Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans
J. Víctor Moreno-Mayar, Ben A. Potter, Lasse Vinner, Matthias Steinrücken, Simon Rasmussen, Jonathan Terhorst, John A. Kamm, Anders Albrechtsen, Anna-Sapfo Malaspinas, Martin Sikora, Joshua D. Reuther, Joel D. Irish, Ripan S. Malhi, Ludovic Orlando, Yun S. Song, Rasmus Nielsen, David J. Meltzer & Eske Willerslev Nature doi:10.1038/nature25173 Download Citation Biological anthropologyNext-generation sequencingPopulation genetics Received: 29 March 2017 Accepted: 26 November 2017 Published online: 03 January 2018
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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What the ancient DNA discovery tells us about Native American ancestry A new genome from a Pleistocene burial in Alaska confirms a longstanding model for the initial peopling of the Americas Surprise as DNA reveals new group of Native Americans: the ancient Beringians
But when the first genetic data from two of the Upward Sun River children was successfully recovered by Justin Tackney et al. in 2015, we (I was a minor co-author on the paper) discovered that they had mitochondrial lineages (C1b and B2) not typical of contemporary peoples of the region.
Jennifer Raff Wed 3 Jan ‘18 13.00 EST Last modified on Wed 3 Jan ‘18 14.42 EST
View more sharing options Comments 158 A little over 11,000 years ago, a grieving family in Central Alaska laid to rest a six-week-old baby girl, a three-year-old child, and a preterm female fetus. According to their custom, the children were interred under a hearth inside their home and provisioned with the carefully crafted stone points and bone foreshafts of hunting lances. We don’t know their names, but the peoples who live in the region today (the Tanana Athabaskans) call one of the girls Xach’itee’aanenh t’eede gaay (sunrise child-girl) and the other Yełkaanenh t’eede gaay (dawn twilight child-girl). Their remains were discovered a few years ago at a site known today as the Upward Sun River.
These children carried the history of their ancestors within their DNA, and with the permission of their descendants they are now teaching us about the early events in the peopling of the Americas. A new paper in Nature, Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans by Moreno-Mayar et al., analyzes the complete genome of one of these children. This genome gives us a glimpse of the genetic diversity present in Late Pleistocene Beringians, the ancestors of Native Americans, and confirms a decades-old hypothesis for the early peopling of the Americas.
To contextualize this work, it helps to start with what we know – and don’t know – about how humans first got to the American continents. We’ve known for a long time that the indigenous peoples of the Americas are descended from a group of people who crossed a land connection between Asia and North America sometime during the Last Glacial Maximum (26,500 to 19,000 years before present, or YBP).
The prevailing model for how this happened is known as the Beringian Standstill (or Pause or Incubation, depending on who you ask), which was originally conceived of based on classical genetic markers and fully developed by the analysis of maternally inherited mitochondrial genomes . This model states that the ancient Beringians must have experienced a long period of isolation from all other populations. (Estimates for the length of this isolation vary, but the lower end – roughly 7,000 years – is about as long as the period between the invention of beer brewing and the Apollo 11 landing). During this period they developed the genetic variation uniquely found in Native American populations.
This isolation likely took place in Beringia. Environmental reconstructions based on ancient plant remains taken from soil cores, as well as computer temperature models show that it was actually a relatively decent place to live during the Last Glacial Maximum (LGM). Large regions of Beringia would have had warmer temperatures than Siberia and shrub tundra with plants and animals available to support a sizeable human population. Although we don’t have any direct archaeological evidence of people living in central Beringia during the LGM – because that region is currently underneath the ocean – we do have evidence that people were living year round in northeastern Beringia (present-day Siberia) at the Yana Rhinocerous Horn sites by 30,000 YBP and in western Beringia (present-day Yukon, in Canada) by about 20-22,000 YBP at the Bluefish Caves site.
At the end of the LGM, temperatures began to rise and the glaciers that covered North America slowly began to melt. The first peoples to enter the Americas from Beringia are thought to have done so shortly after a route opened up along the west coast, about 15,000 years ago. Travel by boat would have allowed very rapid southward movement, making it possible for people to establish themselves at the early site of Monte Verde in Chile by 14,220 YBP, as well as a number of other sites in North America of similar ages. Whether there was southward travel by Clovis peoples via the ice-free corridor once it opened remains unresolved, but there is at least some evidence against it.
Today there remain a number of questions about the details of the Beringian Incubation model: 1) Which population(s) contributed to the ancestry of the earliest Native Americans? 2) When and where did their ancestors become isolated, and how long did this isolation last? 3) How did people initially enter the Americas from Beringia? 4) When and how did the patterned genetic variation that we see in Native American populations emerge?
Ancient genomes from people who lived in the Americas and in Siberia during or shortly after the LGM can help provide answers to some of these questions. But there aren’t very many burials that date to this period, so the Upward Sun River child’s genome is very significant. It strongly confirms the Beringian Incubation/Standstill model. In this region of Alaska today, we only see a subset of Native American-specific mitochondrial haplogroups: those which are uniquely restricted to the Arctic and Subarctic. But the Beringian Standstill model predicted that ancestral Beringians should have all “founder” mitochondrial lineages present in ancient and contemporary Native Americans. In the absence of any ancient DNA dating to the Late Pleistocene, this remained an unsolvable puzzle.
But when the first genetic data from two of the Upward Sun River children was successfully recovered by Justin Tackney et al. in 2015, we (I was a minor co-author on the paper) discovered that they had mitochondrial lineages (C1b and B2) not typical of contemporary peoples of the region. We hypothesized that they might represent the descendants of a remnant ancient Beringian population, but it was impossible to test this hypothesis without additional data from the nuclear genomes. Moreno-Mayar et al.’s nuclear genome results from one of the children (the other didn’t yield enough nuclear DNA for analysis) confirm that she belonged to a group that had remained in Beringia after Native Americans began their migration southward into the Americas. We know that because this child is equally related to all indigenous populations in the Americas. She did not belong to either of the two major Native American genetic groups (Southern and Northern), but was equally related to both of them. One interpretation of this result is that her ancestors must have remained in Alaska after splitting from the ancestors of Native Americans sometime around 20,000 YBP. Her genome, provides new insight into the genetic diversity present in the ancestral Beringian population. One important component of that is that it gives us new estimates of the approximate dates of key events:
~36,000 YBP: The ancestors of the ancient Beringians began to separate from East Asians, but gene flow between them continues until about 25,000 YBP ~25-20,000 YBP: This population experienced gene flow with the ancient North Eurasian population (to which the Mal’ta boy belonged) ~20,000 YBP: The ancestors of the Upward Sun River child diverged from the ancestors of other Native Americans. ~17,000-14,600 YBP: The two major clades (genetic groups) of Native Americans differentiate from one another. While this paper doesn’t yield any tremendous surprises, it does add new details to and confirms the predictions of a hypothesis for the initial peopling of the Americas that has been the focus of much research over the past few years. We ought to temper our excitement, however, with the recognition that a nuclear genome from a single individual might not represent the full range of genetic diversity within a population, and those questions I outlined above will need additional data to fully answer. We still have a tremendous amount to learn about the origins and evolution of the indigenous peoples of the Americas.
Further reading:
Moreno-Mayar et al. 2018. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Nature.
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Proc Natl Acad Sci U S A. 2015 Nov 10; 112(45): 13833–13838. Published online 2015 Oct 26. doi: 10.1073/pnas.1511903112 PMCID: PMC4653186 Anthropology Two contemporaneous mitogenomes from terminal Pleistocene burials in eastern Beringia
Justin C. Tackney,a,1 Ben A. Potter,b Jennifer Raff,c Michael Powers,d W. Scott Watkins,e Derek Warner,d Joshua D. Reuther,b,f Joel D. Irish,g and Dennis H. O’Rourkea
SIGNIFICANCE Beringia gave rise to the first Western Hemisphere colonists, although the genetic characterization of that source population has remained obscure. We report two mitogenomes from human remains within Beringia, with an age (∼11,500 cal B.P.) that postdates the end of the initial colonization by only a few millennia. The mitochondrial lineages identified (B2, C1b) are rare to absent in modern northern populations, indicating greater genetic diversity in early Beringia than in modern populations of the region. The antiquity and geographic location of these two burials, and the combined genomic and archaeological analyses, provide new perspectives on the link between Asia and the Americas, and the genetic makeup of the first Americans.
Keywords: Pleistocene burials, ancient mitochondrial DNA, paleogenomics, peopling, Americas Go to: ABSTRACT Pleistocene residential sites with multiple contemporaneous human burials are extremely rare in the Americas. We report mitochondrial genomic variation in the first multiple mitochondrial genomes from a single prehistoric population: two infant burials (USR1 and USR2) from a common interment at the Upward Sun River Site in central Alaska dating to ∼11,500 cal B.P. Using a targeted capture method and next-generation sequencing, we determined that the USR1 infant possessed variants that define mitochondrial lineage C1b, whereas the USR2 genome falls at the root of lineage B2, allowing us to refine younger coalescence age estimates for these two clades. C1b and B2 are rare to absent in modern populations of northern North America. Documentation of these lineages at this location in the Late Pleistocene provides evidence for the extent of mitochondrial diversity in early Beringian populations, which supports the expectations of the Beringian Standstill Model.
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