Evidence from Cameroon reveals differences in the genetic structure and histories of chimpanzee populations

Abstract

The history of the genus Pan is a topic of enduring interest. Chimpanzees (Pan troglodytes) are often divided into subspecies, but the population structure and genetic history of chimpanzees across Africa remain unclear. Some population genetics studies have led to speculation that, until recently, this species constituted a single population with ongoing gene flow across its range, which resulted in a continuous gradient of allele frequencies. Chimpanzees, designated here as P. t. ellioti, occupy the Gulf of Guinea region that spans southern Nigeria and western Cameroon at the center of the distribution of this species. Remarkably, few studies have included individuals from this region, hindering the examination of chimpanzee population structure across Africa. Here, we analyzed microsatellite genotypes of 94 chimpanzees, including 32 designated as P. t. ellioti. We find that chimpanzees fall into three major populations: (i) Upper Guinea in western Africa (P. t. verus); (ii) the Gulf of Guinea region (P. t. ellioti); and (iii) equatorial Africa (P. t. troglodytes and P. t. schweinfurthii). Importantly, the Gulf of Guinea population is significantly different genetically from the others, sharing a last common ancestor with the populations in Upper Guinea ~0.46 million years ago (mya) and equatorial Africa ~0.32 mya. Equatorial chimpanzees are subdivided into up to three populations occupying southern Cameroon, central Africa, and eastern Africa, which may have constituted a single population until ~0.10-0.11 mya. Finally, occasional hybridization may be occurring between the Gulf of Guinea and southern Cameroon populations.

Fig. 1.

Distribution and current taxonomy of Pan.

Fig. 2.

Cluster analysis of Pan. (A) STRUCTURE plots for K = 4–6. Each vertical line represents an individual, and colors represent their inferred ancestry from K ancestral populations. (B) PCA created on the basis of individual genotypes for the Pan dataset. (C) PCA of the Gulf of Guinea/equatorial Africa chimpanzee dataset. Individuals indicated by open circles showed ≥25% ancestry in more than one ancestral cluster (K) by STRUCTURE analysis.

Fig. 3.

Neighbor-joining phylogram of chimpanzee populations constructed using D² (28) allele frequency differentiation values.

Fig. 4.

Proposed population structure of Pan, including chimpanzees from the Gulf of Guinea region. (A) Population distribution map. (B) T_MRCA between populations and phylogeny.