Reconstructing Prehistoric African Population Structure

• Type of Material: Article
• Authors: Pontus Skoglund, Harvard Medical School; Jessica Thompson, Emory University; Mary E. Prendergast, Radcliffe Institute for Advanced Study; Alissa Mittnik, Max Planck Institute for the Science of Human History; Kendra Sirak, Emory University; Mateja Hajdinjak, Max Planck Institute for Evolutionary Anthropology; Tasneem Salie, University of Cape Town; Nadin Rohland, Harvard Medical School; Swapan Mallick, Harvard Medical School; Alexander Peltzer, Max Planck Institute for the Science of Human History; Anja Heinze, Max Planck Institute for Evolutionary Anthropology; Inigo Olalde, Harvard Medical School; Matthew Ferry, Harvard Medical School; Eadaoin Harney, Harvard Medical School; Megan Michel, Harvard Medical School; Kristin Stewardson, Harvard Medical School; Jessica I. Cerezo-Román, California Polytechnic State University; Chrissy Chiumia, Malawi Department of Museums and Monuments; Alison Crowther, Max Planck Institute for the Science of Human History; Elizabeth Gomani-Chindebvu, Malawi Department of Museums and Monuments
• Language: English
• Date: 2017-09-21
• Publisher: IOS Press
• Publication Version: Author Accepted Manuscript (After Peer Review)
• Copyright Statement: © 2017 Elsevier Inc.
• License: Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1016/j.cell.2017.08.049
• Title of Journal or Parent Work: Analytical Cellular Pathology / Cellular Oncology
• ISSN: 1570-5870
• Volume: 171
• Issue: 1
• Start Page: 59
• End Page: 71.e21
• Grant/Funding Information: A.G.M and J.P. are supported by the National Research Foundation of South Africa.; M.G.T. was supported by Wellcome Trust Senior Investigator Award (grant number 100719/Z/12/Z).; K.Si. was supported by NSF grant BCS-1613577.; R.R was supported by the South African Medical Research Council.; M.H., A.H., M.M. and S.P. were supported by the Max Planck Society.; J.K. and A.M. were supported by the DFG grant KR 4015/1-1 and the Max Planck Society.; N.B. was supported by ERC starting grant SEALINKS (206148), and R.P was supported by ERC starting grant ADNABIOARC (263441).; P.S. was supported by the Wenner-Gren Foundation and the Swedish Research Council (VR grant 2014-453).; D.R. was supported by NIH grant GM100233, by NSF HOMINID BCS-1032255, and is a Howard Hughes Medical Institute investigator.
• Keywords: Africa; ancient DNA; Genome, Human; Male; Fossils; Bone and Bones; African Continental Ancestry Group; Life Style; Genome-Wide Association Study; population genetics; population history; adaptation; Genetics, Medical; hunter-gatherers; Female; DNA, Ancient; natural selection; Genetics, Population; Humans
• Research Categories: Biology, Cell; Anthropology, Medical and Forensic; Anthropology, Cultural

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