Ancient DNA and deep population structure in sub-Saharan African foragers

Multiple lines of genetic and archaeological evidence suggest major demographic changes in the terminal Late Pleistocene and early Holocene of sub-Saharan Africa. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured more ancient population structures. To probe deeper time, we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the last ~18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase data quality on 15 previously published ancient individuals, and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, likely reflecting Pleistocene interactions ~80-20 thousand years ago: deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of central African ancestry. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analysis but remain contested, suggesting increasing regionalisation at the end of the Pleistocene.