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Thread: Late Pleistocene DNA suggests a local origin for the first farmers of centr. Anatolia

  1. #11
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    atalhyk (7100–5950 BC) MtDna U3b, N, K1a17, U, W1c, K, H+73, H, X2b4, U5b2
    genes-10-00207-g001.png
    Last edited by ruslan; 03-20-2019 at 08:06 PM.

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  3. #12
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    When are these samples going to be added on G25?

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  5. #13
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    Quote Originally Posted by Ajeje Brazorf View Post
    When are these samples going to be added on G25?
    Seconded... in particular the 15kya hunter gatherer.

    The BAM files are now available: https://www.ebi.ac.uk/ena/data/view/PRJEB24794

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  7. #14
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    Quote Originally Posted by ruslan View Post
    atalhyk (7100–5950 BC) MtDna U3b, N, K1a17, U, W1c, K, H+73, H, X2b4, U5b2
    genes-10-00207-g001.png
    Interesting that U5 turns up in Neolithic Anatolia. That's the first instance of this yes?
    Collection of 14,000 d-stats: Hidden Content Part 2: Hidden Content Part 3: Hidden Content PM me for d-stats, qpadm, qpgraph, or f3-outgroup nmonte models.

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  9. #15
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    Quote Originally Posted by K33 View Post
    Seconded... in particular the 15kya hunter gatherer.

    The BAM files are now available: https://www.ebi.ac.uk/ena/data/view/PRJEB24794
    I am working on them now

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  11. #16
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    Done, one sample is still missing
    https://1drv.ms/f/s!AqBtywy1BkksiJ4kskb5bN0luytrdA

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  13. #17
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    In order to test the integrity of generated genotypes, I performed a couple of qpAdm tests. The goal was to compare the results to qpAdm results, which have been published in supplementary information of article.

    Admixture models of the Iron Gates hunter-gatherers (Iron Gates HG)

    Ref1 Ref2 Ref3 Ref1 Ref2 Ref3 Ref1 Ref2 Ref3 Pval (rank-1) Outgroups
    AHG WHG EHG 25.8 62.9 11.3 5.0 7.4 3.3 3.08E-01 Basic set

    My rightpop file looks a little bit different to Basic set from original article (instead of Mixe I used Brazil_LapaDoSanto and instead of Mala - Kharia)

    Code:
    left pops:
    Iron_Gates_HG
    AHG
    WHG2
    EHG
    
    right pops:
    Kostenki14
    Han
    Onge
    Mbuti
    Israel_Natufian
    Brazil_LapaDoSanto
    Kharia
    
      0        Iron_Gates_HG   36
      1                  AHG    1
      2                 WHG2    2
      3                  EHG   11
      4           Kostenki14    1
      5                  Han    3
      6                 Onge    6
      7                Mbuti    4
      8      Israel_Natufian    1
      9   Brazil_LapaDoSanto    7
     10               Kharia   12
    jackknife block size:     0.050
    snps: 1148667  indivs: 84
    number of blocks for block jackknife: 713
    ## ncols: 1148667
    coverage:        Iron_Gates_HG 996933
    coverage:                  AHG 802743
    coverage:                 WHG2 1002479
    coverage:                  EHG 1121486
    coverage:           Kostenki14 932536
    coverage:                  Han 1121713
    coverage:                 Onge 720049
    coverage:                Mbuti 1121724
    coverage:      Israel_Natufian 385032
    coverage:   Brazil_LapaDoSanto 973100
    coverage:               Kharia 616242
    dof (jackknife):   587.447
    numsnps used: 260269
    codimension 1
    f4info: 
    f4rank: 2 dof:      4 chisq:     3.211 tail:          0.523126926 dofdiff:      6 chisqdiff:    -3.211 taildiff:                    1
    B:
              scale     1.000     1.000 
                Han     0.866     0.429 
               Onge     0.622     0.361 
              Mbuti     1.053    -0.473 
    Israel_Natufian     0.935    -1.829 
    Brazil_LapaDoSanto     1.471     1.417 
             Kharia     0.845     0.328 
    A:
              scale  1005.108  1181.083 
                AHG     1.183    -1.252 
               WHG2    -0.594     0.188 
                EHG     1.117     1.182 
    
    
    full rank
    f4info: 
    f4rank: 3 dof:      0 chisq:     0.000 tail:                    1 dofdiff:      4 chisqdiff:     3.211 taildiff:          0.523126926
    B:
              scale     1.000     1.000     1.000 
                Han     0.864     0.425     0.942 
               Onge     0.616     0.357     0.471 
              Mbuti     1.060    -0.488     0.652 
    Israel_Natufian     0.972    -1.852    -0.243 
    Brazil_LapaDoSanto     1.449     1.386    -2.074 
             Kharia     0.841     0.319     0.324 
    A:
              scale   965.459  1203.946 10480.024 
                AHG     1.254    -1.190     1.064 
               WHG2    -0.379     0.251     1.353 
                EHG     1.133     1.234     0.193 
    
    
    best coefficients:     0.216     0.661     0.123 
    Jackknife mean:      0.216702035     0.658352367     0.124945597 
          std. errors:     0.053     0.080     0.047 
    
    error covariance (* 1000000)
          2813      -3511        698 
         -3511       6424      -2912 
           698      -2912       2214 
    
    
    summ: Iron_Gates_HG    3      0.523127     0.217     0.658     0.125  2813 -3511   698  6424 -2912  2214 
    
        fixed pat  wt  dof     chisq       tail prob
              000  0     4     3.211        0.523127     0.216     0.661     0.123 
              001  1     5     8.723         0.12062     0.175     0.825     0.000 
              010  1     5    46.410     7.49479e-09     0.624    -0.000     0.376 
              100  1     5    15.736      0.00763892     0.000     0.960     0.040 
              011  2     6    90.568     2.30932e-17     1.000    -0.000     0.000 
              101  2     6    16.173       0.0128564     0.000     1.000     0.000 
              110  2     6   372.017               0     0.000    -0.000     1.000 
    best pat:          000         0.523127              -  -
    best pat:          001          0.12062  chi(nested):     5.512 p-value for nested model:       0.0188844
    best pat:          101        0.0128564  chi(nested):     7.449 p-value for nested model:      0.00634595
    
    coeffs:     0.216     0.661     0.123 
    
    ## dscore:: f_4(Base, Fit, Rbase, right2)
    ## genstat:: f_4(Base, Fit, right1, right2)
    
    details:             AHG             Han     0.000821    2.115872
    details:            WHG2             Han    -0.000135   -0.496687
    details:             EHG             Han     0.001479    6.536762
    dscore:             Han f4:     0.000270 Z:     1.305587
    
    details:             AHG            Onge     0.000525    1.418260
    details:            WHG2            Onge    -0.000109   -0.422641
    details:             EHG            Onge     0.001109    5.388109
    dscore:            Onge f4:     0.000178 Z:     0.871334
    
    details:             AHG           Mbuti     0.001958    4.948978
    details:            WHG2           Mbuti    -0.000429   -1.594124
    details:             EHG           Mbuti     0.000765    3.559666
    dscore:           Mbuti f4:     0.000233 Z:     1.088000
    
    details:             AHG Israel_Natufian     0.003102    6.848291
    details:            WHG2 Israel_Natufian    -0.000808   -2.734621
    details:             EHG Israel_Natufian    -0.000750   -3.015818
    dscore: Israel_Natufian f4:     0.000042 Z:     0.179161
    
    details:             AHG Brazil_LapaDoSanto     0.000328    0.833679
    details:            WHG2 Brazil_LapaDoSanto    -0.000550   -2.044894
    details:             EHG Brazil_LapaDoSanto     0.003095   13.588931
    dscore: Brazil_LapaDoSanto f4:     0.000088 Z:     0.420979
    
    details:             AHG          Kharia     0.000838    2.383397
    details:            WHG2          Kharia    -0.000225   -0.921153
    details:             EHG          Kharia     0.001331    6.664103
    dscore:          Kharia f4:     0.000196 Z:     1.027265
    
    gendstat:           Kostenki14                  Han     1.306
    gendstat:           Kostenki14                 Onge     0.871
    gendstat:           Kostenki14                Mbuti     1.088
    gendstat:           Kostenki14      Israel_Natufian     0.179
    gendstat:           Kostenki14   Brazil_LapaDoSanto     0.421
    gendstat:           Kostenki14               Kharia     1.027
    gendstat:                  Han                 Onge    -0.641
    gendstat:                  Han                Mbuti    -0.250
    gendstat:                  Han      Israel_Natufian    -1.114
    gendstat:                  Han   Brazil_LapaDoSanto    -1.269
    gendstat:                  Han               Kharia    -0.641
    gendstat:                 Onge                Mbuti     0.363
    gendstat:                 Onge      Israel_Natufian    -0.657
    gendstat:                 Onge   Brazil_LapaDoSanto    -0.593
    gendstat:                 Onge               Kharia     0.157
    gendstat:                Mbuti      Israel_Natufian    -0.942
    gendstat:                Mbuti   Brazil_LapaDoSanto    -0.883
    gendstat:                Mbuti               Kharia    -0.282
    gendstat:      Israel_Natufian   Brazil_LapaDoSanto     0.221
    gendstat:      Israel_Natufian               Kharia     0.837
    gendstat:   Brazil_LapaDoSanto               Kharia     0.813

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  15. #18
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    Next, qpADM Admixture models of the Anatolian Aceramic farmers (AAF)

    Ancestral sources Mixture proportions (%) Standard errors (%)
    Ref1 Ref2 Ref3 Ref1 Ref2 Ref3 Ref1 Ref2 Ref3 Pval
    (rank 1) Outgroups
    AHG Iran_N 91.4 8.6 7.2 7.2 5.38E-02 Basic set
    AHG Iran_N 89.7 10.3 3.9 3.9 2.96E-01 Basic set;
    Levant_N;WHG;EHG


    Code:
    left pops:
    AAF
    AHG
    Iran_N
    
    right pops:
    Kostenki14
    Han
    Onge
    Mbuti
    Israel_Natufian
    Brazil_LapaDoSanto
    Kharia
    WHG2
    EHG
    Levant_N
    
      0                  AAF    4
      1                  AHG    1
      2               Iran_N   10
      3           Kostenki14    1
      4                  Han    3
      5                 Onge    6
      6                Mbuti    4
      7      Israel_Natufian    1
      8   Brazil_LapaDoSanto    7
      9               Kharia   12
     10                 WHG2    2
     11                  EHG   11
     12             Levant_N    3
    jackknife block size:     0.050
    snps: 1148901  indivs: 65
    number of blocks for block jackknife: 713
    ## ncols: 1148901
    coverage:                  AAF 971492
    coverage:                  AHG 802743
    coverage:               Iran_N 1004293
    coverage:           Kostenki14 932536
    coverage:                  Han 1121713
    coverage:                 Onge 720049
    coverage:                Mbuti 1121724
    coverage:      Israel_Natufian 385032
    coverage:   Brazil_LapaDoSanto 973100
    coverage:               Kharia 616242
    coverage:                 WHG2 1002479
    coverage:                  EHG 1121486
    coverage:             Levant_N 702722
    dof (jackknife):   594.329
    numsnps used: 300316
    codimension 1
    f4info: 
    f4rank: 1 dof:      8 chisq:     8.324 tail:          0.402478553 dofdiff:     10 chisqdiff:    -8.324 taildiff:                    1
    B:
              scale     1.000 
                Han    -0.561 
               Onge    -0.822 
              Mbuti    -0.422 
    Israel_Natufian     1.548 
    Brazil_LapaDoSanto    -0.607 
             Kharia    -0.830 
               WHG2     1.268 
                EHG     0.093 
           Levant_N     1.662 
    A:
              scale  1104.211 
                AHG     0.087 
             Iran_N    -1.412 
    
    
    full rank
    f4info: 
    f4rank: 2 dof:      0 chisq:     0.000 tail:                    1 dofdiff:      8 chisqdiff:     8.324 taildiff:          0.402478553
    B:
              scale     1.000     1.000 
                Han    -0.586     0.412 
               Onge    -0.823    -0.616 
              Mbuti    -0.429    -1.692 
    Israel_Natufian     1.554     0.353 
    Brazil_LapaDoSanto    -0.612     1.565 
             Kharia    -0.836    -0.389 
               WHG2     1.234     1.426 
                EHG     0.091    -0.099 
           Levant_N     1.666    -0.906 
    A:
              scale  1091.875  7858.968 
                AHG     0.046     1.377 
             Iran_N    -1.413     0.321 
    
    
    best coefficients:     0.942     0.058 
    Jackknife mean:      0.939952230     0.060047770 
          std. errors:     0.052     0.052 
    
    error covariance (* 1000000)
          2756      -2756 
         -2756       2756 
    
    
    summ: AAF    2      0.402479     0.940     0.060  2756 -2756  2756 
    
        fixed pat  wt  dof     chisq       tail prob
               00  0     8     8.324        0.402479     0.942     0.058 
               01  1     9     9.443        0.397428     1.000    -0.000 
               10  1     9   449.040               0     0.000     1.000 
    best pat:           00         0.402479              -  -
    best pat:           01         0.397428  chi(nested):     1.119 p-value for nested model:        0.290137
    
    coeffs:     0.942     0.058 
    
    ## dscore:: f_4(Base, Fit, Rbase, right2)
    ## genstat:: f_4(Base, Fit, right1, right2)
    
    details:             AHG             Han     0.000053    0.170899
    details:          Iran_N             Han     0.000779    3.312669
    dscore:             Han f4:     0.000096 Z:     0.319438
    
    details:             AHG            Onge    -0.000138   -0.475412
    details:          Iran_N            Onge     0.001040    4.508941
    dscore:            Onge f4:    -0.000070 Z:    -0.250558
    
    details:             AHG           Mbuti    -0.000314   -1.022660
    details:          Iran_N           Mbuti     0.000486    2.003786
    dscore:           Mbuti f4:    -0.000267 Z:    -0.909260
    
    details:             AHG Israel_Natufian     0.000129    0.360231
    details:          Iran_N Israel_Natufian    -0.002003   -7.073134
    dscore: Israel_Natufian f4:     0.000005 Z:     0.013554
    
    details:             AHG Brazil_LapaDoSanto     0.000250    0.793477
    details:          Iran_N Brazil_LapaDoSanto     0.000854    3.642143
    dscore: Brazil_LapaDoSanto f4:     0.000285 Z:     0.945073
    
    details:             AHG          Kharia    -0.000095   -0.346584
    details:          Iran_N          Kharia     0.001067    5.079136
    dscore:          Kharia f4:    -0.000028 Z:    -0.105178
    
    details:             AHG            WHG2     0.000312    1.003363
    details:          Iran_N            WHG2    -0.001536   -5.983556
    dscore:            WHG2 f4:     0.000205 Z:     0.684640
    
    details:             AHG             EHG    -0.000004   -0.014847
    details:          Iran_N             EHG    -0.000121   -0.552639
    dscore:             EHG f4:    -0.000011 Z:    -0.041959
    
    details:             AHG        Levant_N    -0.000091   -0.279783
    details:          Iran_N        Levant_N    -0.002198   -8.564835
    dscore:        Levant_N f4:    -0.000213 Z:    -0.686206
    
    gendstat:           Kostenki14                  Han     0.319
    gendstat:           Kostenki14                 Onge    -0.251
    gendstat:           Kostenki14                Mbuti    -0.909
    gendstat:           Kostenki14      Israel_Natufian     0.014
    gendstat:           Kostenki14   Brazil_LapaDoSanto     0.945
    gendstat:           Kostenki14               Kharia    -0.105
    gendstat:           Kostenki14                 WHG2     0.685
    gendstat:           Kostenki14                  EHG    -0.042
    gendstat:           Kostenki14             Levant_N    -0.686
    gendstat:                  Han                 Onge    -0.762
    gendstat:                  Han                Mbuti    -1.567
    gendstat:                  Han      Israel_Natufian    -0.285
    gendstat:                  Han   Brazil_LapaDoSanto     0.933
    gendstat:                  Han               Kharia    -0.705
    gendstat:                  Han                 WHG2     0.427
    gendstat:                  Han                  EHG    -0.508
    gendstat:                  Han             Levant_N    -1.155
    gendstat:                 Onge                Mbuti    -0.899
    gendstat:                 Onge      Israel_Natufian     0.252
    gendstat:                 Onge   Brazil_LapaDoSanto     1.606
    gendstat:                 Onge               Kharia     0.250
    gendstat:                 Onge                 WHG2     1.066
    gendstat:                 Onge                  EHG     0.292
    gendstat:                 Onge             Levant_N    -0.539
    gendstat:                Mbuti      Israel_Natufian     0.896
    gendstat:                Mbuti   Brazil_LapaDoSanto     2.345
    gendstat:                Mbuti               Kharia     1.276
    gendstat:                Mbuti                 WHG2     1.767
    gendstat:                Mbuti                  EHG     1.186
    gendstat:                Mbuti             Levant_N     0.202
    gendstat:      Israel_Natufian   Brazil_LapaDoSanto     0.924
    gendstat:      Israel_Natufian               Kharia    -0.119
    gendstat:      Israel_Natufian                 WHG2     0.603
    gendstat:      Israel_Natufian                  EHG    -0.055
    gendstat:      Israel_Natufian             Levant_N    -0.713
    gendstat:   Brazil_LapaDoSanto               Kharia    -1.708
    gendstat:   Brazil_LapaDoSanto                 WHG2    -0.305
    gendstat:   Brazil_LapaDoSanto                  EHG    -1.518
    gendstat:   Brazil_LapaDoSanto             Levant_N    -1.883
    gendstat:               Kharia                 WHG2     1.035
    gendstat:               Kharia                  EHG     0.105
    gendstat:               Kharia             Levant_N    -0.781
    gendstat:                 WHG2                  EHG    -0.950
    gendstat:                 WHG2             Levant_N    -1.489
    gendstat:                  EHG             Levant_N    -0.833
    Code:
    allsnps: NO
    ## qpAdm version: 810
    seed: 1873935210
    
    left pops:
    AAF
    AHG
    Iran_N
    
    right pops:
    Kostenki14
    Han
    Onge
    Mbuti
    Israel_Natufian
    Brazil_LapaDoSanto
    Kharia
    WHG2
    EHG
    
      0                  AAF    4
      1                  AHG    1
      2               Iran_N   10
      3           Kostenki14    1
      4                  Han    3
      5                 Onge    6
      6                Mbuti    4
      7      Israel_Natufian    1
      8   Brazil_LapaDoSanto    7
      9               Kharia   12
     10                 WHG2    2
     11                  EHG   11
    jackknife block size:     0.050
    snps: 1148901  indivs: 62
    number of blocks for block jackknife: 713
    ## ncols: 1148901
    coverage:                  AAF 971492
    coverage:                  AHG 802743
    coverage:               Iran_N 1004293
    coverage:           Kostenki14 932536
    coverage:                  Han 1121713
    coverage:                 Onge 720049
    coverage:                Mbuti 1121724
    coverage:      Israel_Natufian 385032
    coverage:   Brazil_LapaDoSanto 973100
    coverage:               Kharia 616242
    coverage:                 WHG2 1002479
    coverage:                  EHG 1121486
    dof (jackknife):   594.449
    numsnps used: 307941
    codimension 1
    f4info: 
    f4rank: 1 dof:      7 chisq:     4.372 tail:           0.73601325 dofdiff:      9 chisqdiff:    -4.372 taildiff:                    1
    B:
              scale     1.000 
                Han     0.684 
               Onge     0.997 
              Mbuti     0.582 
    Israel_Natufian    -1.668 
    Brazil_LapaDoSanto     0.765 
             Kharia     0.984 
               WHG2    -1.365 
                EHG    -0.028 
    A:
              scale  1144.558 
                AHG    -0.184 
             Iran_N     1.402 
    
    
    full rank
    f4info: 
    f4rank: 2 dof:      0 chisq:     0.000 tail:                    1 dofdiff:      7 chisqdiff:     4.372 taildiff:           0.73601325
    B:
              scale     1.000     1.000 
                Han     0.692     0.451 
               Onge     0.991    -0.269 
              Mbuti     0.582    -1.359 
    Israel_Natufian    -1.674     0.138 
    Brazil_LapaDoSanto     0.761     2.118 
             Kharia     0.986    -0.298 
               WHG2    -1.358     1.033 
                EHG    -0.042    -0.465 
    A:
              scale  1138.998 10643.459 
                AHG    -0.152     1.364 
             Iran_N     1.406     0.374 
    
    
    best coefficients:     0.884     0.116 
    Jackknife mean:      0.882353503     0.117646497 
          std. errors:     0.052     0.052 
    
    error covariance (* 1000000)
          2679      -2679 
         -2679       2679 
    
    
    summ: AAF    2      0.736013     0.882     0.118  2679 -2679  2679 
    
        fixed pat  wt  dof     chisq       tail prob
               00  0     7     4.372        0.736013     0.884     0.116 
               01  1     8     8.702        0.368053     1.000     0.000 
               10  1     8   342.404               0     0.000     1.000 
    best pat:           00         0.736013              -  -
    best pat:           01         0.368053  chi(nested):     4.330 p-value for nested model:       0.0374563
    
    coeffs:     0.884     0.116 
    
    ## dscore:: f_4(Base, Fit, Rbase, right2)
    ## genstat:: f_4(Base, Fit, right1, right2)
    
    details:             AHG             Han     0.000039    0.116593
    details:          Iran_N             Han     0.000898    3.608257
    dscore:             Han f4:     0.000138 Z:     0.456071
    
    details:             AHG            Onge    -0.000109   -0.357418
    details:          Iran_N            Onge     0.001236    5.115944
    dscore:            Onge f4:     0.000047 Z:     0.169450
    
    details:             AHG           Mbuti    -0.000195   -0.600298
    details:          Iran_N           Mbuti     0.000693    2.732610
    dscore:           Mbuti f4:    -0.000092 Z:    -0.308770
    
    details:             AHG Israel_Natufian     0.000298    0.799399
    details:          Iran_N Israel_Natufian    -0.002044   -6.860542
    dscore: Israel_Natufian f4:     0.000026 Z:     0.077148
    
    details:             AHG Brazil_LapaDoSanto     0.000239    0.713119
    details:          Iran_N Brazil_LapaDoSanto     0.001038    4.170758
    dscore: Brazil_LapaDoSanto f4:     0.000331 Z:     1.080308
    
    details:             AHG          Kharia    -0.000103   -0.350463
    details:          Iran_N          Kharia     0.001231    5.551529
    dscore:          Kharia f4:     0.000052 Z:     0.194077
    
    details:             AHG            WHG2     0.000381    1.148150
    details:          Iran_N            WHG2    -0.001616   -5.954030
    dscore:            WHG2 f4:     0.000150 Z:     0.488248
    
    details:             AHG             EHG     0.000015    0.052192
    details:          Iran_N             EHG    -0.000045   -0.192388
    dscore:             EHG f4:     0.000008 Z:     0.030455
    
    gendstat:           Kostenki14                  Han     0.456
    gendstat:           Kostenki14                 Onge     0.169
    gendstat:           Kostenki14                Mbuti    -0.309
    gendstat:           Kostenki14      Israel_Natufian     0.077
    gendstat:           Kostenki14   Brazil_LapaDoSanto     1.080
    gendstat:           Kostenki14               Kharia     0.194
    gendstat:           Kostenki14                 WHG2     0.488
    gendstat:           Kostenki14                  EHG     0.030
    gendstat:                  Han                 Onge    -0.422
    gendstat:                  Han                Mbuti    -0.985
    gendstat:                  Han      Israel_Natufian    -0.350
    gendstat:                  Han   Brazil_LapaDoSanto     0.960
    gendstat:                  Han               Kharia    -0.489
    gendstat:                  Han                 WHG2     0.044
    gendstat:                  Han                  EHG    -0.622
    gendstat:                 Onge                Mbuti    -0.629
    gendstat:                 Onge      Israel_Natufian    -0.070
    gendstat:                 Onge   Brazil_LapaDoSanto     1.284
    gendstat:                 Onge               Kharia     0.029
    gendstat:                 Onge                 WHG2     0.394
    gendstat:                 Onge                  EHG    -0.194
    gendstat:                Mbuti      Israel_Natufian     0.390
    gendstat:                Mbuti   Brazil_LapaDoSanto     1.798
    gendstat:                Mbuti               Kharia     0.757
    gendstat:                Mbuti                 WHG2     0.900
    gendstat:                Mbuti                  EHG     0.454
    gendstat:      Israel_Natufian   Brazil_LapaDoSanto     1.003
    gendstat:      Israel_Natufian               Kharia     0.094
    gendstat:      Israel_Natufian                 WHG2     0.367
    gendstat:      Israel_Natufian                  EHG    -0.064
    gendstat:   Brazil_LapaDoSanto               Kharia    -1.506
    gendstat:   Brazil_LapaDoSanto                 WHG2    -0.679
    gendstat:   Brazil_LapaDoSanto                  EHG    -1.652
    gendstat:               Kharia                 WHG2     0.433
    gendstat:               Kharia                  EHG    -0.271
    gendstat:                 WHG2                  EHG    -0.622
    
    ## end of run

  16. The Following User Says Thank You to Vadim Verenich For This Useful Post:

     Hando (04-06-2019)

  17. #19
    Registered Users
    Posts
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    mtDNA
    J1c

    qpADM Admixture models of the Anatolian hunter-gatherer (AHG). The proportions estimated for
    each ancestral source (Ref1-4) used to model the target population AHG are given

    Ref1 Ref2 Ref3 Ref1 Ref2 Ref3 Ref1 Ref2 Ref3 Pval (rank - 1) Outgroups
    AHG Levant_N WHG 47.9 52.1 4.5 4.5 0.158 Basic set
    AHG Levant_N WHG Iran_N 46.4 41.7 11.9 4.6 7.1 6.9 0.296 Basic set

    Code:
    ## qpAdm version: 810
    seed: 1638257782
    
    left pops:
    AHG
    Levant_N
    WHG2
    Iran_N
    
    right pops:
    Kostenki14
    Han
    Onge
    Mbuti
    Israel_Natufian
    Brazil_LapaDoSanto
    Kharia
    
      0                  AHG    1
      1             Levant_N    3
      2                 WHG2    2
      3               Iran_N   10
      4           Kostenki14    1
      5                  Han    3
      6                 Onge    6
      7                Mbuti    4
      8      Israel_Natufian    1
      9   Brazil_LapaDoSanto    7
     10               Kharia   12
    jackknife block size:     0.050
    snps: 1148658  indivs: 50
    number of blocks for block jackknife: 713
    ## ncols: 1148658
    coverage:                  AHG 802743
    coverage:             Levant_N 702722
    coverage:                 WHG2 1002479
    coverage:               Iran_N 1004293
    coverage:           Kostenki14 932536
    coverage:                  Han 1121713
    coverage:                 Onge 720049
    coverage:                Mbuti 1121724
    coverage:      Israel_Natufian 385032
    coverage:   Brazil_LapaDoSanto 973100
    coverage:               Kharia 616242
    dof (jackknife):   595.168
    numsnps used: 238772
    codimension 1
    f4info: 
    f4rank: 2 dof:      4 chisq:     3.039 tail:           0.55125069 dofdiff:      6 chisqdiff:    -3.039 taildiff:                    1
    B:
              scale     1.000     1.000 
                Han     0.045     0.888 
               Onge     0.050     1.036 
              Mbuti     0.797     1.170 
    Israel_Natufian     2.311    -0.870 
    Brazil_LapaDoSanto     0.081     0.773 
             Kharia     0.117     1.189 
    A:
              scale   775.896  1128.401 
           Levant_N     0.912     0.115 
               WHG2    -1.391    -0.662 
             Iran_N    -0.482     1.597 
    
    
    full rank
    f4info: 
    f4rank: 3 dof:      0 chisq:     0.000 tail:                    1 dofdiff:      4 chisqdiff:     3.039 taildiff:           0.55125069
    B:
              scale     1.000     1.000     1.000 
                Han     0.037     0.895     1.119 
               Onge     0.042     1.034    -1.799 
              Mbuti     0.780     1.166    -0.183 
    Israel_Natufian     2.317    -0.874     0.475 
    Brazil_LapaDoSanto     0.079     0.771     1.018 
             Kharia     0.106     1.188    -0.467 
    A:
              scale   773.138  1149.231  6919.462 
           Levant_N     0.902    -0.003    -1.044 
               WHG2    -1.397    -0.847    -1.087 
             Iran_N    -0.482     1.511    -0.853 
    
    
    best coefficients:     0.565     0.336     0.099 
    Jackknife mean:      0.564256962     0.335010604     0.100732434 
          std. errors:     0.057     0.112     0.103 
    
    error covariance (* 1000000)
          3266      -2673       -593 
         -2673      12618      -9945 
          -593      -9945      10538 
    
    
    summ: AHG    3      0.551251     0.564     0.335     0.101  3266 -2673  -593 12618 -9945 10538 
    
        fixed pat  wt  dof     chisq       tail prob
              000  0     4     3.039        0.551251     0.565     0.336     0.099 
              001  1     5     4.543        0.474125     0.566     0.434     0.000 
              010  1     5    12.097       0.0334778     0.641    -0.000     0.359 
              100  1     5    78.083     2.11196e-15     0.000     1.509    -0.509  infeasible
              011  2     6    45.097     4.47703e-08     1.000    -0.000     0.000 
              101  2     6    84.532     4.12663e-16     0.000     1.000     0.000 
              110  2     6   156.054               0     0.000    -0.000     1.000 
    best pat:          000         0.551251              -  -
    best pat:          001         0.474125  chi(nested):     1.504 p-value for nested model:        0.220091
    best pat:          011      4.47703e-08  chi(nested):    40.554 p-value for nested model:     1.91276e-10
    
    coeffs:     0.565     0.336     0.099 
    
    ## dscore:: f_4(Base, Fit, Rbase, right2)
    ## genstat:: f_4(Base, Fit, right1, right2)
    
    details:        Levant_N             Han    -0.000135   -0.315180
    details:            WHG2             Han    -0.000941   -2.046224
    details:          Iran_N             Han     0.001011    2.522395
    dscore:             Han f4:    -0.000293 Z:    -0.772682
    
    details:        Levant_N            Onge     0.000314    0.749111
    details:            WHG2            Onge    -0.000590   -1.387933
    details:          Iran_N            Onge     0.001551    3.924327
    dscore:            Onge f4:     0.000132 Z:     0.362939
    
    details:        Levant_N           Mbuti     0.000940    2.194564
    details:            WHG2           Mbuti    -0.002261   -5.043513
    details:          Iran_N           Mbuti     0.001073    2.647544
    dscore:           Mbuti f4:    -0.000124 Z:    -0.326009
    
    details:        Levant_N Israel_Natufian     0.002609    5.012617
    details:            WHG2 Israel_Natufian    -0.003675   -7.198932
    details:          Iran_N Israel_Natufian    -0.002679   -5.644668
    dscore: Israel_Natufian f4:    -0.000026 Z:    -0.059069
    
    details:        Levant_N Brazil_LapaDoSanto    -0.000083   -0.190790
    details:            WHG2 Brazil_LapaDoSanto    -0.000917   -2.017945
    details:          Iran_N Brazil_LapaDoSanto     0.000822    2.025165
    dscore: Brazil_LapaDoSanto f4:    -0.000274 Z:    -0.715971
    
    details:        Levant_N          Kharia     0.000169    0.433789
    details:            WHG2          Kharia    -0.001039   -2.585010
    details:          Iran_N          Kharia     0.001537    4.276744
    dscore:          Kharia f4:    -0.000102 Z:    -0.301866
    
    gendstat:           Kostenki14                  Han    -0.773
    gendstat:           Kostenki14                 Onge     0.363
    gendstat:           Kostenki14                Mbuti    -0.326
    gendstat:           Kostenki14      Israel_Natufian    -0.059
    gendstat:           Kostenki14   Brazil_LapaDoSanto    -0.716
    gendstat:           Kostenki14               Kharia    -0.302
    gendstat:                  Han                 Onge     1.534
    gendstat:                  Han                Mbuti     0.537
    gendstat:                  Han      Israel_Natufian     0.645
    gendstat:                  Han   Brazil_LapaDoSanto     0.068
    gendstat:                  Han               Kharia     0.850
    gendstat:                 Onge                Mbuti    -0.874
    gendstat:                 Onge      Israel_Natufian    -0.413
    gendstat:                 Onge   Brazil_LapaDoSanto    -1.403
    gendstat:                 Onge               Kharia    -1.060
    gendstat:                Mbuti      Israel_Natufian     0.248
    gendstat:                Mbuti   Brazil_LapaDoSanto    -0.471
    gendstat:                Mbuti               Kharia     0.086
    gendstat:      Israel_Natufian   Brazil_LapaDoSanto    -0.631
    gendstat:      Israel_Natufian               Kharia    -0.214
    gendstat:   Brazil_LapaDoSanto               Kharia     0.746
    
    ## end of run
    Code:
    ## qpAdm version: 810
    seed: 2067175192
    
    left pops:
    AHG
    Levant_N
    WHG2
    
    right pops:
    Kostenki14
    Han
    Onge
    Mbuti
    Israel_Natufian
    Brazil_LapaDoSanto
    Kharia
    
      0                  AHG    1
      1             Levant_N    3
      2                 WHG2    2
      3           Kostenki14    1
      4                  Han    3
      5                 Onge    6
      6                Mbuti    4
      7      Israel_Natufian    1
      8   Brazil_LapaDoSanto    7
      9               Kharia   12
    jackknife block size:     0.050
    snps: 1148632  indivs: 40
    number of blocks for block jackknife: 713
    ## ncols: 1148632
    coverage:                  AHG 802743
    coverage:             Levant_N 702722
    coverage:                 WHG2 1002479
    coverage:           Kostenki14 932536
    coverage:                  Han 1121713
    coverage:                 Onge 720049
    coverage:                Mbuti 1121724
    coverage:      Israel_Natufian 385032
    coverage:   Brazil_LapaDoSanto 973100
    coverage:               Kharia 616242
    dof (jackknife):   604.834
    numsnps used: 334867
    codimension 1
    f4info: 
    f4rank: 1 dof:      5 chisq:     4.009 tail:           0.54807637 dofdiff:      7 chisqdiff:    -4.009 taildiff:                    1
    B:
              scale     1.000 
                Han     0.247 
               Onge     0.296 
              Mbuti     1.073 
    Israel_Natufian     2.116 
    Brazil_LapaDoSanto     0.252 
             Kharia     0.395 
    A:
              scale   939.687 
           Levant_N     0.847 
               WHG2    -1.133 
    
    
    full rank
    f4info: 
    f4rank: 2 dof:      0 chisq:     0.000 tail:                    1 dofdiff:      5 chisqdiff:     4.009 taildiff:           0.54807637
    B:
              scale     1.000     1.000 
                Han     0.268     1.209 
               Onge     0.302    -0.205 
              Mbuti     1.076     0.347 
    Israel_Natufian     2.107    -1.660 
    Brazil_LapaDoSanto     0.276     1.081 
             Kharia     0.404     0.670 
    A:
              scale   897.710  4625.799 
           Levant_N     0.646    -1.000 
               WHG2    -1.258    -1.000 
    
    
    best coefficients:     0.572     0.428 
    Jackknife mean:      0.571726954     0.428273046 
          std. errors:     0.059     0.059 
    
    error covariance (* 1000000)
          3506      -3506 
         -3506       3506 
    
    
    summ: AHG    2      0.548076     0.572     0.428  3506 -3506  3506 
    
        fixed pat  wt  dof     chisq       tail prob
               00  0     5     4.009        0.548076     0.572     0.428 
               01  1     6    44.865     4.97881e-08     1.000    -0.000 
               10  1     6    84.474     4.24242e-16     0.000     1.000 
    best pat:           00         0.548076              -  -
    best pat:           01      4.97881e-08  chi(nested):    40.855 p-value for nested model:     1.63912e-10
    
    coeffs:     0.572     0.428 
    
    ## dscore:: f_4(Base, Fit, Rbase, right2)
    ## genstat:: f_4(Base, Fit, right1, right2)
    
    details:        Levant_N             Han    -0.000096   -0.315590
    details:            WHG2             Han    -0.000671   -2.046854
    dscore:             Han f4:    -0.000342 Z:    -1.242608
    
    details:        Levant_N            Onge     0.000224    0.750264
    details:            WHG2            Onge    -0.000421   -1.391644
    dscore:            Onge f4:    -0.000052 Z:    -0.198128
    
    details:        Levant_N           Mbuti     0.000670    2.199054
    details:            WHG2           Mbuti    -0.001612   -5.043861
    dscore:           Mbuti f4:    -0.000306 Z:    -1.113296
    
    details:        Levant_N Israel_Natufian     0.001860    4.999137
    details:            WHG2 Israel_Natufian    -0.002620   -7.191379
    dscore: Israel_Natufian f4:    -0.000056 Z:    -0.172044
    
    details:        Levant_N Brazil_LapaDoSanto    -0.000059   -0.191338
    details:            WHG2 Brazil_LapaDoSanto    -0.000654   -2.019385
    dscore: Brazil_LapaDoSanto f4:    -0.000313 Z:    -1.131063
    
    details:        Levant_N          Kharia     0.000121    0.434161
    details:            WHG2          Kharia    -0.000741   -2.584742
    dscore:          Kharia f4:    -0.000248 Z:    -1.009475
    
    gendstat:           Kostenki14                  Han    -1.243
    gendstat:           Kostenki14                 Onge    -0.198
    gendstat:           Kostenki14                Mbuti    -1.113
    gendstat:           Kostenki14      Israel_Natufian    -0.172
    gendstat:           Kostenki14   Brazil_LapaDoSanto    -1.131
    gendstat:           Kostenki14               Kharia    -1.009
    gendstat:                  Han                 Onge     1.434
    gendstat:                  Han                Mbuti     0.157
    gendstat:                  Han      Israel_Natufian     0.952
    gendstat:                  Han   Brazil_LapaDoSanto     0.141
    gendstat:                  Han               Kharia     0.576
    gendstat:                 Onge                Mbuti    -1.205
    gendstat:                 Onge      Israel_Natufian    -0.015
    gendstat:                 Onge   Brazil_LapaDoSanto    -1.249
    gendstat:                 Onge               Kharia    -1.225
    gendstat:                Mbuti      Israel_Natufian     0.885
    gendstat:                Mbuti   Brazil_LapaDoSanto    -0.032
    gendstat:                Mbuti               Kharia     0.323
    gendstat:      Israel_Natufian   Brazil_LapaDoSanto    -0.904
    gendstat:      Israel_Natufian               Kharia    -0.747
    gendstat:   Brazil_LapaDoSanto               Kharia     0.393
    
    ## end of run
    Code:
    allsnps: YES
    ## qpAdm version: 810
    seed: 1909635723
    
    left pops:
    AHG
    Levant_N
    WHG
    Iran_N
    
    right pops:
    Kostenki14
    Han
    Onge
    Mbuti
    Israel_Natufian
    Brazil_LapaDoSanto
    Kharia
    
      0                  AHG    1
      1             Levant_N    3
      2                  WHG   13
      3               Iran_N   10
      4           Kostenki14    1
      5                  Han    3
      6                 Onge    6
      7                Mbuti    4
      8      Israel_Natufian    1
      9   Brazil_LapaDoSanto    7
     10               Kharia   12
    jackknife block size:     0.050
    snps: 1148658  indivs: 61
    number of blocks for block jackknife: 713
    ## ncols: 1148658
    coverage:                  AHG 802743
    coverage:             Levant_N 702722
    coverage:                  WHG 1004524
    coverage:               Iran_N 1004293
    coverage:           Kostenki14 932536
    coverage:                  Han 1121713
    coverage:                 Onge 720049
    coverage:                Mbuti 1121724
    coverage:      Israel_Natufian 385032
    coverage:   Brazil_LapaDoSanto 973100
    coverage:               Kharia 616242
    dof (jackknife):   610.123
    numsnps used: 1148658
    codimension 1
    f4info: 
    f4rank: 2 dof:      4 chisq:     4.859 tail:          0.302121532 dofdiff:      6 chisqdiff:    -4.859 taildiff:                    1
    B:
              scale     1.000     1.000 
                Han     0.941    -0.418 
               Onge     1.017    -0.546 
              Mbuti     1.549     0.237 
    Israel_Natufian     0.543     2.271 
    Brazil_LapaDoSanto     0.795    -0.420 
             Kharia     0.866    -0.369 
    A:
              scale   512.104   642.376 
           Levant_N     0.467     0.737 
                WHG    -1.217    -0.973 
             Iran_N     1.141    -1.229 
    
    
    full rank
    f4info: 
    f4rank: 3 dof:      0 chisq:     0.000 tail:                    1 dofdiff:      4 chisqdiff:     4.859 taildiff:          0.302121532
    B:
              scale     1.000     1.000     1.000 
                Han     0.936    -0.482     0.674 
               Onge     1.016    -0.610    -1.000 
              Mbuti     1.551     0.129     0.358 
    Israel_Natufian     0.573     2.228    -0.063 
    Brazil_LapaDoSanto     0.788    -0.474    -1.339 
             Kharia     0.857    -0.436     1.619 
    A:
              scale   507.112   647.381  5745.796 
           Levant_N     0.614     0.733    -1.054 
                WHG    -1.159    -0.947    -1.019 
             Iran_N     1.132    -1.251    -0.922 
    
    
    best coefficients:     0.584     0.317     0.099 
    Jackknife mean:      0.583644692     0.316751592     0.099603717 
          std. errors:     0.046     0.066     0.062 
    
    error covariance (* 1000000)
          2081      -1314       -767 
         -1314       4407      -3094 
          -767      -3094       3860 
    
    
    summ: AHG    3      0.302122     0.584     0.317     0.100  2081 -1314  -767  4407 -3094  3860 
    
        fixed pat  wt  dof     chisq       tail prob
              000  0     4     4.859        0.302122     0.584     0.317     0.099 
              001  1     5     7.376        0.194155     0.605     0.395    -0.000 
              010  1     5    27.655     4.25006e-05     0.678    -0.000     0.322 
              100  1     5   153.020               0     0.000     0.729     0.271 
              011  2     6    75.848     2.56695e-14     1.000    -0.000     0.000 
              101  2     6   162.471               0     0.000     1.000     0.000 
              110  2     6   223.544               0     0.000    -0.000     1.000 
    best pat:          000         0.302122              -  -
    best pat:          001         0.194155  chi(nested):     2.517 p-value for nested model:        0.112604
    best pat:          011      2.56695e-14  chi(nested):    68.473 p-value for nested model:     1.28653e-16
    
    coeffs:     0.584     0.317     0.099 
    
    ## dscore:: f_4(Base, Fit, Rbase, right2)
    ## genstat:: f_4(Base, Fit, right1, right2)
    
    details:        Levant_N             Han     0.000506    1.088537
    details:             WHG             Han    -0.001543   -3.127890
    details:          Iran_N             Han     0.002976    6.049829
    dscore:             Han f4:     0.000101 Z:     0.238596
    
    details:        Levant_N            Onge     0.000801    1.517809
    details:             WHG            Onge    -0.001224   -2.322326
    details:          Iran_N            Onge     0.003691    6.822665
    dscore:            Onge f4:     0.000446 Z:     0.944489
    
    details:        Levant_N           Mbuti     0.001987    3.968961
    details:             WHG           Mbuti    -0.003796   -7.498313
    details:          Iran_N           Mbuti     0.003189    6.246590
    dscore:           Mbuti f4:     0.000273 Z:     0.598391
    
    details:        Levant_N Israel_Natufian     0.003262    7.584370
    details:             WHG Israel_Natufian    -0.004548   -9.918670
    details:          Iran_N Israel_Natufian    -0.002981   -6.546083
    dscore: Israel_Natufian f4:     0.000168 Z:     0.422615
    
    details:        Levant_N Brazil_LapaDoSanto     0.000714    1.536414
    details:             WHG Brazil_LapaDoSanto    -0.000847   -1.759847
    details:          Iran_N Brazil_LapaDoSanto     0.002956    6.085490
    dscore: Brazil_LapaDoSanto f4:     0.000442 Z:     1.038062
    
    details:        Levant_N          Kharia     0.000297    0.849362
    details:             WHG          Kharia    -0.001585   -3.888209
    details:          Iran_N          Kharia     0.002556    6.256750
    dscore:          Kharia f4:    -0.000075 Z:    -0.225255
    
    gendstat:           Kostenki14                  Han     0.239
    gendstat:           Kostenki14                 Onge     0.944
    gendstat:           Kostenki14                Mbuti     0.598
    gendstat:           Kostenki14      Israel_Natufian     0.423
    gendstat:           Kostenki14   Brazil_LapaDoSanto     1.038
    gendstat:           Kostenki14               Kharia    -0.225
    gendstat:                  Han                 Onge     1.063
    gendstat:                  Han                Mbuti     0.513
    gendstat:                  Han      Israel_Natufian     0.158
    gendstat:                  Han   Brazil_LapaDoSanto     1.176
    gendstat:                  Han               Kharia    -0.632
    gendstat:                 Onge                Mbuti    -0.511
    gendstat:                 Onge      Israel_Natufian    -0.637
    gendstat:                 Onge   Brazil_LapaDoSanto    -0.012
    gendstat:                 Onge               Kharia    -1.602
    gendstat:                Mbuti      Israel_Natufian    -0.262
    gendstat:                Mbuti   Brazil_LapaDoSanto     0.478
    gendstat:                Mbuti               Kharia    -1.071
    gendstat:      Israel_Natufian   Brazil_LapaDoSanto     0.663
    gendstat:      Israel_Natufian               Kharia    -0.654
    gendstat:   Brazil_LapaDoSanto               Kharia    -1.815
    
    ## end of run

  18. The Following 3 Users Say Thank You to Vadim Verenich For This Useful Post:

     Bas (07-05-2019),  epoch (07-04-2019),  Hando (04-06-2019)

  19. #20
    Gold Class Member
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    Quote Originally Posted by Kale View Post
    Interesting that U5 turns up in Neolithic Anatolia. That's the first instance of this yes?
    Yes I think so. The U5b2 sample from Catalhoyuk probably relates to some sort of migration of Southeastern European (WHG) hunter-gatherers to Anatolia at some point in the remote past.

  20. The Following User Says Thank You to J Man For This Useful Post:

     Helen (07-04-2019)

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