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Thread: Iranian qpAdm modeling

  1. #1
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    Iranian qpAdm modeling

    For the longest time I had no luck getting decent fits for the Iranian members using qpAdm. However, now that I have the Iranian Neolithic genomes things seem to be improving.

    Using Iran Neolithics, project member DMXX is starting to get good fits.

    SAMPLE IRAN NEOL ANATOLIA NEOL LEVANT NEOL ANDRONOVO HAN TAIL PROBABILITY CHISQ
    DMXX 53.0% 0.0% 12.5% 27.5% 7.0% 88.4% 1.7



    Unfortunately, I still have not been able to obtain a decent fit worth posting for Jesus and NK19191

  2. The Following 8 Users Say Thank You to Kurd For This Useful Post:

     DMXX (07-21-2016), Humanist (07-21-2016), khanabadoshi (07-21-2016), NK19191 (07-21-2016), parasar (07-24-2016), persian (07-21-2016), surbakhunWeesste (07-21-2016), vatan (07-21-2016)

  3. #2
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    Hi Kurd, how can I send you my file? I have tested through 23andme, thanks.

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    I tried various combinations using Iran N and Iran Chl with Levant N, to no avail. This is the best I can do so far for Humanist (not a great fit). I was optimistic when I had initially seen such great fits for some of the Kurds using Iran N, but am now starting to wonder whether its genetic contribution was more limited. It is also possible that other members require the use of other base populations, that I have not yet used with Iran N, or perhaps are hitherto not sequenced.

    SAMPLE IRAN RECENT ANATOLIA NEOL LEVANT BA ANDRONOVO HAN TAIL PROBABILITY CHISQ
    HUMANIST 57.5% 0.0% 38.9% 0.0% 3.6% 69.0% 3.9

  5. The Following 3 Users Say Thank You to Kurd For This Useful Post:

     DMXX (07-21-2016), Humanist (07-21-2016), NK19191 (07-21-2016)

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    Very nice. Broadly in keeping with Davidski's Iranian qpAdm results. Specifically, Iranians being a near two-way mixture of Iran_ChL (with extra Iran_N in some cases) and a steppe-derived component.

    Perhaps jesus could be modeled with Iran_N, Iran_ChL, Levant_N, Andronovo and Yoruba, and NK19191 with the same ingroup pops as myself, with Anatolian_N swapped for Iran_N?

  7. The Following 2 Users Say Thank You to DMXX For This Useful Post:

     khanabadoshi (07-23-2016), NK19191 (07-22-2016)

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    How do you get this done?

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    Quote Originally Posted by persian View Post
    Hi Kurd, how can I send you my file? I have tested through 23andme, thanks.
    Check your PM

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     persian (07-23-2016)

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    Quote Originally Posted by DMXX View Post
    Very nice. Broadly in keeping with Davidski's Iranian qpAdm results. Specifically, Iranians being a near two-way mixture of Iran_ChL (with extra Iran_N in some cases) and a steppe-derived component.

    Perhaps jesus could be modeled with Iran_N, Iran_ChL, Levant_N, Andronovo and Yoruba, and NK19191 with the same ingroup pops as myself, with Anatolian_N swapped for Iran_N?
    Iran N with Iran Chl was not a good fit for NK19191, but Iran N with CHG was better. Therefore, it seems that some individuals can be modeled with good to excellent fits without CHG (yourself and some Kurds), others require CHG in combination with Iran N. I will go back and introduce CHG for some of the individuals that had poor fits with Iran N alone. I will also check to see if your fit improves by trading Anatolia N for CHG.

  12. The Following 3 Users Say Thank You to Kurd For This Useful Post:

     DMXX (07-24-2016), khanabadoshi (07-23-2016), NK19191 (07-23-2016)

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    After about a dozen tries, I finally got a decent model for NK19191.

    SAMPLE IRAN CHL LEVANT NEOL ONGE EHG HAN TAIL PROBABILITY CHISQ
    NK19191 45.4% 24.6% 11.8% 18.2% 0.00% 90.0% 1.6

  14. The Following 3 Users Say Thank You to Kurd For This Useful Post:

     DMXX (07-24-2016), khanabadoshi (07-24-2016), NK19191 (07-23-2016)

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    Quote Originally Posted by Kurd View Post
    Iran N with Iran Chl was not a good fit for NK19191, but Iran N with CHG was better. Therefore, it seems that some individuals can be modeled with good to excellent fits without CHG (yourself and some Kurds), others require CHG in combination with Iran N. I will go back and introduce CHG for some of the individuals that had poor fits with Iran N alone. I will also check to see if your fit improves by trading Anatolia N for CHG.
    It might be more difficult for NK19191 as he has some recent ancestry from the South Caucasus, which could explain why CHG and Iran_N was better than Iran_N and Iran_ChL. Perhaps CHG and Iran_ChL would work better for him in light of that. Not sure if that combo's been attempted.

  16. The Following User Says Thank You to DMXX For This Useful Post:

     NK19191 (07-24-2016)

  17. #10
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    Quote Originally Posted by DMXX View Post
    It might be more difficult for NK19191 as he has some recent ancestry from the South Caucasus, which could explain why CHG and Iran_N was better than Iran_N and Iran_ChL. Perhaps CHG and Iran_ChL would work better for him in light of that. Not sure if that combo's been attempted.
    I tried that but it was a failure. The standard errors approached 100%.

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