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 unresolved^1,2,3,4,5. 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 Americans^1,7,8. 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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Commenting on this article is now closed.

1. Don Wilson4 January 2018, 19:31

   I read your abstract with interest and wonder if DNA or other testing has ruled out the possibility of a progenitor peoples migration from/through South and Central America to the north and interbreeding with those peoples migrating across the Bering bridge and moving south? I ask because a working archeologist from Cusco University, guiding us through Machu Pichu 3 yrs. ago seemed adamant that the "Peruvian" progenitors did not migrate from No. America, through the Bering land bridge as taught in U.S. schools, but, most likely either migrated to or from Asia and what is now Peru. He indicated that there are ongoing DNA and other studies underway attempting to resolve the migration direction question. He was clear that there is an Asian connection but speculated that it possibly was accomplished by boat or raft. If that remains a possibility, could that also be an explanation for the genetic differences observed? Thank you.

2. Wim BorsboomReplied toDon Wilson13 March 2018, 15:01

   Hi Don,
   Excellent question, if you get any reasonable answer, please send me an email
   wimjborsboom@gmail.com
   I would very much appreciate that.
   Wim Borsboom

3. NeaAnderthal4 January 2018, 19:54

   It would be interesting to determine the genetic similarities with differing native Siberian populations such as the Kumandinians of the Altay region.

4. John Ensminger11 January 2018, 13:25

   This comment may only be appropriate for certain of the authors of this paper who are associated with the excavations at Sun River. I would appreciate any information as to whether there is any evidence that there may have been dogs at the Sun River site. I do not see any mention in this paper, the Supplementary Info, or the papers by Potter et al. in 2008 and 2014 (nor is Canis listed among the fauna in the Supp Info to the latter), but there may be other sources I haven’t encountered. A number of papers on the genetics of aboriginal American dogs generally refer to dogs coming over the land bridge from Siberia to the Americas with humans but I have not seen consideration being given to the difficulties such generalizations encounter if the evidence regarding a Beringian Standstill has to be taken into account. If human gene flow from Siberia ceased between 25,000 and 18,000 years ago (or even later, depending on the research group), then dogs would presumably not have accompanied humans into Beringia after that. One could postulate some feral dog population moving into the area and becoming associated with a group that previously did not have dogs, or some group of humans moving in and then disappearing without a genetic trace but leaving their dogs, but these seem almost Rube Goldberg constructs. I believe an argument can be made that the first wave of humans into America may not have had dogs (correlating several lines of research) but presumably there had to be dogs in Alaska by the time the land bridge closed, say 12,500 years ago, to explain the archeological record (Paleo-Eskimo and Thule migrations coming too late). If a kind of proto-domestication (Germonpre) is presumed, the flaw here is that this is generally seen as not leading to modern dogs. That leaves the possibility of an earlier domestication leading to modern dogs (Wang et al. 2015), and makes a conservative timeline (Morey, etc.) more difficult to support if there was, in fact, a Standstill. Beringia was a large area during the Last Glacial Maximum and a structured cultural environment has been suggested (Reich and Skoglund), making it possible that some groups within it had dogs while others did not (true, for instance, of some neighboring tribes in California despite similar subsistence patterns). Hence my question as to whether the Sun River site holds any evidence of dogs.

5. Lee Albee27 February 2018, 17:46

   I am a bit concerned by the continued use of the masking methodology. This methodology has a significant bias against the North American populations as they seemingly have a higher level of "western eurasian" genetics. By aggressively stripping away "other" ancestry, the relationship to the native american alleles should be expected to be similar or the same to both north and south america. I am worried this analysis method is baking in a bias