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Thread: Global25 automated nMonte for South/Central Asian members

  1. #5881
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    Quote Originally Posted by Kulin View Post
    I don't think Client said either were better. He was implying that good/reasonable fits on scaled (3 or lower) are different to ones on unscaled (1 or lower). A fit of 2-3 is pretty much horrible with unscaled coordinates. Of course everyone has by now read that Huijbregts said that unscaled coordinates with the default penalty is optimal.
    Based on tests comparing scaled/unscaled coords with formal stats, fst distance and PCA from raw data, scaled with pen=0 looks like the optimal setting.

    Unscaled coords are usually noisy.
    Last edited by Generalissimo; 08-09-2019 at 06:51 AM.

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    Quote Originally Posted by Generalissimo View Post
    Have you checked if adding Mbuti and/or switching the order of the right pops at the base shifts the results? Because it usually does.
    What would the technical reason be that would make shifting order make a difference? In the end it's still generating say.. F4: Tajik Tajiksim Rightpop1 Rightpop2 for every combination of rightpops. The order shouldn't matter.
    I threw Mota as the first right pop in a couple and there was no material change.
    Collection of 14,000 d-stats: Hidden Content Part 2: Hidden Content Part 3: Hidden Content PM me for d-stats, qpadm, qpgraph, or f3-outgroup nmonte models.

  4. #5883
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    Quote Originally Posted by Kale View Post
    What would the technical reason be that would make shifting order make a difference? In the end it's still generating say.. F4: Tajik Tajiksim Rightpop1 Rightpop2 for every combination of rightpops. The order shouldn't matter.
    I threw Mota as the first right pop in a couple and there was no material change.
    I don't know, but I was told that the order of the right pops might change the results, so it's a good idea to check this. And the idea for the African outgroup is also from the makers of the software.

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    Quote Originally Posted by Generalissimo View Post
    I don't know, but I was told that the order of the right pops might change the results, so it's a good idea to check this. And the idea for the African outgroup is also from the makers of the software.
    Randomized the order of the right pops in the earlier Tajik model. It was different which is unexpected, but the difference was again not material.
    Collection of 14,000 d-stats: Hidden Content Part 2: Hidden Content Part 3: Hidden Content PM me for d-stats, qpadm, qpgraph, or f3-outgroup nmonte models.

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  7. #5885
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    Here's a plot of various groups:

    https://www.brownpundits.com/2019/08...medium=twitter

    If you had to label, what would you call the different colors- e.g. the brick red seems to be AASI, the purple- Iran or west-asian and so on? Or am I trying to simplify it too much?

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    Quote Originally Posted by dumbo007 View Post
    Here's a plot of various groups:

    https://www.brownpundits.com/2019/08...medium=twitter

    If you had to label, what would you call the different colors- e.g. the brick red seems to be AASI, the purple- Iran or west-asian and so on? Or am I trying to simplify it too much?
    Based on a quick glance, they appear to just be components maximized in modern populations. So, South Asian, Caucasian/West Asian, Northern Euro, etc. So, your inferences look right.

    The paper is from 2016 and there aren't any references to ancients so that supports those assumptions as well. The focus of the paper was to tease out any potential foreign ancestry in Kashmiri Muslims from Srinagar but the geneticists found them to be identical to the Kashmiri Pandit samples already available.
    Last edited by Sapporo; 08-11-2019 at 02:53 AM.
    pegasus modeling:

    sample": "Punjabi_Jat:Sapporo_AGUser",
    "fit": 1.1506,
    "IRN_Shahr_I_Sokhta_BA3": 43.33,
    "TKM_Gonur1_BA": 31.67,
    "RUS_Sintashta_MLBA": 25,
    "closestDistances": [

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  10. #5887
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    Quote Originally Posted by dumbo007 View Post
    Here's a plot of various groups:

    https://www.brownpundits.com/2019/08...medium=twitter

    If you had to label, what would you call the different colors- e.g. the brick red seems to be AASI, the purple- Iran or west-asian and so on? Or am I trying to simplify it too much?
    That paper is before the Farmer paper dropped so in essence its dated now

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    Quote Originally Posted by pegasus View Post
    That paper is before the Farmer paper dropped so in essence its dated now
    Could you please share a link to the Farmer paper- I'm fairly new to this.

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    Quote Originally Posted by dumbo007 View Post
    Could you please share a link to the Farmer paper- I'm fairly new to this.
    Not a direct answer, but check out the dedicated thread for relevant pop gen papers: https://anthrogenica.com/showthread....Papers/page113 -- basically you can find all relevant papers (links/references) there. User pmokeefe is prolific in posting new papers. If you check out earlier pages, you will find relevant papers.

    Note that paper related discussion is not allowed in that thread, but can be discussed here: https://anthrogenica.com/showthread....Thread/page225
    Last edited by poi; 08-11-2019 at 10:00 PM. Reason: typo correction

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