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-Chindebvu; Agness 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

doi:10.1016/j.cell.2017.08.049

Reconstructing Prehistoric African Population Structure

Cell. 2017 Sep 21;171(1):59-71.e21. doi: 10.1016/j.cell.2017.08.049.

Authors

Pontus Skoglund¹, Jessica C Thompson², Mary E Prendergast³, Alissa Mittnik⁴, Kendra Sirak⁵, Mateja Hajdinjak⁶, Tasneem Salie⁷, Nadin Rohland⁸, Swapan Mallick⁹, Alexander Peltzer¹⁰, Anja Heinze⁶, Iñigo Olalde⁸, Matthew Ferry¹¹, Eadaoin Harney¹², Megan Michel¹¹, Kristin Stewardson¹¹, Jessica I Cerezo-Román¹³, Chrissy Chiumia¹⁴, Alison Crowther¹⁵, Elizabeth Gomani-Chindebvu¹⁴, Agness O Gidna¹⁶, Katherine M Grillo¹⁷, I Taneli Helenius¹⁸, Garrett Hellenthal¹⁸, Richard Helm¹⁹, Mark Horton²⁰, Saioa López¹⁸, Audax Z P Mabulla¹⁶, John Parkington²¹, Ceri Shipton²², Mark G Thomas¹⁸, Ruth Tibesasa²³, Menno Welling²⁴, Vanessa M Hayes²⁵, Douglas J Kennett²⁶, Raj Ramesar⁷, Matthias Meyer⁶, Svante Pääbo⁶, Nick Patterson²⁷, Alan G Morris²¹, Nicole Boivin²⁸, Ron Pinhasi²⁹, Johannes Krause⁴, David Reich³⁰

Affiliations

¹ Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address: skoglund@genetics.med.harvard.edu.
² Department of Anthropology, Emory University, Atlanta, GA 30322, USA.
³ Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA 02138, USA.
⁴ Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archeological Sciences, Eberhard-Karls-University, Tuebingen 72070, Germany.
⁵ Department of Anthropology, Emory University, Atlanta, GA 30322, USA; School of Archaeology and Earth Institute, University College Dublin, Dublin 4, Ireland.
⁶ Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.
⁷ Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa.
⁸ Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
⁹ Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
¹⁰ Max Planck Institute for the Science of Human History, Jena 07745, Germany; Integrative Transcriptomics, Centre for Bioinformatics, University of Tuebingen, Tuebingen 72076, Germany.
¹¹ Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
¹² Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
¹³ Department of Geography and Anthropology, California State Polytechnic University, Pomona, Pomona, CA 91768, USA.
¹⁴ Malawi Department of Museums and Monuments, Lilongwe 3, Malawi.
¹⁵ Max Planck Institute for the Science of Human History, Jena 07745, Germany; School of Social Science, The University of Queensland, Brisbane, Queensland 4072, Australia.
¹⁶ National Museums of Tanzania, Dar es Salaam, Tanzania.
¹⁷ Department of Archaeology and Anthropology, University of Wisconsin - La Crosse, La Crosse, WI 54601, USA.
¹⁸ Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.
¹⁹ Canterbury Archaeological Trust, Canterbury CT1 2LU, UK.
²⁰ Department Archaeology and Anthropology, University of Bristol, Bristol BS8 1UU, UK.
²¹ Department of Archaeology, University of Cape Town, Cape Town 7700, South Africa.
²² McDonald Institute for Archaeological Research, Cambridge CB2 3ER, UK; British Institute in Eastern Africa, Nairobi 30710, Kenya.
²³ Department of Anthropology and Archaeology, University of Pretoria, Pretoria 0083, South Africa.
²⁴ African Studies Centre Leiden, Leiden University, Leiden 2300 RB, Netherlands; African Heritage Ltd, Zomba, Malawi.
²⁵ Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; Central Clinical School, University of Sydney, Camperdown, NSW 2050, Australia; School of Health Systems and Public Health, University of Pretoria, Gezina 0031, South Africa.
²⁶ Department of Anthropology and Institutes for Energy and the Environment, Pennsylvania State University, University Park, PA 16802, USA.
²⁷ Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
²⁸ Max Planck Institute for the Science of Human History, Jena 07745, Germany.
²⁹ School of Archaeology and Earth Institute, University College Dublin, Dublin 4, Ireland; Department of Anthropology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
³⁰ Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. Electronic address: reich@genetics.med.harvard.edu.

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.

Keywords: Africa; adaptation; ancient DNA; hunter-gatherers; natural selection; population genetics; population history.

MeSH terms

Africa
Black People / genetics*
Bone and Bones / chemistry
DNA, Ancient / analysis
Female
Fossils
Genetics, Medical
Genetics, Population
Genome, Human*
Genome-Wide Association Study
Humans
Life Style
Male

Substances

DNA, Ancient

Abstract

MeSH terms

Substances

Grants and funding