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Thread: okarinaofsteiner's East Eurasian GEDmatch megathread

  1. #21
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    Quote Originally Posted by Max_H View Post
    Are you sure this is reliable? Is it not odd that some East Asians get African ancestry? Also Japanese getting South Indian? from where/when?
    HarappaWorld is a South Asia-centric calculator, so the "noise" it picks up among non-South Asian populations might not be super reliable. I think some Dodecad calculators also assign random "African" noise to Han Chinese GEDmatch samples.

    I do think the "Papuan-like/Onge-like" noise these GEDmatch calculators are picking up reflects some sort of Basal ancestry that's found among South Asians, East Asians, Oceanians, Central Asians, etc. I see no reason why some Han Chinese wouldn't have trace levels of Hoabinhian, Jomon, or "Ancient Tibetan"-like ancestry if neighboring East Asian populations also have them.

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    I'm surprised that shanxi and gansu hans are the most northern shifted while the ones from manchuria like HLJ, jilin, liaoning are not. or maybe im misreading the plot.
    Also it seems most of China is quite northern shifted in general. the northern cluster reaches till shanghai, Hubei, Zhejiang. Traditionally these are considered southern regions if im not wrong.

    Seems like Fujian and Hunan and Fujian are the halfway point between northern and southern clusters. The 'northerness' decreases drastically further south of Hunan and Fujian.

  4. #23
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    Quote Originally Posted by naruto View Post
    I'm surprised that shanxi and gansu hans are the most northern shifted while the ones from manchuria like HLJ, jilin, liaoning are not. or maybe im misreading the plot.
    Also it seems most of China is quite northern shifted in general. the northern cluster reaches till shanghai, Hubei, Zhejiang. Traditionally these are considered southern regions if im not wrong.

    Seems like Fujian and Hunan and Fujian are the halfway point between northern and southern clusters. The 'northerness' decreases drastically further south of Hunan and Fujian.
    It's hard to tell because all of the northern provinces are so close to each other. I made my own map of how "northern"/"southern" the Han Chinese of different provinces are- mostly based on Chinese adoptees on GEDmatch. The northern provinces are less accurate because ~90% of the adoptees are from the southern provinces.



    I will post more information about this later.

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  6. #24
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    Quote Originally Posted by okarinaofsteiner View Post
    HarappaWorld is a South Asia-centric calculator, so the "noise" it picks up among non-South Asian populations might not be super reliable. I think some Dodecad calculators also assign random "African" noise to Han Chinese GEDmatch samples.

    I do think the "Papuan-like/Onge-like" noise these GEDmatch calculators are picking up reflects some sort of Basal ancestry that's found among South Asians, East Asians, Oceanians, Central Asians, etc. I see no reason why some Han Chinese wouldn't have trace levels of Hoabinhian, Jomon, or "Ancient Tibetan"-like ancestry if neighboring East Asian populations also have them.
    I was mostly talking about the African, I doubt there has been any San gene flow into China for example. Except maybe some very low gene flow via Middle East?

    As for the South Asian, I also find it odd I am not aware of many Shandong people scoring South Asian in Wegene but could be wrong. Could some of that noise be incomplete lineage sorting?

    I reckon, if Japanese also have it then in reality it reflects Jomon-like ancestry, which would go with the shared Ydna D among Japanese and the Onge populations of the Andaman islands. Ancient Tibetan probably exists in low levels in Shanxi and Gansu imo.

  7. #25
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    Quote Originally Posted by naruto View Post
    I'm surprised that shanxi and gansu hans are the most northern shifted while the ones from manchuria like HLJ, jilin, liaoning are not. or maybe im misreading the plot.
    Also it seems most of China is quite northern shifted in general. the northern cluster reaches till shanghai, Hubei, Zhejiang. Traditionally these are considered southern regions if im not wrong.

    Seems like Fujian and Hunan and Fujian are the halfway point between northern and southern clusters. The 'northerness' decreases drastically further south of Hunan and Fujian.
    NE China should be close to Shandong since most of the people there descent from Han settlers during the late Qing dynasty. Shandong is slightly less northern than Shanxi, it could also be that Shanxi has some Siberian ancestry more than Shandong.

    Genetic south China (if one can say that) is mostly Fujian, Guangdong, Hainan and Guangxi, maybe parts of Yunnan and Guizhou, while traditionally southern China is just meant for the areas south of the Yangtze river.

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  9. #26
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    There was an interesting article on Han Chinese population genetics released sometime in 2018 , based on low-pass, noninvasive prenatal testing samples from various women who were Chinese nationals.

    Among other things they compared the allele distribution of Han women from various provinces with 5 of the 1000 Genomes populations: CHB (Han Chinese from Beijing), CHS (Southern Han Chinese), JPT (ethnic Japanese from Tokyo), CDX (ethnic Dai from Xishuangbanna Yunnan), and KHV (Kinh Vietnamese from Ho Chi Minh City). This basically shows how genetically similar different Han Chinese subgroups are to those populations.

    Screenshots of allele sharing patterns between Han and 1000 Genomes East Asian groups:


    ARTICLE| VOLUME 175, ISSUE 2, P347-359.E14, OCTOBER 04, 2018
    Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History
    Open Archive DOI:https://doi.org/10.1016/j.cell.2018.08.016


    Highlights
    Genome sequencing from low-pass noninvasive prenatal testing samples
    GWAS of 141,431 low-pass genomes reveals 16 unknown genetic associations
    Patterns of clinically relevant viral infection in maternal plasma
    Insights into the genetic structure and history of the Chinese population

    Summary
    We analyze whole-genome sequencing data from 141,431 Chinese women generated for non-invasive prenatal testing (NIPT). We use these data to characterize the population genetic structure and to investigate genetic associations with maternal and infectious traits. We show that the present day distribution of alleles is a function of both ancient migration and very recent population movements. We reveal novel phenotype-genotype associations, including several replicated associations with height and BMI, an association between maternal age and EMB, and between twin pregnancy and NRG1. Finally, we identify a unique pattern of circulating viral DNA in plasma with high prevalence of hepatitis B and other clinically relevant maternal infections. A GWAS for viral infections identifies an exceptionally strong association between integrated herpesvirus 6 and MOV10L1, which affects piwi-interacting RNA (piRNA) processing and PIWI protein function. These findings demonstrate the great value and potential of accumulating NIPT data for worldwide medical and genetic analyses.

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  11. #27
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    As some of you may know I'm a huge fan of the MDLP K23b calculator. It has a lot more ancestry components than many other GEDmatch calculators, which gives it higher resolution. But what makes MDLP K23b really useful is its high number of reference populations (620). Having multiple reference populations for larger ethnic groups is useful for comparing different subgroups within an ethnicity. I don't know of any other calculators that have different Han Chinese reference populations for different language groups or countries like MDLP K23b does. So as an East Asian and ethnic Chinese who's interested in population genetics, this tool has been very useful in learning about how subgroups of different Asian ethnicities differ from each other genetically.


    The MDLP K23b calculator has 23 different reference populations, 21 of which are shown in this graph I found on Anthrogenica. (Some have slightly different names; the ones that aren't shown are Archaic_African and Archaic_Human).

    Using this


    and this


    I was able to create these global PCA plots of the MDLP K23b ancestry components and reference populations.



    This global PCA shows where the East Asian and South Asian reference populations (green) lie on this PCA plot. SE Asian populations are shifted to the left and slightly down compared to East Asians, while Siberian populations are more to the right and also slightly down. The South Asian populations are shown as a cline between "South_Central"Asian/ANI" and "South_Indian/ASI", even though South Asians typically have significant amounts of "EEF", "Caucasian", and "Ancestral_Altaic/ANE" on MDLP K23b as well.
    Last edited by okarinaofsteiner; 04-09-2021 at 05:13 AM.

  12. #28
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    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%)


    "Australoid": Peaks in the Papuan highlands. Non-Papuan Eastern Indonesians and Island SE Asian Negritos generally score 10-20%.

    "Melano-Polynesian": Peaks in the Melanesian islands east of Papua. Non-Papuan Eastern Indonesians and Island SE Asian Negritos generally score ~10%.
    Australian aborigines seem to be a mix of both but slightly more Australoid (~50% Australoid vs ~40% Melano_Polynesian); SE Asians are generally more "Australoid" than "Melano-Polynesian"

    "Amerindian": Native American. Peaks in Asia among Selkup and certain Central Asian groups (~2%).

    "South_Indian": AASI, Onge (~55%), and "East Veddoid". Negritos score 15-20%.

    For the purposes of this thread and in my spreadsheet I defined "East Eurasian" as Paleo_Siberian, East_Siberian, Tungus_Altaic, South_East_Asia, and Austronesian. Arctic and Amerindian are technically still "Mongoloid" in the genetic sense but I wanted to focus on East Asia-specific ancestry components.


    One of the first things I noticed when I started examining my own GEDmatch Genesis results in 2018, and those of my GEDmatch One-to-Many DNA Relatives- was that the Chinese results (and the Han Chinese reference populations) all tended to score similar levels of "South_East_Asia" in MDLP K23b, with most of the variance being in "Tungus_Altaic" and "Austronesian".

    I noticed that Han Chinese have a T_A/Austronesian cline; this basically functions as a North-South cline since almost all Han Chinese score between 45-50% S_EAsian, and the three components T_A, AN, and S_EAsian comprise 95%+ of most individuals’ ancestry in MDLP K23b. I classified samples with more T_A than Austronesian as "Northern" and vicer versa for "Southern" based on how the Han Chinese reference populations scored. I'm pretty sure Han_ and Han_North are from the HGDP dataset , and I think the other South Chinese ones are from the HUGO Pan-Asia SNP Consortium study.

    * Han_North (HGDP): 52.17% S_EA, 15.43% AN, 29.95 T_A, 98.39% East Eurasian
    * Han-Mandarin: 43.51% S_EA, 23.73% AN, 25.29% T_A, 94.59% East Eurasian
    * Hakka (HUGO TW-HB?): 45.23% S_EA, 32.66% AN, 19.67% T_A, 98.89% East Eurasian
    * Chinese_Taiwan (HUGO TW-HA?): 44.18% S_EA, 33.42% AN, 19.59% T_A, 98.6% East Eurasian
    * Han_Singapore (HUGO SG-CN?): 45.54% S_EA, 33.14% AN, 17.67% T_A, 97.93% East Eurasian
    * Han_ (HGDP): 50.37% S_EA, 32.72% AN, 16.41% T_A, 99.82% East Eurasian
    * Cantonese (HUGO CN-GA?): 45.37% S_EA, 38.27% AN, 13.23% T_A, 97.87% East Eurasian



    Out of curiosity, I decided to collect Chinese and other East Asian MDLP K23b results from the GEDmatch One-to-Many database to see how they compared to my own. Won't elaborate on my methodology, but I think a lot of the samples I collected have been removed from public view from now.

    At first glance, there seemed to be a "break" in the Chinese North-South cline, around where there were equal amounts of "Tungus_Altaic" and "Austronesian". I assumed the cluster with more Austronesian broadly represented Han Chinese from south of the Qinling Mountains and Lower Yangtze River, while the cluster with more Tungus_Altaic broadly repsented Han Chinese from north of the Qinling Mountains and the Lower Yangtze.



    Upon further observation, I noticed that actual Chinese samples didn't completely overlap with the reference populations. For example, the "Northern China" like cluster was more Tungus_Altaic and less South_East_Asia than the Han_North and Han-Mandarin reference populations. When I tried splitting my early dataset into 4 smaller clusters, I got:
    1) a "northern" cluster with more T_A than AN closer to Han_North,
    2) a "central" cluster with roughly equal amoutns of T_A and AN positioned closer to Han-Mandarin,
    3) a "south-central" cluster that extended from 2 to the Taiwanese/Hakka/Singapore reference populations,
    4) a "farther south" cluster that extended from the Taiwanese/Hakka/Singapore reference populations to the Cantonese reference population


    For further analysis/ease of displaying information, I created a "North-South" scale for East Asian ancestry, based on the relative proportion of "Tungus_Altaic", "South_East_Asian", and "Austronesian" within the East Asian ancestry component. I did this so it'd be easier to compare different Chinese subgroups to each other, and Chinese from other East/Southeast/Central Asians. It was originally scaled in such a way that a Han Chinese person who was 100% "East Asian" on MDLP K23b and scored equal amounts of "T_A" and "AN" would score 0.5 on my scale. Later I added "East_Siberian" and "Paleo_Siberian" to my scale, weighted more "negatively" than "Tungus_Altaic".

    Below is a chart of the "North-South" scale, versus the "East Asian" (T_A + S_EA + AN + East_Sib + Paleo_Sib) percentage- for the earlier version of my Han Chinese GEDmatch sample dataset. The "online" samples are from Chinese (PRC national) netizens who shared their results on the WeGene forums. Considerably more northern-shifted than the GEDmatch samples, and probably more representative of the Han Chinese in Mainland China.
    Last edited by okarinaofsteiner; 04-09-2021 at 06:54 PM.

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  14. #29
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    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:
    • 7 Tibet/Nepal/Bhutan
    • 4 (South) Chinese/Japanese mix
    • 13 Other Mixed East Asian
    • 16 Thailand/Laos/Myanmar/Hmong
    • 14 Cambodia
    • 22 Nusantara (*probably mostly native Indonesians, but could also be MY, SG, BN, Moros, or Thai Malays)
    • 25 Overseas SEA Chinese (*one person is LatinAm mixed)
    • 31 Japanese
    • 52 Korean
    • 94 Northern Chinese (assigned based on MDLP K23b results, not known ancestry)
    • 160 Southern Chinese (assigned based on MDLP K23b results, not known ancestry)
    • 80 Vietnamese
    • 68 Filipino
    • @redwine, @Shazouzu and @Jortita (found them on GEDmatch)
    • 12 Euro + EastAsian mixes
    • Various non-East Asian samples for the global PCA plots (incl. 6 Latin American mestizos and 10 Central Asians provided by @Tsakhur)



    General comments on the GEDmatch samples:

    1. It was harder to find non-mixed Japanese samples. Many have ASI/Papuan/Melanesian-like "noise" that may reflect Jomon ancestry, which is why there are a lot of "outliers" on the PCA plot.
    2. Koreans are the most homogeneous and have the least non-East Eurasian admixture. They form a tight cluster on the PCA close that partially overlaps with the Japanese but not with the Northern Han.
    3. The Northern Han (labeled as "N_Chinese") have more non-East Eurasian admixture than the Southern Han; many have noticeable East_Siberian, Arctic, and West Eurasian admixture. This is shown on the PCA plots as a downward blue trail from the main CJK line.
    4. The Southern Han are labeled as "Chinese" because most of the Chinese samples I found on GEDmatch were Southern Han and the distribution of Northern Han on the PCA plot stood out to me. Aside from South Chinese from Guangdong and Fujian, they don't have any ASI-like admixture and are equally Papuan/Melanesian-admixed as the Northern Han.
      --> Mainlander outliers aside, Taiwanese generally cluster with the Minnan and Hakka reference populations and HK/Canto generally cluster with the Cantonese and Hakka reference populations. Taiwanese tend to be Austronesian shifted but are also less divergent from the main Chinese cluster on the PCA, while HK/Canto tend to be more non-East Eurasian admixed and Viet/SE Asian shifted.
    5. @redwine was right about the Viet reference populations being off on Tungus_Altaic and Austronesian; they're accurate in terms of predicting where Kinh Vietnamese typically plot on the global PCA though. Non-Hoa Viets are shifted away from the South Chinese on the PCA due to being 1-3% South_Indian, but aside from the Hmong and the more "pure Austronesian" Filipinos they're the most autosomally "CJK East Asian" SE Asians.
    6. @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.
    7. Cambodians and Nusantarans are further away from the "CJK East Asian" cluster on the PCA than Filipinos. Autosomally Indonesians seem to be an hybrid of Filipinos and Cambodians, albeit slightly shifted towards Papuans and Melanesians.
    8. Most Thais, Laotians, Cambodians, Burmese, and West Malaysians/Indonesians score 10-15% "South_Indian"/ASI, which is a significant amount of non-"Mongoloid" admixture. Even Vietnamese and Filipinos tend to score 2-3% "South_Indian" (Filipinos also typically score 2-5% "Australoid" + "Melano_Polynesian"). The only East Asians who commonly scored more than ~1% on any of those components are a few of the Japanese samples, which likely reflects the calculator picking up on Jomon-derived SNPs that are exclusive to Japanese.

      All of these differences shift "Mongoloid" SE Asians farther apart from CJK East Asians than the north-south differences in East Eurasian ancestry among CJK East Asians, because the East Eurasian ancestry components are all very close to each other on the global PCA, whereas "South_Indian" and "Australoid" + "Melano_Polynesian" are quite a bit farther away.






    254 "Han Chinese" GEDmatch samples, with data points of known regional ancestry singled out. T_A vs AN plot. This gave me some idea of what the regional structure of Han Chinese population genetics was. The range and position of the "Guangdong" samples was consistent with where the "Chinese_Taiwan" TW-HA, "Hakka" TW-HB, "Cantonese" CN-GZ, and Chinese Singaporean reference populations plot. All of the northern Chinese samples cluster around the "northernmost" end of the Han Chinese range. (The light green one is of a Chinese immigrant to the US who is of Fuzhounese ancestry, while the red one is from southern Shaanxi province, south of the Qinling mountain range. )
     



    Another version of the above, with ~32 samples of suspected Cantonese speakers labeled "HK/Canto" and ~27 samples suspected to be Taiwanese or ROC-affiliated labeled "TW [ROC]". The "HK/Canto" samples generally fell between the "Cantonese (CN-GZ)" and "Hakka (TW-HB )" ref pops, while the "TW [ROC]" samples that weren't obviously of waishengren ancestry tended to be slightly more T_A shifted than the "Chinese_Taiwan (TW-HA)" ref pop.
     


    Speculative regional clusters for Han Chinese (I made this in late 2018, this was guesswork)





    CJKVP East Asia- T_A vs Austronesian graph


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


    Means and Medians- T_A vs Austronesian graph
     


    Means and Medians- % East Eurasian vs N-S cline graph
     


    East Asians vs Jomon vs Hoabinhian- it was interesting to see how Jomon and Hoabinhian scored on this calculator. This doesn't literally mean Jomon is ~70% "East Asian" or Hoabinhian is 30% "East Asian". Rather, Jomon and Hoabinhian share a certain amount of drift with Proto-East Asian that is distinct from AASI or Papuan proper. Although Jomon seems to share more drift, since it scores higher on MDLP K23b "East Asian".
     





    I also made some plots of what these GEDmatch samples would look like on a global PCA for MDLP K23b

    East Eurasian samples in reference to the East Asian, "Australoid" and "Melano-Polynesian" (left), "Arctic" (@ 11.00, 5.00), and "Amerindian" (@9.60, 3.60) ancestry components)
     


    East Eurasian samples, zoomed in so you can see the different ethnic groups more clearly
     


    East Eurasian samples, density plot
     


    same as above but with "TW [ROC]" and "HK/Canto" Chinese samples singled out
     


    All East Eurasian samples, with smaller groups singled out
     


    All East Eurasian samples, with SEA Chinese individuals singled out


    All East Eurasian samples, with obviously mixed-ethnic Asians singled out (labels are guesses to their ancestry based on their GEDmatch Oracle results)


    Global PCA of North Asian reference populations


    Global PCA of North Asian reference populations, with GEDmatch samples included
    Last edited by okarinaofsteiner; 04-12-2021 at 06:44 AM.

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  16. #30
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    Global MDLP K23b plots of GEDmatch samples. All were made sometime in 2018, maybe early 2019

    Global PCA plot of East Eurasian GEDmatch samples, including 12 Central Asians (Kazakh, Altaian, Mongol, Tuva, Kyrgyz), and 6 mostly Amerindian Latin American mestizos. The Central Asian and Latin American samples were courtesy of @Tsakhur


    Global PCA plot of GEDmatch samples of Euro to Asia ancestry


    Global PCA plot with global GEDmatch samples
    Last edited by okarinaofsteiner; 04-12-2021 at 06:50 AM.

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