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Thread: Global25 automated nMonte for South/Central Asian members

  1. #5071
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    Quote Originally Posted by Kulin View Post
    Could you try with only ancients, thanks.
    That will not result in as good of a fit because there are no AASI rich tribal types as of yet but we can try:

    "sample": "Bengali_Bangladesh:Kulin_AGUser",
    "fit": 2.2227,
    "PAK_Swat_Saidu_Sharif_IA_o": 74.17,
    "RUS_Sintashta_MLBA": 11.67,
    "LAO_BA": 8.33,
    "NPL_Chokhopani_2700BP": 5.83,
    "RUS_West_Siberia_N": 0,

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  3. #5072
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    Quote Originally Posted by Kulin View Post
    Could you try with only ancients, thanks.
    It is impossible to model you with just ancients and get a good fit ,I tried and its because you have much less Iran_N compared with other South Asian groups, so a tribal population is definitely needed.



    {
    "sample": "Bengali_Bangladesh:Kulin_AGUser",
    "fit": 2.4495,
    "PAK_Swat_Saidu_Sharif_IA_o": 70,
    "NPL_Chokhopani_2700BP": 9.17,
    "RUS_Sintashta_MLBA": 7.5,
    "IRN_Shahr_I_Sokhta_BA1": 6.67,
    "LAO_BA": 5.83,
    "RUS_West_Siberia_N": 0.83,
    Last edited by pegasus; 06-11-2019 at 04:21 AM.

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  5. #5073
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    So I promise in the last post that I will try to model SE Asians also using South Asian pops as admixture sources: https://anthrogenica.com/showthread....l=1#post572978

    Well here it is:

    Here are some models for Thai samples. I choose the four most West Eurasian-shifted Thai individuals. I am speculating that some Thai individual samples are from Southern Thailand close to Malaysia because they are scoring some Malaysia_LN. All of them also have some Han Chinese ancestry which reflect the historical massive migration of Chinese migrants from South China into Thailand, which a lot have assimilated and intermarried with the locals.

    Thai DCH002: Interesting this individual seem to be around 20-21% South Asian, being mostly Gujarati+South Indian (represented by North Kannadi) and some North Indian/Paki admixture (represented by Ror from Haryana)

    "sample": "Test1:Thai_-_DCH002",
    "fit": 1.7746,
    "Htin_Mal": 34.17,
    "Han": 22.5,
    "Dai": 10,
    "Malaysia_LN": 10,
    "Gujarati": 8.33,
    "North_Kannadi": 7.5,
    "Ror": 5,

    "Igorot": 2.5,
    "LAO_LN_BA": 0,

    Now compare to the West Eurasian score (using Sarazm and Yamnaya BGR): this Thai individual has around 12% West Eurasian ancestry. So looks like the West Eurasian comes from South Asian ancestry (mostly Gujarati+South Indian+some Ror in this case along with AASI which represented the indigenous part of South Asians). Also I have feeling this sample is from Southern Thailand as it scores around 11% Malaysia_LN.

    "sample": "Test1:Thai_-_DCH002",
    "fit": 1.8391,
    "Htin_Mal": 27.5,
    "Han": 21.67,
    "Dai": 16.67,
    "Malaysia_LN": 10.83,
    "Simulated_AASI_Averaged": 10,
    "TJK_Sarazm_Eneolithic": 5.83,
    "Yamnaya_BGR": 5.83,

    "Igorot": 1.67,
    "LAO_LN_BA": 0,

    Thai DCH008: This sample have around 12% Chinese (represented by Han) admixture. This sample is around 20% South Asian ancestry. Unlike the first individual, this sample seem to be more South Indian (North Kannadi) followed by Gujarati and Northwest Indian/Pakistani-like (Ror) admixture.

    "sample": "Test2:Thai_-_DCH008",
    "fit": 2.1514,
    "Dai": 23.33,
    "Htin_Mal": 23.33,
    "Han": 11.67,
    "LAO_LN_BA": 10,
    "Igorot": 8.33,
    "North_Kannadi": 8.33,
    "Gujarati": 5.83,
    "Ror": 5.83,

    "Malaysia_LN": 3.33,

    Now compare the South Asian score to the West Eurasian (Sarazm+Yamnaya BGR) amount: this Thai is scoring around 12% West Eurasian ancestry. It makes me wonder if most of the West Eurasian comes from the South Asian ancestry this individual is scoring. Also this individual seems to score minor Igorot (Austronesian hill tribe from Phils) admixture which surprises me a bit. It makes me wonder where in Thailand the results are from.

    "sample": "Test2:Thai_-_DCH008",
    "fit": 2.217,
    "Dai": 27.5,
    "Htin_Mal": 21.67,
    "Han": 10.83,
    "LAO_LN_BA": 10.83,
    "Simulated_AASI_Averaged": 8.33,
    "Igorot": 7.5,
    "TJK_Sarazm_Eneolithic": 7.5,
    "Yamnaya_BGR": 4.17,

    "Malaysia_LN": 1.67,

    Thai DCH006: this individual has around 17-18% South Asian ancestry and most of it seems to be Gujarati+Ror followed by South Indian-like (North Kannadi) affinity. This individual also have the smallest Han admixture among all the four Thai samples.

    "sample": "Test1:Thai_-_DCH006",
    "fit": 1.9371,
    "Htin_Mal": 45,
    "Dai": 15,
    "Malaysia_LN": 9.17,
    "Han": 7.5,
    "Gujarati": 6.67,
    "Ror": 6.67,

    "LAO_LN_BA": 5.83,
    "North_Kannadi": 4.17,
    "Igorot": 0,

    Now compare the South Asian score to the West Eurasian score of the same individual. This Thai (Thai DCH006) has around 10% West Eurasian ancestry (Sarazm+Yamnaya BGR) and also 7.5% AASI (which is also likely come from South Asian or Negrito ancestry) which could correlated with the 17-18% South Asian affinity they are scoring

    sample": "Test1:Thai_-_DCH006",
    "fit": 2.0754,
    "Htin_Mal": 38.33,
    "Dai": 15,
    "Malaysia_LN": 15,
    "Han": 10,
    "Simulated_AASI_Averaged": 7.5,
    "TJK_Sarazm_Eneolithic": 5.83,
    "LAO_LN_BA": 4.17,
    "Yamnaya_BGR": 4.17,
    "Igorot": 0,

    Thai DCH010: the fourth sample has around 20% South Asian admixture (mostly Gujarati+South Indian followed by minor NW Indian/Pakistani aka Ror-like ancestry). Also this sample has around 15% Han Chinese admix.

    "sample": "Test2:Thai_-_DCH010",
    "fit": 1.7457,
    "Htin_Mal": 27.5,
    "Dai": 25.83,
    "Han": 15,
    "Malaysia_LN": 10.83,
    "Gujarati": 8.33,
    "North_Kannadi": 7.5,
    "Ror": 4.17,

    "Igorot": 0.83,
    "LAO_LN_BA": 0,

    Now compare the South Asian score to the West Eurasian and AASI score: this individual has around 11% West Eurasian and 9% AASI ancestry. I think this really correlates with the 20% South Asian admixture this Thai is scoring. Am also wondering where in the country this result is from.

    "sample": "Test2:Thai_-_DCH010",
    "fit": 1.8299,
    "Dai": 30,
    "Htin_Mal": 30,
    "Han": 13.33,
    "Simulated_AASI_Averaged": 9.17,
    "Malaysia_LN": 6.67,
    "Yamnaya_BGR": 5.83,
    "TJK_Sarazm_Eneolithic": 5,

    "Igorot": 0,
    "LAO_LN_BA": 0,

    -So these Thai samples have around 17-21% South Asian which is comparable to their 10-12% West Eurasian and 7-10% AASI ancestry.

    I know this topic is not that appropriate for this forum but I am wondering what are the phenotypes of these four Thai individuals? Do you think they look like regular SE Asians or they do look substantially Indian influenced? Also have a feeling that these results are from somewhere in Thailand where there is a lot of interaction between the locals and Indian traders and settlers.

    What are you thoughts on this?
    Last edited by Tsakhur; 06-11-2019 at 12:05 PM.

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  7. #5074
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    Is default penalty really good for similar groups? I've been told that's the case, but in practice I've often noticed it seems to only make things worse.

    "sample": "Hyderabad_Muslim:misanthropy_AGUser",
    "fit": 1.5568,
    "Velamas": 34.17,
    "Brahmin_Gujarat": 31.67,
    "Irula": 26.67,
    "Iranian_Lor": 3.33,
    "Yemenite_Jew": 3.33,
    "Yoruba": 0.83,

    "sample": "Hyderabad_Muslim:misanthropy_brother_AGUser",
    "fit": 2.5922,
    "Velamas": 45.83,
    "Brahmin_Gujarat": 21.67,
    "Irula": 19.17,
    "Iranian_Lor": 8.33,
    "Yemenite_Jew": 3.33,
    "Yoruba": 1.67,

    Now without penalty:
    "sample": "Hyderabad_Muslim:misanthropy_AGUser",
    "fit": 1.1125,
    "Brahmin_Gujarat": 34.17,
    "Irula": 30,
    "Velamas": 28.33,
    "Yemenite_Jew": 6.67,
    "Yoruba": 0.83,
    "Iranian_Lor": 0,


    "sample": "Hyderabad_Muslim:misanthropy_brother_AGUser",
    "fit": 2.1712,
    "Velamas": 43.33,
    "Irula": 24.17,
    "Brahmin_Gujarat": 17.5,
    "Yemenite_Jew": 7.5,
    "Iranian_Lor": 5.83,
    "Yoruba": 1.67,

    Both get Yemeni at the correct amount(~7%). I used two different west asian sources that would both have levant N

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  9. #5075
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    Quote Originally Posted by Censored View Post
    Is default penalty really good for similar groups? I've been told that's the case, but in practice I've often noticed it seems to only make things worse.

    "sample": "Hyderabad_Muslim:misanthropy_AGUser",
    "fit": 1.5568,
    "Velamas": 34.17,
    "Brahmin_Gujarat": 31.67,
    "Irula": 26.67,
    "Iranian_Lor": 3.33,
    "Yemenite_Jew": 3.33,
    "Yoruba": 0.83,

    "sample": "Hyderabad_Muslim:misanthropy_brother_AGUser",
    "fit": 2.5922,
    "Velamas": 45.83,
    "Brahmin_Gujarat": 21.67,
    "Irula": 19.17,
    "Iranian_Lor": 8.33,
    "Yemenite_Jew": 3.33,
    "Yoruba": 1.67,

    Now without penalty:
    "sample": "Hyderabad_Muslim:misanthropy_AGUser",
    "fit": 1.1125,
    "Brahmin_Gujarat": 34.17,
    "Irula": 30,
    "Velamas": 28.33,
    "Yemenite_Jew": 6.67,
    "Yoruba": 0.83,
    "Iranian_Lor": 0,


    "sample": "Hyderabad_Muslim:misanthropy_brother_AGUser",
    "fit": 2.1712,
    "Velamas": 43.33,
    "Irula": 24.17,
    "Brahmin_Gujarat": 17.5,
    "Yemenite_Jew": 7.5,
    "Iranian_Lor": 5.83,
    "Yoruba": 1.67,

    Both get Yemeni at the correct amount(~7%). I used two different west asian sources that would both have levant N
    From my understanding, using no penalty on similar groups tends to cause over fit results, while the default penalty can avoid this.

  10. #5076
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    Quote Originally Posted by Kulin View Post
    Could you try with only ancients, thanks.
    "Bengali_Bangladesh:Kulin_AGUser", (penalty = 0.001)
    "fit": 1.7783,
    "IRN_Shahr_I_Sokhta_BA2": 38.33,
    "Simulated_AASI": 31.67,
    "RUS_Sintashta_MLBA": 16.67,
    "NPL_Samdzong_1500BP": 9.17,
    "LAO_BA": 4.17,

    "Bengali_Bangladesh:Kulin_AGUser", (pen = 0)
    "fit": 1.5646,
    "IRN_Shahr_I_Sokhta_BA2": 36.67,
    "Simulated_AASI": 30.83,
    "RUS_Sintashta_MLBA": 18.33,
    "NPL_Samdzong_1500BP": 9.17,
    "LAO_BA": 5,

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  12. #5077
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    Quote Originally Posted by kush View Post
    "Bengali_Bangladesh:Kulin_AGUser", (penalty = 0.001)
    "fit": 1.7783,
    "IRN_Shahr_I_Sokhta_BA2": 38.33,
    "Simulated_AASI": 31.67,
    "RUS_Sintashta_MLBA": 16.67,
    "NPL_Samdzong_1500BP": 9.17,
    "LAO_BA": 4.17,

    "Bengali_Bangladesh:Kulin_AGUser", (pen = 0)
    "fit": 1.5646,
    "IRN_Shahr_I_Sokhta_BA2": 36.67,
    "Simulated_AASI": 30.83,
    "RUS_Sintashta_MLBA": 18.33,
    "NPL_Samdzong_1500BP": 9.17,
    "LAO_BA": 5,
    Thanks! I wanted it done with the AASIs originally (though ofc technically its not an ancient :p)

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  14. #5078
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    Who are the Gujarati sample on nmonte? They seem to fit me surprisingly well, which I would not expect for a population this far west.

    Also, where is the Kol sample from?
    Last edited by Censored; 06-20-2019 at 05:05 AM.

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  16. #5079
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    Quote Originally Posted by Censored View Post
    Who are the Gujarati sample on nmonte? They seem to fit me surprisingly well, which I would not expect for a population this far west.

    Also, where is the Kol sample from?
    Kol sample is from UP I believe. Not the same as Austro-Asiatic 'Kol' (obviously)

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  18. #5080
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    Quote Originally Posted by Censored View Post
    Who are the Gujarati sample on nmonte? They seem to fit me surprisingly well, which I would not expect for a population this far west.

    Also, where is the Kol sample from?
    I would think they are Patel like. So no wonder they will match with you.

    "sample": "Custom:AGUser_censored",
    "fit": 1.6797,
    "Gujarati": 91.67,
    "Simulated_AASI_South_by_DMXX": 5,
    "IRN_Ganj_Dareh_N": 2.5,
    "Simulated_AA_Basal_by_DMXX": 0.83,

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