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Thread: Gene Flow Between Southern and South-eastern Asia

  1. #71
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    Quote Originally Posted by DMXX View Post
    Right you are - However, I haven't found a clear indication in the paper that they used both samples in their basic qpAdm model. Perhaps I overlooked it? Did you see anything regarding how they treated IVCp in their model?
    Well, no, I haven't been able to find a direct quote from the paper itself but others who've read it have basically said the same thing I have. And the thing is that if they're using strictly SIS3+Onge+Sintashta to model south Asians, it's going to result in a poor fit for a lot of South Asians particularly those originating in the northwest because that's too much AASI and not enough Iran_N. Kalash alone have similar levels of Iran_N compared to SIS3 and way less AASI.

    IVCp apparently was described as being a straight mix of Iranian farmer and AASI ancestry:

    "In fact, it was certainly the case that the peoples of the Indus Valley were genetically
    297 heterogeneous as we observe one of the Indus_Periphery individuals having ~42% AASI
    298 ancestry and the other two individuals having ~14-18% AASI ancestry (but always mixes of the
    299 same two proximal sources of AASI and Iranian agriculturalist-related ancestry)."

    There were 4 total SIS samples, 2 of which belonged to SIS1. So perhaps they've used 3 of the 4? It's quite confusing
    Last edited by Censored; 06-08-2019 at 03:36 AM.

  2. #72
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    Quote Originally Posted by DMXX View Post
    Right you are - However, I haven't found a clear indication in the paper that they used both samples in their basic qpAdm model. Perhaps I overlooked it? Did you see anything regarding how they treated IVCp in their model?
    "Indus_Periphery sample (a pool of three outlier individuals from the BMAC site of Gonur and from Shahr-i-Sokhta)"


    "Gonur2_BA This sample has significant amounts of South Asian HG related ancestry and is part of a genetic grouping we call Indus_Periphery"

    "The following two samples have significant amounts of South Asian HG related admixture, and we call these samples part of the Indus_Periphery genetic grouping.
    ... Shahr-i-Soktha_MLBA2 ... Shahr-i-Soktha_MLBA3"

    For each Indian Cline group X, we estimated the vector of coefficients under qpAdm:
    c(X) = (cS(X), cI(X), cA(X)) (4.1)
    where cj(X) are admixture coefficients for S=Steppe-related (Steppe_MLBA), I=Iranian
    agriculturalist-related (Indus_Periphery), and A=South Asian hunter-gatherer (AASI)-related (Onge).
    https://www.biorxiv.org/content/bior...1/292581-1.pdf
    Last edited by parasar; 06-09-2019 at 05:24 PM.

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  4. #73
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    You guys are right, and that's been my interpretation since reading the paper when the pre-print first came out.

    The question I'm posing is with respect to the qpAdm three pop model they feature - What is being used for their IVCp ref pop? Are they using SiSBA2? SiSBA3? Both (somehow)?

    I vaguely remember reading somewhere (a comment in this forum perhaps) suggesting they used SiSBA3. That made sense prima facie, given SiSBA3 is the most AASI-shifted sample we currently have. Didn't double-check the statement concerning that and assumed it was true, but now I can't find any obvious statement in the paper regarding this, now that Censored's given me/us a valid reason to doubt that assumption is true.

  5. #74
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    Quote Originally Posted by DMXX View Post
    You guys are right, and that's been my interpretation since reading the paper when the pre-print first came out.

    The question I'm posing is with respect to the qpAdm three pop model they feature - What is being used for their IVCp ref pop? Are they using SiSBA2? SiSBA3? Both (somehow)?

    I vaguely remember reading somewhere (a comment in this forum perhaps) suggesting they used SiSBA3. That made sense prima facie, given SiSBA3 is the most AASI-shifted sample we currently have. Didn't double-check the statement concerning that and assumed it was true, but now I can't find any obvious statement in the paper regarding this, now that Censored's given me/us a valid reason to doubt that assumption is true.
    Its a trio of SIS2, SIS3 and Gonur2, I told poi to simulate the averages on G25, it essentially is 70% Iran_N related/30% AASI, their criteria for Iran_N is a more Hotu/Sarazm version so it includes WSHG/AG3 like ancestry, there is 13 of them now, most are still from Shahr I Shokta and they are very likely coming from Balochistan/Sind and I don't think the main cluster is ancestral for most Indian populations they are way too Iran_N shifted, Gangetic and Insular Indians need a more tribal shifted base that is very evident from the figure below. In the new figures they are more broad , Steppe MLBA is now just Steppe (include Dali or WSHG sources I am assuming) and Iran_N is now Iran related source, its a smart way of not admitting error but fixing it at the same time. Rather the 2 outliers are most ancestral and likely coming from further east.

    I wish they included the Daamgard samples so the "ANI" side would be filled up .


    Last edited by pegasus; 06-10-2019 at 02:19 AM.

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