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 Egerup Halager; Maika Malig; Jessica Hernandez-Rodriguez; Irene Hernando-Herraez; 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 Camprubí; 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 Redlef 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 Heide Schierup; Christina Hvilsom; Aida M Andrés; Jeffrey D Wall; Carlos D Bustamante; Michael F Hammer; Evan E Eichler; Tomas Marques-Bonet

doi:10.1038/nature12228

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 Egerup Halager, Maika Malig, Jessica Hernandez-Rodriguez, Irene Hernando-HerraezKay 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 Camprubí, 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 Redlef 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 Heide Schierup, Christina Hvilsom, Aida M Andrés, Jeffrey D Wall, Carlos D Bustamante, Michael F Hammer, Evan E Eichler, Tomas Marques-Bonet

Computational and RNA Biology

453 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 language	English
Journal	Nature
Volume	499
Issue number	7459
Pages (from-to)	471-475
Number of pages	5
ISSN	0028-0836
DOIs	https://doi.org/10.1038/nature12228
Publication status	Published - 2013

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Prado-Martinez, J., Sudmant, P. H., Kidd, J. M., Li, H., Kelley, J. L., Lorente-Galdos, B., Veeramah, K. R., Woerner, A. E., O'Connor, T. D., Santpere, G., Cagan, A., Theunert, C., Casals, F., Laayouni, H., Munch, K., Hobolth, A., Halager, A. E., Malig, M., Hernandez-Rodriguez, J., ... Marques-Bonet, T. (2013). Great ape genetic diversity and population history. Nature, 499(7459), 471-475. https://doi.org/10.1038/nature12228

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, Camprubí, 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, HR, 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

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title = "Great ape genetic diversity and population history",

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.",

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

year = "2013",

doi = "10.1038/nature12228",

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journal = "Nature",

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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 Egerup

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 Redlef

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 Heide

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 - Letter

C2 - 23823723

SN - 0028-0836

VL - 499

SP - 471

EP - 475

JO - Nature

JF - Nature

IS - 7459

ER -

Great ape genetic diversity and population history

Abstract

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