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Thread: Isolating pontic steppe admixture in south asians in nmonte

  1. #21
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    Quote Originally Posted by Censored View Post
    I created this thread because the topic comes up so frequently that its worth having a discussion in its own right. We often struggle to do this when modeling so it might be worth coming up with ideas as to how to do it.

    One model that seems to work well combines ancients and moderns. It is a compact Paniya, Velamas, Krasnoyarsk(or Sintashta), Dzharkutan1, Naxi model. I wanted to use mostly moderns but there is no steppe deficient modern population that is also high Iran_N, so I added Dzharkutan.
    Krasnoyarsk instead of Sintashta to capture slight excess Siberian. It will work for people who are fully indigenous to the region so if you have a foreign ancestor you may need to add something else in.

    Default penalty:
    Attachment 32014

    The fits are decent but more importantly, we see the steppe values we expect. Midi scores .8-1.67% each run(most likely just noise), Tip and Kush both get zero, and importantly they get little to no BMAC, as expected. Meanwhile my friend aaronbee gets about 26% steppe which is also reasonable.

    p.s. im aware the dzarkutan for balochis is inflated
    I still feel like Velamas aren't the greatest population to use for modeling, especially given they have a ~10% BMAC type shift. They're too small a sample size among other things. I like Marathas and Kallars because they provide a decent AASI shifted base from which to evaluate populations IMO.

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  3. #22
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    I personally wouldn't model with any of the modern southern Subcontinental tribals. They all have plenty of Iran_N-related ancestry and something along the ANE-WSHG cline (as I and others have commented on several times elsewhere).

    Including them will result in some inadvertent component soak-up from whichever Iran_N-derived sources you've also included in the model (f.ex. SiSBA1, SiSBA3, SGPT). I suppose an argument could be made that some of the IVC was (at one point/in one area) highly Velamas-Kannadi-like, but I'd counter that the use of SiSBA3 or a steppe-deficient SSo makes more spatio-temporal sense for that.

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  5. #23
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    Quote Originally Posted by DMXX View Post
    I personally wouldn't model with any of the modern southern Subcontinental tribals. They all have plenty of Iran_N-related ancestry and something along the ANE-WSHG cline (as I and others have commented on several times elsewhere).

    Including them will result in some inadvertent component soak-up from whichever Iran_N-derived sources you've also included in the model (f.ex. SiSBA1, SiSBA3, SGPT). I suppose an argument could be made that some of the IVC was (at one point/in one area) highly Velamas-Kannadi-like, but I'd counter that the use of SiSBA3 or a steppe-deficient SSo makes more spatio-temporal sense for that.
    Yeah I was talking more along the lines of which modern to use, but ancient wise I like SISBA3 in conjunction with SISBA1. It seems to work best fit wise and also makes a lot of sense historically.

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  7. #24
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    Quote Originally Posted by 26284729292 View Post
    Yeah I was talking more along the lines of which modern to use, but ancient wise I like SISBA3 in conjunction with SISBA1. It seems to work best fit wise and also makes a lot of sense historically.
    I could do a lot of useful things with SSo, if someone could locate the qpAdm run(s) involving that sample. It'd be a very informative contribution to my AASI_NW simulations. I could also create a steppe-deficient simulation of it, which could ostensibly be used as a stand-in for IVC.

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  9. #25
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    Quote Originally Posted by DMXX View Post
    I personally wouldn't model with any of the modern southern Subcontinental tribals. They all have plenty of Iran_N-related ancestry and something along the ANE-WSHG cline (as I and others have commented on several times elsewhere).

    Including them will result in some inadvertent component soak-up from whichever Iran_N-derived sources you've also included in the model (f.ex. SiSBA1, SiSBA3, SGPT). I suppose an argument could be made that some of the IVC was (at one point/in one area) highly Velamas-Kannadi-like, but I'd counter that the use of SiSBA3 or a steppe-deficient SSo makes more spatio-temporal sense for that.
    The thing about these tribals is that they hold down WSHG and prevent steppe from being elevated. Also, for me the bigger issue is Velamas as they do have something SISBA1-like which can deflate real BMAC in some. As for SIS3, its the lack of ANF which gives even steppe deficient moderns a minor boost in steppe, which is what I want to avoid.

    "sample": "Andhra_Pradesh_Kamma:Average",
    "fit": 1.8694,
    "IRN_Shahr_I_Sokhta_BA3": 65.83,
    "IRN_Shahr_I_Sokhta_BA1": 14.17,
    "Simulated_AASI_South_by_DMXX": 14.17,
    "RUS_Sintashta_MLBA": 5.83,

    "sample": "Reddy:Average",
    "fit": 2.242,
    "IRN_Shahr_I_Sokhta_BA3": 53.33,
    "IRN_Shahr_I_Sokhta_BA1": 20.83,
    "Simulated_AASI_South_by_DMXX": 20,
    "RUS_Sintashta_MLBA": 5.83,

    "sample": "Velamas:Average",
    "fit": 1.2743,
    "IRN_Shahr_I_Sokhta_BA3": 48.33,
    "Simulated_AASI_South_by_DMXX": 24.17,
    "IRN_Shahr_I_Sokhta_BA1": 22.5,
    "RUS_Sintashta_MLBA": 5,

    "sample": "Piramalai:Average",
    "fit": 1.7825,
    "IRN_Shahr_I_Sokhta_BA3": 55,
    "Simulated_AASI_South_by_DMXX": 25.83,
    "IRN_Shahr_I_Sokhta_BA1": 15.83,
    "RUS_Sintashta_MLBA": 3.33,


    I would add one more thing, which is that I have tried such runs many times privately and they seem to work for isolation purposes. I don't understand why they do but it does appear to be the case. As someone already said it could be that the complex mix already present in certain moderns allows specific ancestry to show through more clearly.

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  11. #26
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    Quote Originally Posted by 26284729292 View Post
    I still feel like Velamas aren't the greatest population to use for modeling, especially given they have a ~10% BMAC type shift. They're too small a sample size among other things. I like Marathas and Kallars because they provide a decent AASI shifted base from which to evaluate populations IMO.
    These do also have a SIS1/BMAC-like shift too don't they? If you can think of any modern population without it I would be happy to test it. So far I and others tested similar models using SIS3 instead but it didn't work out.

  12. #27
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    Quote Originally Posted by Censored View Post
    These do also have a SIS1/BMAC-like shift too don't they? If you can think of any modern population without it I would be happy to test it. So far I and others tested similar models using SIS3 instead but it didn't work out.
    Edit: saw your prior post.
    Last edited by 26284729292; 07-28-2019 at 12:38 AM.

  13. #28
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    Quote Originally Posted by Censored View Post
    The thing about these tribals is that they hold down WSHG and prevent steppe from being elevated. Also, for me the bigger issue is Velamas as they do have something SISBA1-like which can deflate real BMAC in some. As for SIS3, its the lack of ANF which gives even steppe deficient moderns a minor boost in steppe, which is what I want to avoid.

    "sample": "Andhra_Pradesh_Kamma:Average",
    "fit": 1.8694,
    "IRN_Shahr_I_Sokhta_BA3": 65.83,
    "IRN_Shahr_I_Sokhta_BA1": 14.17,
    "Simulated_AASI_South_by_DMXX": 14.17,
    "RUS_Sintashta_MLBA": 5.83,

    "sample": "Reddy:Average",
    "fit": 2.242,
    "IRN_Shahr_I_Sokhta_BA3": 53.33,
    "IRN_Shahr_I_Sokhta_BA1": 20.83,
    "Simulated_AASI_South_by_DMXX": 20,
    "RUS_Sintashta_MLBA": 5.83,

    "sample": "Velamas:Average",
    "fit": 1.2743,
    "IRN_Shahr_I_Sokhta_BA3": 48.33,
    "Simulated_AASI_South_by_DMXX": 24.17,
    "IRN_Shahr_I_Sokhta_BA1": 22.5,
    "RUS_Sintashta_MLBA": 5,

    "sample": "Piramalai:Average",
    "fit": 1.7825,
    "IRN_Shahr_I_Sokhta_BA3": 55,
    "Simulated_AASI_South_by_DMXX": 25.83,
    "IRN_Shahr_I_Sokhta_BA1": 15.83,
    "RUS_Sintashta_MLBA": 3.33,


    I would add one more thing, which is that I have tried such runs many times privately and they seem to work for isolation purposes. I don't understand why they do but it does appear to be the case. As someone already said it could be that the complex mix already present in certain moderns allows specific ancestry to show through more clearly.
    This is a good run. If you could add Marathas, that would be great.

    Seemingly, Piramalai (kallars) look like Velamas with an additional 7-8% of SISBA1. The AASI discrepancy is not nearly as large as I thought it would be.

  14. #29
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    Including a BMAC pop with notable ANF such as Gonur1 BA or Dzharkutan should alleviate any issues with inflating Steppe in supposedly steppe deficient groups. I believe they are also both more ANF than SIS BA1. Do formal stats support all those groups have absolutely 0% Pontic Steppe? Does including WSHG reduce the MLBA Steppe scored without worsening fits?

    @Censored

    Including Simulated AASI in that model above is an issue. It is an elemental population and is likely causing SIS BA1 to be inflated for most individuals. This is situation where SISBA3 simply won’t work for individuals who are more than 40% AASI. We’re missing a more AASI shifted ancient and won’t be able to present a realistic archaeological based model for many individuals without mixing in moderns which defeats the purpose of modeling with ancients.
    Last edited by Sapporo; 07-28-2019 at 12:47 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": [

  15. #30
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    Quote Originally Posted by Sapporo View Post
    Do formal stats support all those groups have absolutely 0% Pontic Steppe?
    .
    In short, no. But it's complicated.

    The Narasimhan qpAdm run involving Subcontinental tribal moderns is compromised, as they employed a simple three pop model (MLBA steppe + IVCp + AASI). There, they registered anywhere between 3-6% MLBA steppe, from memory.

    Any surplus ancestry along the ANE-WSHG-EHG cline in said moderns will result in an artificial inflation of MLBA steppe, given the core profile of that population were ~60% ANE-derived (mostly coming from EHG, with the addition of the ~20% ANE-like admixture in the remaining CHG).

    G25 modelling shows that, in terms of fit, Subcontinental southern tribals have a preference rank in the order of MA1 > WSHG > Sintashta when the Narasimhan model is replicated.

    [Edit]: I just remembered that Kale's qpAdm stats for the Irula showed that, for them, Sintashta wasn't preferable to a WSHG-rich Turanian agriculturalist group. So, that indirectly supports that the Irula lack MLBA steppe.

    So, I'll have to revise the above comment to "indirectly, yes, but it's complicated".
    Last edited by DMXX; 07-28-2019 at 12:47 AM. Reason: edit comment

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