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Avian MHC Evolution in the Era of Genomics: Phase 1.0.

O'Connor EA, Westerdahl H, Burri R, Edwards SV.

Cells. 2019 Sep 26;8(10). pii: E1152. doi: 10.3390/cells8101152. Review.


Evolutionary Dynamics of Sex Chromosomes of Paleognathous Birds.

Xu L, Wa Sin SY, Grayson P, Edwards SV, Sackton TB.

Genome Biol Evol. 2019 Aug 1;11(8):2376-2390. doi: 10.1093/gbe/evz154.


Modern Phylogenomics: Building Phylogenetic Trees Using the Multispecies Coalescent Model.

Liu L, Anderson C, Pearl D, Edwards SV.

Methods Mol Biol. 2019;1910:211-239. doi: 10.1007/978-1-4939-9074-0_7.


Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution.

Lamichhaney S, Card DC, Grayson P, Tonini JFR, Bravo GA, Näpflin K, Termignoni-Garcia F, Torres C, Burbrink F, Clarke JA, Sackton TB, Edwards SV.

Philos Trans R Soc Lond B Biol Sci. 2019 Jul 22;374(1777):20180248. doi: 10.1098/rstb.2018.0248. Epub 2019 Jun 3.


Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone.

Cloutier A, Sackton TB, Grayson P, Clamp M, Baker AJ, Edwards SV.

Syst Biol. 2019 Apr 23. pii: syz019. doi: 10.1093/sysbio/syz019. [Epub ahead of print]


Convergent regulatory evolution and loss of flight in paleognathous birds.

Sackton TB, Grayson P, Cloutier A, Hu Z, Liu JS, Wheeler NE, Gardner PP, Clarke JA, Baker AJ, Clamp M, Edwards SV.

Science. 2019 Apr 5;364(6435):74-78. doi: 10.1126/science.aat7244.


Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees.

Hu Z, Sackton TB, Edwards SV, Liu JS.

Mol Biol Evol. 2019 May 1;36(5):1086-1100. doi: 10.1093/molbev/msz049.


Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics.

Bravo GA, Antonelli A, Bacon CD, Bartoszek K, Blom MPK, Huynh S, Jones G, Knowles LL, Lamichhaney S, Marcussen T, Morlon H, Nakhleh LK, Oxelman B, Pfeil B, Schliep A, Wahlberg N, Werneck FP, Wiedenhoeft J, Willows-Munro S, Edwards SV.

PeerJ. 2019 Feb 14;7:e6399. doi: 10.7717/peerj.6399. eCollection 2019.


Museum specimens of terrestrial vertebrates are sensitive indicators of environmental change in the Anthropocene.

Schmitt CJ, Cook JA, Zamudio KR, Edwards SV.

Philos Trans R Soc Lond B Biol Sci. 2018 Nov 19;374(1763). pii: 20170387. doi: 10.1098/rstb.2017.0387. Review.


Conceptual and empirical advances in Neotropical biodiversity research.

Antonelli A, Ariza M, Albert J, Andermann T, Azevedo J, Bacon C, Faurby S, Guedes T, Hoorn C, Lohmann LG, Matos-Maraví P, Ritter CD, Sanmartín I, Silvestro D, Tejedor M, Ter Steege H, Tuomisto H, Werneck FP, Zizka A, Edwards SV.

PeerJ. 2018 Oct 4;6:e5644. doi: 10.7717/peerj.5644. eCollection 2018.


Editorial: Evolutionary Feedbacks Between Population Biology and Genome Architecture.

Ezaz T, Edwards SV.

Front Genet. 2018 Aug 21;9:329. doi: 10.3389/fgene.2018.00329. eCollection 2018. No abstract available.


Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome.

Perry BW, Card DC, McGlothlin JW, Pasquesi GIM, Adams RH, Schield DR, Hales NR, Corbin AB, Demuth JP, Hoffmann FG, Vandewege MW, Schott RK, Bhattacharyya N, Chang BSW, Casewell NR, Whiteley G, Reyes-Velasco J, Mackessy SP, Gamble T, Storey KB, Biggar KK, Passow CN, Kuo CH, McGaugh SE, Bronikowski AM, de Koning APJ, Edwards SV, Pfrender ME, Minx P, Brodie ED 3rd, Brodie ED Jr, Warren WC, Castoe TA.

Genome Biol Evol. 2018 Aug 1;10(8):2110-2129. doi: 10.1093/gbe/evy157.


Ecology can inform genetics: Disassortative mating contributes to MHC polymorphism in Leach's storm-petrels (Oceanodroma leucorhoa).

Hoover B, Alcaide M, Jennings S, Sin SYW, Edwards SV, Nevitt GA.

Mol Ecol. 2018 Jul 16. doi: 10.1111/mec.14801. [Epub ahead of print]


Rapid diversification and hybridization have shaped the dynamic history of the genus Elaenia.

Tang Q, Edwards SV, Rheindt FE.

Mol Phylogenet Evol. 2018 Oct;127:522-533. doi: 10.1016/j.ympev.2018.05.008. Epub 2018 May 18.


Earth BioGenome Project: Sequencing life for the future of life.

Lewin HA, Robinson GE, Kress WJ, Baker WJ, Coddington J, Crandall KA, Durbin R, Edwards SV, Forest F, Gilbert MTP, Goldstein MM, Grigoriev IV, Hackett KJ, Haussler D, Jarvis ED, Johnson WE, Patrinos A, Richards S, Castilla-Rubio JC, van Sluys MA, Soltis PS, Xu X, Yang H, Zhang G.

Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):4325-4333. doi: 10.1073/pnas.1720115115.


Physiological and regulatory underpinnings of geographic variation in reptilian cold tolerance across a latitudinal cline.

Campbell-Staton SC, Bare A, Losos JB, Edwards SV, Cheviron ZA.

Mol Ecol. 2018 May;27(9):2243-2255. doi: 10.1111/mec.14580. Epub 2018 Apr 20.


Reply to Gatesy and Springer: Claims of homology errors and zombie lineages do not compromise the dating of placental diversification.

Liu L, Zhang J, Rheindt FE, Lei F, Qu Y, Wang Y, Zhang Y, Sullivan C, Nie W, Wang J, Yang F, Chen J, Edwards SV, Meng J, Wu S.

Proc Natl Acad Sci U S A. 2017 Nov 7;114(45):E9433-E9434. doi: 10.1073/pnas.1715371114. Epub 2017 Oct 24. No abstract available.


Gene flow during glacial habitat shifts facilitates character displacement in a Neotropical flycatcher radiation.

Chattopadhyay B, Garg KM, Gwee CY, Edwards SV, Rheindt FE.

BMC Evol Biol. 2017 Sep 1;17(1):210. doi: 10.1186/s12862-017-1047-3.


Comparative Genomics as a Foundation for Evo-Devo Studies in Birds.

Grayson P, Sin SYW, Sackton TB, Edwards SV.

Methods Mol Biol. 2017;1650:11-46. doi: 10.1007/978-1-4939-7216-6_2.


Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary.

Liu L, Zhang J, Rheindt FE, Lei F, Qu Y, Wang Y, Zhang Y, Sullivan C, Nie W, Wang J, Yang F, Chen J, Edwards SV, Meng J, Wu S.

Proc Natl Acad Sci U S A. 2017 Aug 29;114(35):E7282-E7290. doi: 10.1073/pnas.1616744114. Epub 2017 Aug 14.


Winter storms drive rapid phenotypic, regulatory, and genomic shifts in the green anole lizard.

Campbell-Staton SC, Cheviron ZA, Rochette N, Catchen J, Losos JB, Edwards SV.

Science. 2017 Aug 4;357(6350):495-498. doi: 10.1126/science.aam5512. Epub 2017 Aug 3.


SNPs across time and space: population genomic signatures of founder events and epizootics in the House Finch (Haemorhous mexicanus).

Shultz AJ, Baker AJ, Hill GE, Nolan PM, Edwards SV.

Ecol Evol. 2016 Sep 28;6(20):7475-7489. doi: 10.1002/ece3.2444. eCollection 2016 Oct.


Genomic footprints of adaptation in a cooperatively breeding tropical bird across a vegetation gradient.

Termignoni-García F, Jaramillo-Correa JP, Chablé-Santos J, Liu M, Shultz AJ, Edwards SV, Escalante-Pliego P.

Mol Ecol. 2017 Sep;26(17):4483-4496. doi: 10.1111/mec.14224. Epub 2017 Jul 29.


Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics.

Edwards SV, Cloutier A, Baker AJ.

Syst Biol. 2017 Nov 1;66(6):1028-1044. doi: 10.1093/sysbio/syx058.


Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird.

Tigano A, Shultz AJ, Edwards SV, Robertson GJ, Friesen VL.

Ecol Evol. 2017 Mar 12;7(7):2370-2381. doi: 10.1002/ece3.2819. eCollection 2017 Apr.


Climate-mediated adaptation after mainland colonization of an ancestrally subtropical island lizard, Anolis carolinensis.

Campbell-Staton SC, Edwards SV, Losos JB.

J Evol Biol. 2016 Nov;29(11):2168-2180. doi: 10.1111/jeb.12935. Epub 2016 Aug 1.


Population Genomics Reveals Low Genetic Diversity and Adaptation to Hypoxia in Snub-Nosed Monkeys.

Zhou X, Meng X, Liu Z, Chang J, Wang B, Li M, Wengel PO, Tian S, Wen C, Wang Z, Garber PA, Pan H, Ye X, Xiang Z, Bruford MW, Edwards SV, Cao Y, Yu S, Gao L, Cao Z, Liu G, Ren B, Shi F, Peterfi Z, Li D, Li B, Jiang Z, Li J, Gladyshev VN, Li R, Li M.

Mol Biol Evol. 2016 Oct;33(10):2670-81. doi: 10.1093/molbev/msw150. Epub 2016 Aug 23.


Time-to-contact estimation errors among older drivers with useful field of view impairments.

Rusch ML, Schall MC Jr, Lee JD, Dawson JD, Edwards SV, Rizzo M.

Accid Anal Prev. 2016 Oct;95(Pt A):284-91. doi: 10.1016/j.aap.2016.07.008. Epub 2016 Jul 26.


Reticulation, divergence, and the phylogeography-phylogenetics continuum.

Edwards SV, Potter S, Schmitt CJ, Bragg JG, Moritz C.

Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):8025-32. doi: 10.1073/pnas.1601066113.


Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes.

Suh A, Witt CC, Menger J, Sadanandan KR, Podsiadlowski L, Gerth M, Weigert A, McGuire JA, Mudge J, Edwards SV, Rheindt FE.

Nat Commun. 2016 Apr 21;7:11396. doi: 10.1038/ncomms11396.


The "Atlantis Forest hypothesis" does not explain Atlantic Forest phylogeography.

Raposo do Amaral F, Edwards SV, Pie MR, Jennings WB, Svensson-Coelho M, d'Horta FM, Schmitt CJ, Maldonado-Coelho M.

Proc Natl Acad Sci U S A. 2016 Apr 12;113(15):E2097-8. doi: 10.1073/pnas.1602213113. Epub 2016 Mar 16. No abstract available.


Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics.

Edwards SV, Xi Z, Janke A, Faircloth BC, McCormack JE, Glenn TC, Zhong B, Wu S, Lemmon EM, Lemmon AR, Leaché AD, Liu L, Davis CC.

Mol Phylogenet Evol. 2016 Jan;94(Pt A):447-62. doi: 10.1016/j.ympev.2015.10.027. Epub 2015 Oct 27. Review.


Multiple phylogenetically distinct events shaped the evolution of limb skeletal morphologies associated with bipedalism in the jerboas.

Moore TY, Organ CL, Edwards SV, Biewener AA, Tabin CJ, Jenkins FA Jr, Cooper KL.

Curr Biol. 2015 Nov 2;25(21):2785-2794. doi: 10.1016/j.cub.2015.09.037. Epub 2015 Oct 8.


Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree".

Liu L, Edwards SV.

Science. 2015 Oct 9;350(6257):171. doi: 10.1126/science.aaa7343.


Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".

Cracraft J, Houde P, Ho SY, Mindell DP, Fjeldså J, Lindow B, Edwards SV, Rahbek C, Mirarab S, Warnow T, Gilbert MT, Zhang G, Braun EL, Jarvis ED.

Science. 2015 Sep 25;349(6255):1460. doi: 10.1126/science.aab1578.


Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses (Phoebastria nigripes) using double digest RADseq: implications for conservation.

Dierickx EG, Shultz AJ, Sato F, Hiraoka T, Edwards SV.

Evol Appl. 2015 Aug;8(7):662-78. doi: 10.1111/eva.12274. Epub 2015 Jun 13.


Physical Mapping and Refinement of the Painted Turtle Genome (Chrysemys picta) Inform Amniote Genome Evolution and Challenge Turtle-Bird Chromosomal Conservation.

Badenhorst D, Hillier LW, Literman R, Montiel EE, Radhakrishnan S, Shen Y, Minx P, Janes DE, Warren WC, Edwards SV, Valenzuela N.

Genome Biol Evol. 2015 Jun 24;7(7):2038-50. doi: 10.1093/gbe/evv119.


Estimating phylogenetic trees from genome-scale data.

Liu L, Xi Z, Wu S, Davis CC, Edwards SV.

Ann N Y Acad Sci. 2015 Dec;1360:36-53. doi: 10.1111/nyas.12747. Epub 2015 Apr 14. Review.


Adaptive Evolution as a Predictor of Species-Specific Innate Immune Response.

Webb AE, Gerek ZN, Morgan CC, Walsh TA, Loscher CE, Edwards SV, O'Connell MJ.

Mol Biol Evol. 2015 Jul;32(7):1717-29. doi: 10.1093/molbev/msv051. Epub 2015 Mar 10.


Phylogenomic analyses data of the avian phylogenomics project.

Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Alfaro-Núñez A, Narula N, Liu L, Burt D, Ellegren H, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G; Avian Phylogenomics Consortium.

Gigascience. 2015 Feb 12;4:4. doi: 10.1186/s13742-014-0038-1. eCollection 2015.


Molecular evolution of Dmrt1 accompanies change of sex-determining mechanisms in reptilia.

Janes DE, Organ CL, Stiglec R, O'Meally D, Sarre SD, Georges A, Graves JA, Valenzuela N, Literman RA, Rutherford K, Gemmell N, Iverson JB, Tamplin JW, Edwards SV, Ezaz T.

Biol Lett. 2014 Dec;10(12):20140809. doi: 10.1098/rsbl.2014.0809.


Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutiérrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, Caballero J, Hubley RM, Smit AF, Platt RN, Lavoie CA, Ramakodi MP, Finger JW Jr, Suh A, Isberg SR, Miles L, Chong AY, Jaratlerdsiri W, Gongora J, Moran C, Iriarte A, McCormack J, Burgess SC, Edwards SV, Lyons E, Williams C, Breen M, Howard JT, Gresham CR, Peterson DG, Schmitz J, Pollock DD, Haussler D, Triplett EW, Zhang G, Irie N, Jarvis ED, Brochu CA, Schmidt CJ, McCarthy FM, Faircloth BC, Hoffmann FG, Glenn TC, Gabaldón T, Paten B, Ray DA.

Science. 2014 Dec 12;346(6215):1254449. doi: 10.1126/science.1254449. Epub 2014 Dec 11.


Whole-genome analyses resolve early branches in the tree of life of modern birds.

Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G.

Science. 2014 Dec 12;346(6215):1320-31. doi: 10.1126/science.1253451.


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.


Feather development genes and associated regulatory innovation predate the origin of Dinosauria.

Lowe CB, Clarke JA, Baker AJ, Haussler D, Edwards SV.

Mol Biol Evol. 2015 Jan;32(1):23-8. doi: 10.1093/molbev/msu309. Epub 2014 Nov 18.


Sensory biology. Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor.

Baldwin MW, Toda Y, Nakagita T, O'Connell MJ, Klasing KC, Misaka T, Edwards SV, Liberles SD.

Science. 2014 Aug 22;345(6199):929-33. doi: 10.1126/science.1255097.


Parallel evolution of tetrodotoxin resistance in three voltage-gated sodium channel genes in the garter snake Thamnophis sirtalis.

McGlothlin JW, Chuckalovcak JP, Janes DE, Edwards SV, Feldman CR, Brodie ED Jr, Pfrender ME, Brodie ED 3rd.

Mol Biol Evol. 2014 Nov;31(11):2836-46. doi: 10.1093/molbev/msu237. Epub 2014 Aug 18.


Inferential reasoning and egg rejection in a cooperatively breeding cuckoo.

Riehl C, Strong MJ, Edwards SV.

Anim Cogn. 2015 Jan;18(1):75-82. doi: 10.1007/s10071-014-0778-4. Epub 2014 Jul 4.


The evolution of bipedalism in jerboas (rodentia: Dipodoidea): origin in humid and forested environments.

Wu S, Zhang F, Edwards SV, Wu W, Ye J, Bi S, Ni X, Quan C, Meng J, Organ CL.

Evolution. 2014 Jul;68(7):2108-18. doi: 10.1111/evo.12404. Epub 2014 May 5.


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