Simplified phylogenetic tree of central (P. t. troglodytes) and western chimpanzees (P. t. verus), bonobos (P. paniscus) and an unknown ‘ghost’ population. Grey arrows represent previously described gene flow events between chimpanzees and bonobos21. The violet arrow represents archaic gene flow into bonobos. The 95% credible intervals for introgression and archaic divergence times as well as introgression amounts are shown, as inferred using S* with ABC modelling (Methods). The divergence times of extant Pan populations were inferred using SFS-based modelling (Methods).