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

[EN] Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa(1-4). Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations(3,5). Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 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, probably reflecting Pleistocene interactions around 80-20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. 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 analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch. DNA analysis of 6 individuals from eastern and south-central Africa spanning the past approximately 18,000 years, and of 28 previously published ancient individuals, provides genetic evidence supporting hypotheses of increasing regionalization at the end of the Pleistocene.We thank the authorities in Kenya, Tanzania, Malawi and Zambia for permission to study these ancient individuals (Supplementary Note 3); J. Stock, A. Manica and D. Bradley for previous work on the individual from Mota Cave, Ethiopia; J. Sealy for helping with the proposal to redate the Hora 1 individual; and L. Eccles for help with radiocarbon dating. Radiocarbon work was supported by the NSF Archaeometry programme (grant no. BCS-1460369) to D.J.K. and B.J.C. Excavations leading to recovery of Kahora 1 and 2 were supported by the National Geographic Society (NGS-53412R-18 to J.C.T.), Yale University and the Hyde Family Foundations. E.A.S. acknowledges support from the Social Sciences and Humanities Research Council of Canada (fellowships 756-2017-0456, BPF 169449). M.E.P. was supported the Radcliffe Institute for Advanced Study during project development. D.R. is an Investigator of the Howard Hughes Medical Institute and was also funded by NIH grants R01-GM100233 and R01-HG012287; by John Templeton Foundation grant 61220; by a private donation from J.-F. Clin; and by the Allen Discovery Center programme, a Paul G. Allen Frontiers Group advised programme of the Paul G. Allen Family Foundation. Open access publication was made possible by The John Templeton Foundation, Yale University Council on African Studies and Rice University School of Social Sciences