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Reconstructing Prehistoric African Population Structure

Abstract

We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers approximately 8,100-2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers approximately 1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a approximately 3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a approximately 1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations. PAPERCLIP.

Type Journal
ISBN 1097-4172 (Electronic) 0092-8674 (Linking)
Authors Skoglund, P.; Thompson, J. C.; Prendergast, M. E.; Mittnik, A.; Sirak, K.; Hajdinjak, M.; Salie, T.; Rohland, N.; Mallick, S.; Peltzer, A.; Heinze, A.; Olalde, I.; Ferry, M.; Harney, E.; Michel, M.; Stewardson, K.; Cerezo-Roman, J. I.; Chiumia, C.; Crowther, A.; Gomani-Chindebvu, E.; Gidna, A. O.; Grillo, K. M.; Helenius, I. T.; Hellenthal, G.; Helm, R.; Horton, M.; Lopez, S.; Mabulla, A. Z. P.; Parkington, J.; Shipton, C.; Thomas, M. G.; Tibesasa, R.; Welling, M.; Hayes, V. M.; Kennett, D. J.; Ramesar, R.; Meyer, M.; Paabo, S.; Patterson, N.; Morris, A. G.; Boivin, N.; Pinhasi, R.; Krause, J.; Reich, D.
Responsible Garvan Author Prof Vanessa Hayes
Publisher Name CELL
Published Date 2017-09-30
Published Volume 171
Published Issue 1
Published Pages 59-71 e21
Status Published in-print
DOI 10.1016/j.cell.2017.08.049
URL link to publisher's version https://www.ncbi.nlm.nih.gov/pubmed/28938123