Reconstructing Prehistoric African Population Structure

Pontus Skoglund, Jessica C. Thompson, Mary E. Prendergast, Alissa Mittnik, Kendra Sirak, Mateja Hajdinjak, Tasneem Salie, Nadin Rohland, Swapan Mallick, Alexander Peltzer, Anja Heinze, Iñigo Olalde, Matthew Ferry, Eadaoin Harney, Megan Michel, Kristin Stewardson, Jessica I. Cerezo-Román, Chrissy Chiumia, Alison Crowther, Elizabeth Gomani-ChindebvuAgness O. Gidna, Katherine M. Grillo, I. Taneli Helenius, Garrett Hellenthal, Richard Helm, Mark Horton, Saioa López, Audax Z.P. Mabulla, John Parkington, Ceri Shipton, Mark G. Thomas, Ruth Tibesasa, Menno Welling, Vanessa M. Hayes, Douglas J. Kennett, Raj Ramesar, Matthias Meyer, Svante Pääbo, Nick Patterson, Alan G. Morris, Nicole Boivin, Ron Pinhasi, Johannes Krause, David Reich

Research output: Contribution to journalArticle

97 Scopus citations

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 ∼8,100–2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼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 ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼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

Original languageEnglish (US)
Pages (from-to)59-71.e21
JournalCell
Volume171
Issue number1
DOIs
StatePublished - Sep 21 2017

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)

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    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-Román, J. I., Chiumia, C., Crowther, A., ... Reich, D. (2017). Reconstructing Prehistoric African Population Structure. Cell, 171(1), 59-71.e21. https://doi.org/10.1016/j.cell.2017.08.049