Great ape genetic diversity and population history

TY - JOUR

T1 - Great ape genetic diversity and population history

AU - Prado-Martinez, Javier

AU - Sudmant, Peter H

AU - Kidd, Jeffrey M

AU - Li, Heng

AU - Kelley, Joanna L

AU - Lorente-Galdos, Belen

AU - Veeramah, Krishna R

AU - Woerner, August E

AU - O'Connor, Timothy D

AU - Santpere, Gabriel

AU - Cagan, Alexander

AU - Theunert, Christoph

AU - Casals, Ferran

AU - Laayouni, Hafid

AU - Munch, Kasper

AU - Hobolth, Asger

AU - Halager, Anders E

AU - Malig, Maika

AU - Hernandez-Rodriguez, Jessica

AU - Hernando-Herraez, Irene

AU - Prüfer, Kay

AU - Pybus, Marc

AU - Johnstone, Laurel

AU - Lachmann, Michael

AU - Alkan, Can

AU - Twigg, Dorina

AU - Petit, Natalia

AU - Baker, Carl

AU - Hormozdiari, Fereydoun

AU - Fernandez-Callejo, Marcos

AU - Dabad, Marc

AU - Wilson, Michael L

AU - Stevison, Laurie

AU - Camprubí, Cristina

AU - Carvalho, Tiago

AU - Ruiz-Herrera, Aurora

AU - Vives, Laura

AU - Mele, Marta

AU - Abello, Teresa

AU - Kondova, Ivanela

AU - Bontrop, Ronald E

AU - Pusey, Anne

AU - Lankester, Felix

AU - Kiyang, John A

AU - Bergl, Richard A

AU - Lonsdorf, Elizabeth

AU - Myers, Simon

AU - Ventura, Mario

AU - Gagneux, Pascal

AU - Comas, David

AU - Siegismund, Hans

AU - Blanc, Julie

AU - Agueda-Calpena, Lidia

AU - Gut, Marta

AU - Fulton, Lucinda

AU - Tishkoff, Sarah A

AU - Mullikin, James C

AU - Wilson, Richard K

AU - Gut, Ivo G

AU - Gonder, Mary Katherine

AU - Ryder, Oliver A

AU - Hahn, Beatrice H

AU - Navarro, Arcadi

AU - Akey, Joshua M

AU - Bertranpetit, Jaume

AU - Reich, David

AU - Mailund, Thomas

AU - Schierup, Mikkel H

AU - Hvilsom, Christina

AU - Andrés, Aida M

AU - Wall, Jeffrey D

AU - Bustamante, Carlos D

AU - Hammer, Michael F

AU - Eichler, Evan E

AU - Marques-Bonet, Tomas

PY - 2013

Y1 - 2013

N2 - 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.

AB - 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.

U2 - 10.1038/nature12228

DO - 10.1038/nature12228

M3 - Journal article

C2 - 23823723

SN - 0028-0836

VL - 499

SP - 471

EP - 475

JO - Nature

JF - Nature

ER -