Great ape genetic diversity and population history
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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 Egerup; 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; Camprubí, 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 Redlef; 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 Heide; 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 journal › Letter › Research › peer-review
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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 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
VL - 499
SP - 471
EP - 475
JO - Nature
JF - Nature
SN - 0028-0836
IS - 7459
ER -
ID: 48838719