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Thread: Looking at South Asia

  1. #1
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    Looking at South Asia

    I have begun looking at the new samples. Below is a basic tree that I use to build up from and create later samples.

    OpeningTree.png

    This second graph includes a combination of all three Indus diaspora samples. It is rough, so I will need to go back and clean this up with a few extra nodes, in my opinion. While the paper asserts there is no Anatolian in the Indus samples, looking at ADMIXTURE and qpAdm, qpGraph begs to differ. There is also these gems that led to it... and make it seem likely

    worst f-stat: Ana Haj Gan Ind -0.001647 -0.004436 -0.002789 0.000883 -3.158

    result: Onge Ganj_Dareh_N Indus_Diaspora -0.009536 0.001749 -5.451 191331
    result: Onge Hajji_Firuz_ChL Indus_Diaspora -0.005081 0.001787 -2.844 193475
    result: Onge Tepe_Anau_EN Indus_Diaspora -0.009280 0.001798 -5.162 185009
    result: Onge Parkhai_EN Indus_Diaspora -0.010915 0.001745 -6.254 190806
    result: Onge Geoksiur_EN Indus_Diaspora -0.012715 0.001863 -6.826 160396
    result: Onge Sarazm_EN Indus_Diaspora -0.009197 0.001955 -4.705 165486

    Indus_Diaspora.png

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    In the process of breaking down Central Asia, then seeing if that goes into the individual Indus Diaspora samples.

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    It's interesting that Anatolian ancestry made it so far East. As I was playing around, similar to your direct F3's, the best simple result I was getting for Indus_Diaspora was like a 75/25 mix of Central Asian neolithic + ENA (though with maybe a bit less Anatolian) The Central Asian neolithics themselves being mostly Iran_N related and with ~20% Anatolian. I think they also have some sort of special relation with CHG (be it actual ancestry or otherwise). Then obviously they have some West_Siberian_N-like mixture.
    Last edited by Kale; 04-17-2018 at 06:53 PM.
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    Quote Originally Posted by Chad Rohlfsen View Post
    I have begun looking at the new samples. Below is a basic tree that I use to build up from and create later samples.

    OpeningTree.png

    This second graph includes a combination of all three Indus diaspora samples. It is rough, so I will need to go back and clean this up with a few extra nodes, in my opinion. While the paper asserts there is no Anatolian in the Indus samples, looking at ADMIXTURE and qpAdm, qpGraph begs to differ. There is also these gems that led to it... and make it seem likely

    worst f-stat: Ana Haj Gan Ind -0.001647 -0.004436 -0.002789 0.000883 -3.158

    result: Onge Ganj_Dareh_N Indus_Diaspora -0.009536 0.001749 -5.451 191331
    result: Onge Hajji_Firuz_ChL Indus_Diaspora -0.005081 0.001787 -2.844 193475
    result: Onge Tepe_Anau_EN Indus_Diaspora -0.009280 0.001798 -5.162 185009
    result: Onge Parkhai_EN Indus_Diaspora -0.010915 0.001745 -6.254 190806
    result: Onge Geoksiur_EN Indus_Diaspora -0.012715 0.001863 -6.826 160396
    result: Onge Sarazm_EN Indus_Diaspora -0.009197 0.001955 -4.705 165486

    Indus_Diaspora.png
    What could explain Ust-Ishim's shared clad with ENA, the lack of inclusion of Paleolithic European samples?

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    Could be a few things. Lack of a Basal-Eu edge to Western hunters, Ust-Ishim really being early ENA, only equally close to West and East due to excess archaic in ancient Westerners... This was just one solution.

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    left pops:
    Brahmin
    Shahr_I_Sokhta_BA1
    Onge
    Sintashta
    West_Siberia_N

    right pops:
    Mota
    Ust_Ishim
    Kostenki14
    MA1
    GoyetQ116-1
    Vestonice16
    Villabruna
    ElMiron
    Iron_Gates
    EHG
    Ganj_Dareh_N
    Natufian
    Boncuklu
    Steppe_EMBA
    Globular_Amphora
    Hajji_Firuz_ChL
    LBK_EN
    Levant_BA

    best coefficients: 0.503 0.370 0.021 0.106
    std. errors: 0.043 0.035 0.050 0.032
    fixed pat wt dof chisq tail prob
    0000 0 14 8.163 0.880656 0.503 0.370 0.021 0.106

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    left pops:
    Brahmin
    Shahr_I_Sokhta_BA3
    Sintashta
    West_Siberia_N

    best coefficients: 0.849 0.144 0.007
    std. errors: 0.039 0.042 0.031

    fixed pat wt dof chisq tail prob
    000 0 15 14.652 0.476798 0.849 0.144 0.007
    001 1 16 24.724 0.0748407 0.853 0.147 0.000
    010 1 16 25.228 0.0659119 0.951 0.000 0.049
    100 1 16 834.300 0 0.000 0.850 0.150
    011 2 17 31.618 0.0167765 1.000 0.000 0.000

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    left pops:
    Brahmin
    Shahr_I_Sokhta_BA1
    West_Siberia_N
    Onge

    right pops:
    Mota
    Ust_Ishim
    Kostenki14
    MA1
    GoyetQ116-1
    Vestonice16
    Villabruna
    ElMiron
    Iron_Gates
    EHG
    Ganj_Dareh_N
    Natufian
    Anatolia_N
    Boncuklu
    Steppe_EMBA
    Globular_Amphora
    LBK_EN
    Ami


    best coefficients: 0.523 0.116 0.361
    std. errors: 0.030 0.025 0.029

    fixed pat wt dof chisq tail prob
    000 0 15 6.921 0.959807 0.523 0.116 0.361

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    Malayan looks to best represent the South Indian ancestry of Brahmins. I tried to add some Iranian admixture, but it was -1.5%. So, I may need an even more West Asian source for another attempt. Certainly an interesting output.

    left pops:
    Brahmin
    Malayan
    Gonur1_BA
    Dali_EBA
    Sintashta

    right pops:
    Mota
    Ust_Ishim
    Kostenki14
    MA1
    GoyetQ116-1
    Vestonice16
    Villabruna
    ElMiron
    Iron_Gates
    EHG
    Ganj_Dareh_N
    Anatolia_N
    Hajji_Firuz_ChL
    Ami
    West_Siberia_N
    Onge


    best coefficients: 0.527 0.365 0.062 0.046
    std. errors: 0.027 0.040 0.029 0.040

    fixed pat wt dof chisq tail prob
    0000 0 12 8.702 0.728139 0.527 0.365 0.062 0.046
    0001 1 13 11.129 0.600042 0.522 0.397 0.081 0.000
    0010 1 13 16.616 0.217443 0.553 0.360 0.000 0.087

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    If IVC ends up being just Iran plus something like Onge, with no Anatolian, then watch BMAC numbers jump and Sintashta or Steppe MLBA really decline. We need IVC samples to be sure. But if this Malayan represents IVC, plus a later SA admixture event into Brahmins, then BMAC is going to go way up, like it is here.

    left pops:
    Brahmin
    Malayan
    Sappali_Tepe_BA
    Krasnoyarsk_MLBA
    Dali_EBA

    right pops:
    Mota
    Ust_Ishim
    Kostenki14
    MA1
    GoyetQ116-1
    Vestonice16
    Villabruna
    ElMiron
    Iron_Gates
    EHG
    Ganj_Dareh_N
    Anatolia_N
    Hajji_Firuz_ChL
    Ami
    West_Siberia_N
    Onge

    best coefficients: 0.508 0.364 0.043 0.085
    std. errors: 0.028 0.038 0.042 0.031

    fixed pat wt dof chisq tail prob
    0000 0 12 8.008 0.784502 0.508 0.364 0.043 0.085
    0001 1 13 15.695 0.26602 0.548 0.334 0.119 0.000
    0010 1 13 9.086 0.766445 0.503 0.392 0.000 0.105

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