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Thread: Pleistocene Alaskan genome reveals first founding population of Native Americans

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    Pleistocene Alaskan genome reveals first founding population of Native Americans

    https://www.nature.com/articles/nature25173

    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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    a, f3 statistics of the form f3(San; X, USR1), for each population in the genotype panel. Warmer colours represent greater shared drift between a population (X) and USR1. b, D statistics of the form D(Native American, Aymara; USR1, Yoruba) (points). The Andean Aymara were used to represent SNA. *Native American populations with Asian admixture (|Z| for D(H1, Aymara; Han, Yoruba) > 3.3) (Supplementary Fig. 5a). Error bars represent 1 and approximately 3.3 standard errors (P ≈ 0.001). Native American populations were grouped by language family1. c, Quantile–quantile plot comparing observed Z scores to the expected normal distribution under the null hypothesis (H0), for all possible D(Native American, USR1; Siberian1, Siberian2). Colours correspond to the Z score obtained for D(H1, Aymara; Han, Yoruba). The expected normal distribution under the null hypothesis was computed for all groups jointly (Supplementary Information section 10.4). Thick and thin lines represent a Z score of approximately 3.3 (P ≈ 0.001) and a Z score of approximately 4.91 (P ≈ 0.01 after applying a Bonferroni correction for 11,322 tests). The bottom-right panel shows the expected tree under the null hypothesis. d, Admixture proportions estimated by ADMIXTURE20 assuming K = 20 ancestral populations. Bars represent individuals, and colours represent admixture proportions from each ancestral component. Admixture proportions in ancient genomes (wider bars) were estimated using a genotype likelihood-based approach21. Nat. Am., Native American; Sib., Siberian.

    https://www.nature.com/articles/nature25173/figures/1

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    Attachment 9602 Attachment 9603 Attachment 9604


    the first arrival was along the seacoast some 15 ka in 2 waves : Q-Z780 followed by Q-M3
    Clovis people were a subclade of Q-Z780
    later most of the Q-Z780 were replaced by the Q-M3
    some Q-M3 are also in Kamtsjatka (Evens) , probably a back migration through the Aleut Islands prior to the present Aleut-Eskimos

    the 2nd arrival was through Beringia into Alaska, trapped behind the ice sheets : C-P39, https://www.yfull.com/tree/C-F3918/
    they arrived 12,5 ka with microliths replacing a prior population with large blades
    they are the Athabaskan speakers
    the south Athabaskan are the Apache and Navajo tribes, a migration coming from the north well documented in the archeological record 0.6 ka

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    Quote Originally Posted by bicicleur View Post
    Too bad I didn't copy and paste the whole paper when it was originally available. But a least I was able to get that graphic before the pay wall went up.

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    1 out of 1 members found this post helpful.
    The title of the paper, and consequently the title of this thread, is wrong. The samples, dated to 11,500 years ago, are from the early Holocene, not the late Pleistocene. The Holocene began 11,700 years ago.

    Another paper by Willerslev, on the Anzick 1 genome, similarly had a false title and misrepresentations regarding dates. The title of that paper declared, without qualification, that Anzick 1 was "from a Clovis burial site", when the reality, swept under the rug by that paper, is that the association between the Anzick 1 remains and the Clovis artifacts at the Anzick site could never be clearly established, given the conditions under which the remains and artifacts were discovered. That paper also gave an incorrect time range for the Clovis period, so that the authors could claim that the Anzick 1 remains date to that period, when in fact they date to after that period. I exposed all of this in the following post on my blog from almost four years ago:

    The dubious association of Anzick 1 with Clovis artifacts

    Quote Originally Posted by bicicleur View Post
    Clovis people were a subclade of Q-Z780
    There's no real evidence for that, because as I explained above, the association between Anzick 1 and Clovis artifacts has never really been established. Also note that the samples in the new paper, which, like Anzick 1, are related to Amerindians, were associated with the Denali complex, which is related to the early stone tool technologies of Siberia and the western parts of the Americas, and which is unrelated to Clovis technology, which is most frequently found in, and appears to have originated from, the eastern United States.

    Quote Originally Posted by bicicleur View Post
    the 2nd arrival was through Beringia into Alaska, trapped behind the ice sheets : C-P39, https://www.yfull.com/tree/C-F3918/
    they arrived 12,5 ka with microliths replacing a prior population with large blades
    they are the Athabaskan speakers
    The latest evidence shows that the speakers of the Na-Dene languages were descended from the Paleo-Eskimos, who crossed the Bering Strait into North America around 5,000 years ago. So that's when C2b1a1-F3918 would have migrated to North America.

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    Quote Originally Posted by Genetiker View Post
    The title of the paper, and consequently the title of this thread, is wrong. The samples, dated to 11,500 years ago, are from the early Holocene, not the late Pleistocene. The Holocene began 11,700 years ago.
    Hmm, that's unfortunate.

    But could it be that it is termed differently for regional location? I admit, I'm not familiar with this.

    In Europe and North America, the Holocene is subdivided into Preboreal, Boreal, Atlantic, Subboreal, and Subatlantic stages of the Blytt–Sernander time scale. There are many regional subdivisions for the Upper or Late Pleistocene; usually these represent locally recognized cold (glacial) and warm (interglacial) periods. The last glacial period ends with the cold Younger Dryas substage.

    https://en.wikipedia.org/wiki/Pleistocene

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    Quote Originally Posted by Genetiker View Post
    The latest evidence shows that the speakers of the Na-Dene languages were descended from the Paleo-Eskimos, who crossed the Bering Strait into North America around 5,000 years ago. So that's when C2b1a1-F3918 would have migrated to North America.
    Is it in this paper?
    I don't have access to it.
    Or is this from an older paper?
    I have read that there was gene flow between Na-Dene and Paleo-Eskimo but not between Na-Dene and neo-Eskimo.
    But I'm not aware that Na-Dene actualy descend from Paleo-Eskimo.

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    2 out of 2 members found this post helpful.
    Quote Originally Posted by bicicleur View Post
    Is it in this paper?
    I don't have access to it.
    Or is this from an older paper?
    I have read that there was gene flow between Na-Dene and Paleo-Eskimo but not between Na-Dene and neo-Eskimo.
    But I'm not aware that Na-Dene actualy descend from Paleo-Eskimo.
    Paleo-Eskimo genetic legacy across North America

    The Na-Dene were partially descended from the Paleo-Eskimos, and partially from the ancestors of the Amerindians, who spread down the Pacific coasts of North and South America around 15,000 years ago. The above paper estimates that ancient Northern Athabaskans had 23–38% Paleo-Eskimo ancestry, and that modern Na-Dene populations have 7–22% Paleo-Eskimo ancestry.

    But it's the Paleo-Eskimo migration around 5,000 years ago that would have brought the Pre-Proto-Na-Dene language and C2b1a1-F3918 to North America. See section 10 of the supplementary information for the above paper, which gives 6,500 years ago as the date of the breakup of Proto-Dene-Yeniseian in Siberia, and 5,000 years ago as the date at which the Paleo-Eskimos brought Pre-Proto-Na-Dene to Alaska.

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    Quote Originally Posted by Genetiker View Post
    The title of the paper, and consequently the title of this thread, is wrong. The samples, dated to 11,500 years ago, are from the early Holocene, not the late Pleistocene. The Holocene began 11,700 years ago.

    Another paper by Willerslev, on the Anzick 1 genome, similarly had a false title and misrepresentations regarding dates. The title of that paper declared, without qualification, that Anzick 1 was "from a Clovis burial site", when the reality, swept under the rug by that paper, is that the association between the Anzick 1 remains and the Clovis artifacts at the Anzick site could never be clearly established, given the conditions under which the remains and artifacts were discovered. That paper also gave an incorrect time range for the Clovis period, so that the authors could claim that the Anzick 1 remains date to that period, when in fact they date to after that period. I exposed all of this in the following post on my blog from almost four years ago:

    The dubious association of Anzick 1 with Clovis artifacts



    There's no real evidence for that, because as I explained above, the association between Anzick 1 and Clovis artifacts has never really been established. Also note that the samples in the new paper, which, like Anzick 1, are related to Amerindians, were associated with the Denali complex, which is related to the early stone tool technologies of Siberia and the western parts of the Americas, and which is unrelated to Clovis technology, which is most frequently found in, and appears to have originated from, the eastern United States.
    Are you still a proponent of the solutrean hypothesis? How do you explain X2a in Kennewick man and the absence of any European related admixture other than ANE from mal'ta boy? The theory is looking increasingly improbable.

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    Quote Originally Posted by Jovialis View Post
    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..
    A 4th migration into the American gene pool? We have thus far this newly "found" Ancient Berigian, the Amerindian (eventually splitting into northern and southern groups), the Paleo-Eskimo\Na-Dene and the Inuit. What should this Koryak-like population inflow be? 11.5 kya is, I think, later than the disappearance of Beringia with the rising sea levels. Do we have other evidences of any new migration between the "old" Native American stock and the "recent" Paleo-Eskimos and Neo-Eskimos?

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    So I am brand new to this and just joined. I have a question about Native American ancient groups, my daughter is 25% documented Native American and a tribal member but when I uploaded her raw DNA to this site all that came back were European ancient groups as Visigoths, Longobords and Franks. Nothing that would fit with Native Americans.

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    Quote Originally Posted by Irisheyes490 View Post
    my daughter is 25% documented Native American and a tribal member but when I uploaded her raw DNA to this site all that came back were European ancient groups as Visigoths, Longobords and Franks. Nothing that would fit with Native Americans.
    If by "this site" you mean MyTrueAncestry.com, then I had a similar experience. I am a registered tribal member and 15-17% Polynesian according to different DNA calculators (which fits with my documented genealogy), but when I uploaded my DNA to MyTrueAncestry all that came back were Gauls, Vikings and Franks. That fits with my majority ancestry (North West European), but doesn't indicate my Polynesian ancestry. If your daughter's ancestry is 75% European, then I suspect her results were dominated by this majority ancestry. To better explore her minority ancestry I suggest uploading her DNA to GEDmatch.com where there are a number of calculators available to explore deep ancestry. My results there suggest that the majority of my Polynesian ancestry is derived from Taiwan, but a substantial minority comes from ancient Melanesia.

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    Quote Originally Posted by Tamakore View Post
    If by "this site" you mean MyTrueAncestry.com, then I had a similar experience. I am a registered tribal member and 15-17% Polynesian according to different DNA calculators (which fits with my documented genealogy), but when I uploaded my DNA to MyTrueAncestry all that came back were Gauls, Vikings and Franks. That fits with my majority ancestry (North West European), but doesn't indicate my Polynesian ancestry. If your daughter's ancestry is 75% European, then I suspect her results were dominated by this majority ancestry. To better explore her minority ancestry I suggest uploading her DNA to GEDmatch.com where there are a number of calculators available to explore deep ancestry. My results there suggest that the majority of my Polynesian ancestry is derived from Taiwan, but a substantial minority comes from ancient Melanesia.
    That website probably just doesn't have any Native American and Pacific Islander DNA samples (a huge flaw in my opinion, as those aren't "tiny" and extremely rare populations on a worldwide basis), so they can't even find a much worse but at least reasonably plausible fit for the sources of a minority of your ancestry, so they will just assign it all to the European populations that form the majority of the analyzed sample's ancestry and "assume" that the lack of a more precise fit is due to "genetic structure" (internal differentiation) in those populations or something like that. They just don't have a database varied and numerous enough to make a more reliable estimation.

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    My results there suggest that the majority of my Polynesian ancestry is derived from Taiwan, but a substantial minority comes from ancient Melanesia.
    This study's two samples (USR1 and USR2) carried mtDNA haplogroups C1 and B2, respectively. B2 or B4b is widespread among Native Americans, while B4a1a1 is referred to as "the Polynesian motif," which is the most common mtDNA haplogroup among Polynesians. Haplogroup B4a1a1 may have dispersed southward out of Taiwan via the Philippines to Near Oceania and Polynesia (Tabbada et al. 2009). The remote ancestors of Austronesian speakers who carried B4a1a1 migrated to Taiwan from Southern China by 5,500 BP, and then onto the Philippines by 4,000 BP.




    Figure 2: Possible geographic locations for the USR1 and NNA–SNA splits.

    The founding population of Native Americans (consisting of Ancient Beringians and NNA and SNA) began to diverge from ancestral Asians as early as around 36 ka, probably in northeast Asia, as there is no evidence of people in Beringia or northwest North America at this period. A high level of gene flow was maintained between them and other Asians until as late as around 25 ka2,13.

    The subsequent isolation of the Native American founding population about 24 ka roughly corresponds to a decline in archaeological evidence for a human presence in Siberia30. Both changes may result from the same underlying cause: the onset of harsh climatic conditions during the LGM2. These findings, coupled with a divergence date of around 20.9 ka between USR1 and other Native Americans, are in agreement with the Beringian standstill model9 (Supplementary Information section 21). Ancient Beringians and the common ancestor of NNA and SNA began to diverge around 20.9 ka, after which gene flow ensued, although whether this only involved the latter or the already differentiated NNA and SNA branches cannot be determined owing to the shallow divergence times among groups.

    Scenarios 1 and 2 are compatible with our evidence of continuous gene flow among these groups, but differ as to the location of the Ancient Beringians versus NNA and SNA split at 20.9 ka, whether in northeast Asia (scenario 1) or eastern Beringia (scenario 2). Each has strengths and weaknesses relative to genetic and archaeological evidence: scenario 1 best fits the archaeological and palaeoecological evidence, as the earliest securely dated sites in Beringia are no older than around 15–14 ka, and the LGM cold period is unlikely to be associated with northward-expanding populations30. Scenario 2 is genetically most parsimonious, given evidence of continuous gene flow between the Ancient Beringians and NNA and SNA, suggesting their geographical proximity 20.9–11.5 ka, and that all three were isolated from Asian and/ or Siberian groups after about 24 ka and form a clade.

    Scenarios 1 and 2 are both consistent with the NNA–SNA split at around 15 ka2 having occurred in a region south of eastern Beringia. The ice sheets were at that time still a substantial barrier to movement that would have helped to maintain separation from the Ancient Beringian population. Although members of the SNA branch have not been documented in regions that were once north of the Pleistocene glaciers1,18, NNA groups (including Athabascan speakers) are present in Alaska today. Therefore, NNA are likely to be descendants of a population that moved north sometime after 11.5 ka25.
    Last edited by ThirdTerm; 11-06-19 at 05:41.
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