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Items: 1 to 50 of 67

1.

Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary.

Springer MS, Foley NM, Brady PL, Gatesy J, Murphy WJ.

Front Genet. 2019 Nov 29;10:1241. doi: 10.3389/fgene.2019.01241. eCollection 2019.

2.

ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets.

Springer MS, Molloy EK, Sloan DB, Simmons MP, Gatesy J.

J Hered. 2019 Dec 14. pii: esz076. doi: 10.1093/jhered/esz076. [Epub ahead of print]

PMID:
31837265
3.

Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations.

Huelsmann M, Hecker N, Springer MS, Gatesy J, Sharma V, Hiller M.

Sci Adv. 2019 Sep 25;5(9):eaaw6671. doi: 10.1126/sciadv.aaw6671. eCollection 2019 Sep.

4.

Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts.

Gatesy J, Sloan DB, Warren JM, Baker RH, Simmons MP, Springer MS.

Mol Phylogenet Evol. 2019 Oct;139:106539. doi: 10.1016/j.ympev.2019.106539. Epub 2019 Jun 18.

PMID:
31226465
5.

Odontogenic ameloblast-associated (ODAM) is inactivated in toothless/enamelless placental mammals and toothed whales.

Springer MS, Emerling CA, Gatesy J, Randall J, Collin MA, Hecker N, Hiller M, Delsuc F.

BMC Evol Biol. 2019 Jan 23;19(1):31. doi: 10.1186/s12862-019-1359-6.

6.

Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses.

Simmons MP, Sloan DB, Springer MS, Gatesy J.

Mol Phylogenet Evol. 2019 Feb;131:80-92. doi: 10.1016/j.ympev.2018.10.001. Epub 2018 Nov 2.

PMID:
30391518
7.

Microstructure and mechanical properties of different keratinous horns.

Zhang Y, Huang W, Hayashi C, Gatesy J, McKittrick J.

J R Soc Interface. 2018 Jun;15(143). pii: 20180093. doi: 10.1098/rsif.2018.0093.

8.

Delimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets.

Springer MS, Gatesy J.

Genes (Basel). 2018 Feb 26;9(3). pii: E123. doi: 10.3390/genes9030123. Review.

9.

Evolution of the MC5R gene in placental mammals with evidence for its inactivation in multiple lineages that lack sebaceous glands.

Springer MS, Gatesy J.

Mol Phylogenet Evol. 2018 Mar;120:364-374. doi: 10.1016/j.ympev.2017.12.010. Epub 2017 Dec 19.

PMID:
29277542
10.

Phylogenomic red flags: Homology errors and zombie lineages in the evolutionary diversification of placental mammals.

Gatesy J, Springer MS.

Proc Natl Acad Sci U S A. 2017 Nov 7;114(45):E9431-E9432. doi: 10.1073/pnas.1715318114. Epub 2017 Oct 24. No abstract available.

11.

Pinniped Diphyly and Bat Triphyly: More Homology Errors Drive Conflicts in the Mammalian Tree.

Springer MS, Gatesy J.

J Hered. 2018 Mar 16;109(3):297-307. doi: 10.1093/jhered/esx089.

PMID:
29077895
12.

Inactivation of the olfactory marker protein (OMP) gene in river dolphins and other odontocete cetaceans.

Springer MS, Gatesy J.

Mol Phylogenet Evol. 2017 Apr;109:375-387. doi: 10.1016/j.ympev.2017.01.020. Epub 2017 Feb 11.

PMID:
28193458
13.

Lineage diversification of fringe-toed lizards (Phrynosomatidae: Uma notata complex) in the Colorado Desert: Delimiting species in the presence of gene flow.

Gottscho AD, Wood DA, Vandergast AG, Lemos-Espinal J, Gatesy J, Reeder TW.

Mol Phylogenet Evol. 2017 Jan;106:103-117. doi: 10.1016/j.ympev.2016.09.008. Epub 2016 Sep 15.

PMID:
27640953
14.

Biases of tree-independent-character-subsampling methods.

Simmons MP, Gatesy J.

Mol Phylogenet Evol. 2016 Jul;100:424-443. doi: 10.1016/j.ympev.2016.04.022. Epub 2016 Apr 19.

PMID:
27103257
15.

The effects of subsampling gene trees on coalescent methods applied to ancient divergences.

Simmons MP, Sloan DB, Gatesy J.

Mol Phylogenet Evol. 2016 Apr;97:76-89. doi: 10.1016/j.ympev.2015.12.013. Epub 2016 Jan 6.

PMID:
26768112
16.

Inactivation of C4orf26 in toothless placental mammals.

Springer MS, Starrett J, Morin PA, Lanzetti A, Hayashi C, Gatesy J.

Mol Phylogenet Evol. 2016 Feb;95:34-45. doi: 10.1016/j.ympev.2015.11.002. Epub 2015 Nov 17.

PMID:
26596502
17.

The gene tree delusion.

Springer MS, Gatesy J.

Mol Phylogenet Evol. 2016 Jan;94(Pt A):1-33. doi: 10.1016/j.ympev.2015.07.018. Epub 2015 Jul 31.

PMID:
26238460
18.

Interordinal gene capture, the phylogenetic position of Steller's sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia.

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, Campbell KL.

Mol Phylogenet Evol. 2015 Oct;91:178-93. doi: 10.1016/j.ympev.2015.05.022. Epub 2015 Jun 4.

PMID:
26050523
19.

Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms.

Simmons MP, Gatesy J.

Mol Phylogenet Evol. 2015 Oct;91:98-122. doi: 10.1016/j.ympev.2015.05.011. Epub 2015 May 19.

PMID:
26002829
20.

Comparative genomics reveals insights into avian genome evolution and adaptation.

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, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-Núñez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farré M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Håstad O, Sawyer RH, Kim H, Kim KW, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O'Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alström P, Fjeldså J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J; Avian Genome Consortium, Jarvis ED, Gilbert MT, Wang J.

Science. 2014 Dec 12;346(6215):1311-20. doi: 10.1126/science.1251385. Epub 2014 Dec 11.

21.

Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum.

Gatesy J, Springer MS.

Mol Phylogenet Evol. 2014 Nov;80:231-66. doi: 10.1016/j.ympev.2014.08.013. Epub 2014 Aug 22.

PMID:
25152276
22.

Molecular evolution tracks macroevolutionary transitions in Cetacea.

McGowen MR, Gatesy J, Wildman DE.

Trends Ecol Evol. 2014 Jun;29(6):336-46. doi: 10.1016/j.tree.2014.04.001. Epub 2014 May 1. Review.

PMID:
24794916
23.

Land plant origins and coalescence confusion.

Springer MS, Gatesy J.

Trends Plant Sci. 2014 May;19(5):267-9. doi: 10.1016/j.tplants.2014.02.012. Epub 2014 Mar 15. No abstract available.

PMID:
24641875
24.

The evolutionary history of cetacean brain and body size.

Montgomery SH, Geisler JH, McGowen MR, Fox C, Marino L, Gatesy J.

Evolution. 2013 Nov;67(11):3339-53. doi: 10.1111/evo.12197. Epub 2013 Jul 23.

PMID:
24152011
25.

Rod monochromacy and the coevolution of cetacean retinal opsins.

Meredith RW, Gatesy J, Emerling CA, York VM, Springer MS.

PLoS Genet. 2013 Apr;9(4):e1003432. doi: 10.1371/journal.pgen.1003432. Epub 2013 Apr 18.

26.

Concatenation versus coalescence versus "concatalescence".

Gatesy J, Springer MS.

Proc Natl Acad Sci U S A. 2013 Mar 26;110(13):E1179. doi: 10.1073/pnas.1221121110. Epub 2013 Mar 4. No abstract available.

27.

Molecular decay of enamel matrix protein genes in turtles and other edentulous amniotes.

Meredith RW, Gatesy J, Springer MS.

BMC Evol Biol. 2013 Jan 23;13:20. doi: 10.1186/1471-2148-13-20.

28.

Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix.

Springer MS, Meredith RW, Gatesy J, Emerling CA, Park J, Rabosky DL, Stadler T, Steiner C, Ryder OA, Janečka JE, Fisher CA, Murphy WJ.

PLoS One. 2012;7(11):e49521. doi: 10.1371/journal.pone.0049521. Epub 2012 Nov 16.

29.

A phylogenetic blueprint for a modern whale.

Gatesy J, Geisler JH, Chang J, Buell C, Berta A, Meredith RW, Springer MS, McGowen MR.

Mol Phylogenet Evol. 2013 Feb;66(2):479-506. doi: 10.1016/j.ympev.2012.10.012. Epub 2012 Oct 26.

PMID:
23103570
30.

Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification.

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, Williams TL, Robinson TJ, Burk-Herrick A, Westerman M, Ayoub NA, Springer MS, Murphy WJ.

Science. 2011 Oct 28;334(6055):521-4. doi: 10.1126/science.1211028. Epub 2011 Sep 22.

31.

A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea.

Geisler JH, McGowen MR, Yang G, Gatesy J.

BMC Evol Biol. 2011 Apr 25;11:112. doi: 10.1186/1471-2148-11-112.

32.

Phylogeny and adaptive evolution of the brain-development gene microcephalin (MCPH1) in cetaceans.

McGowen MR, Montgomery SH, Clark C, Gatesy J.

BMC Evol Biol. 2011 Apr 14;11:98. doi: 10.1186/1471-2148-11-98.

33.

A phylogenetic hypothesis for Crocodylus (Crocodylia) based on mitochondrial DNA: evidence for a trans-Atlantic voyage from Africa to the New World.

Meredith RW, Hekkala ER, Amato G, Gatesy J.

Mol Phylogenet Evol. 2011 Jul;60(1):183-91. doi: 10.1016/j.ympev.2011.03.026. Epub 2011 Apr 1.

PMID:
21459152
34.

Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales.

Meredith RW, Gatesy J, Cheng J, Springer MS.

Proc Biol Sci. 2011 Apr 7;278(1708):993-1002. doi: 10.1098/rspb.2010.1280. Epub 2010 Sep 22.

35.

Nuclear-mitochondrial sequences as witnesses of past interbreeding and population diversity in the jumping bristletail Mesomachilis.

Baldo L, de Queiroz A, Hedin M, Hayashi CY, Gatesy J.

Mol Biol Evol. 2011 Jan;28(1):195-210. doi: 10.1093/molbev/msq193. Epub 2010 Jul 28.

PMID:
20667982
36.

Relationships of Cetacea (Artiodactyla) among mammals: increased taxon sampling alters interpretations of key fossils and character evolution.

Spaulding M, O'Leary MA, Gatesy J.

PLoS One. 2009 Sep 23;4(9):e7062. doi: 10.1371/journal.pone.0007062.

37.

Molecular decay of the tooth gene Enamelin (ENAM) mirrors the loss of enamel in the fossil record of placental mammals.

Meredith RW, Gatesy J, Murphy WJ, Ryder OA, Springer MS.

PLoS Genet. 2009 Sep;5(9):e1000634. doi: 10.1371/journal.pgen.1000634. Epub 2009 Sep 4.

38.

Divergence date estimation and a comprehensive molecular tree of extant cetaceans.

McGowen MR, Spaulding M, Gatesy J.

Mol Phylogenet Evol. 2009 Dec;53(3):891-906. doi: 10.1016/j.ympev.2009.08.018. Epub 2009 Aug 21.

PMID:
19699809
39.

Evolution and phylogenetic utility of the melanocortin-1 receptor gene (MC1R) in Cetartiodactyla.

Ayoub NA, McGowen MR, Clark C, Springer MS, Gatesy J.

Mol Phylogenet Evol. 2009 Aug;52(2):550-7. doi: 10.1016/j.ympev.2009.03.008. Epub 2009 Mar 19. No abstract available.

PMID:
19303453
40.

The vestigial olfactory receptor subgenome of odontocete whales: phylogenetic congruence between gene-tree reconciliation and supermatrix methods.

McGowen MR, Clark C, Gatesy J.

Syst Biol. 2008 Aug;57(4):574-90. doi: 10.1080/10635150802304787.

PMID:
18686195
41.

The rapid accumulation of consistent molecular support for intergeneric crocodylian relationships.

Gatesy J, Amato G.

Mol Phylogenet Evol. 2008 Sep;48(3):1232-7. doi: 10.1016/j.ympev.2008.02.009. Epub 2008 Feb 23. No abstract available.

PMID:
18372192
42.

Morphological and molecular evidence for a stepwise evolutionary transition from teeth to baleen in mysticete whales.

Deméré TA, McGowen MR, Berta A, Gatesy J.

Syst Biol. 2008 Feb;57(1):15-37. doi: 10.1080/10635150701884632.

PMID:
18266181
43.

A tenth crucial question regarding model use in phylogenetics.

Gatesy J.

Trends Ecol Evol. 2007 Oct;22(10):509-10. Epub 2007 Sep 4. No abstract available.

PMID:
17804115
44.

How many genes should a systematist sample? Conflicting insights from a phylogenomic matrix characterized by replicated incongruence.

Gatesy J, DeSalle R, Wahlberg N.

Syst Biol. 2007 Apr;56(2):355-63. No abstract available.

PMID:
17464890
45.

The supermatrix approach to systematics.

de Queiroz A, Gatesy J.

Trends Ecol Evol. 2007 Jan;22(1):34-41. Epub 2006 Oct 13. Review.

PMID:
17046100
46.

Hidden likelihood support in genomic data: can forty-five wrongs make a right?

Gatesy J, Baker RH.

Syst Biol. 2005 Jun;54(3):483-92.

PMID:
16012113
47.

Inconsistencies in arguments for the supertree approach: supermatrices versus supertrees of Crocodylia.

Gatesy J, Baker RH, Hayashi C.

Syst Biol. 2004 Apr;53(2):342-55. No abstract available.

PMID:
15205058
48.

Are the dental data really at odds with the molecular data? Morphological evidence for whale phylogeny (re)reexamined.

O'Leary MA, Gatesy J, Novacek MJ.

Syst Biol. 2003 Dec;52(6):853-64; discussion 864-5. No abstract available.

PMID:
14668123
49.

The evolution of HOM-C homeoboxes in the Dipteran family Drosophilidae.

DeSalle R, Branham MA, O'Grady P, Gatesy J.

Insect Mol Biol. 2003 Aug;12(4):345-51.

PMID:
12864914
50.

Combined support for wholesale taxic atavism in gavialine crocodylians.

Gatesy J, Amato G, Norell M, DeSalle R, Hayashi C.

Syst Biol. 2003 Jun;52(3):403-22. Erratum in: Syst Biol. 2003 Oct;52(5):734.

PMID:
12775528

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