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Thread: New blog featuring aDNA

  1. #21
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    Quote Originally Posted by Chad Rohlfsen View Post
    I really don't think so. What makes you think that Harappans have to be way more Iran/Turan-related than AASI? Velamas are essentially Irula, with some Shahr I Sokhta excess. There was a large movement of late BMAC and related groups into the Indus region in the late BA, so I think using anyone from this area now is going to get results like this and not reflect the early or mature Harappan. Velamas may just have some IE admixture, as even Sintashta admixture is at the standard error, using SIS, Irula, and Sintashta.
    I guess my argument is that SISBA3 is a better representative than Irulas as its much more preferred as an ancestral source for South Asians than Irulas who likely have excess ancient peninsular ancestry

    Model Sample Sample Age BCE Fit Irula Shahr I Sokhta BA3
    2 Irula +Shahr_I_Sokhta_BA3 Custom_-_AGUser_midichlorian_patel 5.3085 0 100
    3 Irula +Shahr_I_Sokhta_BA3 Velamas_-_VELZ260 4.2532 0 100
    4 Irula +Shahr_I_Sokhta_BA3 Velamas_-_VELZ264 2.737 36.6 63.4
    5 Irula +Shahr_I_Sokhta_BA3 Velamas_-_VELZ267 3.521 8.2 91.8

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  3. #22
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    Nah, I think SIS3 is a mix of Harappan and SIS1. We'll see soon. Could there be an odd sample like SIS3 at Harappan sites? Possibly, being as urban as it was, but I think the majority of the population will be more like the Irula. SIS3 only works better than Irula as it is the mixture of SIS1 and Irula that makes up 80-90% of IE Indian DNA. We'll see soon enough.

    left pops:
    Shahr_I_Sokhta3
    Shahr_I_Sokhta1
    Irula

    right pops:
    Mbuti_DG
    Ust_Ishim
    Kostenki14
    EHG
    Iron_Gates
    Anatolia_N
    Ganj_Dareh_N
    Karitiana
    Ami
    Onge

    numsnps used: 195765

    best coefficients: 0.222 0.778

    std. errors: 0.039 0.039

    fixed pat wt dof chisq tail prob
    00 0 8 3.371 0.908949 0.222 0.778

  4. #23
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    There was probably some significant substructure within the Harappan population, even if it was totally contained within the so called AASI > Indus_Periphery genetic cline.

    So one Harappan sample, or even a few, will just give us another indication of where along this cline some Harappan groups sat, rather than an all purpose data point for modeling South Asian ancestry.

    But I think what we'll see is a sample free of all that ANE-related "noise" from Central Asia, which will help in estimating more accurately the levels of actual Bronze Age steppe ancestry in most Indians.

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  6. #24
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    Don't count on that. ANE increases relative to BE away from the Zagros. NW India should not ruin that cline.

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  8. #25
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    A couple more interesting ones

    left pops:
    Brahmin
    Irula
    Dzharkutan1_BA
    Sintashta

    right pops:
    Mbuti_DG
    Ust_Ishim
    Kostenki14
    EHG
    Iron_Gates
    Anatolia_N
    Ganj_Dareh_N
    Karitiana
    Ami
    Onge

    numsnps used: 322784

    best coefficients: 0.681 0.203 0.116

    std. errors: 0.023 0.034 0.028

    fixed pat wt dof chisq tail prob
    000 0 7 6.954 0.433685 0.681 0.203 0.116


    left pops:
    Brahmin
    Irula
    Dzharkutan1_BA
    Steppe_MLBA_East

    right pops:
    Mbuti_DG
    Ust_Ishim
    Kostenki14
    EHG
    Iron_Gates
    Anatolia_N
    Ganj_Dareh_N
    Karitiana
    Ami
    Onge

    numsnps used: 324413

    best coefficients: 0.678 0.198 0.124

    std. errors: 0.023 0.034 0.028

    fixed pat wt dof chisq tail prob
    000 0 7 6.294 0.505837 0.678 0.198 0.124

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  10. #26
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    Quote Originally Posted by Chad Rohlfsen View Post
    Nah, I think SIS3 is a mix of Harappan and SIS1. We'll see soon. Could there be an odd sample like SIS3 at Harappan sites? Possibly, being as urban as it was, but I think the majority of the population will be more like the Irula. SIS3 only works better than Irula as it is the mixture of SIS1 and Irula that makes up 80-90% of IE Indian DNA. We'll see soon enough.

    left pops:
    Shahr_I_Sokhta3
    Shahr_I_Sokhta1
    Irula

    right pops:
    Mbuti_DG
    Ust_Ishim
    Kostenki14
    EHG
    Iron_Gates
    Anatolia_N
    Ganj_Dareh_N
    Karitiana
    Ami
    Onge

    numsnps used: 195765

    best coefficients: 0.222 0.778

    std. errors: 0.039 0.039

    fixed pat wt dof chisq tail prob
    00 0 8 3.371 0.908949 0.222 0.778
    Well then these pure Harappans didn't provide much ancestry to moderns as SISBA3 works better and in larger quantities for the majority of non-Tribal South Indians from what I've seen.

    And this was prior to Indo-Europeans as SISBA3 has no steppe and Velamas and most Gujarati Patels also have minimal steppe ancestry
    Last edited by bmoney; 08-09-2018 at 03:47 AM.

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  12. #27
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    Quote Originally Posted by Chad Rohlfsen View Post
    Don't count on that. ANE increases relative to BE away from the Zagros. NW India should not ruin that cline.
    What does BE mean?

  13. #28
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    Quote Originally Posted by Chad Rohlfsen View Post
    Don't count on that. ANE increases relative to BE away from the Zagros. NW India should not ruin that cline.
    We'll see.

  14. #29
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    Quote Originally Posted by Generalissimo View Post
    There was probably some significant substructure within the Harappan population, even if it was totally contained within the so called AASI > Indus_Periphery genetic cline.

    So one Harappan sample, or even a few, will just give us another indication of where along this cline some Harappan groups sat, rather than an all purpose data point for modeling South Asian ancestry.

    But I think what we'll see is a sample free of all that ANE-related "noise" from Central Asia, which will help in estimating more accurately the levels of actual Bronze Age steppe ancestry in most Indians.
    Why does SISBA3 work so well for the non-Steppe ancestry of the bulk of South Asians outside the NW?

    Substructure doesn't seem to have impacted the preference for SISBA3
    Last edited by bmoney; 08-09-2018 at 03:53 AM.

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  16. #30
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    Quote Originally Posted by bmoney View Post
    Why does SISBA3 work so well for the non-Steppe ancestry of the bulk of South Asians outside the NW?

    Substructure doesn't seem to have impacted the preference for SISBA3
    Because this sample is overwhelmingly of South Asian origin, but the Harappan sample might work even better.

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