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Thread: Brahmin Genetics

  1. #331
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    Quote Originally Posted by GeneXplore View Post
    So I just ran the f3 calculation of the form f3(South Asian, Steppe; Chimp.REF), with Steppe as Yamnaya and then Botai. The f3 tells us how close the populations are genetically.

    You can see that for Yamnaya, Ror, Pathan and Kalash are closest, followed by Jatt in 4th position. But for Botai, Jatt is the closest.

    The ethnonym Jatt and Getae etc these are pre-Aryan so it is likely the Jatts had this Central Asian connection but it is not related to Yamnaya or Steppe MLBA, but Botai and similar cultures.

    Russia_EBA_Yamnaya_Samara Kazakhstan_Botai.SG
    Ror 225.180172 Jatt 224.236276
    Kalash 224.850646 Kalash 223.934442
    Pathan 224.476636 Ror 223.873757
    Jatt 224.395778 Burusho 223.524471
    Balochi 223.796471 Pathan 223.148042
    Burusho 223.648028 GujaratiA 223.085037
    GujaratiA 223.6379 UBR.SG 222.674328
    GujaratiB 223.204934 GujaratiB 222.658732
    UBR.SG 222.320355 GujaratiD 221.904322
    Guj-Muslim 221.707925 Balochi 221.894449
    GujaratiD 221.628776 Guj-Muslim 219.833526

    Most of us here are amateurs in regards to f3 and such. You may want to contact the following youtuber , who was a former user of the forum with extensive knowledge in that field.

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  3. #332
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    Quote Originally Posted by GeneXplore View Post
    The first column is how close each one is to Yamnaya, the second column is how close it is to Botai. The bigger the number the closer they are, and I put them in order, highest to lowest.

    "Russia_EBA_Yamnaya_Samara Jatt 224.395778, second column Kazakhstan_Botai.SG Jatt 224.236276" means f3(Jatt, Yamnaya; Chimp) = 224.39577, f3(Jatt, Botai; Chimp.REF) = 224.23627. The bigger the number the closer they are. So Botai is closest to Jatt while Yamnaya is closest to Ror.
    Did u compute z scores for these?
    Target: Kapisa_scaled
    Distance: 1.9111% / 0.01911125
    45.0 Shahr_I_Sokhta_BA3_2650BCE_
    35.2 UZB_Bustan_BA
    18.0 KAZ_Oy_Dzhaylau_MLBA
    1.8 NPL_Chokhopani_2700BP
    World K134
    Distance to: Kapisa_scaled
    0.01898797 Khatri-Kohistani-Sindhi-Kamboj
    Mitochondrial Haplogroup: R30b found in Shahr-I-Sokhta_BA1 subclades found in Swat IA:Leobanr, Katelai & Barikot Historic.

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  5. #333
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    Quote Originally Posted by GeneXplore View Post
    The first column is how close each one is to Yamnaya, the second column is how close it is to Botai. The bigger the number the closer they are, and I put them in order, highest to lowest.

    "Russia_EBA_Yamnaya_Samara Jatt 224.395778, second column Kazakhstan_Botai.SG Jatt 224.236276" means f3(Jatt, Yamnaya; Chimp) = 224.39577, f3(Jatt, Botai; Chimp.REF) = 224.23627. The bigger the number the closer they are. So Botai is closest to Jatt while Yamnaya is closest to Ror.
    Aren't Jatt still closer to Yamnaya Samara than to Botai? I am sure there were many other cultures not too far away from those two, why check their genetic relationship to Yamnaya and Botai only?

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  7. #334
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    Quote Originally Posted by GeneXplore View Post
    The first column is how close each one is to Yamnaya, the second column is how close it is to Botai. The bigger the number the closer they are, and I put them in order, highest to lowest.

    "Russia_EBA_Yamnaya_Samara Jatt 224.395778, second column Kazakhstan_Botai.SG Jatt 224.236276" means f3(Jatt, Yamnaya; Chimp) = 224.39577, f3(Jatt, Botai; Chimp.REF) = 224.23627. The bigger the number the closer they are. So Botai is closest to Jatt while Yamnaya is closest to Ror.
    What jatts samples you are taking in consideration? Your stuff is at very preliminary stage, you are looking in hurry in passing judgement, pre Aryan ,aryan, closeness etc

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  9. #335
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    Quote Originally Posted by GeneXplore View Post
    The first column is how close each one is to Yamnaya, the second column is how close it is to Botai. The bigger the number the closer they are, and I put them in order, highest to lowest.

    "Russia_EBA_Yamnaya_Samara Jatt 224.395778, second column Kazakhstan_Botai.SG Jatt 224.236276" means f3(Jatt, Yamnaya; Chimp) = 224.39577, f3(Jatt, Botai; Chimp.REF) = 224.23627. The bigger the number the closer they are. So Botai is closest to Jatt while Yamnaya is closest to Ror.
    From which study are these samples (Jatt, Ror, Burusho etc) ?

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    Quote Originally Posted by GeneXplore View Post
    Samples are from the Reich and Pathak datasets. I dont know if the Jatt sample is representative of all Jatts but it looks about right.

    In HarrappaDNA Gujarati Muslim is closest to Jatt out of these groups and that is also consistent with f3 (from these datasets) from my other thread.
    There is also problem with data in some studies, in one of them there are samples from Bathinda which were not Jatt samples at all. Sapporo and others here can tell you more about it. Also you need to place Muslim, Sikh and Hindu jatts into different categories as they have mixed with different castes to a different degree, I believe.

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  13. #337
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    Quote Originally Posted by GeneXplore View Post
    Yeah, I know, but we dont have enough data atm so this is just preliminary. There will be differences in the samples to some extent.

    However, what's interesting is my own Gujarati-Muslim results in Harrappa


    # Population (source) Distance
    1 gujarati-muslim (harappa) 4.12
    2 up-muslim (harappa) 6.24
    3 punjabi-jatt-muslim (harappa) 8.3

    Closest to UP Muslim and then Jatt. This is consistent with the data from the Pathak dataset, where the Jatt is the closest match for Gujarati Muslim. So there does seem to be consistency in the samples between Harrappa DNA and the Pathak set. However, in HarrappaDNA "Sikh Jatt" appears much lower for me so yes there will be differences amongst different Jatts so not sure if the above results should apply to any specific individuals.

    We have to look at why Gujarati-Muslim, UP Muslim and Jatt are so close, and who are they far from.
    Are you a Gujarati Ismaili/Khoja?

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    Quote Originally Posted by GeneXplore View Post
    No they are different, I'm Bharuchi Patel.
    https://anthrogenica.com/showthread....l=1#post748499
    Thanks. I see that Pegasus have already questioned your motives, he excels in many fields and one of them that we all here know is genetics.

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  17. #339
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    Quote Originally Posted by GeneXplore View Post
    I can have another closer look again, but if I remember correctly, the Jatts are not particularly close to Steppe EMBA or MLBA (Yamnaya or Sintashta) which is what people mean when they say "Steppe DNA" but the Jatts are actuallly quite close to Botai/MA1 type of ancestry, which is strange, but points to an older and different type of relationship to the Steppes than Rors and others.

    That makes no sense since Rors are essentially a subgroup within the Jats, since many of the other Jats in that region are pretty much the same. If you are using the Jat samples from the Reich Lab, those are not Jats. Though that does not change the fact its not Botai or Krotov people bringing Steppe ancestry for pretty much all populations in Southern Eurasia. I even looked at SPGT populations with low Steppe ancestry ( IVC shifted outliers) and they even ended up slightly more Steppe MLBA/CWC than expected. Yamnaya shifted sources work better (70-73%) vs Sintashta which is 65-68%, though they are still very closely related populations. The p value is 0.93 , it does not get better than that. We all know where you are going with this.
     
    left pops:
    Pakistan_IA_KatelaiSubset
    SIS1459/8728
    Russia_Srubnaya
    Alalakh_MLBA_outlier

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

    0 Pakistan_IA_KatelaiSubset 3
    1 SIS1459/8728 2
    2 Russia_Srubnaya 3
    3 Alalakh_MLBA_outlier 1
    4 Cameroon_SMA.DG 1
    5 Russia_Steppe_Eneolithic 3
    6 Onge 6
    7 PPNB 11
    8 Anatolia_N 30
    9 Iran_GanjDareh_N 4
    10 DevilsCave_N.SG 4
    11 Russia_UstBelaya_Angara 11
    12 EHG 3
    13 WSHG 2
    14 Russia_MA1_HG.SG 1
    15 CHG 2
    16 Sweden_HG_Motala 6
    jackknife block size: 0.050
    snps: 1150513 indivs: 93
    number of blocks for block jackknife: 714
    ## ncols: 1150513
    coverage: Pakistan_IA_KatelaiSubset 835199
    coverage: SIS1459/8728 715615
    coverage: Russia_Srubnaya 521923
    coverage: Alalakh_MLBA_outlier 733730
    coverage: Cameroon_SMA.DG 1140138
    coverage: Russia_Steppe_Eneolithic 1008226
    coverage: Onge 1143397
    coverage: PPNB 871625
    coverage: Anatolia_N 1141220
    coverage: Iran_GanjDareh_N 1014826
    coverage: DevilsCave_N.SG 1149702
    coverage: Russia_UstBelaya_Angara 1092594
    coverage: EHG 1027057
    coverage: WSHG 856695
    coverage: Russia_MA1_HG.SG 805960
    coverage: CHG 1149558
    coverage: Sweden_HG_Motala 1038843
    Effective number of blocks: 620.143
    numsnps used: 1150513
    codimension 1
    f4info:
    f4rank: 2 dof: 10 chisq: 4.420 tail: 0.926403311 dofdiff: 12 chisqdiff: -4.420 taildiff: 1
    B:
    scale 1.000 1.000
    Russia_Steppe_Eneolithic 1.115 -0.498
    Onge -0.630 0.732
    PPNB 1.098 -0.292
    Anatolia_N 1.558 0.051
    Iran_GanjDareh_N 0.388 -2.294
    DevilsCave_N.SG -0.432 0.472
    Russia_UstBelaya_Angara -0.158 0.360
    EHG 1.291 1.101
    WSHG 0.976 0.288
    Russia_MA1_HG.SG 0.723 0.384
    CHG 0.758 -1.383
    Sweden_HG_Motala 1.627 1.470
    A:
    scale 552.548 2077.943
    SIS1459/8728 -0.403 0.120
    Russia_Srubnaya 1.446 0.762
    Alalakh_MLBA_outlier 0.865 -1.551


    full rank
    f4info:
    f4rank: 3 dof: 0 chisq: 0.000 tail: 1 dofdiff: 10 chisqdiff: 4.420 taildiff: 0.926403311
    B:
    scale 1624.142 361.539 566.267
    Russia_Steppe_Eneolithic -1.096 1.040 1.264
    Onge 1.293 -0.432 -0.762
    PPNB -1.206 1.029 1.115
    Anatolia_N -1.524 1.529 1.416
    Iran_GanjDareh_N -0.480 0.100 1.374
    DevilsCave_N.SG 0.744 -0.305 -0.512
    Russia_UstBelaya_Angara 0.620 -0.034 -0.200
    EHG -1.098 1.422 0.753
    WSHG -0.331 1.055 0.907
    Russia_MA1_HG.SG -0.679 0.762 0.468
    CHG -0.474 0.602 1.390
    Sweden_HG_Motala -1.476 1.776 0.915
    A:
    scale 1.732 1.732 1.732
    SIS1459/8728 1.732 0.000 0.000
    Russia_Srubnaya 0.000 1.732 0.000
    Alalakh_MLBA_outlier 0.000 0.000 1.732


    best coefficients: 0.743 0.134 0.123
    Jackknife mean: 0.742249812 0.133316264 0.124433924
    std. errors: 0.038 0.041 0.061

    error covariance (* 1,000,000)
    1480 309 -1790
    309 1643 -1952
    -1790 -1952 3742


    summ: Pakistan_IA_KatelaiSubset 3 0.926403 0.742 0.133 0.124
    Last edited by pegasus; 02-23-2021 at 01:04 PM.

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  19. #340
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    Quote Originally Posted by GeneXplore View Post
    The Jatt sample is from Pathak, not from Reich. I already mentioned it matches with the Jatt samples from HarappaDNA as both are closest to Gujarati-Muslim, and that sample is the same in HarrapaDNA and ADMIXTOOLS (my own data).

    Either way whatever is the Jatt sample from Pathak definitely has some additional Botai-type ancestry from the above f3 data. You are not even running f3s or f4s in your data, you are going straight into qpAdm. You are free to provide any other explanation of the f3 data showing Botai is close to some type of 'Jatt'.

    Nice qpAdm btw, you know who gave you those right pops dont you? 2 years ago no one here was running qpADM with those outgroups, now everyone is using them and you dont even know who that came from...
    You linked rors with arora/Khatris. Rors is a small population just 7-8 lacs akin to haryana jats in Karnal/kurukshetra area. They are nowhere related to Khatris/ aroras. I don't know this f3/qpadm but on Harappa they score very similar to haryana jats

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