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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.


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]


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.


How conflict shapes evolution in poeciliid fishes.

Furness AI, Pollux BJA, Meredith RW, Springer MS, Reznick DN.

Nat Commun. 2019 Jul 26;10(1):3335. doi: 10.1038/s41467-019-11307-5.


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.


Emergence of a Chimeric Globin Pseudogene and Increased Hemoglobin Oxygen Affinity Underlie the Evolution of Aquatic Specializations in Sirenia.

Signore AV, Paijmans JLA, Hofreiter M, Fago A, Weber RE, Springer MS, Campbell KL.

Mol Biol Evol. 2019 Jun 1;36(6):1134-1147. doi: 10.1093/molbev/msz044.


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.


In love and war: The morphometric and phylogenetic basis of ornamentation, and the evolution of male display behavior, in the livebearer genus Poecilia.

Goldberg DL, Landy JA, Travis J, Springer MS, Reznick DN.

Evolution. 2019 Feb;73(2):360-377. doi: 10.1111/evo.13671. Epub 2019 Jan 17.


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.


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.


Appropriate fossil calibrations and tree constraints uphold the Mesozoic divergence of solenodons from other extant mammals.

Springer MS, Murphy WJ, Roca AL.

Mol Phylogenet Evol. 2018 Apr;121:158-165. doi: 10.1016/j.ympev.2018.01.007. Epub 2018 Jan 10.


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.


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.


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.


Their loss is our gain: regressive evolution in vertebrates provides genomic models for uncovering human disease loci.

Emerling CA, Widjaja AD, Nguyen NN, Springer MS.

J Med Genet. 2017 Dec;54(12):787-794. doi: 10.1136/jmedgenet-2017-104837. Epub 2017 Aug 16. Review.


Inactivation of thermogenic UCP1 as a historical contingency in multiple placental mammal clades.

Gaudry MJ, Jastroch M, Treberg JR, Hofreiter M, Paijmans JLA, Starrett J, Wales N, Signore AV, Springer MS, Campbell KL.

Sci Adv. 2017 Jul 12;3(7):e1602878. doi: 10.1126/sciadv.1602878. eCollection 2017 Jul.


The origin and biogeographic diversification of fishes in the family Poeciliidae.

Reznick DN, Furness AI, Meredith RW, Springer MS.

PLoS One. 2017 Mar 9;12(3):e0172546. doi: 10.1371/journal.pone.0172546. eCollection 2017.


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.


Talpid Mole Phylogeny Unites Shrew Moles and Illuminates Overlooked Cryptic Species Diversity.

He K, Shinohara A, Helgen KM, Springer MS, Jiang XL, Campbell KL.

Mol Biol Evol. 2017 Jan;34(1):78-87. doi: 10.1093/molbev/msw221. Epub 2016 Oct 30.


Waking the undead: Implications of a soft explosive model for the timing of placental mammal diversification.

Springer MS, Emerling CA, Meredith RW, Janečka JE, Eizirik E, Murphy WJ.

Mol Phylogenet Evol. 2017 Jan;106:86-102. doi: 10.1016/j.ympev.2016.09.017. Epub 2016 Sep 19.


Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates.

Mason VC, Li G, Minx P, Schmitz J, Churakov G, Doronina L, Melin AD, Dominy NJ, Lim NT, Springer MS, Wilson RK, Warren WC, Helgen KM, Murphy WJ.

Sci Adv. 2016 Aug 10;2(8):e1600633. doi: 10.1126/sciadv.1600633. eCollection 2016 Aug.


Mammal madness: is the mammal tree of life not yet resolved?

Foley NM, Springer MS, Teeling EC.

Philos Trans R Soc Lond B Biol Sci. 2016 Jul 19;371(1699). pii: 20150140. doi: 10.1098/rstb.2015.0140. Review.


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.


Spectral shifts of mammalian ultraviolet-sensitive pigments (short wavelength-sensitive opsin 1) are associated with eye length and photic niche evolution.

Emerling CA, Huynh HT, Nguyen MA, Meredith RW, Springer MS.

Proc Biol Sci. 2015 Nov 22;282(1819). pii: 20151817. doi: 10.1098/rspb.2015.1817.


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.


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.


Convergent evolution of alternative developmental trajectories associated with diapause in African and South American killifish.

Furness AI, Reznick DN, Springer MS, Meredith RW.

Proc Biol Sci. 2015 Mar 7;282(1802). pii: 20142189. doi: 10.1098/rspb.2014.2189.


Genomic evidence for rod monochromacy in sloths and armadillos suggests early subterranean history for Xenarthra.

Emerling CA, Springer MS.

Proc Biol Sci. 2015 Feb 7;282(1800):20142192. doi: 10.1098/rspb.2014.2192.


Evidence for a single loss of mineralized teeth in the common avian ancestor.

Meredith RW, Zhang G, Gilbert MT, Jarvis ED, Springer MS.

Science. 2014 Dec 12;346(6215):1254390. doi: 10.1126/science.1254390. Epub 2014 Dec 11.


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.


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.


The evolution of the placenta drives a shift in sexual selection in livebearing fish.

Pollux BJ, Meredith RW, Springer MS, Garland T, Reznick DN.

Nature. 2014 Sep 11;513(7517):233-6. doi: 10.1038/nature13451. Epub 2014 Jul 9.


Eyes underground: regression of visual protein networks in subterranean mammals.

Emerling CA, Springer MS.

Mol Phylogenet Evol. 2014 Sep;78:260-70. doi: 10.1016/j.ympev.2014.05.016. Epub 2014 May 22.


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.


The evolution of the sexually selected sword in Xiphophorus does not compromise aerobic locomotor performance.

Oufiero CE, Meredith RW, Jugo KN, Tran P, Chappell MA, Springer MS, Reznick DN, Garland T Jr.

Evolution. 2014 Jun;68(6):1806-23. doi: 10.1111/evo.12391. Epub 2014 Mar 28.


Phylogenetics: bats united, microbats divided.

Springer MS.

Curr Biol. 2013 Nov 18;23(22):R999-R1001. doi: 10.1016/j.cub.2013.09.053.


Technical comment on "The placental mammal ancestor and the post-K-Pg radiation of placentals".

Springer MS, Meredith RW, Teeling EC, Murphy WJ.

Science. 2013 Aug 9;341(6146):613. doi: 10.1126/science.1238025.


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.


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.


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.


11β-HSD1 inhibition reduces atherosclerosis in mice by altering proinflammatory gene expression in the vasculature.

Luo MJ, Thieringer R, Springer MS, Wright SD, Hermanowski-Vosatka A, Plump A, Balkovec JM, Cheng K, Ding GJ, Kawka DW, Koo GC, Grand CB, Luo Q, Maletic MM, Malkowitz L, Shah K, Singer I, Waddell ST, Wu KK, Yuan J, Zhu J, Stepaniants S, Yang X, Lum PY, Wang IM.

Physiol Genomics. 2013 Jan 7;45(1):47-57. doi: 10.1152/physiolgenomics.00109.2012. Epub 2012 Nov 20.


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.


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.


Phylogenetic relationships of living and recently extinct bandicoots based on nuclear and mitochondrial DNA sequences.

Westerman M, Kear BP, Aplin K, Meredith RW, Emerling C, Springer MS.

Mol Phylogenet Evol. 2012 Jan;62(1):97-108. doi: 10.1016/j.ympev.2011.09.009. Epub 2011 Nov 11.


Metabolic syndrome in mice induced by expressing a transcriptional activator in adipose tissue.

Zhang L, Zhou Y, Zhu AY, Li XQ, Mundt SS, Gao L, Lisnock J, Hernandez M, Alonso-Galicia M, Springer MS, O'Neill EA, Daugherty BL, Puig O.

Transgenic Res. 2012 Jun;21(3):633-44. doi: 10.1007/s11248-011-9562-2. Epub 2011 Oct 26.


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.


The historical biogeography of Mammalia.

Springer MS, Meredith RW, Janecka JE, Murphy WJ.

Philos Trans R Soc Lond B Biol Sci. 2011 Sep 12;366(1577):2478-502. doi: 10.1098/rstb.2011.0023. Review.


Molecular phylogenetic relationships and the coevolution of placentotrophy and superfetation in Poecilia (Poeciliidae: Cyprinodontiformes).

Meredith RW, Pires MN, Reznick DN, Springer MS.

Mol Phylogenet Evol. 2011 Apr;59(1):148-57. doi: 10.1016/j.ympev.2011.01.014. Epub 2011 Feb 1.


Effects of an 11β-hydroxysteroid dehydrogenase type 1 inhibitor, MK-0916, in patients with type 2 diabetes mellitus and metabolic syndrome.

Feig PU, Shah S, Hermanowski-Vosatka A, Plotkin D, Springer MS, Donahue S, Thach C, Klein EJ, Lai E, Kaufman KD.

Diabetes Obes Metab. 2011 Jun;13(6):498-504. doi: 10.1111/j.1463-1326.2011.01375.x.


A Phylogeny and Timescale for the Evolution of Pseudocheiridae (Marsupialia: Diprotodontia) in Australia and New Guinea.

Meredith RW, Mendoza MA, Roberts KK, Westerman M, Springer MS.

J Mamm Evol. 2010 Jun;17(2):75-99. Epub 2010 Mar 2.

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