Great ape genetic diversity and population history

Bibliographic Collection: 
CARTA-Inspired Publication
Publication Type: Journal Article
Authors: Prado-Martinez, J; Sudmant, PH; Kidd, JM; Li, H; Kelley, JL; Lorente-Galdos, B; Veeramah, KR; Woerner, AE; O'Connor, TD; Santpere, G; Cagan, A; Theunert, C; Casals, F; Laayouni, H; Munch, K; Hobolth, A; Halager, AE; Malig, M; Hernandez-Rodriguez, J; Hernando-Herraez, I; Prüfer, K; Pybus, M; Johnstone, L; Lachmann, M; Alkan, C; Twigg, D; Petit, N; Baker, C; Hormozdiari, F; Fernández-Callejo, M; Dabad, M; Wilson, ML; Stevison, L; Camprubi, C; Carvalho, T; Ruiz-Herrera, A; Vives, L; Melé, M; Abelló, T; Kondova, I; Bontrop, RE; Pusey, A; Lankester, F; Kiyang, JA; Bergl, RA; Lonsdorf, E; Myers, S; Ventura, M; Gagneux, P; Comas, D; Siegismund, H; Blanc, J; Agueda-Calpena, L; Gut, M; Fulton, L; Tishkoff, SA; Mullikin, JC; Wilson, RK; Gut, IG; Gonder, MK; Ryder, OA; Hahn, BH; Navarro, A; Akey, JM; Bertranpetit, J; Reich, D; Mailund, T; Schierup, MH; Hvilsom, C; Andres, AM; Wall, JD; Bustamante, CD; Hammer, MF; Eichler, EE; Marquès-Bonet, T
Year of Publication: 2013
Journal: Nature
Volume: 499
Edition: 2013/07/05
Number: 7459
Pagination: 471-5
Date Published: Jul 25
Type of Article: Research Support, N.I.H., ExtramuralResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, Non-P.H.S.
Publication Language: eng
ISBN Number: 1476-4687 (Electronic)00
Accession Number: 23823723
Abstract:

Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.

Notes:

Nature. 2013 Jul 25;499(7459):471-5. doi: 10.1038/nature12228. Epub 2013 Jul 3.

Alternate Journal: Nature
Author Address:

Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.

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