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Genomic Evidence for Local Adaptation of Hunter-Gatherers to the African Rainforest.

Lopez M, Choin J, Sikora M, Siddle K, Harmant C, Costa HA, Silvert M, Mouguiama-Daouda P, Hombert JM, Froment A, Le Bomin S, Perry GH, Barreiro LB, Bustamante CD, Verdu P, Patin E, Quintana-Murci L.

Curr Biol. 2019 Jul 13. pii: S0960-9822(19)30858-9. doi: 10.1016/j.cub.2019.07.013. [Epub ahead of print]


Natural selection contributed to immunological differences between hunter-gatherers and agriculturalists.

Harrison GF, Sanz J, Boulais J, Mina MJ, Grenier JC, Leng Y, Dumaine A, Yotova V, Bergey CM, Nsobya SL, Elledge SJ, Schurr E, Quintana-Murci L, Perry GH, Barreiro LB.

Nat Ecol Evol. 2019 Aug;3(8):1253-1264. doi: 10.1038/s41559-019-0947-6. Epub 2019 Jul 29.


Impact of DNA degradation on massively parallel sequencing-based autosomal STR, iiSNP, and mitochondrial DNA typing systems.

Zavala EI, Rajagopal S, Perry GH, Kruzic I, Bašić Ž, Parsons TJ, Holland MM.

Int J Legal Med. 2019 Jul 2. doi: 10.1007/s00414-019-02110-4. [Epub ahead of print]


Horse Paleogenomes and Human-Animal Interactions in Prehistory.

Perry GH, Makarewicz CA.

Trends Genet. 2019 Jul;35(7):473-475. doi: 10.1016/j.tig.2019.04.006. Epub 2019 May 17.


Polygenic adaptation and convergent evolution on growth and cardiac genetic pathways in African and Asian rainforest hunter-gatherers.

Bergey CM, Lopez M, Harrison GF, Patin E, Cohen JA, Quintana-Murci L, Barreiro LB, Perry GH.

Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):E11256-E11263. doi: 10.1073/pnas.1812135115. Epub 2018 Nov 9.


An environmental DNA sampling method for aye-ayes from their feeding traces.

Aylward ML, Sullivan AP, Perry GH, Johnson SE, Louis EE Jr.

Ecol Evol. 2018 Jul 31;8(18):9229-9240. doi: 10.1002/ece3.4341. eCollection 2018 Sep.


The demographic history and mutational load of African hunter-gatherers and farmers.

Lopez M, Kousathanas A, Quach H, Harmant C, Mouguiama-Daouda P, Hombert JM, Froment A, Perry GH, Barreiro LB, Verdu P, Patin E, Quintana-Murci L.

Nat Ecol Evol. 2018 Apr;2(4):721-730. doi: 10.1038/s41559-018-0496-4. Epub 2018 Mar 12.


Monkeys overharvest shellfish.

Perry GH, Codding BF.

Elife. 2017 Sep 13;6. pii: e30865. doi: 10.7554/eLife.30865.


Harnessing ancient genomes to study the history of human adaptation.

Marciniak S, Perry GH.

Nat Rev Genet. 2017 Nov;18(11):659-674. doi: 10.1038/nrg.2017.65. Epub 2017 Sep 11. Review.


Transposable elements are the primary source of novelty in primate gene regulation.

Trizzino M, Park Y, Holsbach-Beltrame M, Aracena K, Mika K, Caliskan M, Perry GH, Lynch VJ, Brown CD.

Genome Res. 2017 Oct;27(10):1623-1633. doi: 10.1101/gr.218149.116. Epub 2017 Aug 30.


Human behaviour as a long-term ecological driver of non-human evolution.

Sullivan AP, Bird DW, Perry GH.

Nat Ecol Evol. 2017 Feb 21;1(3):65. doi: 10.1038/s41559-016-0065. Review.


Testing Convergent Evolution in Auditory Processing Genes between Echolocating Mammals and the Aye-Aye, a Percussive-Foraging Primate.

Bankoff RJ, Jerjos M, Hohman B, Lauterbur ME, Kistler L, Perry GH.

Genome Biol Evol. 2017 Jul 1;9(7):1978-1989. doi: 10.1093/gbe/evx140.


A massively parallel strategy for STR marker development, capture, and genotyping.

Kistler L, Johnson SM, Irwin MT, Louis EE, Ratan A, Perry GH.

Nucleic Acids Res. 2017 Sep 6;45(15):e142. doi: 10.1093/nar/gkx574.


An evolutionary medicine perspective on Neandertal extinction.

Sullivan AP, de Manuel M, Marques-Bonet T, Perry GH.

J Hum Evol. 2017 Jul;108:62-71. doi: 10.1016/j.jhevol.2017.03.004. Epub 2017 May 16.


Dispersals and genetic adaptation of Bantu-speaking populations in Africa and North America.

Patin E, Lopez M, Grollemund R, Verdu P, Harmant C, Quach H, Laval G, Perry GH, Barreiro LB, Froment A, Heyer E, Massougbodji A, Fortes-Lima C, Migot-Nabias F, Bellis G, Dugoujon JM, Pereira JB, Fernandes V, Pereira L, Van der Veen L, Mouguiama-Daouda P, Bustamante CD, Hombert JM, Quintana-Murci L.

Science. 2017 May 5;356(6337):543-546. doi: 10.1126/science.aal1988.


Archaeogenomic evidence reveals prehistoric matrilineal dynasty.

Kennett DJ, Plog S, George RJ, Culleton BJ, Watson AS, Skoglund P, Rohland N, Mallick S, Stewardson K, Kistler L, LeBlanc SA, Whiteley PM, Reich D, Perry GH.

Nat Commun. 2017 Feb 21;8:14115. doi: 10.1038/ncomms14115.


Functional preservation and variation in the cone opsin genes of nocturnal tarsiers.

Moritz GL, Ong PS, Perry GH, Dominy NJ.

Philos Trans R Soc Lond B Biol Sci. 2017 Apr 5;372(1717). pii: 20160075. doi: 10.1098/rstb.2016.0075.


Phylogenomic Reconstruction of Sportive Lemurs (genus Lepilemur) Recovered from Mitogenomes with Inferences for Madagascar Biogeography.

Lei R, Frasier CL, Hawkins MT, Engberg SE, Bailey CA, Johnson SE, McLain AT, Groves CP, Perry GH, Nash SD, Mittermeier RA, Louis EE.

J Hered. 2017 Mar 1;108(2):107-119. doi: 10.1093/jhered/esw072.


Divergent Ah Receptor Ligand Selectivity during Hominin Evolution.

Hubbard TD, Murray IA, Bisson WH, Sullivan AP, Sebastian A, Perry GH, Jablonski NG, Perdew GH.

Mol Biol Evol. 2016 Oct;33(10):2648-58. doi: 10.1093/molbev/msw143. Epub 2016 Aug 2.


Hunter-gatherer genomics: evolutionary insights and ethical considerations.

Bankoff RJ, Perry GH.

Curr Opin Genet Dev. 2016 Dec;41:1-7. doi: 10.1016/j.gde.2016.06.015. Epub 2016 Jul 9. Review.


Implications of lemuriform extinctions for the Malagasy flora.

Federman S, Dornburg A, Daly DC, Downie A, Perry GH, Yoder AD, Sargis EJ, Richard AF, Donoghue MJ, Baden AL.

Proc Natl Acad Sci U S A. 2016 May 3;113(18):5041-6. doi: 10.1073/pnas.1523825113. Epub 2016 Apr 11.


Euarchontan Opsin Variation Brings New Focus to Primate Origins.

Melin AD, Wells K, Moritz GL, Kistler L, Orkin JD, Timm RM, Bernard H, Lakim MB, Perry GH, Kawamura S, Dominy NJ.

Mol Biol Evol. 2016 Apr;33(4):1029-41. doi: 10.1093/molbev/msv346. Epub 2016 Jan 6.


Gourds and squashes (Cucurbita spp.) adapted to megafaunal extinction and ecological anachronism through domestication.

Kistler L, Newsom LA, Ryan TM, Clarke AC, Smith BD, Perry GH.

Proc Natl Acad Sci U S A. 2015 Dec 8;112(49):15107-12. doi: 10.1073/pnas.1516109112. Epub 2015 Nov 16.


The epigenomic landscape of African rainforest hunter-gatherers and farmers.

Fagny M, Patin E, MacIsaac JL, Rotival M, Flutre T, Jones MJ, Siddle KJ, Quach H, Harmant C, McEwen LM, Froment A, Heyer E, Gessain A, Betsem E, Mouguiama-Daouda P, Hombert JM, Perry GH, Barreiro LB, Kobor MS, Quintana-Murci L.

Nat Commun. 2015 Nov 30;6:10047. doi: 10.1038/ncomms10047.


Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic.

Lynch VJ, Bedoya-Reina OC, Ratan A, Sulak M, Drautz-Moses DI, Perry GH, Miller W, Schuster SC.

Cell Rep. 2015 Jul 14;12(2):217-28. doi: 10.1016/j.celrep.2015.06.027. Epub 2015 Jul 2.


Parasites and human evolution.

Perry GH.

Evol Anthropol. 2014 Nov-Dec;23(6):218-28. doi: 10.1002/evan.21427. Review.


Ancient DNA and human evolution.

Perry GH, Orlando L.

J Hum Evol. 2015 Feb;79:1-3. doi: 10.1016/j.jhevol.2014.12.002. Epub 2015 Jan 22. No abstract available.


Insights into hominin phenotypic and dietary evolution from ancient DNA sequence data.

Perry GH, Kistler L, Kelaita MA, Sams AJ.

J Hum Evol. 2015 Feb;79:55-63. doi: 10.1016/j.jhevol.2014.10.018. Epub 2015 Jan 3.


Comparative and population mitogenomic analyses of Madagascar's extinct, giant 'subfossil' lemurs.

Kistler L, Ratan A, Godfrey LR, Crowley BE, Hughes CE, Lei R, Cui Y, Wood ML, Muldoon KM, Andriamialison H, McGraw JJ, Tomsho LP, Schuster SC, Miller W, Louis EE, Yoder AD, Malhi RS, Perry GH.

J Hum Evol. 2015 Feb;79:45-54. doi: 10.1016/j.jhevol.2014.06.016. Epub 2014 Dec 16.


Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history.

Kim HL, Ratan A, Perry GH, Montenegro A, Miller W, Schuster SC.

Nat Commun. 2014 Dec 4;5:5692. doi: 10.1038/ncomms6692.


Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers.

Perry GH, Foll M, Grenier JC, Patin E, Nédélec Y, Pacis A, Barakatt M, Gravel S, Zhou X, Nsobya SL, Excoffier L, Quintana-Murci L, Dominy NJ, Barreiro LB.

Proc Natl Acad Sci U S A. 2014 Sep 2;111(35):E3596-603. doi: 10.1073/pnas.1402875111. Epub 2014 Aug 18.


Comparative metabolomics in primates reveals the effects of diet and gene regulatory variation on metabolic divergence.

Blekhman R, Perry GH, Shahbaz S, Fiehn O, Clark AG, Gilad Y.

Sci Rep. 2014 Jul 28;4:5809. doi: 10.1038/srep05809.


Natural selection for the Duffy-null allele in the recently admixed people of Madagascar.

Hodgson JA, Pickrell JK, Pearson LN, Quillen EE, Prista A, Rocha J, Soodyall H, Shriver MD, Perry GH.

Proc Biol Sci. 2014 Aug 22;281(1789):20140930. doi: 10.1098/rspb.2014.0930.


The impact of agricultural emergence on the genetic history of African rainforest hunter-gatherers and agriculturalists.

Patin E, Siddle KJ, Laval G, Quach H, Harmant C, Becker N, Froment A, Régnault B, Lemée L, Gravel S, Hombert JM, Van der Veen L, Dominy NJ, Perry GH, Barreiro LB, Verdu P, Heyer E, Quintana-Murci L.

Nat Commun. 2014;5:3163. doi: 10.1038/ncomms4163.


Galaxy tools to study genome diversity.

Bedoya-Reina OC, Ratan A, Burhans R, Kim HL, Giardine B, Riemer C, Li Q, Olson TL, Loughran TP Jr, Vonholdt BM, Perry GH, Schuster SC, Miller W.

Gigascience. 2013 Dec 30;2(1):17. doi: 10.1186/2047-217X-2-17.


Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar.

Perry GH, Louis EE Jr, Ratan A, Bedoya-Reina OC, Burhans RC, Lei R, Johnson SE, Schuster SC, Miller W.

Proc Natl Acad Sci U S A. 2013 Apr 9;110(15):5823-8. doi: 10.1073/pnas.1211990110. Epub 2013 Mar 25.


ASPM and the evolution of cerebral cortical size in a community of New World monkeys.

Villanea FA, Perry GH, Gutiérrez-Espeleta GA, Dominy NJ.

PLoS One. 2012;7(9):e44928. doi: 10.1371/journal.pone.0044928. Epub 2012 Sep 27.


Regulatory element copy number differences shape primate expression profiles.

Iskow RC, Gokcumen O, Abyzov A, Malukiewicz J, Zhu Q, Sukumar AT, Pai AA, Mills RE, Habegger L, Cusanovich DA, Rubel MA, Perry GH, Gerstein M, Stone AC, Gilad Y, Lee C.

Proc Natl Acad Sci U S A. 2012 Jul 31;109(31):12656-61. doi: 10.1073/pnas.1205199109. Epub 2012 Jul 13.


Evolutionary genetics of the human Rh blood group system.

Perry GH, Xue Y, Smith RS, Meyer WK, Calışkan M, Yanez-Cuna O, Lee AS, Gutiérrez-Arcelus M, Ober C, Hollox EJ, Tyler-Smith C, Lee C.

Hum Genet. 2012 Jul;131(7):1205-16. doi: 10.1007/s00439-012-1147-5. Epub 2012 Feb 25.


Comparative RNA sequencing reveals substantial genetic variation in endangered primates.

Perry GH, Melsted P, Marioni JC, Wang Y, Bainer R, Pickrell JK, Michelini K, Zehr S, Yoder AD, Stephens M, Pritchard JK, Gilad Y.

Genome Res. 2012 Apr;22(4):602-10. doi: 10.1101/gr.130468.111. Epub 2011 Dec 29.


A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar.

Perry GH, Reeves D, Melsted P, Ratan A, Miller W, Michelini K, Louis EE Jr, Pritchard JK, Mason CE, Gilad Y.

Genome Biol Evol. 2012;4(2):126-35. doi: 10.1093/gbe/evr132. Epub 2011 Dec 7.


Spatial association and clinical development of equine influenza in horses yarded overnight at an equestrian event at Maitland prior to propagating the 2007 epidemic in Australia.

Britton AL, Major DA, Perry GH, Read AJ.

Aust Vet J. 2011 Jul;89 Suppl 1:68-9. doi: 10.1111/j.1751-0813.2011.00751.x.


Genomic-scale capture and sequencing of endogenous DNA from feces.

Perry GH, Marioni JC, Melsted P, Gilad Y.

Mol Ecol. 2010 Dec;19(24):5332-44. doi: 10.1111/j.1365-294X.2010.04888.x. Epub 2010 Nov 3.


More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure.

Stone AC, Battistuzzi FU, Kubatko LS, Perry GH Jr, Trudeau E, Lin H, Kumar S.

Philos Trans R Soc Lond B Biol Sci. 2010 Oct 27;365(1556):3277-88. doi: 10.1098/rstb.2010.0096.


Evolutionary adaptations to dietary changes.

Luca F, Perry GH, Di Rienzo A.

Annu Rev Nutr. 2010 Aug 21;30:291-314. doi: 10.1146/annurev-nutr-080508-141048. Review.


A rod cell marker of nocturnal ancestry.

Perry GH, Pickrell JK.

J Hum Evol. 2010 Feb;58(2):207-10. doi: 10.1016/j.jhevol.2009.09.007. Epub 2009 Nov 25. No abstract available.


Evolution of the human pygmy phenotype.

Perry GH, Dominy NJ.

Trends Ecol Evol. 2009 Apr;24(4):218-25. doi: 10.1016/j.tree.2008.11.008. Epub 2009 Feb 24. Review.


Different selective pressures shape the molecular evolution of color vision in chimpanzee and human populations.

Verrelli BC, Lewis CM Jr, Stone AC, Perry GH.

Mol Biol Evol. 2008 Dec;25(12):2735-43. doi: 10.1093/molbev/msn220. Epub 2008 Oct 1.


Copy number variation and evolution in humans and chimpanzees.

Perry GH, Yang F, Marques-Bonet T, Murphy C, Fitzgerald T, Lee AS, Hyland C, Stone AC, Hurles ME, Tyler-Smith C, Eichler EE, Carter NP, Lee C, Redon R.

Genome Res. 2008 Nov;18(11):1698-710. doi: 10.1101/gr.082016.108. Epub 2008 Sep 4.

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