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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European Nucleotide Archive
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.