Evidence for multiple past introgressions among chimpanzee subspecies during warming periods

The evolutionary history of common chimpanzee (Pan troglodytes) subspecies is complex, marked by several past introgression events whose dating and location are unknown and are at odds with the current strong geographic segregation of the subspecies. We reconstruct the historical biogeography of common chimpanzee subspecies. Our findings reveal that cranial morphology reflects genetic differentiation, with the western chimpanzee being the most derived lineage. This is consistent with its current geographic isolation, which we find was punctuated by periods of potential contact with the other subspecies. These moments coincide with warming periods creating increased tree cover across the geographic barrier, the Dahomey Gap, currently separating western chimpanzee from the other subspecies. This integrative framework of a climate-mediated dynamical biogeography provides unprecedented insights into the dynamics of chimpanzee evolution, demonstrating how past climatic fluctuations and vegetation changes profoundly shaped the present-day distribution of Pan troglodytes subspecies along with their genetic differences.