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Thread: A Working Tree for Ancient Eurasia

  1. #1
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    A Working Tree for Ancient Eurasia


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    For this graph...
    https://populationgenomics.files.wor...7070131561.png
    The reason Clovis is a bit underfit to Ust_Ishim is likely due to the Vanuatu samples having the excess Denisovan associated with Oceanian populations, as well as Tianyuan being drawn away from everybody (except Goyet) for whatever reason.
    F3: Vanuatu_ancient Ust_Ishim Mbuti.DG = 0.227309
    F3: Tianyuan Ust_Ishim Mbuti.DG = 0.227507
    Compare to other East Eurasians...
    Andaman_100BP = 0.231864
    Jomon = 0.230349
    Nepal_ancient = 0.230525
    XiongNu = 0.229852
    And MA1 and Anzick...
    MA1 = 0.231976
    Anzick = 0.231033

    Additionally, hypothetically MA1 and GoyetQ116-1 should behave the same way in relation to Ust_Ishim and East Eurasians as per that topology, but d-stats contradict that.
    D: outgroup GoyetQ116-1 Ust_Ishim Onge/Han/etc. will be 0
    Whereas D: outgroup MA1 Ust_Ishim Onge/Han/etc. will be significantly positive
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    Vanuatu 2900BP is like the Ami, not Papuans. You also shouldn't get too carried away on stats mixing ancients and moderns.

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    Let's see if I understand it. Crucial to this is the idea that Ust'Ishim is more or less Basal West-Eurasian. Tianyuan however likes MA1 and GoyetQ116 over Us'Ishim, so these two have basal East-Asian ancestry added. And Tianyuan likes GoyetQ116 over SunghirIV and Ust'Ishim likes over SunghirIV as well. Since you began with Ust'Ishim being basal West-Eurasian you must have something pushing SunghirIV from both basal East-Asian and basal West-Eurasian, therefore SunghirIV is Basal-Eurasian admixted.

    But the Z-scores in what led you to believe Ust'Ishim is basal West-Eurasian are all lower than 3. I have seen people using lower Z-scores, but doesn't this mean there is a very real possibility that Ust'Ishim isn't basal West-Eurasian?

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    The best way to fit it is Ust-Ishim branching from West Eurasians. Goyet is closer to Ust-Ishim than ENA is and closer to ENA than Ust-Ishim is. Makes perfect sense. SunghirIV being further from both Ust-Ishim and ENA than Goyet is exactly as expected for Bssal Eurasian.

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    A very interesting pre-print came out at the tail end of last year that I don't think got much play on this forum, but is very pertinent to understanding deep Eurasian population structure: Extreme selective sweeps displaced archaic admixture across the human X chromosome around 50,000 years ago

    The X chromosome in non-African populations has less diversity and less Neanderthal introgression than expected. We analyzed X chromosome diversity across the globe and discovered seventeen chromosomal regions, where haplotypes of several hundred kilobases have recently reached high frequencies in non-African populations only. The selective sweeps must have occurred more than 45,000 years ago because the ancient Ust'-Ishim male also carries its expected proportion of these haplotypes. Surprisingly, the swept haplotypes are entirely devoid of Neanderthal introgression, which implies that a population without Neanderthal admixture contributed the swept haplotypes. It also implies that the sweeps must have happened after the main interbreeding event with Neanderthals about 55,000 BP. These swept haplotypes may thus be the only genetic remnants of an earlier out-of-Africa event.
    Basically, possible evidence for Basal Eurasian ancestry in even Ust-Ishim. Anyway you could try teasing something like this out via D-stats or qpGraph?

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    I'll clarify a little more. ENA to Goyet and MA1 depresses the relationship to Ust-Ishim. Without the ENA, the Z may be 3+.

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    Quote Originally Posted by Chad Rohlfsen View Post
    Vanuatu 2900BP is like the Ami, not Papuans. You also shouldn't get too carried away on stats mixing ancients and moderns.
    O my bad, Vanuatu_2900BP wasn't in my Vanuatu_ancient label because they all have pretty bad coverage; the rest of the Vanuatu samples are very Oceanian. You should use some of the ancient Nepalese samples or XiongNu or something as your East Asian.
    And for the mixing of ancients and moderns in D-stats, fine
    D: outgroup GoyetQ116-1 Ust_Ishim Andaman_100BP/XiongNu/etc. will be 0
    D: outgroup MA1 Ust_Ishim Andaman_100BP/XiongNu/etc. will be significantly positive.

    Surprisingly, the swept haplotypes are entirely devoid of Neanderthal introgression, which implies that a population without Neanderthal admixture contributed the swept haplotypes.
    Or the Neanderthal version of those haplotypes were swept because they were disadvantageous?
    Last edited by Kale; 05-06-2019 at 02:32 PM.
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    Quote Originally Posted by Chad Rohlfsen View Post
    The best way to fit it is Ust-Ishim branching from West Eurasians. Goyet is closer to Ust-Ishim than ENA is and closer to ENA than Ust-Ishim is. Makes perfect sense. SunghirIV being further from both Ust-Ishim and ENA than Goyet is exactly as expected for Bssal Eurasian.
    Chad, "Basal West Eurasian" is an interesting result for Ust Ishim. I have previously been harping on a similar concept, which I have called "Ancient Central Eurasian", or Basal Crown Eurasian, in other posts. Ust Ishim and Sunghir are dead ends because they wandered off the reservation too soon, so to speak. But presumably, if we get DNA from 50kya and earlier from the Pontic-Caspian-Aral Sea region, we will find a population that was the direct ancestor of both ANE and Aurignacians.

    One thing unanswered within the East Eurasian phylogeny, is "Northeast Asian"/Neosiberian ancestry just SE Asian HG who ventured north and admixed with Paleolithic ANE? Or is the Northeast Asian/SE Asian differentiation due to a 2-way cleavage and tens of thousands of years of drift between the unified Paleolithic E Eurasian population?

    Tianyuan seems more closely related to Vanuatu/Ami-like people than to Baikal HG and Devils Gate, right?

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    Quote Originally Posted by K33 View Post
    Tianyuan seems more closely related to Vanuatu/Ami-like people than to Baikal HG and Devils Gate, right?
    Negative. Tianyuan is just about equally related to all East Asian (Han, Ami, Ulchi, Baikal_EN, Sherpa, Japanese, Hezhen, Oroqen, etc.)
    Tianyuan is less related to Onge and Onge-like groups, and also perhaps Jomon to some degree, though there's only 1 decent quality Jomon sample so I'd hesitate to place any bets on that.

    One thing unanswered within the East Eurasian phylogeny, is "Northeast Asian"/Neosiberian ancestry just SE Asian HG who ventured north and admixed with Paleolithic ANE? Or is the Northeast Asian/SE Asian differentiation due to a 2-way cleavage and tens of thousands of years of drift between the unified Paleolithic E Eurasian population?
    If East-Asian/Northeast-Asians are differentiated from Southeast-Asians/Oceanians on the basis of ANE ancestry (which is primarily West Eurasian), we should expect East Asians to pull towards other West Eurasians as well.
    Using the range of affinities among 27 East/Northeast-Asian populations as well as Onge; Onge is within the East/Northeast-Asian range of affinities in relation to the following populations...
    Ust_Ishim, GoyetQ116-1, Gravettians (Vestonice16, Ostuni1, and KremsWA3 grouped), Kostenki14, Sunghir
    Below the East/Northeast-Asian range of affinities in relation to these populations...
    Barcin_N, Levant_N, Iran_N, CHG, Taforalt, MA1, EHG, WHG, Native-Americans, Jomon, Tianyuan
    And above the East/Northeast-Asian range of affinities in relation to Papuan
    Last edited by Kale; 05-07-2019 at 03:45 AM.
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