Population dynamics and genetic connectivity in recent chimpanzee history

Knowledge on the population history of free-ranging endangered species is critical for conservation and population management, but whole-genome data on chimpanzees (Pan troglodytes) is geographically sparse. Here, we produced the first non-invasive geolocalized catalogue of genomic diversity by capturing chromosome 21 from 828 non-invasive samples collected at 48 sampling sites across Africa. The four recognized subspecies diverged during the Middle Pleistocene, with clear genetic differentiation correlating with known geographical barriers, while previously undescribed genetic exchange suggests that these have been permeable on a local scale. We obtain a detailed reconstruction of population stratification and fine-scale patterns of isolation, migration and connectivity until recently, including a comprehensive picture of their admixture with bonobos (Pan paniscus). We find that, unlike humans, chimpanzees did not experience extended episodes of long-distance migrations, which might have limited cultural transmission between populations. Finally, based on local rare variation, we implement a fine-grained geolocalization approach, with unprecedented precision in comparison to previous studies in this and other species. This could be used as a more accurate tool in conservation to determine the geographical origin of poached or confiscated chimpanzees.