Fig. 6.

Four possible scenarios of genetic mixture involving Neandertals. Scenario 1 represents gene flow into Neandertal from other archaic hominins, here collectively referred to as Homo erectus. This would manifest itself as segments of the Neandertal genome with unexpectedly high divergence from present-day humans. Scenario 2 represents gene flow between late Neandertals and early modern humans in Europe and/or western Asia. We see no evidence of this because Neandertals are equally distantly related to all non-Africans. However, such gene flow may have taken place without leaving traces in the present-day gene pool. Scenario 3 represents gene flow between Neandertals and the ancestors of all non-Africans. This is the most parsimonious explanation of our observation. Although we detect gene flow only from Neandertals into modern humans, gene flow in the reverse direction may also have occurred. Scenario 4 represents old substructure in Africa that persisted from the origin of Neandertals until the ancestors of non-Africans left Africa. This scenario is also compatible with the current data.