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

Mark Lipson (), Elizabeth A. Sawchuk (), Jessica C. Thompson (), Jonas Oppenheimer, Christian A. Tryon, Kathryn L. Ranhorn, Kathryn M. Luna, Kendra A. Sirak, Iñigo Olalde, Stanley H. Ambrose, John W. Arthur, Kathryn J. W. Arthur, George Ayodo, Alex Bertacchi, Jessica I. Cerezo-Román, Brendan J. Culleton, Matthew C. Curtis, Jacob Davis, Agness O. Gidna, Annalys Hanson, Potiphar Kaliba, Maggie Katongo, Amandus Kwekason, Myra F. Laird, Jason Lewis, Audax Z. P. Mabulla, Fredrick Mapemba, Alan Morris, George Mudenda, Raphael Mwafulirwa, Daudi Mwangomba, Emmanuel Ndiema, Christine Ogola, Flora Schilt, Pamela R. Willoughby, David K. Wright, Andrew Zipkin, Ron Pinhasi, Douglas J. Kennett, Fredrick Kyalo Manthi, Nadin Rohland, Nick Patterson, David Reich () and Mary E. Prendergast ()
Additional contact information
Mark Lipson: Harvard Medical School
Elizabeth A. Sawchuk: University of Alberta
Jessica C. Thompson: Yale University
Jonas Oppenheimer: University of California, Santa Cruz
Christian A. Tryon: University of Connecticut
Kathryn L. Ranhorn: Arizona State University
Kathryn M. Luna: Georgetown University
Kendra A. Sirak: Harvard Medical School
Iñigo Olalde: Harvard Medical School
Stanley H. Ambrose: University of Illinois Urbana-Champaign
John W. Arthur: University of South Florida,
Kathryn J. W. Arthur: University of South Florida,
George Ayodo: Jaramogi Oginga Odinga University of Science and Technology
Alex Bertacchi: Yale University
Jessica I. Cerezo-Román: University of Oklahoma
Brendan J. Culleton: Pennsylvania State University
Matthew C. Curtis: California State University—Channel Islands
Jacob Davis: Independent researcher
Agness O. Gidna: National Museums of Tanzania
Annalys Hanson: Sol Solutions LLC
Potiphar Kaliba: Malawi Department of Museums and Monuments
Maggie Katongo: Rice University
Amandus Kwekason: National Museums of Tanzania
Myra F. Laird: University of Southern California
Jason Lewis: Stony Brook University
Audax Z. P. Mabulla: University of Dar es Salaam
Fredrick Mapemba: Malawi Department of Museums and Monuments
Alan Morris: University of Cape Town
George Mudenda: Livingstone Museum
Raphael Mwafulirwa: Mzuzu University
Daudi Mwangomba: University of Malawi
Emmanuel Ndiema: National Museums of Kenya
Christine Ogola: National Museums of Kenya
Flora Schilt: Universidade do Algarve
Pamela R. Willoughby: University of Alberta
David K. Wright: University of Oslo
Andrew Zipkin: Arizona State University
Ron Pinhasi: University of Vienna
Douglas J. Kennett: University of California
Fredrick Kyalo Manthi: National Museums of Kenya
Nadin Rohland: Harvard Medical School
Nick Patterson: Harvard University
David Reich: Harvard Medical School
Mary E. Prendergast: Harvard Medical School

Nature, 2022, vol. 603, issue 7900, 290-296

Abstract: Abstract 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 Africa1–4. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations3,5. 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.

Date: 2022
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DOI: 10.1038/s41586-022-04430-9

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