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Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans

Nature volume 553, pages 203–207 (2018)Cite this article

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Abstract

Despite broad agreement that the Americas were initially populated via Beringia, the land bridge that connected far northeast Asia with northwestern North America during the Pleistocene epoch, when and how the peopling of the Americas occurred remains unresolved1,2,3,4,5. Analyses of human remains from Late Pleistocene Alaska are important to resolving the timing and dispersal of these populations. The remains of two infants were recovered at Upward Sun River (USR), and have been dated to around 11.5 thousand years ago (ka)6. Here, by sequencing the USR1 genome to an average coverage of approximately 17 times, we show that USR1 is most closely related to Native Americans, but falls basal to all previously sequenced contemporary and ancient Native Americans1,7,8. As such, USR1 represents a distinct Ancient Beringian population. Using demographic modelling, we infer that the Ancient Beringian population and ancestors of other Native Americans descended from a single founding population that initially split from East Asians around 36 ± 1.5 ka, with gene flow persisting until around 25 ± 1.1 ka. Gene flow from ancient north Eurasians into all Native Americans took place 25–20 ka, with Ancient Beringians branching off around 22–18.1 ka. Our findings support a long-term genetic structure in ancestral Native Americans, consistent with the Beringian ‘standstill model’9. We show that the basal northern and southern Native American branches, to which all other Native Americans belong, diverged around 17.5–14.6 ka, and that this probably occurred south of the North American ice sheets. We also show that after 11.5 ka, some of the northern Native American populations received gene flow from a Siberian population most closely related to Koryaks, but not Palaeo-Eskimos1, Inuits or Kets10, and that Native American gene flow into Inuits was through northern and not southern Native American groups1. Our findings further suggest that the far-northern North American presence of northern Native Americans is from a back migration that replaced or absorbed the initial founding population of Ancient Beringians.

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Figure 1: Genetic affinities between USR1, present-day Native Americans and world-wide populations.
Figure 2: Possible geographic locations for the USR1 and NNA–SNA splits.
Figure 3: A model for the formation of the different Native American populations.
Figure 4: USR1 demographic history in the context of East Asians, Siberians and other Native Americans.

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Acknowledgements

The Upward Sun River excavations and analysis were conducted under a Memorandum of Agreement (MOA) signed by the State of Alaska, the National Science Foundation, the Healy Lake Tribal Council and the Tanana Chiefs Conference. We appreciate the cooperation of all parties. We thank M. Allentoft, S. Gopalakrishnan, T. Korneliussen, P. Librado, J. Ramos-Madrigal, G. Renaud and F. Vieira for discussions, and the Danish National High-throughput Sequencing Centre for assistance with data generation. GeoGenetics members were supported by the Lundbeck Foundation and the Danish National Research Foundation (DNRF94) and KU2016. J.V.M.-M. was supported by Conacyt (Mexico). Samples were recovered during excavations by B.A.P. supported by NSF Grants 1138811 and 1223119. Research was supported in part by NIH grant R01-GM094402 (M.St., J.T., J.A.K. and Y.S.S.) and a Packard Fellowship for Science and Engineering (Y.S.S.). Y.S.S. is a Chan Zuckerberg Biohub investigator. D.J.M. is supported by the Quest Archaeological Research Fund. A.-S.M. is supported by the Swiss National Science Foundation and the ERC.

Author information

Author notes

  1. J. Víctor Moreno-Mayar, Ben A. Potter and Lasse Vinner: These authors contributed equally to this work.

Authors and Affiliations

  1. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 1350, Denmark

    J. Víctor Moreno-Mayar, Lasse Vinner, Anna-Sapfo Malaspinas, Martin Sikora, Ludovic Orlando, Rasmus Nielsen, David J. Meltzer & Eske Willerslev

  2. Department of Anthropology, University of Alaska, Fairbanks, 99775, Alaska, USA

    Ben A. Potter & Joshua D. Reuther

  3. Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, Massachusetts, 01003, USA

    Matthias Steinrücken

  4. Department of Ecology and Evolution, University of Chicago, Chicago, 60637, Illinois, USA

    Matthias Steinrücken

  5. Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, 2800, Denmark

    Simon Rasmussen

  6. Department of Statistics, University of California, Berkeley, 94720, California, USA

    Jonathan Terhorst, John A. Kamm, Yun S. Song & Rasmus Nielsen

  7. Department of Statistics, University of Michigan, Ann Arbor, 48109, Michigan, USA

    Jonathan Terhorst

  8. Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

    John A. Kamm & Eske Willerslev

  9. Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, 2200, Denmark

    Anders Albrechtsen

  10. Department of Computational Biology, University of Lausanne, Lausanne, Switzerland

    Anna-Sapfo Malaspinas

  11. Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland

    Anna-Sapfo Malaspinas

  12. Research Centre in Evolutionary Anthropology and Palaeoecology, Liverpool John Moores University, Liverpool, L3 3AF, UK

    Joel D. Irish

  13. Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, 61801, Illinois, USA

    Ripan S. Malhi

  14. Carle R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, Illinois, USA

    Ripan S. Malhi

  15. Computer Science Division, University of California, Berkeley, California, 94720, USA

    Yun S. Song

  16. Chan Zuckerberg Biohub, San Francisco, California, 94158, USA

    Yun S. Song

  17. Department of Integrative Biology, University of California, Berkeley, 94720, California, USA

    Rasmus Nielsen

  18. Department of Anthropology, Southern Methodist University, Dallas, 75275, Texas, USA

    David J. Meltzer

  19. Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK

    Eske Willerslev

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  1. J. Víctor Moreno-Mayar
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Contributions

The project was conceived by E.W. and B.A.P. and headed by E.W. L.V. processed ancient DNA. J.V.M.-M. and S.R. assembled datasets. J.V.M.-M., M.St., J.T., J.A.K. and A.A. analysed genetic data. B.A.P. led the USR field investigation and B.A.P. and D.J.M. provided anthropological contextualization. B.A.P., J.D.R. and J.D.I. conducted archaeological and bioanthropological work. R.N., Y.S.S., M.Si., A.-S.M., and L.O. supervised bioinformatic and statistical analyses. B.A.P. engaged with indigenous communities. J.V.M.-M., B.A.P., D.J.M. and E.W. wrote the manuscript with input from L.V., A.-S.M., M.Si., R.S.M., L.O., Y.S.S, R.N. and the other authors.

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Correspondence to Eske Willerslev.

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Moreno-Mayar, J., Potter, B., Vinner, L. et al. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Nature 553, 203–207 (2018). https://doi.org/10.1038/nature25173

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