Alternative demographic models for two African populations.

A) Simple model of population divergence. The San and Yoruba populations are assumed to have split from an ancestral African population and to have gone through a recent populations size increase. They also had a single pulse of asymmetrical gene flow (admixture) T_a generations ago. B) More complex scenario, where the San and Yoruba demes belong to two distinct continent-island structures, which have also admixed asymmetrically T_a generations ago. The ancestral Yoruba and San populations would have gone through exponential growth at different times, and have exchanged genes just after their divergence until T_EY generations ago. In both models, we assumed that the Denisova population diverged from the ancestral human population 16,000 generations ago, as estimated in [58] based on an ancestral population size of 10,000 diploids (see Table S11.2 in Suppl. Mat. of ref. [58]). This date would correspond to ≈400,000 years assuming a generation time of 25 y. The models and their parameters are further described in the Material and Methods section.