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Thread: Global25 automated nMonte for South/Central Asian members

  1. #7741
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    One more - my maternal aunt:

    Shazia_scaled,0.061464,-0.006093,-0.113513,0.069122,-0.065243,0.04769,0.00235,0,0.001432,0.00164,-0.002923,0.003597,-0.003419,-0.005643,0.008822,0.00411,-0.007953,-0.003801,-0.005782,-0.011255,0.000374,-0.001484,-0.001602,-0.006025,0.002634

    Shazia,0.0054,-0.0006,-0.0301,0.0214,-0.0212,0.0171,0.001,0,0.0007,0.0009,-0.0018,0.0024,-0.0023,-0.0041,0.0065,0.0031,-0.0061,-0.003,-0.0046,-0.009,0.0003,-0.0012,-0.0013,-0.005,0.0022

    Target: Shazia_scaled
    Distance: 1.7251% / 0.01725128
    49.0 IRN_Shahr_I_Sokhta_BA2
    24.2 TJK_Sarazm_En
    11.4 RUS_Sintashta_MLBA
    10.0 Anatolia_Tepecik_Ciftlik_N
    3.2 Han
    1.4 MAR_Iberomaurusian
    0.8 WHG

    Background: 1/2 Bains Rajput; 1/4 Awan; 1/4 Hazarewal.
    Last edited by Ahmed Ali; 10-16-2020 at 09:20 PM.

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  3. #7742
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    Quote Originally Posted by maroco View Post

    the fit looks terrible
    Yes, I'm trying to use groups from the study that I listed. I'm not going for the lowest fits.
    BMAC pre Steppe should be Iranian farmer + Anatolian + WSGH. It seems the Steppe is actually a mix of MLBA +WSHG. There might be CHG in there as well. Remember we are going across thousands of years with different timelines. This is technically not a great run. Neolithic to LBA is long break.
    Last edited by agent_lime; 10-16-2020 at 07:40 PM.

  4. #7743
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    Quote Originally Posted by agent_lime View Post
    Thanks Pegasus. I cannot replicate the results from the paper. I tried different WSHG and HG Steppe groups. Even Gonur1 seems to prefer RUS_Khvalynsk_En. What would be the appropriate groups to replicate Narasimhan.


    My results-
    Narasimhan's ANF values are inflated and thats why he gets crappy p values, they didn't include CHG , they did the same for Steppe EMBA/MLBA and they don't have any Iran_N. They had Afansievo with 18% ANF using Iran_N, with Eneolithic Steppe it falls to 6-7% ANF/7-8% EEF. Khvalynsk has WSHG btw, I would not use them they seem to have been largely obliterated once Fatyanovo groups moved into the Volga. They did not contribute to anyone.

    With Turan/BMAC populations there is a CHG shift, with it ANF goes down to 10-15%. With that modern like sample I posted , ANF/CHG /AG3 goes up because of Steppe ancestry. She has almost 6% AASI as well, whereas with the main cluster its 1-2%. SIS2/IVC populations completely lack this CHG shift.

    Target: TKM_Gonur1_BA:I1793
    Distance: 4.5975% / 0.04597523
    47.0 IRN_Ganj_Dareh_N
    19.6 GEO_CHG
    18.6 TUR_Barcin_N
    8.6 RUS_AfontovaGora3
    6.2 AASI

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  6. #7744
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    While modeling myself over G25, I observed that I am able to model myself using either of SIS BA2 or BA3 with no difference in fit whatsoever. However, the implications it has for the amount of direct BMAC input estimated between the two models is substantial.

    Here are the models:

    sample: kamil154
    distance: 2.3073
    Gonur1_BA: 46.5
    Shahr_I_Sokhta_BA3: 34.5
    CG_CentralSteppeMLBA: 15
    Chokhopani_2700BP: 4

    sample: kamil154
    distance: 2.2918
    Shahr_I_Sokhta_BA2: 49
    Gonur1_BA: 30.5
    Srubnaya_Alakul_MLBA: 16
    Chokhopani_2700BP: 4.5

    There is a paucity of IVC proper samples from the Indus tributaries region, and so for now all we can rely upon IVCp such as SIS or Rakhigarhi from Yamuna/Ganga region, so how exactly the admixture was in the Indus tributaries region is still purely speculative. However, based on what we know from archaeogenetics and Indo-Iranian literature, there seems to have been significant BMAC-rich incursion either into a high ASI/Low Caucasian base in PGW, East of the Indus tributaries region, or then later in history with the Southward push of an East Iranic, Pamirid type Proto-Pashtun population into a primarily SPGT type base, west of the Indus tributaries.

    Based on Iron Age SPGT (Pre-Pashtun ethnogenesis) samples however, it is apparent that whatever little NE-Euro found in them was likely referred traces due to interactions with Vedic pops to their east. To me, it seems that the population of IVC proper was already more Caucasian shifted and lower SI shifted in comparison to samples such as Rakhigarhi or SIS BA3, which could explain why certain Punjab pops score the way they do in terms of West Asian shift, despite being lower Euro than certain other pops to their East and West. In other words, I am considering that Indus proper pops might be a case of low to moderate BMAC movement into a high Iran N/low SI base, whereas PGW would be a case of significant BMAC movement into a high SI/low Iran N base.

    I think the model involving SIS BA2 for instance might be closer to reality in my case, and that of SPGT shifted Punjabi's.

    Thoughts?
    Last edited by kamil154; 10-17-2020 at 08:17 PM.
    G25 Neolithic model

    "sample": "kamil154",
    "distance": 2.2284,
    "Ganj_Dareh_N": 41,
    "Barcin_N": 18,
    "Simulated_AASI_NW_by_DMXX": 17,
    "Karelia_HG": 10.5,
    "GEO_CHG": 3.5,
    "Tyumen_HG": 3,
    "LAO_Hoabinhian": 2.5,
    "LapaDoSanto_9600BP": 2.5,
    "Boshan_N": 2

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  8. #7745
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    Quote Originally Posted by kamil154 View Post
    While modeling myself over G25, I observed that I am able to model myself using either of SIS BA2 or BA3 with no difference in fit whatsoever. However, the implications it has for the amount of direct BMAC input estimated between the two models is substantial.

    Here are the models:

    sample: kamil154
    distance: 2.3073
    Gonur1_BA: 46.5
    Shahr_I_Sokhta_BA3: 34.5
    CG_CentralSteppeMLBA: 15
    Chokhopani_2700BP: 4

    sample: kamil154
    distance: 2.2918
    Shahr_I_Sokhta_BA2: 49
    Gonur1_BA: 30.5
    Srubnaya_Alakul_MLBA: 16
    Chokhopani_2700BP: 4.5

    There is a paucity of IVC proper samples from the Indus tributaries region, and so for now all we can rely upon IVCp such as SIS or Rakhigarhi from Yamuna/Ganga region, so how exactly the admixture was in the Indus tributaries region is still purely speculative. However, based on what we know from archaeogenetics and Indo-Iranian literature, there seems to have been significant BMAC-rich incursion either into a high ASI/Low Caucasian base in PGW, East of the Indus tributaries region, or then later in history with the Southward push of an East Iranic, Pamirid type Proto-Pashtun population into a primarily SPGT type base, west of the Indus tributaries.

    Based on Iron Age SPGT (Pre-Pashtun ethnogenesis) samples however, it is apparent that whatever little NE-Euro found in them was likely referred traces due to interactions with Vedic pops to their east. To me, it seems that the population of IVC proper was already more Caucasian shifted and lower SI shifted in comparison to samples such as Rakhigarhi for SIS BA3, which could explain why certain Punjab pops score the way they do in terms of West Asian shift, despite being lower Euro than certain other pops to their East and West. In other words, I am considering that Indus proper pops might be a case of low to moderate BMAC movement into a high Iran N/low SI base, whereas PGW would be a case of significant BMAC movement into a high SI/low Iran N base.

    I think the model involving SIS BA2 for instance might be closer to reality in my case, and that of SPGT shifted Punjabi's.

    Thoughts?

    Modern Punjabi populations with exception of some Gujjars afaik, cannot model solely with the SIS2 average or 1456, she has 31-32% AASI, they generally have 18-25%, with all the components being introduced by these hybrid IIr groups , that makes it impossible and leads to inflated Steppe values. Matt's IVC ghost for SPGT which he based of his PCA analysis was between 8728 and 1459, which is Rakghigarhi like. So between the IVC collapse and arrival of IIr related groups, AASI increased for sure. If you look at the IVC heavy SPGT and Bustan_o2 samples it reflects that as well.

    SPGT/Gandharan populations are more archaic than the PGW Vedic group, that culture forms post 1200 BC. Also, the lack of L657 would exclude them.

    I really would be cautious of utilizing HW admixture components and superimposing them on G25, because its often not accurate and admixture calculators are limited.
    Last edited by pegasus; 10-18-2020 at 07:57 AM.

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  10. #7746
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    Quote Originally Posted by pegasus View Post

    I really would be cautious of utilizing HW admixture components and superimposing them on G25, because its often not accurate and admixture calculators are limited.
    Unfortunately doesn't seem like anyones trynna leave that sorry ass calculator alone any time soon

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  12. #7747
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    Good fit:
    "distance": 2.1048,
    "Tepe_Hissar_C": 49.5,
    "Dali_MLBA": 21.5,
    "Simulated_AASI_by_DMXX": 18,
    "West_Siberia_N": 7,
    "Ganj_Dareh_N": 4

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  14. #7748
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    New Kandahar Pashtun sample ,

    "sample": "Kandahar2",
    "distance": 1.8006,
    "Sappali_Tepe_BA": 36.5,
    "Srubnaya_MLBA": 29.5,
    "CG_IVCp": 29,
    "Devils_Gate_Cave_N": 5


    "sample": "Kandahar2 ",
    "distance": 1.6332,
    "KAZ_Kangju": 46.5,
    "CG_IVCp": 34.5,
    "Caucasus_lowlands_LN": 10.5,
    "Gonur1_BA": 8.5,



    "sample": "Kandahar2",
    "distance": 1.6627,
    "CG_IVCp": 32,
    "KAZ_Kangju": 30,
    "TKM_IA": 18.5,
    "Caucasus_lowlands_LN": 9,
    "Gonur1_BA": 9,
    "Devils_Gate_Cave_N": 1.5




    "sample": "Kandahar2",
    "distance": 1.797,
    "TKM_IA": 47,
    "CG_IVCp": 31,
    "Caucasus_lowlands_LC": 10.5,
    "Sappali_Tepe_BA": 8,
    "Upper_Yellow_River_LN": 3.5

    distal proportions


    "sample": "Kandahar2",
    "distance": 2.8198,
    "Ganj_Dareh_N": 40.5,
    "Barcin_N": 21.5,
    "Simulated_AASI_by_DMXX": 10.5,
    "Sidelkino_HG": 9.5,
    "Tyumen_HG": 7.5,
    "GEO_CHG": 6,
    "Devils_Gate_Cave_N": 4.5
    Last edited by pegasus; 10-24-2020 at 08:17 PM.

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  16. #7749
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    @pegasus

    What settings did you use for that Kandahari's runs? Default pen + scaled with which batch and cycles settings? I wanted to do some similar runs on Genoplot.

    @kamil

    Same question to you for your SIS BA3 vs. SIS BA2 runs.
    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": [

    avatar credit goes out to aaronbee2010

  17. #7750
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    Quote Originally Posted by Sapporo View Post
    @pegasus

    What settings did you use for that Kandahari's runs? Default pen + scaled with which batch and cycles settings? I wanted to do some similar runs on Genoplot.

    @kamil

    Same question to you for your SIS BA3 vs. SIS BA2 runs.
    I didn't use default penalty , just regular settings , penalty =0 . Its not the average on Genoplot , I will send you the coordinates.

    With the whole SIS2 average , it does not work well at all with Punjabi populations like I mentioned earlier.


    "sample": "Punjabi Sikh India:Average",
    "distance": 2.1756,
    "Shahr_I_Sokhta_BA2": 70.5,
    "Srubnaya_MLBA": 27,
    "Dzharkutan1_BA": 2.5

    With SIS3 thrown in


    "sample": "Punjabi Sikh India:Average",
    "distance": 1.7649,
    "Shahr_I_Sokhta_BA3": 42.5,
    "Srubnaya_MLBA": 24.5,
    "Dzharkutan1_BA": 21,
    "Shahr_I_Sokhta_BA2": 12


    With TKM IA ( 55% Steppe MLBA/45% BMAC)


    "sample": "Punjabi Sikh India:Average",
    "distance": 1.1896,
    "Shahr_I_Sokhta_BA3": 46,
    "TKM_IA": 46,
    "Shahr_I_Sokhta_BA2": 8

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