Genetic structure of chimpanzee populations

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.

Figure 1. STRUCTURE Analysis, Blinded to Population Labels, Recapitulates the Reported Population Structure of the Chimpanzees

Individuals 76–78 are reported hybrids. Only two individuals with a >5% proportion of ancestry in more than one inferred cluster are wild born: number 54 and number 17. Red, central; blue, eastern; green, western; yellow, bonobo.

Figure 2. PCA, Without Using Population Labels, Divides the 84 Chimpanzees into Four Apparently Discontinuous Populations of Western, Central, Eastern, and Bonobo

Plots of eigenvectors 1 versus 2, and eigenvectors 2 versus 3, show clustering into populations, with the expected assignments for the 75 individuals identified as all of one ancestry by STRUCTURE (solid circles). The nine individuals identified by STRUCTURE as hybrids (open circles) are for the most part identified as hybrids by PCA as well. There are two individuals (red open circles) reported as being of a particular population but that in fact appear to be hybrids: number 23, reported as eastern but in fact a western-eastern hybrid, and number 54, a wild-born individual reported as western but in fact a western-central hybrid.