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Genome-wide patterns of selection in 230 ancient Eurasians

Author

Listed:
  • Iain Mathieson

    (Harvard Medical School)

  • Iosif Lazaridis

    (Harvard Medical School
    Broad Institute of MIT and Harvard)

  • Nadin Rohland

    (Harvard Medical School
    Broad Institute of MIT and Harvard)

  • Swapan Mallick

    (Harvard Medical School
    Broad Institute of MIT and Harvard
    Howard Hughes Medical Institute, Harvard Medical School)

  • Nick Patterson

    (Broad Institute of MIT and Harvard)

  • Songül Alpaslan Roodenberg

    (Independent researcher)

  • Eadaoin Harney

    (Harvard Medical School
    Howard Hughes Medical Institute, Harvard Medical School)

  • Kristin Stewardson

    (Harvard Medical School
    Howard Hughes Medical Institute, Harvard Medical School)

  • Daniel Fernandes

    (School of Archaeology and Earth Institute, Belfield, University College Dublin)

  • Mario Novak

    (School of Archaeology and Earth Institute, Belfield, University College Dublin
    Institute for Anthropological Research)

  • Kendra Sirak

    (School of Archaeology and Earth Institute, Belfield, University College Dublin
    Emory University)

  • Cristina Gamba

    (School of Archaeology and Earth Institute, Belfield, University College Dublin
    Smurfit Institute of Genetics, Trinity College Dublin
    † Present addresses: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5–7, 1350 Copenhagen, Denmark (C.G.); New York Genome Center, New York, New York 10013, USA (J.P.).)

  • Eppie R. Jones

    (Smurfit Institute of Genetics, Trinity College Dublin)

  • Bastien Llamas

    (Australian Centre for Ancient DNA, School of Biological Sciences & Environment Institute, University of Adelaide)

  • Stanislav Dryomov

    (Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences
    Institute of Archaeology and Ethnography, Siberian Branch of the Russian Academy of Sciences)

  • Joseph Pickrell

    (Harvard Medical School
    † Present addresses: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5–7, 1350 Copenhagen, Denmark (C.G.); New York Genome Center, New York, New York 10013, USA (J.P.).)

  • Juan Luís Arsuaga

    (Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos
    Facultad Ciencias Geológicas, Universidad Complutense de Madrid)

  • José María Bermúdez de Castro

    (Centro Nacional de Investigacíon sobre Evolución Humana (CENIEH))

  • Eudald Carbonell

    (IPHES. Institut Català de Paleoecologia Humana i Evolució Social, Campus Sescelades-URV
    Area de Prehistoria, Universitat Rovira i Virgili (URV))

  • Fokke Gerritsen

    (Netherlands Institute in Turkey, Istiklal Caddesi, Nur-i Ziya Sokak 5)

  • Aleksandr Khokhlov

    (Volga State Academy of Social Sciences and Humanities)

  • Pavel Kuznetsov

    (Volga State Academy of Social Sciences and Humanities)

  • Marina Lozano

    (IPHES. Institut Català de Paleoecologia Humana i Evolució Social, Campus Sescelades-URV
    Area de Prehistoria, Universitat Rovira i Virgili (URV))

  • Harald Meller

    (State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory)

  • Oleg Mochalov

    (Volga State Academy of Social Sciences and Humanities)

  • Vyacheslav Moiseyev

    (Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS)

  • Manuel A. Rojo Guerra

    (University of Valladolid)

  • Jacob Roodenberg

    (The Netherlands Institute for the Near East)

  • Josep Maria Vergès

    (IPHES. Institut Català de Paleoecologia Humana i Evolució Social, Campus Sescelades-URV
    Area de Prehistoria, Universitat Rovira i Virgili (URV))

  • Johannes Krause

    (Max Planck Institute for the Science of Human History
    Institute for Archaeological Sciences, University of Tübingen)

  • Alan Cooper

    (Australian Centre for Ancient DNA, School of Biological Sciences & Environment Institute, University of Adelaide)

  • Kurt W. Alt

    (State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory
    Danube Private University
    Institute for Prehistory and Archaeological Science, University of Basel)

  • Dorcas Brown

    (Hartwick College)

  • David Anthony

    (Hartwick College)

  • Carles Lalueza-Fox

    (Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra))

  • Wolfgang Haak

    (Australian Centre for Ancient DNA, School of Biological Sciences & Environment Institute, University of Adelaide
    Max Planck Institute for the Science of Human History)

  • Ron Pinhasi

    (School of Archaeology and Earth Institute, Belfield, University College Dublin)

  • David Reich

    (Harvard Medical School
    Broad Institute of MIT and Harvard
    Howard Hughes Medical Institute, Harvard Medical School)

Abstract

Ancient DNA makes it possible to observe natural selection directly by analysing samples from populations before, during and after adaptation events. Here we report a genome-wide scan for selection using ancient DNA, capitalizing on the largest ancient DNA data set yet assembled: 230 West Eurasians who lived between 6500 and 300 bc, including 163 with newly reported data. The new samples include, to our knowledge, the first genome-wide ancient DNA from Anatolian Neolithic farmers, whose genetic material we obtained by extracting from petrous bones, and who we show were members of the population that was the source of Europe’s first farmers. We also report a transect of the steppe region in Samara between 5600 and 300 bc, which allows us to identify admixture into the steppe from at least two external sources. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.

Suggested Citation

  • Iain Mathieson & Iosif Lazaridis & Nadin Rohland & Swapan Mallick & Nick Patterson & Songül Alpaslan Roodenberg & Eadaoin Harney & Kristin Stewardson & Daniel Fernandes & Mario Novak & Kendra Sirak & , 2015. "Genome-wide patterns of selection in 230 ancient Eurasians," Nature, Nature, vol. 528(7583), pages 499-503, December.
    • Handle: RePEc:nat:nature:v:528:y:2015:i:7583:d:10.1038_nature16152
    DOI: 10.1038/nature16152
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    Cited by:

    1. Selina Carlhoff & Wibhu Kutanan & Adam B. Rohrlach & Cosimo Posth & Mark Stoneking & Kathrin Nägele & Rasmi Shoocongdej & Johannes Krause, 2023. "Genomic portrait and relatedness patterns of the Iron Age Log Coffin culture in northwestern Thailand," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    2. Quamrul H. Ashraf & Oded Galor & Marc P. B. Klemp, 2020. "The Ancient Origins of the Wealth of Nations," CESifo Working Paper Series 8624, CESifo.
    3. Joaquim Fort & Joaquim Pérez-Losada, 2024. "Interbreeding between farmers and hunter-gatherers along the inland and Mediterranean routes of Neolithic spread in Europe," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    4. Kendra A. Sirak & Daniel M. Fernandes & Mark Lipson & Swapan Mallick & Matthew Mah & Iñigo Olalde & Harald Ringbauer & Nadin Rohland & Carla S. Hadden & Éadaoin Harney & Nicole Adamski & Rebecca Berna, 2021. "Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    5. Douglas J. Kennett & Mark Lipson & Keith M. Prufer & David Mora-Marín & Richard J. George & Nadin Rohland & Mark Robinson & Willa R. Trask & Heather H. J. Edgar & Ethan C. Hill & Erin E. Ray & Paige L, 2022. "South-to-north migration preceded the advent of intensive farming in the Maya region," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    6. Leonardo Vallini & Carlo Zampieri & Mohamed Javad Shoaee & Eugenio Bortolini & Giulia Marciani & Serena Aneli & Telmo Pievani & Stefano Benazzi & Alberto Barausse & Massimo Mezzavilla & Michael D. Pet, 2024. "The Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    7. Isabel Alves & Joanna Giemza & Michael G. B. Blum & Carolina Bernhardsson & Stéphanie Chatel & Matilde Karakachoff & Aude Pierre & Anthony F. Herzig & Robert Olaso & Martial Monteil & Véronique Gallie, 2024. "Human genetic structure in Northwest France provides new insights into West European historical demography," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    8. Owen Alexander Higgins & Alessandra Modi & Costanza Cannariato & Maria Angela Diroma & Federico Lugli & Stefano Ricci & Valentina Zaro & Stefania Vai & Antonino Vazzana & Matteo Romandini & He Yu & Fr, 2024. "Life history and ancestry of the late Upper Palaeolithic infant from Grotta delle Mura, Italy," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    9. Chi-Chun Liu & David Witonsky & Anna Gosling & Ju Hyeon Lee & Harald Ringbauer & Richard Hagan & Nisha Patel & Raphaela Stahl & John Novembre & Mark Aldenderfer & Christina Warinner & Anna Di Rienzo &, 2022. "Ancient genomes from the Himalayas illuminate the genetic history of Tibetans and their Tibeto-Burman speaking neighbors," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    10. Maciej Chyleński & Przemysław Makarowicz & Anna Juras & Maja Krzewińska & Łukasz Pospieszny & Edvard Ehler & Agnieszka Breszka & Jacek Górski & Halina Taras & Anita Szczepanek & Marta Polańska & Piotr, 2023. "Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    11. Bárbara Sousa da Mota & Simone Rubinacci & Diana Ivette Cruz Dávalos & Carlos Eduardo G. Amorim & Martin Sikora & Niels N. Johannsen & Marzena H. Szmyt & Piotr Włodarczak & Anita Szczepanek & Marcin M, 2023. "Imputation of ancient human genomes," Nature Communications, Nature, vol. 14(1), pages 1-17, December.

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