Ancient genomes from southern Africa pushes modern human divergence beyond 260,000 years ago

Southern Africa is consistently placed as one of the potential regions for the evolution of Homo sapiens. To examine the region9s human prehistoryprior to the arrival of migrants from East and West Africa or Eurasia in the last 1,700 years, we generated and analyzed genome sequence data from seven ancient individuals from KwaZulu-Natal, South Africa. Three Stone Age hunter-gatherersdate to ~2,000 years ago, and we show that they were related to current-day southern San groups such as the Karretjie People. Four Iron Agefarmers (300-500 years old) have genetic signatures similar to present day Bantu-speakers. The genome sequence (13x coverage) of a juvenile boy from Ballito Bay, who lived ~2,000 years ago, demonstrates that southern African Stone Age hunter-gathererswere not impacted by recent admixture; however, we estimate that all modern-day Khoekhoe and San groups have been influenced by 9-22% genetic admixturefrom East African/Eurasian pastoralist groups arriving >1,000 years ago, including the Ju|9hoansi San, previously thought to have very low levels of admixture. Using traditional and new approaches, we estimate the population divergence time between the Ballito Bay boy and other groups to beyond 260,000 years ago. These estimates dramatically increases the deepest divergence amongst modern humans, coincide with the onset of the Middle Stone Agein sub-Saharan Africa, and coincide with anatomical developments of archaic humansinto modern humans as represented in the local fossil record. Cumulatively, cross-disciplinary records increasingly point to southern Africa as a potential (not necessarily exclusive) 9hot spot9 for the evolution of our species.