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. de 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; Mary E. Prendergast

doi:10.1038/s41586-022-04430-9

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. de 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, Mary E. Prendergast

Research output: Contribution to Journal › Article › Academic › peer-review

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.

Original language	English
Pages (from-to)	290-296
Journal	Nature
Volume	603
Issue number	7900
DOIs	https://doi.org/10.1038/s41586-022-04430-9
Publication status	Published - 10 Mar 2022
Externally published	Yes

Funding

We thank the authorities in Kenya, Tanzania, Malawi and Zambia for permission to study these ancient individuals (Supplementary Note ); 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. 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.

Funders	Funder number
Radcliffe Institute for Advanced Study, Harvard University
Hyde Family Foundation
Yale University Council on African Studies and Rice University School of Social Sciences
National Institutes of Health
Yale University
Howard Hughes Medical Institute
National Science Foundation	1460369
National Geographic Society	NGS-53412R-18
National Institute of General Medical Sciences	R01GM100233
Horizon 2020 Framework Programme	101032025
Social Sciences and Humanities Research Council of Canada	BPF 169449, 756-2017-0456
National Human Genome Research Institute	R01HG012287
John Templeton Foundation	61220

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Lipson, M., Sawchuk, E. A., Thompson, J. C., Oppenheimer, J., Tryon, C. A., Ranhorn, K. L., de Luna, K. M., Sirak, K. A., Olalde, I., Ambrose, S. H., Arthur, J. W., Arthur, K. J. W., Ayodo, G., Bertacchi, A., Cerezo-Román, J. I., Culleton, B. J., Curtis, M. C., Davis, J., Gidna, A. O., ... Prendergast, M. E. (2022). Ancient DNA and deep population structure in sub-Saharan African foragers. Nature, 603(7900), 290-296. https://doi.org/10.1038/s41586-022-04430-9

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title = "Ancient DNA and deep population structure in sub-Saharan African foragers",

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.",

author = "Mark Lipson and Sawchuk, \{Elizabeth A.\} and Thompson, \{Jessica C.\} and Jonas Oppenheimer and Tryon, \{Christian A.\} and Ranhorn, \{Kathryn L.\} and \{de Luna\}, \{Kathryn M.\} and Sirak, \{Kendra A.\} and I{\~n}igo Olalde and Ambrose, \{Stanley H.\} and Arthur, \{John W.\} and Arthur, \{Kathryn J. W.\} and George Ayodo and Alex Bertacchi and Cerezo-Rom{\'a}n, \{Jessica I.\} and Culleton, \{Brendan J.\} and Curtis, \{Matthew C.\} and Jacob Davis and Gidna, \{Agness O.\} and Annalys Hanson and Potiphar Kaliba and Maggie Katongo and Amandus Kwekason and Laird, \{Myra F.\} and Jason Lewis and Mabulla, \{Audax Z. P.\} and Fredrick Mapemba and Alan Morris and George Mudenda and Raphael Mwafulirwa and Daudi Mwangomba and Emmanuel Ndiema and Christine Ogola and Flora Schilt and Willoughby, \{Pamela R.\} and Wright, \{David K.\} and Andrew Zipkin and Ron Pinhasi and Kennett, \{Douglas J.\} and Manthi, \{Fredrick Kyalo\} and Nadin Rohland and Nick Patterson and David Reich and Prendergast, \{Mary E.\}",

year = "2022",

month = mar,

day = "10",

doi = "10.1038/s41586-022-04430-9",

language = "English",

volume = "603",

pages = "290--296",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "7900",

}

Lipson, M, Sawchuk, EA, Thompson, JC, Oppenheimer, J, Tryon, CA, Ranhorn, KL, de Luna, KM, Sirak, KA, Olalde, I, Ambrose, SH, Arthur, JW, Arthur, KJW, Ayodo, G, Bertacchi, A, Cerezo-Román, JI, Culleton, BJ, Curtis, MC, Davis, J, Gidna, AO, Hanson, A, Kaliba, P, Katongo, M, Kwekason, A, Laird, MF, Lewis, J, Mabulla, AZP, Mapemba, F, Morris, A, Mudenda, G, Mwafulirwa, R, Mwangomba, D, Ndiema, E, Ogola, C, Schilt, F, Willoughby, PR, Wright, DK, Zipkin, A, Pinhasi, R, Kennett, DJ, Manthi, FK, Rohland, N, Patterson, N, Reich, D & Prendergast, ME 2022, 'Ancient DNA and deep population structure in sub-Saharan African foragers', Nature, vol. 603, no. 7900, pp. 290-296. https://doi.org/10.1038/s41586-022-04430-9

TY - JOUR

T1 - Ancient DNA and deep population structure in sub-Saharan African foragers

AU - Lipson, Mark

AU - Sawchuk, Elizabeth A.

AU - Thompson, Jessica C.

AU - Oppenheimer, Jonas

AU - Tryon, Christian A.

AU - Ranhorn, Kathryn L.

AU - de Luna, Kathryn M.

AU - Sirak, Kendra A.

AU - Olalde, Iñigo

AU - Ambrose, Stanley H.

AU - Arthur, John W.

AU - Arthur, Kathryn J. W.

AU - Ayodo, George

AU - Bertacchi, Alex

AU - Cerezo-Román, Jessica I.

AU - Culleton, Brendan J.

AU - Curtis, Matthew C.

AU - Davis, Jacob

AU - Gidna, Agness O.

AU - Hanson, Annalys

AU - Kaliba, Potiphar

AU - Katongo, Maggie

AU - Kwekason, Amandus

AU - Laird, Myra F.

AU - Lewis, Jason

AU - Mabulla, Audax Z. P.

AU - Mapemba, Fredrick

AU - Morris, Alan

AU - Mudenda, George

AU - Mwafulirwa, Raphael

AU - Mwangomba, Daudi

AU - Ndiema, Emmanuel

AU - Ogola, Christine

AU - Schilt, Flora

AU - Willoughby, Pamela R.

AU - Wright, David K.

AU - Zipkin, Andrew

AU - Pinhasi, Ron

AU - Kennett, Douglas J.

AU - Manthi, Fredrick Kyalo

AU - Rohland, Nadin

AU - Patterson, Nick

AU - Reich, David

AU - Prendergast, Mary E.

PY - 2022/3/10

Y1 - 2022/3/10

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/85125051210

U2 - 10.1038/s41586-022-04430-9

DO - 10.1038/s41586-022-04430-9

M3 - Article

SN - 0028-0836

VL - 603

SP - 290

EP - 296

JO - Nature

JF - Nature

IS - 7900

ER -

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

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