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Thread: okarinaofsteiner's East Eurasian GEDmatch megathread

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    I also did polynomial regression fits on the populations with larger sample sizes to see if there was any relationship between '% East Eurasian' and 'northern/southerness'. There weren't any clear patterns for the Japanese or Korean samples (didn't even bother doing this for the Korean samples because there was so little non-East Eurasian "noise"/admixture). But there were some patterns for the Chinese, Vietnamese, and Filipino samples.

    The most northern-shifted and most southern-shifted Chinese samples have slightly more non-East Eurasian admixture, which I now know to be from "Silk Road" West Eurasian admixture in inland Northern Han (Shanxi, Shaanxi, Gansu, etc. but also the coastal northern provinces to a lesser extent), and slightly higher levels of trace Hoabinhian/Papuan-like ancestry closer to the Vietnam/Myanmar border.

    The most northern-shifted Vietnamese are almost certainly Hoa (ethnic Chinese), who generally lack the 1-2% "South Indian" than most Kinh samples have. More "southern-shifted" Kinh don't seem noticeably more Hoabinhian-shifted than more "northern-shifted" Kinh. The trendline is probably due to a few unusually "southern-shifted" outliers in my dataset who might have some Khmer, Cham, or other ethnic minority like ancestry?

    The most northern-shifted and southern-shifted Filipino samples are the most "pure East Eurasian". The more "pure Austronesian" samples are obviously going to score less on non-East Eurasian components; I think these were a bit more likely to have "precolonial" sounding surnames? The more "northern-shifted" samples probably have more colonial-era Chinese ancestry, which would also cause them to score less on Hoabinhian, Papuan, and West Eurasian.




    Individual "Han Chinese" results, sorted based on how they score on my N-S cline. Here the "HK/Canto" (n = 37) and "Taiwan [ROC]" (n = 31) subsets are displayed separately.


    Individual "Han Chinese" results, sorted based on how they score on my N-S cline. This excludes the "HK/Canto" and "Taiwan [ROC]" subsets. I think I'm around 53?


    Individual "Japanese" results, sorted based on how they score on my N-S cline.


    Individual "Vietnamese" results, sorted based on how they score on my N-S cline.


    Individual "Filipino" results, sorted based on how they score on my N-S cline.
    Last edited by okarinaofsteiner; 05-10-2021 at 08:29 PM.

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    Quote Originally Posted by okarinaofsteiner View Post
    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).




    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)





    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, 31.13% 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, 32.17% 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

    There was a typo in the quoted section. Spotted it too late to edit the original post, so I edited it out here.




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

    For reference, this is how La386 (Hoabinhian sample from Laos) and the Onge reference populations score:

    La368: 42.70% S_Ind, 8.40% Australoid, 4.91% Melano_Polynesian, 12.16% AN, 11.79% S_EA. 29.07% East Eurasian (~30% shared drift with "East Eurasian") and the N-S cline for the East Eurasian ancestry is 0.5760.

    Onge: 54.36% S_Ind, 13.17% Australoid, 0.98% Melano_Polynesian, 13.57% AN, 13.21% S_EA. 28.55% East Eurasian (~30% shared drift with "East Eurasian") and the N-S cline for the East Eurasian ancestry is 0.6882.

    This is what that looks like compared to actual East Eurasians:
     


    It's worth pointing out that MDLP K23b models modern-day Onge and prehistoric Hoabinhian as being "part East Asian" and not just some combination of AASI-like "S_Indian", "Australoid", and "Melano_Polynesian". It means AASI is an imperfect proxy for the non-Papuan, non-Australian aborigine ancestry/genetic drift in this population.

    Modern-day SE Asians generally score more "S_Ind" than "Australoid" + "Melano_Polynesian" combined, often by similar ratios as in La368 and Onge. This is probably more true for Vietnamese than other SE Asian groups which might have non-negligible amounts of actual South Asian/subcontinental ancestry.

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    Quote Originally Posted by okarinaofsteiner View Post
    La368: 42.70% S_Ind, 8.40% Australoid, 4.91% Melano_Polynesian, 12.16% AN, 11.79% S_EA. 29.07% East Eurasian (~30% shared drift with "East Eurasian") and the N-S cline for the East Eurasian ancestry is 0.5760.
    Which components did you add to get total East Eurasian? 12.16 + 11.79 = 23.95 ... how did you get 29.07?
    Last edited by thejkhan; 05-12-2021 at 04:29 PM. Reason: 12.61 -> 12.16

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    Quote Originally Posted by thejkhan View Post
    Which components did you add to get total East Eurasian? 12.61 + 11.79 = 24.48 ... how did you get 29.07?
    My “East Eurasian” = Austronesian + South_East_Asian + Tungus_Altaic + East_Siberian + Paleo_Siberian.

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    Quote Originally Posted by okarinaofsteiner View Post
    My “East Eurasian” = Austronesian + South_East_Asian + Tungus_Altaic + East_Siberian + Paleo_Siberian.
    How do you explain the significantly more West Eurasian in Lao_Hoabinhian vs Onge?

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    Quote Originally Posted by thejkhan View Post
    How do you explain the significantly more West Eurasian in Lao_Hoabinhian vs Onge?
    La368 is ~5% more West Eurasian (EHG + EEF + Caucasian + N_African + Near_East + S_Central_Asian) and ~5% more African than Onge. I'm guessing that's more of an issue with the calculator working with ancient samples.

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    Quote Originally Posted by okarinaofsteiner View Post
    La368 is ~5% more West Eurasian (EHG + EEF + Caucasian + N_African + Near_East + S_Central_Asian) and ~5% more African than Onge. I'm guessing that's more of an issue with the calculator working with ancient samples.
    I see the same trend modeling Hoabinhian and Onge with Vahaduo + G25.

    Capture.PNG

    More Kostenki in Hoabinhian, and some Natufian too which is non-existent in Onge. Neither score any Yoruba.
    Last edited by thejkhan; 05-12-2021 at 09:09 PM. Reason: regarding Yoruba score

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    More Global PCA plots for your viewing pleasure...



    Global PCA of all of my original East Eurasian samples (CJKVP + Nusantara + other samples that aren't obviously part Euro), plotted with some Central Asian and Latin American GEDmatch samples provided by @Tsakhur.



    Same as the above, but with La368 (Hoabinhian) and Ikawazu Jomon plotted for reference. Note how La368 (Hoabinhian) is close to a straight line between "South_Indian" and "Australoid" + "Melano_Polynesian", but slightly closer to the former than the latter. By contrast, the Jomon samples are close to the modern-day Cambodians.




    At this point, my interest shifted towards trying to figure out what kind of regional/spatial structure there was within the Han Chinese results I had. This wasn't possible for my Japanese/Korean/Vietnamese/Filipino samples because I had fewer samples on hand, and no way to determine where their regional ancestry within their country(ies) of origin might be from. However, many of the Chinese samples I found were associated with certain cities or provinces- either because they had names like "Guangxi girl", or because their names used Taiwan/Hong Kong/non-Mainland China specific romanization schemes.



    This is a global PCA plot of some of the "Han Chinese" samples in my original dataset, plus some additional samples I stumbled upon some time later, in early 2019. I know the labels look a bit confusing and all over the place, but I wanted to see if there were any obvious regional patterns on the global PCA.

    The labeled samples are individuals of known regional/provincial ancestry, and they didn't seem to fall into clear regional clusters due to having variable levels of noise in their MDLP K23b results. But based on how the "northern" Chinese, "Taiwanese [ROC]", and "HK/Canto" subsets scored, I was able to guess where I might expect Han Chinese from certain regions to plot on the global PCA relative to other East Asians.

    1) Some northern Chinese (possibly inland?)- shifted left on PC1 and down on PC2 from the "main series". (9.80, 5.60) to (10.00, 5.85)
    2) Many northern/eastern Chinese (coastal)- rightmost end on PC1 of the "main series", closest to the Korean samples. (10.00, 5.90) to (10.05, 5.95)
    3) Northern shifted end of the "Taiwanese" cluster (probably south-central?)- right end of TW/ROC cluster [red circles]. (9.90, 5.90) to (9.96, 5.95)
    4) Southern shifted end of the "Taiwanese" cluster (around Fujian and Guangdong??)- left end of TW/ROC cluster [red circles]. (9.85, 5.90)
    5) Most southern-shifted portion of the "main series". Yue-speaking part of Guangdong? Most of the HK/Canto cluster [triangles]. (9.80, 5.85) to (9.90, 5.90)
    Last edited by okarinaofsteiner; 05-16-2021 at 03:10 AM.

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    Quote Originally Posted by okarinaofsteiner View Post
    More Global PCA plots for your viewing pleasure...



    Global PCA of all of my original East Eurasian samples (CJKVP + Nusantara + other samples that aren't obviously part Euro), plotted with some Central Asian and Latin American GEDmatch samples provided by @Tsakhur.



    Same as the above, but with La368 (Hoabinhian) and Ikawazu Jomon plotted for reference. Note how La368 (Hoabinhian) is close to a straight line between "South_Indian" and "Australoid" + "Melano_Polynesian", but slightly closer to the former than the latter. By contrast, the Jomon samples are close to the modern-day Cambodians.




    At this point, my interest shifted towards trying to figure out what kind of regional/spatial structure there was within the Han Chinese results I had. This wasn't possible for my Japanese/Korean/Vietnamese/Filipino samples because I had fewer samples on hand, and no way to determine where their regional ancestry within their country(ies) of origin might be from. However, many of the Chinese samples I found were associated with certain cities or provinces- either because they had names like "Guangxi girl", or because their names used Taiwan/Hong Kong/non-Mainland China specific romanization schemes.



    This is a global PCA plot of some of the "Han Chinese" samples in my original dataset, plus some additional samples I stumbled upon some time later, in early 2019. I know the labels look a bit confusing and all over the place, but I wanted to see if there were any obvious regional patterns on the global PCA.

    The labeled samples are individuals of known regional/provincial ancestry, and they didn't seem to fall into clear regional clusters due to having variable levels of noise in their MDLP K23b results. But based on how the "northern" Chinese, "Taiwanese [ROC]", and "HK/Canto" subsets scored, I was able to guess where I might expect Han Chinese from certain regions to plot on the global PCA relative to other East Asians.

    1) Some northern Chinese (possibly inland?)- shifted left on PC1 and down on PC2 from the "main series". (9.80, 5.60) to (10.00, 5.85)
    2) Many northern/eastern Chinese (coastal)- rightmost end on PC1 of the "main series", closest to the Korean samples. (10.00, 5.90) to (10.05, 5.95)
    3) Northern shifted end of the "Taiwanese" cluster (probably south-central?)- right end of TW/ROC cluster [red circles]. (9.90, 5.90) to (9.96, 5.95)
    4) Southern shifted end of the "Taiwanese" cluster (around Fujian and Guangdong??)- left end of TW/ROC cluster [red circles]. (9.85, 5.90)
    5) Most southern-shifted portion of the "main series". Yue-speaking part of Guangdong? Most of the HK/Canto cluster [triangles]. (9.80, 5.85) to (9.90, 5.90)
    Fascinating. What is the ethnicity of the Nusantara individual that plot a bit near and as Western-shifted as the Kyrgyz and Altaian samples? He/she seem to possess a lot of South Asian and West Eurasian ancestry for her/him to plot really Western compared to other Nusantara samples and seem rather distant from the East Asian clusters.

    Also what are the nationalities/ethnicities of the "OTHER Gedmatch" individuals that plot near and seem to be as West Eurasian as some Altaians, Tuvans and Mongols?

    Btw, the Latin American samples that is located close to the Altaian, Kyrgyz and Kazakh or even more Western Eurasian than them are actually predominantly Amerindian individuals with some European ancestry. I believe the Latin American individual that plot in the Altaian cluster is literally a Native American with very European admix. It really proves that Amerindians have significant ancient Western Eurasian ancestry mainly from their ANE ancestors.
    Last edited by Tsakhur; 05-16-2021 at 12:38 PM.

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    Quote Originally Posted by Tsakhur View Post
    Fascinating. What is the ethnicity of the Nusantara individual that plot a bit near and as Western-shifted as the Kyrgyz and Altaian samples? He/she seem to possess a lot of South Asian and West Eurasian ancestry for her/him to plot really Western compared to other Nusantara samples and seem rather distant from the East Asian clusters.
    This individual wasn't in my original n=18 Nusantara dataset, and they score 69.02% East Eurasian (the lowest scoring person is in my original n=18 dataset is 67.32% and they have a lot of Papuan-like ancestry). This person seems ~12% Euro.

    Quote Originally Posted by Tsakhur View Post
    Also what are the nationalities/ethnicities of the "OTHER Gedmatch" individuals that plot near and seem to be as West Eurasian as some Altaians, Tuvans and Mongols?
    Two of them have Burmese-sounding names and two of them seem to be Thai. The likely Burmese samples are at (6.85, 1.98) and (7.46, 2.65)- they score ~62% and ~72% East Eurasian respectively. The other 2 are probably not Burmese because they score higher on my N-S East Eurasian cline- those two are around 77% and 66% East Eurasian.

    On an unrelated note, one of the "Filipino" samples in my original n=80 dataset is Guamanian/Chamorro, but has partial Filipino ancestry through a grandparent. This person scored 54% AN, 20% S_EA, 6% T_A, 3-4% Amerind, and ~81% East_Eurasian.

    Quote Originally Posted by Tsakhur View Post
    Btw, the Latin American samples that is located close to the Altaian, Kyrgyz and Kazakh or even more Western Eurasian than them are actually predominantly Amerindian individuals with some European ancestry. I believe the Latin American individual that plot in the Altaian cluster is literally a Native American with very European admix. It really proves that Amerindians have significant ancient Western Eurasian ancestry mainly from their ANE ancestors.
    That may be true, but it isn't obvious from where the "Amerind" ancestry component plots on the Global PCA. It is directly below "Austronesian" and "South_East_Asian" on the PC2 axis, at somewhere around (9.60, 3.80) or so.

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