Southern African ancient genomes estimate modern human divergence to 350,000-260,000 years ago

Southern Africa is consistently placed as a potential region for the evolution of Homo sapiens. We present genome sequences, up to 13x coverage, from seven ancient individuals from KwaZulu-Natal, South Africa. Three Stone Age hunter-gatherers (~2,000 years old), were genetically similar to current-day southern San groups, while four Iron Age farmers (300-500 years old) were genetically similar to present-day Bantu-speakers. We estimate that all modern-day Khoe-San groups have been influenced by 9-30% genetic admixture from East Africans/Eurasians. Using traditional and new approaches, we estimate the first modern human population divergence time to between 350,000 and 260,000 years ago. This estimate increases the deepest divergence amongst modern humans, coinciding with anatomical developments of archaic humans into modern humans as represented in the local fossil record. There are two bam files per individual, one ('dr') contains the damage repaired libraries which was used for all major analyses.