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Thread: okarinaofsteiner's East Eurasian GEDmatch megathread

  1. #31
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    I think Jomon ancestry being less drifted than other East Asian components often creates this pseudo-AASI noise, sometimes if I run Han on G25 they score some low Onge in Shandong which goes away if I add Jomon. Perhaps that's an explanation for the scores of some Japanese as well.

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    Quote Originally Posted by Max_H View Post
    I think Jomon ancestry being less drifted than other East Asian components often creates this pseudo-AASI noise, sometimes if I run Han on G25 they score some low Onge in Shandong which goes away if I add Jomon. Perhaps that's an explanation for the scores of some Japanese as well.
    Yeah this is how one of the Ikawazu Jomon GEDmatch samples scores on MDLP K23b




    I think this is HarappaWorld for the other Ikawazu Jomon sample on GEDmatch


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  4. #33
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    Quote Originally Posted by okarinaofsteiner View Post
    Yeah this is how one of the Ikawazu Jomon GEDmatch samples scores on MDLP K23b




    I think this is HarappaWorld for the other Ikawazu Jomon sample on GEDmatch

    Considering that Jomon and Onge or even AASI probably share some deep uniparental connection it makes sense to me. Though I remember Fu's paper on East Asia last year found little direct affinity Onge-Jomon based on D stats which probably means that whatever they share is very old and it might instead share more with AASI or Tibetan Hunter Gatherers that get interpreted as Onge. It's still something that confuses me tbh.

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    Quote Originally Posted by Max_H View Post
    I think Jomon ancestry being less drifted than other East Asian components often creates this pseudo-AASI noise, sometimes if I run Han on G25 they score some low Onge in Shandong which goes away if I add Jomon. Perhaps that's an explanation for the scores of some Japanese as well.
    The Jomon are not ancestral to Han, and Jomon likely shows up due to shared "onge-related ancestry" in East Asia. Jomon would be a greater fit in that their genome is majority North-East Asian-like, and calculators would pick Jomon up rather than other samples used if both are used together. It's in a similar fashion how a lot of runs of my own genome would pick Iron Age steppe samples (who have East Asian admixture), like Saka (not ancestral) rather than Steppe_MLBA samples (ancestral to me but no East Asian) because I share both Steppe_MLBA + East Asian admixture. Also keep in mind, most Northern Han also have 4-5% West Eurasian admixture (Steppe_MLBA like), probably picked up in ancient times from populations such as the Xiongnu or similar nomads so that needs to be accounted for as well.

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    Quote Originally Posted by okarinaofsteiner View Post
    Description of East Eurasian ancestry components:
    • "Arctic": indigenous peoples of the Arctic. Peaks in Eskimo/Inuit (~90%+) and Chukchi (~60%) in Asia
    • "Paleo_Siberian": northeast Russian Far East. Peaks in Itelmen, Koryak (~90%), and Chukchi (~40%)
    • "East_Siberian": general native Siberian. Peaks in Nganassan (~97%) and Nenets (60-70%)
    • "Tungus_Altaic": general "NE Asian/CJK". Peaks in Ulchi (62%) and Daur + Hezhen (~50%)
    • "South_East_Asia": general Continental East Asia + Tibeto-Burman. Peaks in Naga (~70%), Naxi + Yi, Lahu, and Tibetans (~63%)
    "Austronesian": general Southern Mongoloid. Peaks in Taiwanese aborigines and in Igorot (~100%)

    Quote Originally Posted by okarinaofsteiner View Post
    General comments on the GEDmatch samples:

    [LIST=1][*]@Tsakhur and @Sage75 are both right about Filipinos' autosomal DNA. Filipinos are more Australoid and Melano_Polynesian admixed than Mainland SE Asians but most are at least 90% East Eurasian. The ones with native-sounding names tend to score higher on Austronesian; some score over 60%. I'm guessing the Filipinos scoring more than 10% Tungus_Altaic are Chinese mixed. Many are Hispanic/LatinAm mixed and can score 3-5% European/Amerindian/SSA.[*]

    CJKVP East Asia- T_A vs Austronesian graph


    CJKVP East Asia- % East Eurasian vs N-S cline graph

    Just saw this Razib Khan blog post- A new paper, Genomic insights into population history and biological adaptation in Oceania, is worth reading.
    I’m going to sidestep the new inference that Austronesian expansion may predate the movement out of Taiwan.


    https://www.nature.com/articles/s41586-021-03236-5

    We infer that the East Asian ancestors of Pacific populations may have diverged from Taiwanese Indigenous peoples before the Neolithic expansion, which is thought to have started from Taiwan around 5,000 years ago2,3,4
    https://www.pnas.org/content/118/13/e2026132118

    Here, we report ∼2.3 million genotypes from 1,028 individuals representing 115 indigenous Philippine populations and genome-sequence data from two ∼8,000-y-old individuals from Liangdao in the Taiwan Strait... The ancestors of Cordillerans diverged from indigenous peoples of Taiwan at least ∼8,000 y ago, prior to the arrival of paddy field rice agriculture in the Philippines ∼2,500 y ago, where some of their descendants remain to be the least admixed East Asian groups carrying an ancestry shared by all Austronesian-speaking populations. These observations contradict an exclusive “out-of-Taiwan” model of farming–language–people dispersal within the last four millennia for the Philippines and Island Southeast Asia.
    This actually explains why Amis, Atatyal, and Igorot score ~100% Austronesian in MDLP K23b, while "mainstream" lowland Filipinos like Ilocanos and Tagalogs usually score less than 60%. Most rice-farming Austronesian groups have additional "non-pure Austronesian" East Eurasian ancestry from the southward expansion of rice agriculture, which MDLP K23b probably models as "South_East_Asian" due to being distinct from the Cordilleran "pure Austronesian" ancestry of Igorot and Amis.

    This raises questions of how lowland Plains Taiwanese aborigines would have scored on MDLP K23b. I'm guessing they would be less pure "Austronesian" and more "South_East_Asian" than Amis and Atayal, although I have no idea if they'd be a good proxy for the donor population that introduced "non-pure Austronesian" ancestry to modern-day Filipinos.
    Last edited by okarinaofsteiner; 04-18-2021 at 02:50 AM.

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  9. #36
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    Quote Originally Posted by okarinaofsteiner View Post
    Just saw this Razib Khan blog post- A new paper, Genomic insights into population history and biological adaptation in Oceania, is worth reading.
    I’m going to sidestep the new inference that Austronesian expansion may predate the movement out of Taiwan.


    https://www.nature.com/articles/s41586-021-03236-5



    https://www.pnas.org/content/118/13/e2026132118



    This actually explains why Amis, Atatyal, and Igorot score ~100% Austronesian in MDLP K23b, while "mainstream" lowland Filipinos like Igorot usually score less than 60%. Most rice-farming Austronesian groups have additional "non-pure Austronesian" East Eurasian ancestry from the southward expansion of rice agriculture, which MDLP K23b probably models as "South_East_Asian" due to being distinct from the Cordilleran "pure Austronesian" ancestry of Igorot and Amis.

    This raises questions of how lowland Plains Taiwanese aborigines would have scored on MDLP K23b. I'm guessing they would be less pure "Austronesian" and more "South_East_Asian" than Amis and Atayal, although I have no idea if they'd be a good proxy for the donor population that introduced "non-pure Austronesian" ancestry to modern-day Filipinos.
    Hmm, thanks for linking this. So would they be closer to Liangdao-type population?

    And if so which ancient population would be closest to Yangtze river rice farmers? Would they be more northern than Austronesians?

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    Quote Originally Posted by Max_H View Post
    Hmm, thanks for linking this. So would they be closer to Liangdao-type population?

    And if so which ancient population would be closest to Yangtze river rice farmers? Would they be more northern than Austronesians?


    From https://www.biorxiv.org/content/10.1...11.08.373225v1

    I have absolutely no idea about the Yangtze rice farmers (I’m guessing they would be somewhere below the Austronesians), but it looks like Neolithic Fujian clusters around where modern-day Tagalogs do (who are more NEA-shifted than Visayans and Ilocanos), while Neolithic Coastal Fujian + Taiwan cluster with Visayan and Dusun/Murut? In any case Neolithic Fujian/Taiwan was clearly Austronesian-related.

    I have more stuff from Anthroscape to post here- will do so over the next few days to weeks.

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    Quote Originally Posted by okarinaofsteiner View Post


    From https://www.biorxiv.org/content/10.1...11.08.373225v1

    I have absolutely no idea about the Yangtze rice farmers (I’m guessing they would be somewhere below the Austronesians), but it looks like Neolithic Fujian clusters around where modern-day Tagalogs do (who are more NEA-shifted than Visayans and Ilocanos), while Neolithic Coastal Fujian + Taiwan cluster with Visayan and Dusun/Murut? In any case Neolithic Fujian/Taiwan was clearly Austronesian-related.

    I have more stuff from Anthroscape to post here- will do so over the next few days to weeks.
    On the PCA it almost seems as Fujian_N is more NEA-shifted than Ami while in the Wang et al recent publication on East Asia, Ami are about 20% NEA in ancestry. As for Visayans and Ilocanos, I think they have higher southern ancestry not from the mainland but from the Philippines itself.

    Looking forward to your posts!

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    Quote Originally Posted by Max_H View Post
    On the PCA it almost seems as Fujian_N is more NEA-shifted than Ami while in the Wang et al recent publication on East Asia, Ami are about 20% NEA in ancestry. As for Visayans and Ilocanos, I think they have higher southern ancestry not from the mainland but from the Philippines itself.

    Looking forward to your posts!
    Thanks! I think the "Demographic History of Southern Chinese" PCA plot shows how different populations score on MDLP K23b. Ami is further away from Visayans and Ilocanos, which also score higher on "South_East_Asian" and lower on "Austronesian" than Ami in MDLP K23b (and therefore are closer to Mainland SE Asians and Han Chinese).



    Quote Originally Posted by okarinaofsteiner View Post
    Posting my full East Eurasian dataset from Sept 2018 now. All MDLP K23b data samples were obtained through the One-to-Many DNA Comparison tool on GEDmatch Genesis during 2018. I verified the ethnicity/nationality of each sample by checking their listed name, email address (incl. foreign country email domains), and cross-checking their calculator results with the reference populations.

    I can't guarantee that all of the gathered samples are of the ethnic background I assigned them as, since I didn't contact any of the sample providers directly. I also can't guarantee that these are all unrelated individuals, even though One-to-Many lets you see if any matches are close relatives.

    GEDmatch One-to-Many Sample count:
    • Cambodia (n = 14)
    • Nusantara (n = 22)
    • Japanese (n = 31)
    • Korean (n = 52)
    • Northern Chinese (n=94) (assigned based on MDLP K23b results, not known ancestry)
    • Southern Chinese (n = 160) (assigned based on MDLP K23b results, not known ancestry)
    • Vietnamese (n = 80)
    • Filipino (n = 68)


    Means and Medians for my East Asian population samples | N-S cline vs % East Eurasian. I think the grey dots are "normalized" medians, calculated from the aggregate results (sum of all the ancestry components), whereas the black dots are calculated from finding the median of each ancestry component.


    Means and Medians for my East Asian population samples | Global PCA cline. Means are shifted away from the East Eurasian ancestry components because of outliers with more "non-East Eurasian" noise and/or more Hoabinhian/Papuan/South Asian-like ancestry.





    Japanese mean- 42.12% T_A, 35.13% S_EA, 19.51% AN, 0.84% Paleo_Sib, 0.60% E_Sib, 0.46% Amerind, 0.42% S_Indian. 98.20% East Eurasian, 0.3702
    Japanese median- 42.07% T_A, 35.09% S_EA, 19.47% AN, 0.72% Paleo_Sib, 0.14% E_Sib, 0.12% Amerind, 0% S_Indian. 98.24% East Eurasian, 0.3687

    Korean mean- 40.73% S_EA, 38.24% T_A, 18.49% AN, 1.68% E_Sib, 0.21% Paleo_Sib, 0.19% Amerind. 99.36% East Eurasian, 0.3816
    Korean median- 40.87% S_EA, 38.21% T_A, 18.35% AN, 1.67% E_Sib, 0% Paleo_Sib, 0% Amerind. 99.80% East Eurasian, 0.3798

    "N"_Chinese mean- 46.39% S_EA, 29.94% T_A, 21.22% AN, 0.91% E_Sib, 0.18% Paleo_Sib, 0.21% Amerind. 98.62% East Eurasian, 0.4448
    "N"_Chinese median- 46.25% S_EA, 29.95% T_A, 21.06% AN, 0.36% E_Sib, 0% Paleo_Sib, 0% Amerind. 99.31% East Eurasian, 0.4456

    "S"_Chinese mean- 46.99% S_EA, 33.15% AN, 18.85% T_A, 0.91% E_Sib, 0.10% Paleo_Sib, 0.21% Amerind. 99.25% East Eurasian, 0.5694
    "S"_Chinese median- 46.93% S_EA, 32.59% AN, 19.51% T_A, 0% E_Sib, 0% Paleo_Sib, 0.21% Amerind. 99.39% East Eurasian, 0.5607

    TW [ROC] mean- 46.71% S_EA, 32.17% AN, 21.18% T_A, 0.08% S_Ind, 0.11% Aus, 0.17% E_Sib, 0.14% Paleo_Sib, 0.07% Amerind. 99.34% East Eurasian, 0.5485
    TW [ROC] median- 47.06% S_EA, 31.13% AN, 20.37% T_A, 0% S_Ind, 0% Aus, 0% E_Sib, 0% Paleo_Sib, 0% Amerind. 99.69% East Eurasian, 0.5583

    HK/Canto mean- 46.50% S_EA, 33.62% AN, 18.47% T_A, 0.14% S_Ind, 0.11% Aus, 0.23% E_Sib, 0.09% Paleo_Sib, 0.17% Amerind. 98.92% East Eurasian, 0.5733
    HK/Canto median- 46.45% S_EA, 35.62% AN, 16.74% T_A, 0% S_Ind, 0% Aus, 0% E_Sib, 0% Paleo_Sib, 0% Amerind. 99.15% East Eurasian, 0.5983

    Viet mean- 45.04% S_EA, 40.61% AN, 10.14% T_A, 2.05% S_Ind, 0.45% Aus, 0.17% Mel-Poly, 0.13% E_Sib, 0.22% Paleo_Sib, 0.17% Amerind. 96.14% East Eurasian, 0.6549
    Viet median- 45.06% S_EA, 41.07% AN, 9.69% T_A, 1.93% S_Ind, 0.24% Aus, 0% Mel-Poly, 0% E_Sib, 0% Paleo_Sib, 0% Amerind. 96.45% East Eurasian, 0.6601

    Filipino mean- 52.51% AN, 29.88% S_EA, 7.46% T_A, 2.96% S_Ind, 1.25% Aus, 2.44% Mel-Poly, 0.27% Amerind. 90.11% East Eurasian, 0.7471
    Filipino median- 52.67% AN, 29.21% S_EA, 7.15% T_A, 2.78% S_Ind, 1.08% Aus, 2.28% Mel-Poly, 0% Amerind. 90.06% East Eurasian, 0.7544

    Not posting the "Cambodian" and "Nusantara" means/medians because the sample sizes were pretty small (< 20).
    Last edited by okarinaofsteiner; 05-10-2021 at 08:28 PM.

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