Genetic Structure of Chimpanzee Populations

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Abstract
Little is known about the history and population structure of our closest living relatives, the chimpanzees, in part because of an extremely poor fossil record. To address this, we report the largest genetic study of the chimpanzees to date, examining 310 microsatellites in 84 common chimpanzees and bonobos. We infer three common chimpanzee populations, which correspond to the previously defined labels of “western,” “central,” and “eastern,” and find little evidence of gene flow between them. There is tentative evidence for structure within western chimpanzees, but we do not detect distinct additional populations. The data also provide historical insights, demonstrating that the western chimpanzee population diverged first, and that the eastern and central populations are more closely related in time. Common chimpanzees have been traditionally classified into three populations: western, central, and eastern. While the morphological or behavioral differences are very small, genetic studies of mitochondrial DNA and the Y chromosome have supported the geography-based designations. To obtain a crisp picture of chimpanzee population structure, we gather far more data than previously available: 310 microsatellite markers genotyped in 78 common chimpanzees and six bonobos, allowing a high resolution genetic analysis of chimpanzee population structure analogous to recent studies that have elucidated human structure. We show that the traditional chimpanzee population designations—western, central, and eastern—accurately label groups of individuals that can be defined from the genetic data without any prior knowledge about where the samples were collected. The populations appear to be discontinuous, and we find little evidence for gradients of variation reflecting hybridization among chimpanzee populations. Regarding chimpanzee history, we demonstrate that central and eastern chimpanzees are more closely related to each other in time than either is to western chimpanzees.