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Thread: Global25 automated nMonte for South/Central Asian members

  1. #7821
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    Quote Originally Posted by Kirtan24 View Post
    Don't you think that Simulated_AASI_by_DMXX inflates the AASI a little bit (3-4%)? This is what Kashmiri Pandit average scores on Genoplot (penalty off) with this particular model:

    sample: Kashmiri Pandit:Average
    distance: 1.8314
    Ganj_Dareh_N: 31
    Simulated_AASI_by_DMXX: 25.5
    Sidelkino_HG: 9
    Barcin_N: 20
    Tyumen_HG: 14.5

    penalty on:

    sample: Kashmiri Pandit:Average
    distance: 2.9794
    Ganj_Dareh_N: 45
    Simulated_AASI_by_DMXX: 23.5
    Barcin_N: 15
    Tyumen_HG: 8.5
    Sidelkino_HG: 8

    On other models the AASI for KPs limits itself to 20-21%. For me it has typically been at 24-26%. Or am I reading too much into it?

    Some other groups (penalty on):

    sample: Brahmin Gujarat:Average
    distance: 2.1267
    Ganj_Dareh_N: 40.5
    Simulated_AASI_by_DMXX: 30
    Barcin_N: 14
    Tyumen_HG: 9.5
    Sidelkino_HG: 6

    sample: Bihar Brahmin Bhumihar:mean
    distance: 3.1936
    Ganj_Dareh_N: 36.5
    Simulated_AASI_by_DMXX: 30
    Barcin_N: 15
    Tyumen_HG: 13
    Sidelkino_HG: 5.5

    sample: Brahmin Uttar Pradesh:Average
    distance: 3.2536
    Ganj_Dareh_N: 35.5
    Simulated_AASI_by_DMXX: 34.5
    Barcin_N: 12
    Tyumen_HG: 10.5
    Sidelkino_HG: 7.5
    Hmm I think something in both our models is off or different from whatever pegasus is using primarily because of Barcin's inflation. Maybe we both are using older sims?

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  3. #7822
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    Quote Originally Posted by ThaYamamoto View Post
    Hmm I think something in both our models is off or different from whatever pegasus is using primarily because of Barcin's inflation. Maybe we both are using older sims?
    I just used the sims on Genoplot, so they should be up to date.
    “Some of you say, “Joy is greater than sorrow,” and others say, “Nay, sorrow is the greater.”
    But I say unto you, they are inseparable.
    Together they come, and when one sits alone with you at your board, remember that the other is asleep upon your bed.”
    ― Khalil Gibran, The Prophet, 1923

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  5. #7823
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    Quote Originally Posted by Kirtan24 View Post
    I just used the sims on Genoplot, so they should be up to date.
    Aite in that case gonna have to see what pegasus says.

  6. #7824
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    Quote Originally Posted by Kirtan24 View Post
    Don't you think that Simulated_AASI_by_DMXX inflates the AASI a little bit (3-4%)? This is what Kashmiri Pandit average scores on Genoplot (penalty off) with this particular model:

    sample: Kashmiri Pandit:Average
    distance: 1.8314
    Ganj_Dareh_N: 31
    Simulated_AASI_by_DMXX: 25.5
    Sidelkino_HG: 9
    Barcin_N: 20
    Tyumen_HG: 14.5

    penalty on:

    sample: Kashmiri Pandit:Average
    distance: 2.9794
    Ganj_Dareh_N: 45
    Simulated_AASI_by_DMXX: 23.5
    Barcin_N: 15
    Tyumen_HG: 8.5
    Sidelkino_HG: 8

    On other models the AASI for KPs limits itself to 20-21%. For me it has typically been at 24-26%. Or am I reading too much into it?

    Some other groups (penalty on):

    sample: Brahmin Gujarat:Average
    distance: 2.1267
    Ganj_Dareh_N: 40.5
    Simulated_AASI_by_DMXX: 30
    Barcin_N: 14
    Tyumen_HG: 9.5
    Sidelkino_HG: 6

    sample: Bihar Brahmin Bhumihar:mean
    distance: 3.1936
    Ganj_Dareh_N: 36.5
    Simulated_AASI_by_DMXX: 30
    Barcin_N: 15
    Tyumen_HG: 13
    Sidelkino_HG: 5.5

    sample: Brahmin Uttar Pradesh:Average
    distance: 3.2536
    Ganj_Dareh_N: 35.5
    Simulated_AASI_by_DMXX: 34.5
    Barcin_N: 12
    Tyumen_HG: 10.5
    Sidelkino_HG: 7.5
    Kashmiri pandits have Tibetan related admixture, pretty much all Himalayan populations do. There is 2-4% SE but its within range till they find actual HGs. Penalty =0 does inflates AASI and deflates Iran_N a bit . Here with default penalty, with better outgroups it's not too different though.


    sample: Kirtan
    distance: 2.439
    Ganj_Dareh_N: 44.5
    Simulated_AASI_by_DMXX: 27.5
    Karelia_HG: 8
    Barcin_N: 8.5
    Tyumen_HG: 9
    GEO_CHG: 2.5

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  8. #7825
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    What is the age of the Tyumen_HG sample?

    While it is definitely a site which has importance for the infusion of Steppe ancestry in South Asia, from late bronze age to Iron age onward, however if we try going back to the any older samples, such as early bronze or late neolithic, especially from the Eurasia, we might have a better chance instead with South Asian samples for the period, for instance Chokhopani and Shahr e Sohta 2 samples. For that is has been the source of most South Asian ancestry from the Himalayas and among many groups, such as the older Gujarati Brahmin G25 samples, minus Kirtan, because the caste identities for these groups had not solidified anytime before 600-800 AD, for the GBs, and much later for the KPs. Speaking of Chokhopani, even many Punjabis show NE Asian, which likely derived from a Chokhopani-like population that might have trickled down from Tibet. And for the GBs there might have been some infusion of it from the Himalayas, ranging from the NW to the Uttarakhand area, during medieval and the period immediately before it, of the Indian History.

    Here is what I get on Vahaduo, without using simulated AASI coordinates. All groups prefer Sintashta/Chokhopani over Tyumen HG.

    Distance: 3.1667% / 0.03166696
    Target: KPB_Scaled
    69.7 IRN_Shahr_I_Sokhta_BA2
    21.0 RUS_Srubnaya_MLBA
    5.0 TUR_Barcin_N
    4.3 NPL_Chokhopani_2700BP

    Distance: 2.5378% / 0.02537828
    Target: Kashmiri_Pandit
    67.6 IRN_Shahr_I_Sokhta_BA2
    25.1 RUS_Srubnaya_MLBA
    5.5 NPL_Chokhopani_2700BP
    1.6 TUR_Barcin_N
    0.2 RUS_Tyumen_HG

    Distance: 2.2224% / 0.02222437
    Target: Brahmin_Gujarat
    76.4 IRN_Shahr_I_Sokhta_BA2
    16.1 RUS_Srubnaya_MLBA
    3.8 NPL_Chokhopani_2700BP
    1.9 RUS_Tyumen_HG
    1.8 TUR_Barcin_N

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  10. #7826
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    Another interesting qpAdm , this is one of the Ghaznavids 7716, he surprisingly needed a Levantine source-based of the stats . On G25 looked similar to other Pashtuns but he is not typical at all of them ,given his excess Levantine-like ancestry,. His Y DNA is not Pashtun like at all either. Though his higher IVC ancestry ties him to the region, so my guess he was a warrior or a religious figure who had both local and foreign origins. The only vector to my mind which would have brought Levantine type ancestry would be via the Saffarids . He came out 25% Steppe related, 35% IVC related ,25% BMAC, 16% Caananite. Its a good working model, but more genomes would be needed to properly resolve this. The usual models failed miserably.

    left pops:
    Pakistan_Medieval_Udegram_Ghaznavid
    ShahrISokhtaSubset
    Kazakhstan_MLBA_OyDzhaylau
    Alalakh_MLBA_outlier
    Levant_BA


    right pops:
    Cameroon_SMA.DG
    Russia_Steppe_Eneolithic
    ONG.SG
    PPNB
    Iran_GanjDareh_N
    DevilsCave_N.SG
    Russia_UstBelaya_Angara
    EHG
    Anatolia_N
    WSHG
    Russia_MA1_HG.SG
    CHG
    Russia_MLBA_Sintashta
    Sweden_HG_Motala

    0 Pakistan_Medieval_Udegram_Ghaznavid 1
    1 ShahrISokhtaSubset 4
    2 Kazakhstan_MLBA_OyDzhaylau 6
    3 Alalakh_MLBA_outlier 1
    4 Levant_BA 3
    5 Cameroon_SMA.DG 1
    6 Russia_Steppe_Eneolithic 3
    7 ONG.SG 6
    8 PPNB 11
    9 Iran_GanjDareh_N 8
    10 DevilsCave_N.SG 4
    11 Russia_UstBelaya_Angara 11
    12 EHG 3
    13 Anatolia_N 30
    14 WSHG 3
    15 Russia_MA1_HG.SG 1
    16 CHG 2
    17 Russia_MLBA_Sintashta 19
    18 Sweden_HG_Motala 6
    jackknife block size: 0.050
    snps: 1150513 indivs: 123
    number of blocks for block jackknife: 714
    ## ncols: 1150513
    coverage: Pakistan_Medieval_Udegram_Ghaznavid 613682
    coverage: ShahrISokhtaSubset 841356
    coverage: Kazakhstan_MLBA_OyDzhaylau 999558
    coverage: Alalakh_MLBA_outlier 733730
    coverage: Levant_BA 870086
    coverage: Cameroon_SMA.DG 1140138
    coverage: Russia_Steppe_Eneolithic 1008226
    coverage: ONG.SG 1143397
    coverage: PPNB 871625
    coverage: Iran_GanjDareh_N 1057358
    coverage: DevilsCave_N.SG 1149702
    coverage: Russia_UstBelaya_Angara 1092594
    coverage: EHG 1027057
    coverage: Anatolia_N 1141220
    coverage: WSHG 858019
    coverage: Russia_MA1_HG.SG 805960
    coverage: CHG 1149558
    coverage: Russia_MLBA_Sintashta 1115156
    coverage: Sweden_HG_Motala 1038843
    Effective number of blocks: 621.675
    numsnps used: 1150513
    codimension 1
    f4info:
    f4rank: 3 dof: 10 chisq: 9.081 tail: 0.524420183 dofdiff: 12 chisqdiff: -9.081 taildiff: 1
    B:
    scale 1.000 1.000 1.000
    Russia_Steppe_Eneolithic 1.141 0.315 0.709
    ONG.SG -0.069 1.157 -0.545
    PPNB 0.398 -2.057 -0.269
    Iran_GanjDareh_N 0.024 0.350 2.830
    DevilsCave_N.SG 0.138 1.028 0.004
    Russia_UstBelaya_Angara 0.436 1.073 -0.198
    EHG 1.612 0.387 -0.916
    Anatolia_N 0.711 -1.791 -0.284
    WSHG 1.465 0.999 0.159
    Russia_MA1_HG.SG 0.925 0.682 0.051
    CHG 0.488 -0.035 1.253
    Russia_MLBA_Sintashta 1.480 -0.391 -0.460
    Sweden_HG_Motala 1.670 -0.160 -1.161
    A:
    scale 690.949 926.907 2671.743
    ShahrISokhtaSubset -1.046 0.967 -0.665
    Kazakhstan_MLBA_OyDzhaylau 1.600 -0.142 -0.538
    Alalakh_MLBA_outlier 0.200 -0.060 1.781
    Levant_BA -0.554 -1.744 -0.310


    full rank
    f4info:
    f4rank: 4 dof: 0 chisq: 0.000 tail: 1 dofdiff: 10 chisqdiff: 9.081 taildiff: 0.524420183
    B:
    scale 520.670 438.653 1509.354 447.656
    Russia_Steppe_Eneolithic -0.991 0.998 0.849 -0.835
    ONG.SG 0.663 -0.119 -0.797 -0.991
    PPNB -1.532 0.533 -0.187 1.516
    Iran_GanjDareh_N -0.260 -0.249 2.759 -0.500
    DevilsCave_N.SG 0.159 -0.125 -0.716 -1.144
    Russia_UstBelaya_Angara 0.121 0.311 -0.376 -1.178
    EHG -0.992 1.719 -0.222 -0.883
    Anatolia_N -1.663 0.815 -0.128 1.150
    WSHG -0.910 1.238 0.012 -1.597
    Russia_MA1_HG.SG -0.520 0.796 0.037 -1.042
    CHG -0.564 0.425 1.731 -0.215
    Russia_MLBA_Sintashta -1.452 1.529 0.010 -0.269
    Sweden_HG_Motala -1.360 1.797 -0.528 -0.466
    A:
    scale 2.000 2.000 2.000 2.000
    ShahrISokhtaSubset 2.000 0.000 0.000 0.000
    Kazakhstan_MLBA_OyDzhaylau 0.000 2.000 0.000 0.000
    Alalakh_MLBA_outlier 0.000 0.000 2.000 0.000
    Levant_BA 0.000 0.000 0.000 2.000


    best coefficients: 0.347 0.254 0.235 0.164
    Jackknife mean: 0.347787428 0.254622772 0.233704917 0.163884884
    std. errors: 0.050 0.031 0.076 0.032

    error covariance (* 1,000,000)
    2475 302 -3241 464
    302 955 -1157 -99
    -3241 -1157 5814 -1416
    464 -99 -1416 1051


    summ: Pakistan_Medieval_Udegram_Ghaznavid 4 0.524420 0.348 0.255 0.234 0.164 2475 302 -3241 464 955 ...
    -1157 -99 5814 -1416 1051

    fixed pat wt dof chisq tail prob
    0000 0 10 9.081 0.52442 0.347 0.254 0.235 0.164
    0001 1 11 198.240 0 -0.114 0.045 1.069 0.000 infeasible
    0010 1 11 23.589 0.0145832 0.479 0.300 0.000 0.222
    0100 1 11 62.246 3.53768e-09 0.196 0.000 0.655 0.149
    1000 1 11 48.943 9.68444e-07 0.000 0.192 0.732 0.077
    0011 2 12 85.532 3.59629e-13 0.579 0.421 0.000 0.000
    0101 2 12 73.941 5.82284e-11 0.080 0.000 0.920 0.000
    0110 2 12 133.463 1.24327e-22 0.637 0.000 0.000 0.363
    1001 2 12 57.278 7.04133e-08 0.000 0.216 0.784 0.000
    1010 2 12 323.658 0 0.000 0.531 0.000 0.469
    1100 2 12 84.219 6.42941e-13 0.000 0.000 0.899 0.101
    0111 3 13 307.752 0 1.000 0.000 0.000 0.000
    1011 3 13 562.432 0 0.000 1.000 0.000 0.000
    1101 3 13 76.122 5.88156e-11 0.000 0.000 1.000 0.000
    1110 3 13 636.601 0 0.000 0.000 0.000 1.000
    best pat: 0000 0.52442 - -
    best pat: 0010 0.0145832 chi(nested): 14.508 p-value for nested model: 0.0001396
    best pat: 1001 7.04133e-08 not nested
    best pat: 1101 5.88156e-11 chi(nested): 18.844 p-value for nested model: 1.41883e-05

    coeffs: 0.347 0.254 0.235 0.164

    ## dscore:: f_4(Base, Fit, Rbase, right2)
    ## genstat:: f_4(Base, Fit, right1, right2)

    details: ShahrISokhtaSubset Russia_Steppe_Eneolithic -0.001902 -5.507816
    details: Kazakhstan_MLBA_OyDzhaylau Russia_Steppe_Eneolithic 0.002275 7.013775
    details: Alalakh_MLBA_outlier Russia_Steppe_Eneolithic 0.000563 1.490381
    details: Levant_BA Russia_Steppe_Eneolithic -0.001865 -5.519242
    dscore: Russia_Steppe_Eneolithic f4: -0.000255 Z: -0.864982

    details: ShahrISokhtaSubset ONG.SG 0.001273 3.757871
    details: Kazakhstan_MLBA_OyDzhaylau ONG.SG -0.000271 -0.853529
    details: Alalakh_MLBA_outlier ONG.SG -0.000528 -1.420694
    details: Levant_BA ONG.SG -0.002213 -6.833597
    dscore: ONG.SG f4: -0.000113 Z: -0.392467

    details: ShahrISokhtaSubset PPNB -0.002943 -8.414631
    details: Kazakhstan_MLBA_OyDzhaylau PPNB 0.001215 3.715002
    details: Alalakh_MLBA_outlier PPNB -0.000124 -0.320154
    details: Levant_BA PPNB 0.003386 9.728007
    dscore: PPNB f4: -0.000188 Z: -0.621043

    details: ShahrISokhtaSubset Iran_GanjDareh_N -0.000500 -1.571595
    details: Kazakhstan_MLBA_OyDzhaylau Iran_GanjDareh_N -0.000567 -1.901114
    details: Alalakh_MLBA_outlier Iran_GanjDareh_N 0.001828 5.020231
    details: Levant_BA Iran_GanjDareh_N -0.001117 -3.507134
    dscore: Iran_GanjDareh_N f4: -0.000071 Z: -0.256933

    details: ShahrISokhtaSubset DevilsCave_N.SG 0.000306 0.899993
    details: Kazakhstan_MLBA_OyDzhaylau DevilsCave_N.SG -0.000285 -0.875879
    details: Alalakh_MLBA_outlier DevilsCave_N.SG -0.000475 -1.301721
    details: Levant_BA DevilsCave_N.SG -0.002556 -7.736192
    dscore: DevilsCave_N.SG f4: -0.000496 Z: -1.695529

    details: ShahrISokhtaSubset Russia_UstBelaya_Angara 0.000231 0.744884
    details: Kazakhstan_MLBA_OyDzhaylau Russia_UstBelaya_Angara 0.000709 2.402924
    details: Alalakh_MLBA_outlier Russia_UstBelaya_Angara -0.000249 -0.727779
    details: Levant_BA Russia_UstBelaya_Angara -0.002631 -8.497344
    dscore: Russia_UstBelaya_Angara f4: -0.000228 Z: -0.866418

    details: ShahrISokhtaSubset EHG -0.001904 -5.302990
    details: Kazakhstan_MLBA_OyDzhaylau EHG 0.003918 11.405673
    details: Alalakh_MLBA_outlier EHG -0.000147 -0.356890
    details: Levant_BA EHG -0.001973 -5.428512
    dscore: EHG f4: -0.000022 Z: -0.070131

    details: ShahrISokhtaSubset Anatolia_N -0.003195 -9.802161
    details: Kazakhstan_MLBA_OyDzhaylau Anatolia_N 0.001858 6.164440
    details: Alalakh_MLBA_outlier Anatolia_N -0.000085 -0.236733
    details: Levant_BA Anatolia_N 0.002570 8.084175
    dscore: Anatolia_N f4: -0.000236 Z: -0.858723

    details: ShahrISokhtaSubset WSHG -0.001748 -4.276795
    details: Kazakhstan_MLBA_OyDzhaylau WSHG 0.002821 7.417244
    details: Alalakh_MLBA_outlier WSHG 0.000008 0.017260
    details: Levant_BA WSHG -0.003568 -8.906077
    dscore: WSHG f4: -0.000471 Z: -1.332582

    details: ShahrISokhtaSubset Russia_MA1_HG.SG -0.000998 -2.625186
    details: Kazakhstan_MLBA_OyDzhaylau Russia_MA1_HG.SG 0.001814 4.945375
    details: Alalakh_MLBA_outlier Russia_MA1_HG.SG 0.000024 0.059011
    details: Levant_BA Russia_MA1_HG.SG -0.002329 -6.219682
    dscore: Russia_MA1_HG.SG f4: -0.000260 Z: -0.785746

    details: ShahrISokhtaSubset CHG -0.001084 -3.213672
    details: Kazakhstan_MLBA_OyDzhaylau CHG 0.000969 3.007423
    details: Alalakh_MLBA_outlier CHG 0.001147 3.087752
    details: Levant_BA CHG -0.000480 -1.431633
    dscore: CHG f4: 0.000061 Z: 0.210226

    details: ShahrISokhtaSubset Russia_MLBA_Sintashta -0.002788 -9.043499
    details: Kazakhstan_MLBA_OyDzhaylau Russia_MLBA_Sintashta 0.003486 12.417777
    details: Alalakh_MLBA_outlier Russia_MLBA_Sintashta 0.000007 0.020201
    details: Levant_BA Russia_MLBA_Sintashta -0.000601 -2.006932
    dscore: Russia_MLBA_Sintashta f4: -0.000178 Z: -0.684682

    details: ShahrISokhtaSubset Sweden_HG_Motala -0.002611 -7.676428
    details: Kazakhstan_MLBA_OyDzhaylau Sweden_HG_Motala 0.004097 13.152831
    details: Alalakh_MLBA_outlier Sweden_HG_Motala -0.000350 -0.912400
    details: Levant_BA Sweden_HG_Motala -0.001042 -3.106908
    dscore: Sweden_HG_Motala f4: -0.000117 Z: -0.406573
    Last edited by pegasus; 12-01-2020 at 02:36 AM.

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  12. #7827
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    That distance for me is kind of high, at least compared to the other two. I wonder why

  13. #7828
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    Quote Originally Posted by kpb View Post
    That distance for me is kind of high, at least compared to the other two. I wonder why
    You have an extra CHG like affinity which has to be accounted for. Kamil has it too.

    sample: :kpb
    distance: 1.8566
    Saidu_Sharif_H_o: 41.5
    Gonur1_BA: 28
    Srubnaya_Alakul_MLBA: 16
    CG_IVCp: 12
    Chokhopani_2700BP: 2.5

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  15. #7829
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    Wife (P) : R1a-Z280

    Quote Originally Posted by pegasus View Post
    Another interesting qpAdm , this is one of the Ghaznavids 7716, he surprisingly needed a Levantine source-based of the stats . On G25 looked similar to other Pashtuns but he is not typical at all of them ,given his excess Levantine-like ancestry,. His Y DNA is not Pashtun like at all either. Though his higher IVC ancestry ties him to the region, so my guess he was a warrior or a religious figure who had both local and foreign origins. The only vector to my mind which would have brought Levantine type ancestry would be via the Saffarids . He came out 25% Steppe related, 35% IVC related ,25% BMAC, 16% Caananite. Its a good working model, but more genomes would be needed to properly resolve this. The usual models failed miserably.

    left pops:
    Pakistan_Medieval_Udegram_Ghaznavid
    ShahrISokhtaSubset
    Kazakhstan_MLBA_OyDzhaylau
    Alalakh_MLBA_outlier
    Levant_BA


    right pops:
    Cameroon_SMA.DG
    Russia_Steppe_Eneolithic
    ONG.SG
    PPNB
    Iran_GanjDareh_N
    DevilsCave_N.SG
    Russia_UstBelaya_Angara
    EHG
    Anatolia_N
    WSHG
    Russia_MA1_HG.SG
    CHG
    Russia_MLBA_Sintashta
    Sweden_HG_Motala

    0 Pakistan_Medieval_Udegram_Ghaznavid 1
    1 ShahrISokhtaSubset 4
    2 Kazakhstan_MLBA_OyDzhaylau 6
    3 Alalakh_MLBA_outlier 1
    4 Levant_BA 3
    5 Cameroon_SMA.DG 1
    6 Russia_Steppe_Eneolithic 3
    7 ONG.SG 6
    8 PPNB 11
    9 Iran_GanjDareh_N 8
    10 DevilsCave_N.SG 4
    11 Russia_UstBelaya_Angara 11
    12 EHG 3
    13 Anatolia_N 30
    14 WSHG 3
    15 Russia_MA1_HG.SG 1
    16 CHG 2
    17 Russia_MLBA_Sintashta 19
    18 Sweden_HG_Motala 6
    jackknife block size: 0.050
    snps: 1150513 indivs: 123
    number of blocks for block jackknife: 714
    ## ncols: 1150513
    coverage: Pakistan_Medieval_Udegram_Ghaznavid 613682
    coverage: ShahrISokhtaSubset 841356
    coverage: Kazakhstan_MLBA_OyDzhaylau 999558
    coverage: Alalakh_MLBA_outlier 733730
    coverage: Levant_BA 870086
    coverage: Cameroon_SMA.DG 1140138
    coverage: Russia_Steppe_Eneolithic 1008226
    coverage: ONG.SG 1143397
    coverage: PPNB 871625
    coverage: Iran_GanjDareh_N 1057358
    coverage: DevilsCave_N.SG 1149702
    coverage: Russia_UstBelaya_Angara 1092594
    coverage: EHG 1027057
    coverage: Anatolia_N 1141220
    coverage: WSHG 858019
    coverage: Russia_MA1_HG.SG 805960
    coverage: CHG 1149558
    coverage: Russia_MLBA_Sintashta 1115156
    coverage: Sweden_HG_Motala 1038843
    Effective number of blocks: 621.675
    numsnps used: 1150513
    codimension 1
    f4info:
    f4rank: 3 dof: 10 chisq: 9.081 tail: 0.524420183 dofdiff: 12 chisqdiff: -9.081 taildiff: 1
    B:
    scale 1.000 1.000 1.000
    Russia_Steppe_Eneolithic 1.141 0.315 0.709
    ONG.SG -0.069 1.157 -0.545
    PPNB 0.398 -2.057 -0.269
    Iran_GanjDareh_N 0.024 0.350 2.830
    DevilsCave_N.SG 0.138 1.028 0.004
    Russia_UstBelaya_Angara 0.436 1.073 -0.198
    EHG 1.612 0.387 -0.916
    Anatolia_N 0.711 -1.791 -0.284
    WSHG 1.465 0.999 0.159
    Russia_MA1_HG.SG 0.925 0.682 0.051
    CHG 0.488 -0.035 1.253
    Russia_MLBA_Sintashta 1.480 -0.391 -0.460
    Sweden_HG_Motala 1.670 -0.160 -1.161
    A:
    scale 690.949 926.907 2671.743
    ShahrISokhtaSubset -1.046 0.967 -0.665
    Kazakhstan_MLBA_OyDzhaylau 1.600 -0.142 -0.538
    Alalakh_MLBA_outlier 0.200 -0.060 1.781
    Levant_BA -0.554 -1.744 -0.310


    full rank
    f4info:
    f4rank: 4 dof: 0 chisq: 0.000 tail: 1 dofdiff: 10 chisqdiff: 9.081 taildiff: 0.524420183
    B:
    scale 520.670 438.653 1509.354 447.656
    Russia_Steppe_Eneolithic -0.991 0.998 0.849 -0.835
    ONG.SG 0.663 -0.119 -0.797 -0.991
    PPNB -1.532 0.533 -0.187 1.516
    Iran_GanjDareh_N -0.260 -0.249 2.759 -0.500
    DevilsCave_N.SG 0.159 -0.125 -0.716 -1.144
    Russia_UstBelaya_Angara 0.121 0.311 -0.376 -1.178
    EHG -0.992 1.719 -0.222 -0.883
    Anatolia_N -1.663 0.815 -0.128 1.150
    WSHG -0.910 1.238 0.012 -1.597
    Russia_MA1_HG.SG -0.520 0.796 0.037 -1.042
    CHG -0.564 0.425 1.731 -0.215
    Russia_MLBA_Sintashta -1.452 1.529 0.010 -0.269
    Sweden_HG_Motala -1.360 1.797 -0.528 -0.466
    A:
    scale 2.000 2.000 2.000 2.000
    ShahrISokhtaSubset 2.000 0.000 0.000 0.000
    Kazakhstan_MLBA_OyDzhaylau 0.000 2.000 0.000 0.000
    Alalakh_MLBA_outlier 0.000 0.000 2.000 0.000
    Levant_BA 0.000 0.000 0.000 2.000


    best coefficients: 0.347 0.254 0.235 0.164
    Jackknife mean: 0.347787428 0.254622772 0.233704917 0.163884884
    std. errors: 0.050 0.031 0.076 0.032

    error covariance (* 1,000,000)
    2475 302 -3241 464
    302 955 -1157 -99
    -3241 -1157 5814 -1416
    464 -99 -1416 1051


    summ: Pakistan_Medieval_Udegram_Ghaznavid 4 0.524420 0.348 0.255 0.234 0.164 2475 302 -3241 464 955 ...
    -1157 -99 5814 -1416 1051

    fixed pat wt dof chisq tail prob
    0000 0 10 9.081 0.52442 0.347 0.254 0.235 0.164
    0001 1 11 198.240 0 -0.114 0.045 1.069 0.000 infeasible
    0010 1 11 23.589 0.0145832 0.479 0.300 0.000 0.222
    0100 1 11 62.246 3.53768e-09 0.196 0.000 0.655 0.149
    1000 1 11 48.943 9.68444e-07 0.000 0.192 0.732 0.077
    0011 2 12 85.532 3.59629e-13 0.579 0.421 0.000 0.000
    0101 2 12 73.941 5.82284e-11 0.080 0.000 0.920 0.000
    0110 2 12 133.463 1.24327e-22 0.637 0.000 0.000 0.363
    1001 2 12 57.278 7.04133e-08 0.000 0.216 0.784 0.000
    1010 2 12 323.658 0 0.000 0.531 0.000 0.469
    1100 2 12 84.219 6.42941e-13 0.000 0.000 0.899 0.101
    0111 3 13 307.752 0 1.000 0.000 0.000 0.000
    1011 3 13 562.432 0 0.000 1.000 0.000 0.000
    1101 3 13 76.122 5.88156e-11 0.000 0.000 1.000 0.000
    1110 3 13 636.601 0 0.000 0.000 0.000 1.000
    best pat: 0000 0.52442 - -
    best pat: 0010 0.0145832 chi(nested): 14.508 p-value for nested model: 0.0001396
    best pat: 1001 7.04133e-08 not nested
    best pat: 1101 5.88156e-11 chi(nested): 18.844 p-value for nested model: 1.41883e-05

    coeffs: 0.347 0.254 0.235 0.164

    ## dscore:: f_4(Base, Fit, Rbase, right2)
    ## genstat:: f_4(Base, Fit, right1, right2)

    details: ShahrISokhtaSubset Russia_Steppe_Eneolithic -0.001902 -5.507816
    details: Kazakhstan_MLBA_OyDzhaylau Russia_Steppe_Eneolithic 0.002275 7.013775
    details: Alalakh_MLBA_outlier Russia_Steppe_Eneolithic 0.000563 1.490381
    details: Levant_BA Russia_Steppe_Eneolithic -0.001865 -5.519242
    dscore: Russia_Steppe_Eneolithic f4: -0.000255 Z: -0.864982

    details: ShahrISokhtaSubset ONG.SG 0.001273 3.757871
    details: Kazakhstan_MLBA_OyDzhaylau ONG.SG -0.000271 -0.853529
    details: Alalakh_MLBA_outlier ONG.SG -0.000528 -1.420694
    details: Levant_BA ONG.SG -0.002213 -6.833597
    dscore: ONG.SG f4: -0.000113 Z: -0.392467

    details: ShahrISokhtaSubset PPNB -0.002943 -8.414631
    details: Kazakhstan_MLBA_OyDzhaylau PPNB 0.001215 3.715002
    details: Alalakh_MLBA_outlier PPNB -0.000124 -0.320154
    details: Levant_BA PPNB 0.003386 9.728007
    dscore: PPNB f4: -0.000188 Z: -0.621043

    details: ShahrISokhtaSubset Iran_GanjDareh_N -0.000500 -1.571595
    details: Kazakhstan_MLBA_OyDzhaylau Iran_GanjDareh_N -0.000567 -1.901114
    details: Alalakh_MLBA_outlier Iran_GanjDareh_N 0.001828 5.020231
    details: Levant_BA Iran_GanjDareh_N -0.001117 -3.507134
    dscore: Iran_GanjDareh_N f4: -0.000071 Z: -0.256933

    details: ShahrISokhtaSubset DevilsCave_N.SG 0.000306 0.899993
    details: Kazakhstan_MLBA_OyDzhaylau DevilsCave_N.SG -0.000285 -0.875879
    details: Alalakh_MLBA_outlier DevilsCave_N.SG -0.000475 -1.301721
    details: Levant_BA DevilsCave_N.SG -0.002556 -7.736192
    dscore: DevilsCave_N.SG f4: -0.000496 Z: -1.695529

    details: ShahrISokhtaSubset Russia_UstBelaya_Angara 0.000231 0.744884
    details: Kazakhstan_MLBA_OyDzhaylau Russia_UstBelaya_Angara 0.000709 2.402924
    details: Alalakh_MLBA_outlier Russia_UstBelaya_Angara -0.000249 -0.727779
    details: Levant_BA Russia_UstBelaya_Angara -0.002631 -8.497344
    dscore: Russia_UstBelaya_Angara f4: -0.000228 Z: -0.866418

    details: ShahrISokhtaSubset EHG -0.001904 -5.302990
    details: Kazakhstan_MLBA_OyDzhaylau EHG 0.003918 11.405673
    details: Alalakh_MLBA_outlier EHG -0.000147 -0.356890
    details: Levant_BA EHG -0.001973 -5.428512
    dscore: EHG f4: -0.000022 Z: -0.070131

    details: ShahrISokhtaSubset Anatolia_N -0.003195 -9.802161
    details: Kazakhstan_MLBA_OyDzhaylau Anatolia_N 0.001858 6.164440
    details: Alalakh_MLBA_outlier Anatolia_N -0.000085 -0.236733
    details: Levant_BA Anatolia_N 0.002570 8.084175
    dscore: Anatolia_N f4: -0.000236 Z: -0.858723

    details: ShahrISokhtaSubset WSHG -0.001748 -4.276795
    details: Kazakhstan_MLBA_OyDzhaylau WSHG 0.002821 7.417244
    details: Alalakh_MLBA_outlier WSHG 0.000008 0.017260
    details: Levant_BA WSHG -0.003568 -8.906077
    dscore: WSHG f4: -0.000471 Z: -1.332582

    details: ShahrISokhtaSubset Russia_MA1_HG.SG -0.000998 -2.625186
    details: Kazakhstan_MLBA_OyDzhaylau Russia_MA1_HG.SG 0.001814 4.945375
    details: Alalakh_MLBA_outlier Russia_MA1_HG.SG 0.000024 0.059011
    details: Levant_BA Russia_MA1_HG.SG -0.002329 -6.219682
    dscore: Russia_MA1_HG.SG f4: -0.000260 Z: -0.785746

    details: ShahrISokhtaSubset CHG -0.001084 -3.213672
    details: Kazakhstan_MLBA_OyDzhaylau CHG 0.000969 3.007423
    details: Alalakh_MLBA_outlier CHG 0.001147 3.087752
    details: Levant_BA CHG -0.000480 -1.431633
    dscore: CHG f4: 0.000061 Z: 0.210226

    details: ShahrISokhtaSubset Russia_MLBA_Sintashta -0.002788 -9.043499
    details: Kazakhstan_MLBA_OyDzhaylau Russia_MLBA_Sintashta 0.003486 12.417777
    details: Alalakh_MLBA_outlier Russia_MLBA_Sintashta 0.000007 0.020201
    details: Levant_BA Russia_MLBA_Sintashta -0.000601 -2.006932
    dscore: Russia_MLBA_Sintashta f4: -0.000178 Z: -0.684682

    details: ShahrISokhtaSubset Sweden_HG_Motala -0.002611 -7.676428
    details: Kazakhstan_MLBA_OyDzhaylau Sweden_HG_Motala 0.004097 13.152831
    details: Alalakh_MLBA_outlier Sweden_HG_Motala -0.000350 -0.912400
    details: Levant_BA Sweden_HG_Motala -0.001042 -3.106908
    dscore: Sweden_HG_Motala f4: -0.000117 Z: -0.406573
    I would say you need to account for more "West-Asian"-shifted Proto-Pashtun ancestry from South Afghanistan + West Iranic geneflow starting to arrive from the achaemaenid period, which is more western shifted than BMAC or Shar-i-Sokhta ancestry. We dont have genomes from Iron Age Afghanistan to compare him with. Pashtuns from these region definetly have something more Seh_Gabi-shifted compared to Shar-i-Sokhta and BMAC. Compared to other Pashtun samples especially from Afghanistan these Udegram sample does not seem to pick more Levantine ancestry at least not more compared to other Afghan Pashtun samples when using Kandahari as reference for Proto-Pashtuns. Also his J2a-F3133>FGC9942>Y14698 Y-DNA was already found among ancient Karluk and Karakhanid samples from Central Asia so there is a good chance it is of local (BMAC?) origin. But it also could be from a "back" migration from Iran. This clade is definetly rare among modern day Pashtuns but we don't know if this was also true 1000 years ago.

    Distance: 1.4885% / 0.01488517
    Target: PAK_Udegram_MA_Ghaznavid:I7716
    48.1 PAK_Udegram_IA
    42.1 Pashtun_Kandahar
    7.6 Saka_Tian_Shan_o
    2.2 Levant_Hazor_MLBA

    Distance: 1.3425% / 0.01342522
    Target: Pashtun_Kabul_AVG
    43.7 Pashtun_Kandahar
    34.8 PAK_Udegram_IA
    14.0 KAZ_Wusun
    5.7 Levant_Megiddo_MLBA
    1.8 Saka_Tian_Shan_o

    Distance: 1.4491% / 0.01449136
    Target: Pashtun_North_Afghanistan_AVG
    56.1 Pashtun_Kandahar
    28.2 PAK_Udegram_IA
    10.3 Turk
    5.4 Levant_Megiddo_MLBA

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  17. #7830
    Gold Class Member
    Posts
    4,260
    Location
    Shangri La

    Afghanistan Jammu and Kashmir United States of America Canada
    Quote Originally Posted by Coldmountains View Post
    I would say you need to account for more "West-Asian"-shifted Proto-Pashtun ancestry from South Afghanistan + West Iranic geneflow starting to arrive from the achaemaenid period, which is more western shifted than BMAC or Shar-i-Sokhta ancestry. We dont have genomes from Iron Age Afghanistan to compare him with. Pashtuns from these region definetly have something more Seh_Gabi-shifted compared to Shar-i-Sokhta and BMAC. Compared to other Pashtun samples especially from Afghanistan these Udegram sample does not seem to pick more Levantine ancestry at least not more compared to other Afghan Pashtun samples when using Kandahari as reference for Proto-Pashtuns. Also his J2a-F3133>FGC9942>Y14698 Y-DNA was already found among ancient Karluk and Karakhanid samples from Central Asia so there is a good chance it is of local (BMAC?) origin. But it also could be from a "back" migration from Iran. This clade is definetly rare among modern day Pashtuns but we don't know if this was also true 1000 years ago.

    Distance: 1.4885% / 0.01488517
    Target: PAK_Udegram_MA_Ghaznavid:I7716
    48.1 PAK_Udegram_IA
    42.1 Pashtun_Kandahar
    7.6 Saka_Tian_Shan_o
    2.2 Levant_Hazor_MLBA

    Distance: 1.3425% / 0.01342522
    Target: Pashtun_Kabul_AVG
    43.7 Pashtun_Kandahar
    34.8 PAK_Udegram_IA
    14.0 KAZ_Wusun
    5.7 Levant_Megiddo_MLBA
    1.8 Saka_Tian_Shan_o

    Distance: 1.4491% / 0.01449136
    Target: Pashtun_North_Afghanistan_AVG
    56.1 Pashtun_Kandahar
    28.2 PAK_Udegram_IA
    10.3 Turk
    5.4 Levant_Megiddo_MLBA
    Using Iran Chl or Hasanlu/Hajji Firuz IA alone failed surprisingly, he needed a distinctively Levantine source , Ebla or Levant BA, and a lot of it. Even if you look at the stats , he still needs a more Levantine source, not Iran more Syrian/Lebanese type ancestry. I guess there was more gene flow from Levant than I thought. Yes, Most Kandahar/Helmand Pashtuns definitely would have gotten further Plateau Iranian ancestry, along with Balochis, when it arrives is a good question. What was the subclade of the R1a for Ghaznavid 2959??

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