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Great ape genetic diversity and population history.

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 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 - Nature (2013)

Bottom Line: 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.

View Article: PubMed Central - PubMed

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

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.

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PSMC analysisInferred historical population sizes by PSMC. The lower x-axis gives time measured by pairwise sequence divergence and the y-axis gives the effective population size measured by the scaled mutation rate. The upper x-axis indicates scaling in years, assuming a mutation rate ranging from 10−9 to 5·10−10 per site per year. The top left panel shows the inference for modern human populations. In the rest of the three panels, thin light lines of the same color correspond to PSMC inferences on 100 rounds of bootstrapped sequences.
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Figure 3: PSMC analysisInferred historical population sizes by PSMC. The lower x-axis gives time measured by pairwise sequence divergence and the y-axis gives the effective population size measured by the scaled mutation rate. The upper x-axis indicates scaling in years, assuming a mutation rate ranging from 10−9 to 5·10−10 per site per year. The top left panel shows the inference for modern human populations. In the rest of the three panels, thin light lines of the same color correspond to PSMC inferences on 100 rounds of bootstrapped sequences.

Mentions: PSMC analyses of historical Ne (Figure 3) suggests that the ancestral Pan lineage had the largest effective population size of all lineages >3 million years ago (Mya), after which the ancestral bonobo-chimpanzee population experienced a dramatic decline. Both PSMC and ABC analyses support a model of subsequent increase in chimpanzee Ne starting ~1 Mya, prior to their divergence into separate subspecies. Following an Eastern chimpanzee increase in Ne (~500 thousand years ago, kya), the Central chimpanzees reached their zenith ~200–300 kya followed by the Western chimpanzee ~150 kya. Although the PSMC profiles of the two subspecies within each of the major chimpanzee clades (Eastern/Central and Nigeria-Cameroon/Western) closely shadow each other between 100 kya and 1 Mya, the Western chimpanzee PSMC profile is notable for its initial separation from that of the other chimpanzees, followed by its sudden rise and decline (Supplementary Note, Figure 3). The different gorilla species also show variable demographic histories over the past ~200 ky. Eastern lowland gorillas have the smallest historical Ne, consistent with smaller present-day populations and a history of inbreeding (Figure 1c). A comparison of effective population sizes with the ratio of non-synonymous to synonymous substitutions finds that selection has acted more efficiently in populations wit higher Ne, consistent with neutral theory (Supplementary Note).


Great ape genetic diversity and population history.

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 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 - Nature (2013)

PSMC analysisInferred historical population sizes by PSMC. The lower x-axis gives time measured by pairwise sequence divergence and the y-axis gives the effective population size measured by the scaled mutation rate. The upper x-axis indicates scaling in years, assuming a mutation rate ranging from 10−9 to 5·10−10 per site per year. The top left panel shows the inference for modern human populations. In the rest of the three panels, thin light lines of the same color correspond to PSMC inferences on 100 rounds of bootstrapped sequences.
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Related In: Results  -  Collection

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Figure 3: PSMC analysisInferred historical population sizes by PSMC. The lower x-axis gives time measured by pairwise sequence divergence and the y-axis gives the effective population size measured by the scaled mutation rate. The upper x-axis indicates scaling in years, assuming a mutation rate ranging from 10−9 to 5·10−10 per site per year. The top left panel shows the inference for modern human populations. In the rest of the three panels, thin light lines of the same color correspond to PSMC inferences on 100 rounds of bootstrapped sequences.
Mentions: PSMC analyses of historical Ne (Figure 3) suggests that the ancestral Pan lineage had the largest effective population size of all lineages >3 million years ago (Mya), after which the ancestral bonobo-chimpanzee population experienced a dramatic decline. Both PSMC and ABC analyses support a model of subsequent increase in chimpanzee Ne starting ~1 Mya, prior to their divergence into separate subspecies. Following an Eastern chimpanzee increase in Ne (~500 thousand years ago, kya), the Central chimpanzees reached their zenith ~200–300 kya followed by the Western chimpanzee ~150 kya. Although the PSMC profiles of the two subspecies within each of the major chimpanzee clades (Eastern/Central and Nigeria-Cameroon/Western) closely shadow each other between 100 kya and 1 Mya, the Western chimpanzee PSMC profile is notable for its initial separation from that of the other chimpanzees, followed by its sudden rise and decline (Supplementary Note, Figure 3). The different gorilla species also show variable demographic histories over the past ~200 ky. Eastern lowland gorillas have the smallest historical Ne, consistent with smaller present-day populations and a history of inbreeding (Figure 1c). A comparison of effective population sizes with the ratio of non-synonymous to synonymous substitutions finds that selection has acted more efficiently in populations wit higher Ne, consistent with neutral theory (Supplementary Note).

Bottom Line: 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.

View Article: PubMed Central - PubMed

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

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.

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