctander P. Evidence from milk casein genes that cetaceans are close relatives of hippopotamid artiodactyls. Molecular Biology and Evolution. 13: 954-63. PMID 8752004 DOI: 10.1093/Oxfordjournals.Molbev.A025663  1
1995 Wheeler WC, Gatesy J, DeSalle R. Elision: a method for accommodating multiple molecular sequence alignments with alignment-ambiguous sites. Molecular Phylogenetics and Evolution. 4: 1-9. PMID 7620631 DOI: 10.1006/Mpev.1995.1001  1
1994 Gatesy J, Hayashi C, DeSalle R, Vrba E. RATE LIMITS FOR MISPAIRING AND COMPENSATORY CHANGE: THE MITOCHONDRIAL RIBOSOMAL DNA OF ANTELOPES. Evolution; International Journal of Organic Evolution. 48: 188-196. PMID 28567784 DOI: 10.1111/J.1558-5646.1994.Tb01305.X  1
1994 Amato G, Gatesy J. PCR assays of variable nucleotide sites for identification of conservation units. Exs. 69: 215-226. PMID 7994108  1
1994 Vrba ES, Vaisnys JR, Gatesy JE, Desalle R, Wei KY. Analysis of paedomorphosis using allometric characters: The example of Reduncini antelopes (Bovidae, Mammalia) Systematic Biology. 43: 92-116. DOI: 10.1093/Sysbio/43.1.92  1
1994 Gatesy J, Hayashi C, DeSalle R, Vrba E. Rate limits for mispairing and compensatory change: The mitochondrial ribosomal DNA of antelopes Evolution. 48: 188-196.  1
1994 Vrba ES, Gatesy J. New antelope fossils from Awash, Ethiopia, and phylogenetic analysis of hippotragini (Bovidae, Mammalia) Palaeontologia Africana. 31: 55-72.  1
1993 Gatesy J, DeSalle R, Wheeler W. Alignment-ambiguous nucleotide sites and the exclusion of systematic data. Molecular Phylogenetics and Evolution. 2: 152-7. PMID 8025721 DOI: 10.1006/Mpev.1993.1015  1
1992 Gatesy J, Yelon D, DeSalle R, Vrba ES. Phylogeny of the Bovidae (Artiodactyla, Mammalia), based on mitochondrial ribosomal DNA sequences. Molecular Biology and Evolution. 9: 433-46. PMID 1584013 DOI: 10.1093/Oxfordjournals.Molbev.A040734  1
1992 DeSalle R, Gatesy J, Wheeler W, Grimaldi D. DNA sequences from a fossil termite in Oligo-Miocene amber and their phylogenetic implications. Science (New York, N.Y.). 257: 1933-6. PMID 1411508 DOI: 10.1126/Science.1411508  1
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