Great ape genetic diversity and population history

Javier Prado-Martinez, Peter H. Sudmant, Jeffrey M. Kidd, Heng Li, Joanna L. Kelley, Belen Lorente-Galdos, Krishna R. Veeramah, August E. Woerner, Timothy D. O'Connor, Gabriel Santpere, Alexander Cagan, Christoph Theunert, Ferran Casals, Hafid Laayouni, Kasper Munch, Asger Hobolth, Anders E. Halager, Maika Malig, Jessica Hernandez-Rodriguez, Irene Hernando-Herraez & 55 others Kay Prüfer, Marc Pybus, Laurel Johnstone, Michael Lachmann, Can Alkan, Dorina Twigg, Natalia Petit, Carl Baker, Fereydoun Hormozdiari, Marcos Fernandez-Callejo, Marc Dabad, Michael L. Wilson, Laurie Stevison, Cristina Camprub, Tiago Carvalho, Aurora Ruiz-Herrera, Laura Vives, Marta Mele, Teresa Abello, Ivanela Kondova, Ronald E. Bontrop, Anne Pusey, Felix Lankester, John A. Kiyang, Richard A. Bergl, Elizabeth Lonsdorf, Simon Myers, Mario Ventura, Pascal Gagneux, David Comas, Hans Siegismund, Julie Blanc, Lidia Agueda-Calpena, Marta Gut, Lucinda Fulton, Sarah A. Tishkoff, James C. Mullikin, Richard K. Wilson, Ivo G. Gut, Mary Katherine Gonder, Oliver A. Ryder, Beatrice H. Hahn, Arcadi Navarro, Joshua M. Akey, Jaume Bertranpetit, David Reich, Thomas Mailund, Mikkel H. Schierup, Christina Hvilsom, Aida M. Andrés, Jeffrey D. Wall, Carlos D. Bustamante, Michael F Hammer, Evan E. Eichler, Tomas Marques-Bonet

Research output: Contribution to journalArticle

349 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)471-475
Number of pages5
JournalNature
Volume499
Issue number7459
DOIs
StatePublished - 2013

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Hominidae
Population
Gorilla gorilla
Cameroon
Inbreeding
Pan troglodytes
Gene Flow
Disease Susceptibility
Phylogeny
Nigeria
Population Density
Genetic Recombination
Genes
Single Nucleotide Polymorphism
Genome

ASJC Scopus subject areas

  • General

Cite this

Prado-Martinez, J., Sudmant, P. H., Kidd, J. M., Li, H., Kelley, J. L., Lorente-Galdos, B., ... Marques-Bonet, T. (2013). Great ape genetic diversity and population history. Nature, 499(7459), 471-475. https://doi.org/10.1038/nature12228

Great ape genetic diversity and population history. / Prado-Martinez, Javier; Sudmant, Peter H.; Kidd, Jeffrey M.; Li, Heng; Kelley, Joanna L.; Lorente-Galdos, Belen; Veeramah, Krishna R.; Woerner, August E.; O'Connor, Timothy D.; Santpere, Gabriel; Cagan, Alexander; Theunert, Christoph; Casals, Ferran; Laayouni, Hafid; Munch, Kasper; Hobolth, Asger; Halager, Anders E.; Malig, Maika; Hernandez-Rodriguez, Jessica; Hernando-Herraez, Irene; Prüfer, Kay; Pybus, Marc; Johnstone, Laurel; Lachmann, Michael; Alkan, Can; Twigg, Dorina; Petit, Natalia; Baker, Carl; Hormozdiari, Fereydoun; Fernandez-Callejo, Marcos; Dabad, Marc; Wilson, Michael L.; Stevison, Laurie; Camprub, Cristina; Carvalho, Tiago; Ruiz-Herrera, Aurora; Vives, Laura; Mele, Marta; Abello, Teresa; Kondova, Ivanela; Bontrop, Ronald E.; Pusey, Anne; Lankester, Felix; Kiyang, John A.; Bergl, Richard A.; Lonsdorf, Elizabeth; Myers, Simon; Ventura, Mario; Gagneux, Pascal; Comas, David; Siegismund, Hans; Blanc, Julie; Agueda-Calpena, Lidia; Gut, Marta; Fulton, Lucinda; Tishkoff, Sarah A.; Mullikin, James C.; Wilson, Richard K.; Gut, Ivo G.; Gonder, Mary Katherine; Ryder, Oliver A.; Hahn, Beatrice H.; Navarro, Arcadi; Akey, Joshua M.; Bertranpetit, Jaume; Reich, David; Mailund, Thomas; Schierup, Mikkel H.; Hvilsom, Christina; Andrés, Aida M.; Wall, Jeffrey D.; Bustamante, Carlos D.; Hammer, Michael F; Eichler, Evan E.; Marques-Bonet, Tomas.

In: Nature, Vol. 499, No. 7459, 2013, p. 471-475.

Research output: Contribution to journalArticle

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, Fernandez-Callejo, M, Dabad, M, Wilson, ML, Stevison, L, Camprub, C, Carvalho, T, Ruiz-Herrera, A, Vives, L, Mele, M, Abello, 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, Andrés, AM, Wall, JD, Bustamante, CD, Hammer, MF, Eichler, EE & Marques-Bonet, T 2013, 'Great ape genetic diversity and population history', Nature, vol. 499, no. 7459, pp. 471-475. https://doi.org/10.1038/nature12228
Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B et al. Great ape genetic diversity and population history. Nature. 2013;499(7459):471-475. https://doi.org/10.1038/nature12228
Prado-Martinez, Javier ; Sudmant, Peter H. ; Kidd, Jeffrey M. ; Li, Heng ; Kelley, Joanna L. ; Lorente-Galdos, Belen ; Veeramah, Krishna R. ; Woerner, August E. ; O'Connor, Timothy D. ; Santpere, Gabriel ; Cagan, Alexander ; Theunert, Christoph ; Casals, Ferran ; Laayouni, Hafid ; Munch, Kasper ; Hobolth, Asger ; Halager, Anders E. ; Malig, Maika ; Hernandez-Rodriguez, Jessica ; Hernando-Herraez, Irene ; Prüfer, Kay ; Pybus, Marc ; Johnstone, Laurel ; Lachmann, Michael ; Alkan, Can ; Twigg, Dorina ; Petit, Natalia ; Baker, Carl ; Hormozdiari, Fereydoun ; Fernandez-Callejo, Marcos ; Dabad, Marc ; Wilson, Michael L. ; Stevison, Laurie ; Camprub, Cristina ; Carvalho, Tiago ; Ruiz-Herrera, Aurora ; Vives, Laura ; Mele, Marta ; Abello, Teresa ; Kondova, Ivanela ; Bontrop, Ronald E. ; Pusey, Anne ; Lankester, Felix ; Kiyang, John A. ; Bergl, Richard A. ; Lonsdorf, Elizabeth ; Myers, Simon ; Ventura, Mario ; Gagneux, Pascal ; Comas, David ; Siegismund, Hans ; Blanc, Julie ; Agueda-Calpena, Lidia ; Gut, Marta ; Fulton, Lucinda ; Tishkoff, Sarah A. ; Mullikin, James C. ; Wilson, Richard K. ; Gut, Ivo G. ; Gonder, Mary Katherine ; Ryder, Oliver A. ; Hahn, Beatrice H. ; Navarro, Arcadi ; Akey, Joshua M. ; Bertranpetit, Jaume ; Reich, David ; Mailund, Thomas ; Schierup, Mikkel H. ; Hvilsom, Christina ; Andrés, Aida M. ; Wall, Jeffrey D. ; Bustamante, Carlos D. ; Hammer, Michael F ; Eichler, Evan E. ; Marques-Bonet, Tomas. / Great ape genetic diversity and population history. In: Nature. 2013 ; Vol. 499, No. 7459. pp. 471-475.
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