Genetic Structure of Chimpanzee Populations

Becquet, Céline; Patterson, Nick; Stone, Anne C.; Przeworski, Molly; Reich, David

doi:10.1371/journal.pgen.0030066

Cited by 136 publications

(120 citation statements)

References 32 publications

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“…Given the proximity of Central and Eastern chimpanzees and their low F ST , one possibility is that, rather than a split model, a model of isolation by distance is more appropriate . Interestingly, though, there does not appear to be substantial gene flow between the Eastern and Central ranges (see the estimates of the migration rate in this study and Becquet et al 2007). We also find that, while the model fits most aspects of the bonobo data quite well, the observed Tajima's D is lower than expected (Supplemental Fig.…”

Section: Goodness-of-fit Testmentioning

confidence: 54%

“…Analyses of genetic polymorphism data from apes can help to characterize the geographic distribution of variation (e.g., Becquet et al 2007), shed light on their demographic history, and place the evolutionary history of humans in context (Stone and Verrelli 2006). Here, we considered the largest set of polymorphism data to date for all three species of nonhuman great apes, and estimated parameters of a simple isolation-migration model.…”

Section: Analyses Of Ape Polymorphism Datamentioning

confidence: 99%

“…The meaning of the term "subspecies" is unclear, at least to us, but the labels are thought to correspond to the most pronounced population structure within the species. This view is supported by a recent analysis of 310 microsatellites, which found three populations within common chimpanzees, which correspond to the three subspecies, and little evidence of recent gene flow between them (Becquet et al 2007).…”

mentioning

confidence: 96%

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A new approach to estimate parameters of speciation models with application to apes

Becquet¹,

Przeworski²

2007

Genome Res.

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237

307

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How populations diverge and give rise to distinct species remains a fundamental question in evolutionary biology, with important implications for a wide range of fields, from conservation genetics to human evolution. A promising approach is to estimate parameters of simple speciation models using polymorphism data from multiple loci. Existing methods, however, make a number of assumptions that severely limit their applicability, notably, no gene flow after the populations split and no intralocus recombination. To overcome these limitations, we developed a new Markov chain Monte Carlo method to estimate parameters of an isolation-migration model. The approach uses summaries of polymorphism data at multiple loci surveyed in a pair of diverging populations or closely related species and, importantly, allows for intralocus recombination. To illustrate its potential, we applied it to extensive polymorphism data from populations and species of apes, whose demographic histories are largely unknown. The isolation-migration model appears to provide a reasonable fit to the data. It suggests that the two chimpanzee species became reproductively isolated in allopatry ∼850 Kya, while Western and Central chimpanzee populations split ∼440 Kya but continued to exchange migrants. Similarly, Eastern and Western gorillas and Sumatran and Bornean orangutans appear to have experienced gene flow since their splits ∼90 and over 250 Kya, respectively.

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Section: Goodness-of-fit Testmentioning

confidence: 54%

Section: Analyses Of Ape Polymorphism Datamentioning

confidence: 99%

mentioning

confidence: 96%

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A new approach to estimate parameters of speciation models with application to apes

Becquet¹,

Przeworski²

2007

Genome Res.

Self Cite

237

307

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“…Distinct clusters are evident within the species of chimpanzees and bonobos, which largely correspond to subspecies or regional populations (Becquet et al. 2007; Kawamoto et al. 2013).…”

Section: Resultsmentioning

confidence: 99%

Bridging two scholarly islands enriches both: COI DNA barcodes for species identification versus human mitochondrial variation for the study of migrations and pathologies

Thaler

Stoeckle

2016

Ecology and Evolution

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DNA barcodes for species identification and the analysis of human mitochondrial variation have developed as independent fields even though both are based on sequences from animal mitochondria. This study finds questions within each field that can be addressed by reference to the other. DNA barcodes are based on a 648‐bp segment of the mitochondrially encoded cytochrome oxidase I. From most species, this segment is the only sequence available. It is impossible to know whether it fairly represents overall mitochondrial variation. For modern humans, the entire mitochondrial genome is available from thousands of healthy individuals. SNPs in the human mitochondrial genome are evenly distributed across all protein‐encoding regions arguing that COI DNA barcode is representative. Barcode variation among related species is largely based on synonymous codons. Data on human mitochondrial variation support the interpretation that most – possibly all – synonymous substitutions in mitochondria are selectively neutral. DNA barcodes confirm reports of a low variance in modern humans compared to nonhuman primates. In addition, DNA barcodes allow the comparison of modern human variance to many other extant animal species. Birds are a well‐curated group in which DNA barcodes are coupled with census and geographic data. Putting modern human variation in the context of intraspecies variation among birds shows humans to be a single breeding population of average variance.

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“…Although direct comparisons are difficult, the available evidence suggests that the fitness consequences of between-group competition are as high in chimpanzees as they are in humans; for example, the fraction of adult mortality owing to between-group violence in chimpanzees may match [26] or even exceed [27] that of humans living in traditional societies. However, whether levels of genetic differentiation between competing groups are higher in humans than chimpanzees is unknown, as almost all studies on genetic differentiation in chimpanzees have been conducted at broad geographical scales [28,29] or have used uniparentally inherited markers [30,31], and thus suffer from the same limitations as the data used in Bowles' [15,16] models.…”

Section: Introductionmentioning

confidence: 99%

Genetic differentiation and the evolution of cooperation in chimpanzees and humans

et al. 2011

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It has been proposed that human cooperation is unique among animals for its scale and complexity, its altruistic nature and its occurrence among large groups of individuals that are not closely related or are even strangers. One potential solution to this puzzle is that the unique aspects of human cooperation evolved as a result of high levels of lethal competition (i.e. warfare) between genetically differentiated groups. Although between-group migration would seem to make this scenario unlikely, the plausibility of the between-group competition model has recently been supported by analyses using estimates of genetic differentiation derived from contemporary human groups hypothesized to be representative of those that existed during the time period when human cooperation evolved. Here, we examine levels of between-group genetic differentiation in a large sample of contemporary human groups selected to overcome some of the problems with earlier estimates, and compare them with those of chimpanzees. We find that our estimates of between-group genetic differentiation in contemporary humans are lower than those used in previous tests, and not higher than those of chimpanzees. Because levels of between-group competition in contemporary humans and chimpanzees are also similar, these findings suggest that the identification of other factors that differ between chimpanzees and humans may be needed to provide a compelling explanation of why humans, but not chimpanzees, display the unique features of human cooperation.

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Genetic Structure of Chimpanzee Populations

Cited by 136 publications

References 32 publications

A new approach to estimate parameters of speciation models with application to apes

A new approach to estimate parameters of speciation models with application to apes

Bridging two scholarly islands enriches both: COI DNA barcodes for species identification versus human mitochondrial variation for the study of migrations and pathologies

Genetic differentiation and the evolution of cooperation in chimpanzees and humans

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