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Thread: Genetic analysis of the 34000 years old Salkhit Skull from Mongolia

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    Genetic analysis of the 34000 years old Salkhit Skull from Mongolia

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    Denisovan ancestry and population history of early East Asians

    Diyendo Massilani, Laurits Skov, Mateja Hajdinjak, Byambaa Gunchinsuren, Damdinsuren Tseveendorj, Seonbok Yi, Jungeun Lee, Sarah Nagel, Birgit Nickel, Thibaut Deviese, Tom Higham, Matthias Meyer, Janet Kelso, Benjamin M Peter, Svante Paabo

    doi: https://doi.org/10.1101/2020.06.03.131995

    Abstract
    We present analyses of the genome of a ~34,000-year-old hominin skull cap discovered in the Salkhit Valley in North East Mongolia. We show that this individual was a female member of a modern human population that, following the split between East and West Eurasians, experienced substantial gene flow from West Eurasians. Both she and a 40,000-year-old individual from Tianyuan outside Beijing carried genomic segments of Denisovan ancestry. These segments derive from the same Denisovan admixture event(s) that contributed to present-day mainland Asians but are distinct from the Denisovan DNA segments in present-day Papuans and Aboriginal Australians.
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    Using data from ~1.7 million SNPs where
    Neandertal and/or Denisovan genomes differ from present-day African genomes, we detect 18
    segments of Denisovan ancestry longer than 0.2 cM in the Salkhit genome (Fig. 3, Table S18, Fig.
    S16 and S27) and 20 such segments in the Tianyuan genome (Table S18, Fig. S17 and S27). We
    detect about a third as many segments of Denisovan DNA in the genomes of the ancient Siberians
    Yana 1 and Yana 2, and Mal’ta 1 (Table S18, Fig. S18-20 and S27), consistent with that they carry
    lower proportions of East Asian ancestry.
    In contrast, no Denisovan ancestry is detected in the
    genome of the ~45,000-year-old Siberian individual from Ust’Ishim in West Siberia, nor in any
    European individual older than 20,000 years (Table S18, Fig. S21-24 and S27).
    Recently, there was that paper that used deep sequencing of Icelandics to reveal that Icelanders have some segments that could be attributed to Denisovans, IIRC 3% of all archaic segments. The above may show how such ancestry ended up so far West among West Eurasian groups.
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    Quote Originally Posted by Ryukendo View Post
    Recently, there was that paper that used deep sequencing of Icelandics to reveal that Icelanders have some segments that could be attributed to Denisovans, IIRC 3% of all archaic segments. The above may show how such ancestry ended up so far West among West Eurasian groups.
    Alternatively, isn't there some evidence of low level Native American admixture in Icelanders deriving from Norse colonies in Greenland or possibly North America? That is a plausible alternative source of East Asian, and thus Denisovan, ancestry.

    https://onlinelibrary.wiley.com/doi/...002/ajpa.21419

    Although most mtDNA lineages observed in contemporary Icelanders can be traced to neighboring populations in the British Isles and Scandinavia, one may have a more distant origin. This lineage belongs to haplogroup C1, one of a handful that was involved in the settlement of the Americas around 14,000 years ago. Contrary to an initial assumption that this lineage was a recent arrival, preliminary genealogical analyses revealed that the C1 lineage was present in the Icelandic mtDNA pool at least 300 years ago. This raised the intriguing possibility that the Icelandic C1 lineage could be traced to Viking voyages to the Americas that commenced in the 10th century.

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    Quote Originally Posted by Psynome View Post
    Alternatively, isn't there some evidence of low level Native American admixture in Icelanders deriving from Norse colonies in Greenland or possibly North America? That is a plausible alternative source of East Asian, and thus Denisovan, ancestry.

    https://onlinelibrary.wiley.com/doi/...002/ajpa.21419

    That admixture probably happened before West/East Eurasians diverged according to the >27,000 Icelander genomes article (traces of Denisovan DNA are detected in virtually all non-African populations). There are two possibilities: either direct gene flow from Denisovans into the ancestors of all Eurasians and/or the introgressing Neanderthals were already mixed with the former (we know they interbred frequently in Central Asia).

    unnamed.jpg

    I find it surprising that in the Salkhit paper they're not able to find any Denisovan ancestry in >20,000 year old West Eurasians (including Ust'Ishim). Likewise, the proportion of Denisovan ancestry (0.2%) is very low in the mainland. I wonder why are there so many differences between certain SE Asian and Oceanian populations that carry relatively high levels of this ancestry (>4%) but it is so low and uniform among Eurasians.
    Last edited by Milkyway; 06-04-2020 at 06:15 PM.

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    Quote Originally Posted by Psynome View Post
    Alternatively, isn't there some evidence of low level Native American admixture in Icelanders deriving from Norse colonies in Greenland or possibly North America? That is a plausible alternative source of East Asian, and thus Denisovan, ancestry.

    https://onlinelibrary.wiley.com/doi/...002/ajpa.21419
    I would think though that 300 years (so the 1700s) is not all that interesting. Now if they find a 1,000 year old sample, that would be something!
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    Wow this is cool. Will definitely require rethinking of UP East-West interactions.
    So D: Mbuti X Tianyuan Salkhit is ~Z = 3 for paleo-Europeans and MA1, but for Yana it's ~Z = 6, huge difference.
    Is that something specifically Yana (xMA1) into Salkhit, or Salkhit specifically into Yana? Yana has excess affinity to Tianyuan as well relative to MA1, so I'd be more inclined to say it's the latter.
    It looks like Salkhit (-23-26% Paleo-European as per the qpgraph models) would form only a slight clade with Tianyuan to the exclusion of other East-Eurasians though, not sure if that complicates things.

    Hmmm, how about this for a ridiculously wacky but I think honestly plausible scenario...
    - CI-Eruption devastates populations (Ust-Ishim/Oase/Bachokiro?-like) of Southeast-Europe & Western Steppe.
    - Population from Near East (typified by presence of y-hg IJ) fill the void mixing heavily with survivors in the process (result = Kostenki-like) all the way to Western Siberia.
    - Now in Western Siberia - One group goes East (Yana) and mixes with Salkhit, the rest stay put and over time mix with their Central-Asian Onge-like neighbors (MA1)
    And in all this when we get y-hg from Bachokiro most of them turn out to be C1a and we get one P/pre-P1
    Last edited by Kale; 06-05-2020 at 04:07 AM.
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    Quote Originally Posted by Kale View Post
    And in all this when we get y-hg from Bachokiro most of them turn out to be C1a and we get one P/pre-P1
    I read all 11 pages of Bacho-Kiro thread thinking they had actually typed the Y chromosomes.
    As for prediction, Why not K2a like Oase or Ust Ishim? Actually even C1a would be surprising; earlier European C's tend to be C1b like Kostenski.
    If they find C2 instead of C1, that would be shocking much the way Oase and Ust Ishim were K2a.

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    I think Kostenki and co. were the fusion of an Ust-Ishim/Oase/Bachokiro?-like group and a Near Eastern one that entered after the CI-eruption. If that's true than Ust/Oase/Bachokiro? are actually Early East-Eurasians.
    So besides Kostenki14's odd-one-out C1b, all the other post-CI paleo-Europeans possess y-hg C1a/C1a2 and IJ/I. I'd assume C1a/C1a2 represents the Eastern ancestry and IJ/I represents the Near Eastern ancestry.
    I think the safest bet on the y-hg of Bachokiro will be C1a, but considering Oase and Ust_Ishim are K2a, I wouldn't be surprised to see more of that, though it doesn't seem to have persisted so I suspect it's a minor lineage.
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    Quote Originally Posted by Ryukendo View Post
    Recently, there was that paper that used deep sequencing of Icelandics to reveal that Icelanders have some segments that could be attributed to Denisovans, IIRC 3% of all archaic segments. The above may show how such ancestry ended up so far West among West Eurasian groups.
    Icelanders are largely derived from western Norwegian Vikings. And it's very likely that some of them had Saami ancestry.

    If you look at the Salkhit prerpint, the Saami show the highest affinity to Salkhit relative to all of the other modern European groups.

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    Currently, Tianyuan and Salkhit are the paleolithic samples that share the specific East Asian drift and sit on the East Asian branch of modern variation. Ust Ishim precedes the Western/Eastern Eurasian split and sits on the Western side of the tree. I think that the reason why it is closer to ENA in some statistics is that it lacks some ancestry that is shared by Western Eurasians and not by ENA populations.

    Did you notice that the proportion of eastern and western ancestry in Salkhit in northern Mongolia, 34 kya, is already very close to that of Native Americans, 60-80% East Eurasian and 20-40% ANE? The results of the Yana paper are against an admixture in Beringia between Yana and ENA. This new paper and Ust-Kyakhta paper point to continuous mixing already in Mongolia starting from more than 30 kya ago.

    Another interesting observation concerns Native American mtDNA. Native Americans do not carry any U like Yana and Malta, but Eastern haplogroups A (directly under N), B4b/B2, C1, D1 and Iranian/Basal X. Tianyuan is B, Salkhit is N and Ust-Kyakhta is C4. D will probably be found along the Paleolithic Pacific Coast. Therefore, also MtDNA points to a route via Mongolia/South Baikal and then Pacific Coast.

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