Understanding the demographic history of a species can elucidate patterns of behavioural and genetic diversity as well as provide context to guide conservation efforts for endangered species.
Although many species display a general pattern of isolation by distance (IBD), geographic barriers can lead to differentiation that it is greater than expected from geographical distance. Chimpanzees (Pan troglodytes) have a trans-continental distribution with four recognized subspecies demarcated by geographic barriers. However, this taxonomy is controversial: while several studies have found evidence to support these subspecies designations, others suggest they are artefacts of biased sampling. The Pan African Programme: The Cultured Chimpanzee (PanAf) comprises genetic, ecological, demographic and behavioural data collected throughout the entire geographic range of chimpanzees. Here we present the most comprehensive study to date on chimpanzee population demography based on microsatellite analyses of over 5000 geo-referenced, non-invasively collected faecal samples spanning 57 locations across the ranges of all four subspecies. We aimed to test for the presence of genetic structure, estimate effective migration rates and map the distribution of genetic diversity across the species. The broad pattern of genetic variation in our dataset is characterised by IBD with some local substructure, possibly due to recent isolation of several populations. Western populations have considerably lower diversity and higher effective migration rates relative to the rest of the species. We identified signals of longitudinal gene flow in the eastern populations as expected, but contrary to expectations, evidence of latitudinal gene flow was also present. Together, these results highlight the high degree of geographic mobility in this endangered species, indicating that conservation approaches should intensify efforts to improve and protect connectivity among populations to ensure their survival.