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Thread: How to model non-Yamnaya steppe ancestry? Difference between western and eastern euro

  1. #31
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    Quote Originally Posted by Dame View Post
    Other examples of what has been said. Notice how the high EHG value is not accompanied by a proportional CHG value in the east. In the West a proportional value of CHG accompanies the value of EHG.

    Target: Danish
    Distance: 7.0380% / 0.07037953
    45.2 Anatolia_Barcin_N
    35.0 RUS_Karelia_HG
    11.2 GEO_CHG
    8.6 WHG

    Target: Irish
    Distance: 7.1123% / 0.07112300
    45.0 Anatolia_Barcin_N
    34.0 RUS_Karelia_HG
    12.4 GEO_CHG
    8.6 WHG

    Target: Estonian
    Distance: 6.8846% / 0.06884590
    48.8 RUS_Karelia_HG
    36.4 Anatolia_Barcin_N
    7.6 WHG
    7.2 GEO_CHG

    Target: Russian_Kostroma
    Distance: 5.8178% / 0.05817808
    51.0 RUS_Karelia_HG
    36.8 Anatolia_Barcin_N
    10.2 GEO_CHG
    2.0 WHG

    Target: Finnish
    Distance: 5.9233% / 0.05923289
    50.6 RUS_Karelia_HG
    36.2 Anatolia_Barcin_N
    8.0 GEO_CHG
    5.2 WHG

    Even if the Yamnaya option is removed from the source it is still possible to observe where the Yamnaya signal is strongest based on the ratio between EHG / CHG. In the west, the CHG component proportionally accompanies the EHG element in a proportion very similar to the EHG / CHG ratio in Yamnaya. In the order, there is much more EHG than CHG in terms of ratios coming out of the western Yamnaya standard. Just calculate the EHG / CHG ratio and understand why the Yamnaya signal is stronger in the Northwest, although the EHG component is definitely stronger in the Northeast.

    Some NW Europeans:
    https://www.mupload.nl/img/6jcqov9isp.10.50.png

  2. #32
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    Dame calculator
    Target: Mis_scaled { EE }
    Distance: 5.4182% / 0.05418165 | ADC: 0.25x
    37.8 Anatolia_Barcin_N
    35.4 Yamnaya_RUS_Samara
    25.8 UKR_Meso
    1.0 RUS_Karelia_HG
    Distance: 5.3378% / 0.05337777
    40.6 Anatolia_Barcin_N
    28.0 Yamnaya_RUS_Samara
    21.0 UKR_Meso
    10.4 RUS_Karelia_HG

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    Last edited by Mis; 07-26-2020 at 10:28 AM.

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  4. #33
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    ++delete++
    Last edited by Finn; 07-26-2020 at 08:52 AM.

  5. #34
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    WHG is not suitable for modeling HG ancestry in Eastern Europe. In the Mesolithic / Neolithic period, WHG blended ostensibly with EHG in Eastern Europe. UKR-Meso is much more appropriate as it represents this mixture already in the Eastern European Mesolithic.

    Target: UKR_Meso: I5885
    Distance: 5.1320% / 0.05132014
    52.6 RUS_Karelia_HG
    39.6 WHG
    7.8 Anatolia_Pinarbasi_HG

    Distance to: UKR_Meso: I5885
    0.14705745 RUS_Karelia_HG: I0211
    0.18456149 WHG
    0.36821495 Anatolia_Pinarbasi_HG: ZBC_IPB001

    When the eastern European HG component does not appear at the source, an artificially high level of steppe appears because the steppe component is basically EHG + CHG. In the beginning of CW, the steppe component was high, but over time it was diluted because northeastern Europe was considerably populated with HGs.

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  7. #35
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    If this theory was true, we should get a significant improvement of the models Steppe/Early_Neo/HG by choosing a HG proxy with a known EHG affinity. This is not what happens. I used qpfstats+qpAdm (option allsnps fixed to "YES"),Reich_1240K_HO restricted to the transversions, the following right_list:
    Russia_Ust_Ishim.DG
    Iran_GanjDareh_N
    Jordan_PPNB
    Czech_Vestonice16
    Belgium_UP_GoyetQ116_1_published
    Iberia_ElMiron
    Russia_HG_Tyumen
    Russia_MA1_HG.SG
    Georgia_Kotias.SG

    I used as modern populations the Ukrainians, northern Ukrainians, Belarusians (unfortunately Reich has only one Polish individual, and I frankly had no envy to merge files for a so little topic). I will show what happens with the Ukrainians, hopefully you have nothing against them, but the same observations occur with the others.

    left pops:
    Ukrainian
    Poland_CWC_early
    Germany_EN_LBK
    Hungary_EN_HG_Koros

    best coefficients: 0.604 0.329 0.066
    std. errors: 0.042 0.038 0.033

    chisq / tail prob: 9.910 / 0.128493


    left pops:
    Ukrainian
    Poland_CWC_early
    Germany_EN_LBK
    Ukraine_Mesolithic

    best coefficients: 0.534 0.378 0.087
    std. errors: 0.075 0.037 0.051

    chisq / tail prob: 10.952 / 0.0898779


    left pops:
    Ukrainian
    Poland_CWC_early
    Germany_EN_LBK
    Hungary_EN_HG_Koros
    Ukraine_Mesolithic

    best coefficients: 0.571 0.345 0.050 0.034
    std. errors: 0.097 0.060 0.056 0.089

    chisq / tail prob: 9.735 / 0.0830946


    Of course, there are far better models than these ones, including the first one. For example:

    left pops:
    Ukrainian
    Poland_CWC_early
    Ukraine_Globular_Amphora

    best coefficients: 0.603 0.397
    std. errors: 0.043 0.043

    chisq/tail prob: 9.341 / 0.229084


    In the case you would contest the choice of Poz81 as the "Steppe" proxy, I recall you that he is under an autosomal point of view nearly identical to the Ukrainian Yamnayas:

    left pops:
    Poland_CWC_early
    Ukraine_EBA_Yamnaya
    Ukraine_Globular_Amphora

    best coefficients: 0.978 0.022
    std. errors: 0.077 0.077

    tai prob: 0.128737
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  9. #36
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    That right pop list isn't very robust.
    No WHG? No ANF? No Steppe-proxy?
    Right pops: Barcin, GanjDareh, CHG, Karelia_HG, WSHG, Steppe_Eneolithic...
    if trying to tease out the specific type of WHG ancestry I'd put even two in there, maybe Bichon and IronGates
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  10. #37
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    Quote Originally Posted by Kale View Post
    That right pop list isn't very robust.
    No WHG? No ANF? No Steppe-proxy?
    Right pops: Barcin, GanjDareh, CHG, Karelia_HG, WSHG, Steppe_Eneolithic...
    if trying to tease out the specific type of WHG ancestry I'd put even two in there, maybe Bichon and IronGates
    Is qpAdm easily manipulated depending on what right pops one uses?

    I’m curious what you think is the most accurate run for Eastern Euros with qpAdm and using early CW + MN/CA Farmers + excessive HG input(if they have any), if you don’t mind.

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  12. #38
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    I added Afanasievo to the @Dame calculator

    Target: Mis_scaled {EE}
    Distance: 5.1430% / 0.05143009 | ADC: 0.25x
    37.4 RUS_Afanasievo
    35.8 Anatolia_Barcin_N
    26.8 UKR_Meso {OK}

    Target: Mis_scaled
    Distance: 5.0372% / 0.05037244
    38.2 Anatolia_Barcin_N
    33.6 RUS_Afanasievo
    11.0 RUS_Karelia_HG
    10.2 UKR_Meso
    7.0 WHG

    Distance to: Mis_scaled
    0.14651385 RUS_Afanasievo:I3388
    0.15562199 Yamnaya_RUS_Samara
    0.18183708 IRN_Ganj_Dareh_Historic:I1955
    0.21112192 UKR_Meso:I5885
    0.21689054 Baltic_LTU_Narva
    0.22237812 Anatolia_Barcin_N
    0.24195907 RUS_Karelia_HG:I0211
    0.28164798 GEO_CHG:KK1
    0.31922316 WHG:I1875
    0.32707192 WHG
    0.33729863 WHG:Rochedane
    0.34253829 IRN_Shahr_I_Sokhta_BA2:I11466
    0.48137421 MAR_Iberomaurusian
    0.61925070 Nganassan

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