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Thread: Medieval genomes from Nubia

  1. #41
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    The results aren't suprising a lot of this was known already, it just confirms things even more and i said as much in a different thread: When did Nubia become Nubian?

    If that is the case then there should be a demonstrateable discontinuity for which there isn't. Aside from the noticeable mixture with Arabs there hasn't be any radical population change or replacement.
    Then there is also 2015 study where they sucessfully extract endogenous DNA from specimens from the early Christian Period when the Alodia/Alwah, Nobatia and Makuria kingdoms ruled. They found out the specimens ancestry was West-Euroasian. Which shows that the Coptic/Ethio-Somali ancestral component that defines modern Nubians is most likely the same West Eurasian-affiliated ancestral component that defines the KulR17 specimen from Kulubnarti.

  2. #42
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    There's a preprint for a paper with samples from Roman sites in modern-day Serbia dated to ~1st century CE. One of the individuals may have been a Nubian Legionnaire or Auxilliary. Interestingly, his uniparentals are reported as E-V32 and L2a1j. I don't think that mtDNA has ever been found in Nile populations but has been mostly detected in Somalia and a couple of samples in Saudi Arabia and Jordan.

    In the pre-print, they ran qpAdm with the following populations:

    West_Africa_ancient, Sudan_EarlyChristian, Tianyuan, EHG, Iron_Gates_HG, Levant_N, Anatolia_N, Iran_N, Yamnaya_Samara, Alalakh_MLBA, Iberia_IA, Mycenaean, Slovenia_EIA, Netherlands_IA, Russia_Ingria_IA, Steppe_IA
    and the only model that worked was a one-way model with Sudan_EarlyChristian, but it wasn't a great fit (p=~0.13), but that makes sense as this roman sample is ~600+ years older than those at Kulubnarti, who already showed recent signs of admixture.

    PCA:

     



    Source: BioXiv (pre-print + suppl. material).
    Last edited by blackflash16; 09-01-2021 at 11:23 PM.

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  4. #43
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    I found a paper looking at the biological affinities of Nubians that is pretty interesting especially if the results can ever be confirmed by aDNA. They find that there is discontinuity between late pleistocene lower Nubians and holocene lower Nubians. This has been an observation for years. And the change has been suggested as either gene flow, population replacement or local evolution. This study suggests there was continuity in Nubia but with late pleistocene upper Nubians at Al Khiday
    In sum, the most parsimonious explanation is ancestors of Holocene agriculturalists were in Nubia—just not at Wadi Halfa, Gebel Sahaba, and Tushka. Though cultural diffusion with incorporation of non-local resources occurred [70-71], with perhaps some immigration, it is unnecessary to hypothesize a significant post-Pleistocene influx of agriculturalists. The results suggest most future Nubian agriculturalists were in residence the entire time, though previously in the guise of Neolithic agro-pastoralists and intensive collectors. It would seem likely that, soil deflation aside, more Late Palaeolithic skeletal remains akin to Al Khiday may yet be discovered, possibly including Lower Nubia. So, long term population continuity appears likely after all, perhaps including in situ selection for reduction in cranial robusticity, as well as dental size (only), during the transition from hunting-gathering to agriculture.
    https://royalsocietypublishing.org/d...rspb.2021.0969

    Another interesting observation is that Jebel Sahaba shows the highest affinity to Sub Saharan African populations in particular West Africans. To me suggesting these Lower Nubians might be ancestral to current day West Africans.
    Last edited by Srananšao; 11-27-2021 at 04:19 AM.

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  6. #44
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    Is there data available from this yet?

  7. #45
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    Quote Originally Posted by Chad Rohlfsen View Post
    Is there data available from this yet?
    The BAM files have been released but we are waiting for someone to convert them.

  8. #46
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    Any g25 coordinates for nubians?

  9. #47
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    Quote Originally Posted by Mnemonics View Post
    The BAM files have been released but we are waiting for someone to convert them.
    Here they are in BED and Ancestrymap format.

    Plink
    Geno

    I've already emailed them to Davidski.

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  11. #48
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    Quote Originally Posted by altvred View Post
    Here they are in BED and Ancestrymap format.

    Plink
    Geno

    I've already emailed them to Davidski.
    Have you considered looking at the 2017 Hollfelder Northeast African genomes?

    Sudan.tar.gz in the link below:
    http://jakobssonlab.iob.uu.se/data/

    My understanding is that there was too low of a SNP overlap for these to be included in the G25 a few years ago when they were first released-- could that have been a processing problem? At 3.9 million SNP coverage you'd think they'd be good to go. The Nubians from it are even included on the PCA in the new Kulubnarti study. It's a big hole in the G25 not to have these great samples so is there some magic you can work perhaps?
    Ελευθερία ή θάνατος.

  12. #49
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    Quote Originally Posted by altvred View Post
    Here they are in BED and Ancestrymap format.

    Plink
    Geno

    I've already emailed them to Davidski.
    Thanks!

    Most of their SSA seems to be Dinka-like but they seem to need some extra Mota affinity which is interesting. The Egyptians seem fine as a source for their MENA ancestry when you don't add Iberomaurusians to the right pops list

    Code:
    left pops:
    Kulubnarti_MA
    Dinka.DG
    EgyptianAnc
    
    right pops:
    Cameroon_SMA.SG
    Anatolia_N.SG
    Iran_TepeAbdulHosein_N.SG
    CHG
    Mota
    DevilsGate_N
    Iberia_HG
    Lebanon_MBA.SG
    Russia_Afanasievo.SG
    Rome_Imperial
    Greece_Logkas_MBA.SG
    
      0        Kulubnarti_MA   60
      1             Dinka.DG    3
      2          EgyptianAnc    4
      3      Cameroon_SMA.SG    2
      4        Anatolia_N.SG    5
      5 Iran_TepeAbdulHosein_N.SG    3
      6                  CHG    2
      7                 Mota    1
      8         DevilsGate_N    4
      9            Iberia_HG    2
     10       Lebanon_MBA.SG    5
     11 Russia_Afanasievo.SG    2
     12        Rome_Imperial   43
     13 Greece_Logkas_MBA.SG    2
    jackknife block size:     0.050
    snps: 1150518  indivs: 138
    number of blocks for block jackknife: 714
    ## ncols: 1150518
    coverage:        Kulubnarti_MA 1111256
    coverage:             Dinka.DG 1150400
    coverage:          EgyptianAnc 816220
    coverage:      Cameroon_SMA.SG 1148760
    coverage:        Anatolia_N.SG 1056084
    coverage: Iran_TepeAbdulHosein_N.SG 1061032
    coverage:                  CHG 1134595
    coverage:                 Mota 1134612
    coverage:         DevilsGate_N 1134715
    coverage:            Iberia_HG 1042845
    coverage:       Lebanon_MBA.SG 1138714
    coverage: Russia_Afanasievo.SG 1147532
    coverage:        Rome_Imperial 1128057
    coverage: Greece_Logkas_MBA.SG 1149733
    Effective number of blocks:   632.705
    numsnps used: 745497
    codimension 1
    f4info: 
    f4rank: 1 dof:      9 chisq:    10.432 tail:          0.316684155 dofdiff:     11 chisqdiff:   -10.432 taildiff:                    1
    B:
              scale     1.000 
      Anatolia_N.SG     1.153 
    Iran_TepeAbdulHosein_N.SG     0.977 
                CHG     1.038 
               Mota     0.093 
       DevilsGate_N     0.830 
          Iberia_HG     1.030 
     Lebanon_MBA.SG     1.121 
    Russia_Afanasievo.SG     1.053 
      Rome_Imperial     1.123 
    Greece_Logkas_MBA.SG     1.121 
    A:
              scale    65.112 
           Dinka.DG    -1.175 
        EgyptianAnc     0.788 
    
    
    full rank
    f4info: 
    f4rank: 2 dof:      0 chisq:     0.000 tail:                    1 dofdiff:      9 chisqdiff:    10.432 taildiff:          0.316684155
    B:
              scale    54.811    82.226 
      Anatolia_N.SG    -1.151     1.147 
    Iran_TepeAbdulHosein_N.SG    -0.975     0.995 
                CHG    -1.036     1.059 
               Mota    -0.112     0.079 
       DevilsGate_N    -0.835     0.833 
          Iberia_HG    -1.033     1.019 
     Lebanon_MBA.SG    -1.118     1.118 
    Russia_Afanasievo.SG    -1.057     1.046 
      Rome_Imperial    -1.120     1.116 
    Greece_Logkas_MBA.SG    -1.119     1.116 
    A:
              scale     1.414     1.414 
           Dinka.DG     1.414     0.000 
        EgyptianAnc     0.000     1.414 
    
    
    best coefficients:     0.401     0.599 
    Jackknife mean:      0.401368881     0.598631119 
          std. errors:     0.004     0.004 
    
    error covariance (* 1,000,000)
            20        -20 
           -20         20 
    
    
    summ: Kulubnarti_MA    2      0.316684     0.401     0.599         20        -20         20 
    
        fixed pat  wt  dof     chisq       tail prob
               00  0     9    10.432        0.316684     0.401     0.599 
               01  1    10  7920.073               0     1.000     0.000 
               10  1    10  3354.608               0     0.000     1.000 
    best pat:           00         0.316684              -  -
    best pat:           01                0  chi(nested):  7909.641 p-value for nested model:               0
    
    coeffs:     0.401     0.599 
    
    ## dscore:: f_4(Base, Fit, Rbase, right2)
    ## genstat:: f_4(Base, Fit, right1, right2)
    
    details:             Dinka.DG        Anatolia_N.SG    -0.021007  -77.015740
    details:          EgyptianAnc        Anatolia_N.SG     0.013953   46.904095
    dscore:        Anatolia_N.SG f4:    -0.000079 Z:    -0.403438
    
    details:             Dinka.DG Iran_TepeAbdulHosein_N.SG    -0.017783  -65.618377
    details:          EgyptianAnc Iran_TepeAbdulHosein_N.SG     0.012098   42.162627
    dscore: Iran_TepeAbdulHosein_N.SG f4:     0.000105 Z:     0.560877
    
    details:             Dinka.DG                  CHG    -0.018899  -66.734818
    details:          EgyptianAnc                  CHG     0.012873   41.406740
    dscore:                  CHG f4:     0.000121 Z:     0.609781
    
    details:             Dinka.DG                 Mota    -0.002052   -9.536272
    details:          EgyptianAnc                 Mota     0.000956    4.107228
    dscore:                 Mota f4:    -0.000251 Z:    -1.546190
    
    details:             Dinka.DG         DevilsGate_N    -0.015236  -55.411509
    details:          EgyptianAnc         DevilsGate_N     0.010136   35.010382
    dscore:         DevilsGate_N f4:    -0.000048 Z:    -0.252177
    
    details:             Dinka.DG            Iberia_HG    -0.018842  -66.909529
    details:          EgyptianAnc            Iberia_HG     0.012395   41.373918
    dscore:            Iberia_HG f4:    -0.000143 Z:    -0.724356
    
    details:             Dinka.DG       Lebanon_MBA.SG    -0.020403  -79.447092
    details:          EgyptianAnc       Lebanon_MBA.SG     0.013591   49.736151
    dscore:       Lebanon_MBA.SG f4:    -0.000053 Z:    -0.306480
    
    details:             Dinka.DG Russia_Afanasievo.SG    -0.019289  -69.877523
    details:          EgyptianAnc Russia_Afanasievo.SG     0.012723   43.454202
    dscore: Russia_Afanasievo.SG f4:    -0.000125 Z:    -0.665457
    
    details:             Dinka.DG        Rome_Imperial    -0.020429  -83.934731
    details:          EgyptianAnc        Rome_Imperial     0.013572   55.484904
    dscore:        Rome_Imperial f4:    -0.000075 Z:    -0.473547
    
    details:             Dinka.DG Greece_Logkas_MBA.SG    -0.020415  -75.881701
    details:          EgyptianAnc Greece_Logkas_MBA.SG     0.013572   45.942596
    dscore: Greece_Logkas_MBA.SG f4:    -0.000070 Z:    -0.359041
    
    gendstat:      Cameroon_SMA.SG        Anatolia_N.SG    -0.403
    gendstat:      Cameroon_SMA.SG Iran_TepeAbdulHosein_N.SG     0.561
    gendstat:      Cameroon_SMA.SG                  CHG     0.610
    gendstat:      Cameroon_SMA.SG                 Mota    -1.546
    gendstat:      Cameroon_SMA.SG         DevilsGate_N    -0.252
    gendstat:      Cameroon_SMA.SG            Iberia_HG    -0.724
    gendstat:      Cameroon_SMA.SG       Lebanon_MBA.SG    -0.306
    gendstat:      Cameroon_SMA.SG Russia_Afanasievo.SG    -0.665
    gendstat:      Cameroon_SMA.SG        Rome_Imperial    -0.474
    gendstat:      Cameroon_SMA.SG Greece_Logkas_MBA.SG    -0.359
    gendstat:        Anatolia_N.SG Iran_TepeAbdulHosein_N.SG     1.159
    gendstat:        Anatolia_N.SG                  CHG     1.298
    gendstat:        Anatolia_N.SG                 Mota    -0.811
    gendstat:        Anatolia_N.SG         DevilsGate_N     0.183
    gendstat:        Anatolia_N.SG            Iberia_HG    -0.382
    gendstat:        Anatolia_N.SG       Lebanon_MBA.SG     0.195
    gendstat:        Anatolia_N.SG Russia_Afanasievo.SG    -0.301
    gendstat:        Anatolia_N.SG        Rome_Imperial     0.036
    gendstat:        Anatolia_N.SG Greece_Logkas_MBA.SG     0.065
    gendstat: Iran_TepeAbdulHosein_N.SG                  CHG     0.098
    gendstat: Iran_TepeAbdulHosein_N.SG                 Mota    -1.782
    gendstat: Iran_TepeAbdulHosein_N.SG         DevilsGate_N    -0.908
    gendstat: Iran_TepeAbdulHosein_N.SG            Iberia_HG    -1.394
    gendstat: Iran_TepeAbdulHosein_N.SG       Lebanon_MBA.SG    -1.115
    gendstat: Iran_TepeAbdulHosein_N.SG Russia_Afanasievo.SG    -1.496
    gendstat: Iran_TepeAbdulHosein_N.SG        Rome_Imperial    -1.459
    gendstat: Iran_TepeAbdulHosein_N.SG Greece_Logkas_MBA.SG    -1.056
    gendstat:                  CHG                 Mota    -1.779
    gendstat:                  CHG         DevilsGate_N    -0.937
    gendstat:                  CHG            Iberia_HG    -1.483
    gendstat:                  CHG       Lebanon_MBA.SG    -1.173
    gendstat:                  CHG Russia_Afanasievo.SG    -1.502
    gendstat:                  CHG        Rome_Imperial    -1.551
    gendstat:                  CHG Greece_Logkas_MBA.SG    -1.135
    gendstat:                 Mota         DevilsGate_N     0.976
    gendstat:                 Mota            Iberia_HG     0.505
    gendstat:                 Mota       Lebanon_MBA.SG     1.019
    gendstat:                 Mota Russia_Afanasievo.SG     0.607
    gendstat:                 Mota        Rome_Imperial     0.977
    gendstat:                 Mota Greece_Logkas_MBA.SG     0.855
    gendstat:         DevilsGate_N            Iberia_HG    -0.535
    gendstat:         DevilsGate_N       Lebanon_MBA.SG    -0.035
    gendstat:         DevilsGate_N Russia_Afanasievo.SG    -0.457
    gendstat:         DevilsGate_N        Rome_Imperial    -0.192
    gendstat:         DevilsGate_N Greece_Logkas_MBA.SG    -0.125
    gendstat:            Iberia_HG       Lebanon_MBA.SG     0.559
    gendstat:            Iberia_HG Russia_Afanasievo.SG     0.101
    gendstat:            Iberia_HG        Rome_Imperial     0.502
    gendstat:            Iberia_HG Greece_Logkas_MBA.SG     0.432
    gendstat:       Lebanon_MBA.SG Russia_Afanasievo.SG    -0.494
    gendstat:       Lebanon_MBA.SG        Rome_Imperial    -0.246
    gendstat:       Lebanon_MBA.SG Greece_Logkas_MBA.SG    -0.117
    gendstat: Russia_Afanasievo.SG        Rome_Imperial     0.416
    gendstat: Russia_Afanasievo.SG Greece_Logkas_MBA.SG     0.355
    gendstat:        Rome_Imperial Greece_Logkas_MBA.SG     0.050

    Popping Iberomaurusians into the right pop list creates a strong need for Iberomaurusian related ancestry without a need for less CHG/Iran_N ancestry and a need for more Anatolia_N which I think might indicate admixture from a pristinely Iberomaurusian like source.




    Code:
    left pops:
    Kulubnarti_MA
    Dinka.DG
    EgyptianAnc
    
    right pops:
    Cameroon_SMA.SG
    Anatolia_N.SG
    Iran_TepeAbdulHosein_N.SG
    CHG
    Mota
    DevilsGate_N
    Iberia_HG
    Lebanon_MBA.SG
    Russia_Afanasievo.SG
    Rome_Imperial
    Greece_Logkas_MBA.SG
    Iberomaurusian
    
      0        Kulubnarti_MA   60
      1             Dinka.DG    3
      2          EgyptianAnc    4
      3      Cameroon_SMA.SG    2
      4        Anatolia_N.SG    5
      5 Iran_TepeAbdulHosein_N.SG    3
      6                  CHG    2
      7                 Mota    1
      8         DevilsGate_N    4
      9            Iberia_HG    2
     10       Lebanon_MBA.SG    5
     11 Russia_Afanasievo.SG    2
     12        Rome_Imperial   43
     13 Greece_Logkas_MBA.SG    2
     14       Iberomaurusian    4
    jackknife block size:     0.050
    snps: 1150523  indivs: 142
    number of blocks for block jackknife: 714
    ## ncols: 1150523
    coverage:        Kulubnarti_MA 1111256
    coverage:             Dinka.DG 1150400
    coverage:          EgyptianAnc 816220
    coverage:      Cameroon_SMA.SG 1148760
    coverage:        Anatolia_N.SG 1056084
    coverage: Iran_TepeAbdulHosein_N.SG 1061032
    coverage:                  CHG 1134595
    coverage:                 Mota 1134612
    coverage:         DevilsGate_N 1134715
    coverage:            Iberia_HG 1042845
    coverage:       Lebanon_MBA.SG 1138714
    coverage: Russia_Afanasievo.SG 1147532
    coverage:        Rome_Imperial 1128057
    coverage: Greece_Logkas_MBA.SG 1149733
    coverage:       Iberomaurusian 1086672
    Effective number of blocks:   632.830
    numsnps used: 737799
    codimension 1
    f4info: 
    f4rank: 1 dof:     10 chisq:    81.342 tail:       2.73852251e-13 dofdiff:     12 chisqdiff:   -81.342 taildiff:                    1
    B:
              scale     1.000 
      Anatolia_N.SG     1.177 
    Iran_TepeAbdulHosein_N.SG     0.997 
                CHG     1.058 
               Mota     0.094 
       DevilsGate_N     0.851 
          Iberia_HG     1.052 
     Lebanon_MBA.SG     1.142 
    Russia_Afanasievo.SG     1.075 
      Rome_Imperial     1.145 
    Greece_Logkas_MBA.SG     1.141 
     Iberomaurusian     0.767 
    A:
              scale    66.299 
           Dinka.DG    -1.177 
        EgyptianAnc     0.783 
    
    
    full rank
    f4info: 
    f4rank: 2 dof:      0 chisq:     0.000 tail:                    1 dofdiff:     10 chisqdiff:    81.342 taildiff:       2.73852251e-13
    B:
              scale    55.601    84.359 
      Anatolia_N.SG    -1.172     1.182 
    Iran_TepeAbdulHosein_N.SG    -0.991     1.023 
                CHG    -1.054     1.088 
               Mota    -0.115     0.082 
       DevilsGate_N    -0.851     0.858 
          Iberia_HG    -1.051     1.049 
     Lebanon_MBA.SG    -1.138     1.151 
    Russia_Afanasievo.SG    -1.076     1.075 
      Rome_Imperial    -1.140     1.148 
    Greece_Logkas_MBA.SG    -1.139     1.147 
     Iberomaurusian    -0.800     0.644 
    A:
              scale     1.414     1.414 
           Dinka.DG     1.414     0.000 
        EgyptianAnc     0.000     1.414 
    
    
    best coefficients:     0.400     0.600 
    Jackknife mean:      0.399489578     0.600510422 
          std. errors:     0.005     0.005 
    
    error covariance (* 1,000,000)
            20        -20 
           -20         20 
    
    
    summ: Kulubnarti_MA    2      0.000000     0.399     0.601         20        -20         20 
    
        fixed pat  wt  dof     chisq       tail prob
               00  0    10    81.342     2.73852e-13     0.400     0.600 
               01  1    11  7945.842               0     1.000     0.000 
               10  1    11  3353.653               0     0.000     1.000 
    best pat:           00      2.73852e-13              -  -
    best pat:           01                0  chi(nested):  7864.500 p-value for nested model:               0
    
    coeffs:     0.400     0.600 
    
    ## dscore:: f_4(Base, Fit, Rbase, right2)
    ## genstat:: f_4(Base, Fit, right1, right2)
    
    details:             Dinka.DG        Anatolia_N.SG    -0.021073  -77.249799
    details:          EgyptianAnc        Anatolia_N.SG     0.014009   46.914437
    dscore:        Anatolia_N.SG f4:    -0.000007 Z:    -0.035732
    
    details:             Dinka.DG Iran_TepeAbdulHosein_N.SG    -0.017832  -65.892606
    details:          EgyptianAnc Iran_TepeAbdulHosein_N.SG     0.012130   42.007489
    dscore: Iran_TepeAbdulHosein_N.SG f4:     0.000159 Z:     0.849611
    
    details:             Dinka.DG                  CHG    -0.018965  -67.126077
    details:          EgyptianAnc                  CHG     0.012903   41.291537
    dscore:                  CHG f4:     0.000171 Z:     0.862709
    
    details:             Dinka.DG                 Mota    -0.002073   -9.650261
    details:          EgyptianAnc                 Mota     0.000970    4.156128
    dscore:                 Mota f4:    -0.000246 Z:    -1.516967
    
    details:             Dinka.DG         DevilsGate_N    -0.015310  -55.579881
    details:          EgyptianAnc         DevilsGate_N     0.010166   34.835130
    dscore:         DevilsGate_N f4:    -0.000012 Z:    -0.065473
    
    details:             Dinka.DG            Iberia_HG    -0.018907  -67.162355
    details:          EgyptianAnc            Iberia_HG     0.012431   41.362080
    dscore:            Iberia_HG f4:    -0.000089 Z:    -0.450542
    
    details:             Dinka.DG       Lebanon_MBA.SG    -0.020468  -79.635738
    details:          EgyptianAnc       Lebanon_MBA.SG     0.013646   49.749883
    dscore:       Lebanon_MBA.SG f4:     0.000017 Z:     0.094547
    
    details:             Dinka.DG Russia_Afanasievo.SG    -0.019346  -70.029090
    details:          EgyptianAnc Russia_Afanasievo.SG     0.012744   43.242256
    dscore: Russia_Afanasievo.SG f4:    -0.000077 Z:    -0.404412
    
    details:             Dinka.DG        Rome_Imperial    -0.020496  -84.219793
    details:          EgyptianAnc        Rome_Imperial     0.013608   55.284887
    dscore:        Rome_Imperial f4:    -0.000017 Z:    -0.107284
    
    details:             Dinka.DG Greece_Logkas_MBA.SG    -0.020494  -76.031557
    details:          EgyptianAnc Greece_Logkas_MBA.SG     0.013600   45.802017
    dscore: Greece_Logkas_MBA.SG f4:    -0.000021 Z:    -0.109041
    
    details:             Dinka.DG       Iberomaurusian    -0.014388  -58.696005
    details:          EgyptianAnc       Iberomaurusian     0.007634   28.390996
    dscore:       Iberomaurusian f4:    -0.001164 Z:    -6.675463
    
    gendstat:      Cameroon_SMA.SG        Anatolia_N.SG    -0.036
    gendstat:      Cameroon_SMA.SG Iran_TepeAbdulHosein_N.SG     0.850
    gendstat:      Cameroon_SMA.SG                  CHG     0.863
    gendstat:      Cameroon_SMA.SG                 Mota    -1.517
    gendstat:      Cameroon_SMA.SG         DevilsGate_N    -0.065
    gendstat:      Cameroon_SMA.SG            Iberia_HG    -0.451
    gendstat:      Cameroon_SMA.SG       Lebanon_MBA.SG     0.095
    gendstat:      Cameroon_SMA.SG Russia_Afanasievo.SG    -0.404
    gendstat:      Cameroon_SMA.SG        Rome_Imperial    -0.107
    gendstat:      Cameroon_SMA.SG Greece_Logkas_MBA.SG    -0.109
    gendstat:      Cameroon_SMA.SG       Iberomaurusian    -6.675
    gendstat:        Anatolia_N.SG Iran_TepeAbdulHosein_N.SG     1.049
    gendstat:        Anatolia_N.SG                  CHG     1.150
    gendstat:        Anatolia_N.SG                 Mota    -1.126
    gendstat:        Anatolia_N.SG         DevilsGate_N    -0.032
    gendstat:        Anatolia_N.SG            Iberia_HG    -0.488
    gendstat:        Anatolia_N.SG       Lebanon_MBA.SG     0.179
    gendstat:        Anatolia_N.SG Russia_Afanasievo.SG    -0.449
    gendstat:        Anatolia_N.SG        Rome_Imperial    -0.097
    gendstat:        Anatolia_N.SG Greece_Logkas_MBA.SG    -0.098
    gendstat:        Anatolia_N.SG       Iberomaurusian    -6.587
    gendstat: Iran_TepeAbdulHosein_N.SG                  CHG     0.072
    gendstat: Iran_TepeAbdulHosein_N.SG                 Mota    -2.040
    gendstat: Iran_TepeAbdulHosein_N.SG         DevilsGate_N    -1.027
    gendstat: Iran_TepeAbdulHosein_N.SG            Iberia_HG    -1.389
    gendstat: Iran_TepeAbdulHosein_N.SG       Lebanon_MBA.SG    -1.009
    gendstat: Iran_TepeAbdulHosein_N.SG Russia_Afanasievo.SG    -1.520
    gendstat: Iran_TepeAbdulHosein_N.SG        Rome_Imperial    -1.432
    gendstat: Iran_TepeAbdulHosein_N.SG Greece_Logkas_MBA.SG    -1.094
    gendstat: Iran_TepeAbdulHosein_N.SG       Iberomaurusian    -7.280
    gendstat:                  CHG                 Mota    -1.989
    gendstat:                  CHG         DevilsGate_N    -1.019
    gendstat:                  CHG            Iberia_HG    -1.458
    gendstat:                  CHG       Lebanon_MBA.SG    -1.040
    gendstat:                  CHG Russia_Afanasievo.SG    -1.506
    gendstat:                  CHG        Rome_Imperial    -1.484
    gendstat:                  CHG Greece_Logkas_MBA.SG    -1.146
    gendstat:                  CHG       Iberomaurusian    -7.049
    gendstat:                 Mota         DevilsGate_N     1.119
    gendstat:                 Mota            Iberia_HG     0.731
    gendstat:                 Mota       Lebanon_MBA.SG     1.353
    gendstat:                 Mota Russia_Afanasievo.SG     0.817
    gendstat:                 Mota        Rome_Imperial     1.272
    gendstat:                 Mota Greece_Logkas_MBA.SG     1.057
    gendstat:                 Mota       Iberomaurusian    -4.817
    gendstat:         DevilsGate_N            Iberia_HG    -0.428
    gendstat:         DevilsGate_N       Lebanon_MBA.SG     0.178
    gendstat:         DevilsGate_N Russia_Afanasievo.SG    -0.376
    gendstat:         DevilsGate_N        Rome_Imperial    -0.033
    gendstat:         DevilsGate_N Greece_Logkas_MBA.SG    -0.050
    gendstat:         DevilsGate_N       Iberomaurusian    -6.168
    gendstat:            Iberia_HG       Lebanon_MBA.SG     0.657
    gendstat:            Iberia_HG Russia_Afanasievo.SG     0.070
    gendstat:            Iberia_HG        Rome_Imperial     0.531
    gendstat:            Iberia_HG Greece_Logkas_MBA.SG     0.398
    gendstat:            Iberia_HG       Iberomaurusian    -5.896
    gendstat:       Lebanon_MBA.SG Russia_Afanasievo.SG    -0.640
    gendstat:       Lebanon_MBA.SG        Rome_Imperial    -0.380
    gendstat:       Lebanon_MBA.SG Greece_Logkas_MBA.SG    -0.274
    gendstat:       Lebanon_MBA.SG       Iberomaurusian    -7.272
    gendstat: Russia_Afanasievo.SG        Rome_Imperial     0.490
    gendstat: Russia_Afanasievo.SG Greece_Logkas_MBA.SG     0.351
    gendstat: Russia_Afanasievo.SG       Iberomaurusian    -5.863
    gendstat:        Rome_Imperial Greece_Logkas_MBA.SG    -0.036
    gendstat:        Rome_Imperial       Iberomaurusian    -7.794
    gendstat: Greece_Logkas_MBA.SG       Iberomaurusian    -6.205


    I'll try out some more models.

  13. The Following 7 Users Say Thank You to Mnemonics For This Useful Post:

     Aben Aboo (11-28-2021),  altvred (11-27-2021),  Angoliga (11-27-2021),  drobbah (11-27-2021),  Kale (01-16-2022),  Lank (11-28-2021),  Sabz (11-27-2021)

  14. #50
    Registered Users
    Posts
    379
    Sex
    Location
    Canada
    Ethnicity
    Somali
    Y-DNA (P)
    T-L208
    mtDNA (M)
    N1b2

    Canada Somaliland
    The best model for the Kulubnarti Nubians seems to be Kenya_PastoralIA + Ancient Egyptians + Morocco_EN

    Code:
    left pops:
    Kulubnarti_MA
    Kenya_PastoralIA
    EgyptianAnc
    Morocco_EN
    
    right pops:
    Cameroon_SMA.SG
    Anatolia_N.SG
    Iran_TepeAbdulHosein_N.SG
    CHG
    Mota
    DevilsGate_N
    Iberia_HG
    Lebanon_MBA.SG
    Russia_Afanasievo.SG
    Rome_Imperial
    Greece_Logkas_MBA.SG
    Iberomaurusian
    PPNB
    
      0        Kulubnarti_MA   60
      1     Kenya_PastoralIA    4
      2          EgyptianAnc    4
      3           Morocco_EN    3
      4      Cameroon_SMA.SG    2
      5        Anatolia_N.SG    5
      6 Iran_TepeAbdulHosein_N.SG    3
      7                  CHG    2
      8                 Mota    1
      9         DevilsGate_N    4
     10            Iberia_HG    2
     11       Lebanon_MBA.SG    5
     12 Russia_Afanasievo.SG    2
     13        Rome_Imperial   43
     14 Greece_Logkas_MBA.SG    2
     15       Iberomaurusian    4
     16                 PPNB   12
    jackknife block size:     0.050
    snps: 1150438  indivs: 158
    number of blocks for block jackknife: 714
    ## ncols: 1150438
    coverage:        Kulubnarti_MA 1111256
    coverage:     Kenya_PastoralIA 661264
    coverage:          EgyptianAnc 816220
    coverage:           Morocco_EN 653097
    coverage:      Cameroon_SMA.SG 1148760
    coverage:        Anatolia_N.SG 1056084
    coverage: Iran_TepeAbdulHosein_N.SG 1061032
    coverage:                  CHG 1134595
    coverage:                 Mota 1134612
    coverage:         DevilsGate_N 1134715
    coverage:            Iberia_HG 1042845
    coverage:       Lebanon_MBA.SG 1138714
    coverage: Russia_Afanasievo.SG 1147532
    coverage:        Rome_Imperial 1128057
    coverage: Greece_Logkas_MBA.SG 1149733
    coverage:       Iberomaurusian 1086672
    coverage:                 PPNB 862586
    Effective number of blocks:   631.346
    numsnps used: 329481
    codimension 1
    f4info: 
    f4rank: 2 dof:     10 chisq:     5.665 tail:          0.842612619 dofdiff:     12 chisqdiff:    -5.665 taildiff:                    1
    B:
              scale     1.000     1.000 
      Anatolia_N.SG     1.079     0.520 
    Iran_TepeAbdulHosein_N.SG     0.958     0.426 
                CHG     0.984     0.409 
               Mota     0.060    -0.169 
       DevilsGate_N     0.797     0.132 
          Iberia_HG     0.979     0.251 
     Lebanon_MBA.SG     1.080     0.422 
    Russia_Afanasievo.SG     1.004     0.421 
      Rome_Imperial     1.063     0.469 
    Greece_Logkas_MBA.SG     1.087     0.446 
     Iberomaurusian     1.287    -3.226 
               PPNB     1.100     0.300 
    A:
              scale   131.755   251.842 
    Kenya_PastoralIA    -1.078    -0.333 
        EgyptianAnc     1.248     0.482 
         Morocco_EN     0.528    -1.630 
    
    
    full rank
    f4info: 
    f4rank: 3 dof:      0 chisq:     0.000 tail:                    1 dofdiff:     10 chisqdiff:     5.665 taildiff:          0.842612619
    B:
              scale   120.942   102.107   129.139 
      Anatolia_N.SG    -1.136     1.169     0.142 
    Iran_TepeAbdulHosein_N.SG    -1.029     1.028     0.145 
                CHG    -1.035     1.056     0.184 
               Mota    -0.027     0.050     0.191 
       DevilsGate_N    -0.810     0.819     0.306 
          Iberia_HG    -0.996     1.025     0.314 
     Lebanon_MBA.SG    -1.125     1.148     0.214 
    Russia_Afanasievo.SG    -1.078     1.061     0.176 
      Rome_Imperial    -1.135     1.131     0.169 
    Greece_Logkas_MBA.SG    -1.164     1.145     0.194 
     Iberomaurusian    -0.762     0.632     3.383 
               PPNB    -1.131     1.142     0.331 
    A:
              scale     1.732     1.732     1.732 
    Kenya_PastoralIA     1.732     0.000     0.000 
        EgyptianAnc     0.000     1.732     0.000 
         Morocco_EN     0.000     0.000     1.732 
    
    
    best coefficients:     0.529     0.447     0.024 
    Jackknife mean:      0.529078945     0.446810636     0.024110419 
          std. errors:     0.010     0.009     0.006 
    
    error covariance (* 1,000,000)
           101        -75        -25 
           -75         88        -13 
           -25        -13         38 
    
    
    summ: Kulubnarti_MA    3      0.842613     0.529     0.447     0.024        101        -75        -25         88        -13   ...
            38 
    
        fixed pat  wt  dof     chisq       tail prob
              000  0    10     5.665        0.842613     0.529     0.447     0.024 
              001  1    11    21.861       0.0254715     0.547     0.453     0.000 
              010  1    11   994.305               0     1.007     0.000    -0.007  infeasible
              100  1    11  2080.762               0     0.000     0.897     0.103 
              011  2    12   996.278               0     1.000     0.000     0.000 
              101  2    12  2176.863               0     0.000     1.000     0.000 
              110  2    12  4461.711               0     0.000     0.000     1.000 
    best pat:          000         0.842613              -  -
    best pat:          010                0  chi(nested):   988.640 p-value for nested model:    5.29546e-217
    best pat:          011     1.18269e-205  chi(nested):     1.973 p-value for nested model:        0.160093
    
    coeffs:     0.529     0.447     0.024 
    
    ## dscore:: f_4(Base, Fit, Rbase, right2)
    ## genstat:: f_4(Base, Fit, right1, right2)
    
    details:     Kenya_PastoralIA        Anatolia_N.SG    -0.009396  -24.672121
    details:          EgyptianAnc        Anatolia_N.SG     0.011450   37.376822
    details:           Morocco_EN        Anatolia_N.SG     0.001098    2.945026
    dscore:        Anatolia_N.SG f4:     0.000172 Z:     0.681466
    
    details:     Kenya_PastoralIA Iran_TepeAbdulHosein_N.SG    -0.008506  -22.232757
    details:          EgyptianAnc Iran_TepeAbdulHosein_N.SG     0.010065   31.998309
    details:           Morocco_EN Iran_TepeAbdulHosein_N.SG     0.001127    2.934722
    dscore: Iran_TepeAbdulHosein_N.SG f4:     0.000025 Z:     0.101072
    
    details:     Kenya_PastoralIA                  CHG    -0.008558  -21.436979
    details:          EgyptianAnc                  CHG     0.010346   31.871745
    details:           Morocco_EN                  CHG     0.001427    3.526370
    dscore:                  CHG f4:     0.000130 Z:     0.494550
    
    details:     Kenya_PastoralIA                 Mota    -0.000224   -0.646928
    details:          EgyptianAnc                 Mota     0.000486    1.707858
    details:           Morocco_EN                 Mota     0.001481    4.013705
    dscore:                 Mota f4:     0.000134 Z:     0.579764
    
    details:     Kenya_PastoralIA         DevilsGate_N    -0.006698  -18.129234
    details:          EgyptianAnc         DevilsGate_N     0.008024   26.800489
    details:           Morocco_EN         DevilsGate_N     0.002370    6.170634
    dscore:         DevilsGate_N f4:     0.000099 Z:     0.418936
    
    details:     Kenya_PastoralIA            Iberia_HG    -0.008232  -20.772962
    details:          EgyptianAnc            Iberia_HG     0.010041   30.852812
    details:           Morocco_EN            Iberia_HG     0.002433    6.108523
    dscore:            Iberia_HG f4:     0.000190 Z:     0.733412
    
    details:     Kenya_PastoralIA       Lebanon_MBA.SG    -0.009304  -26.211089
    details:          EgyptianAnc       Lebanon_MBA.SG     0.011243   39.703007
    details:           Morocco_EN       Lebanon_MBA.SG     0.001656    4.598007
    dscore:       Lebanon_MBA.SG f4:     0.000142 Z:     0.618402
    
    details:     Kenya_PastoralIA Russia_Afanasievo.SG    -0.008912  -23.458832
    details:          EgyptianAnc Russia_Afanasievo.SG     0.010387   32.751570
    details:           Morocco_EN Russia_Afanasievo.SG     0.001361    3.394666
    dscore: Russia_Afanasievo.SG f4:    -0.000041 Z:    -0.163827
    
    details:     Kenya_PastoralIA        Rome_Imperial    -0.009382  -28.457057
    details:          EgyptianAnc        Rome_Imperial     0.011074   42.981981
    details:           Morocco_EN        Rome_Imperial     0.001307    3.949103
    dscore:        Rome_Imperial f4:     0.000017 Z:     0.080232
    
    details:     Kenya_PastoralIA Greece_Logkas_MBA.SG    -0.009622  -25.160298
    details:          EgyptianAnc Greece_Logkas_MBA.SG     0.011214   35.114942
    details:           Morocco_EN Greece_Logkas_MBA.SG     0.001501    3.822187
    dscore: Greece_Logkas_MBA.SG f4:    -0.000043 Z:    -0.170034
    
    details:     Kenya_PastoralIA       Iberomaurusian    -0.006301  -17.556329
    details:          EgyptianAnc       Iberomaurusian     0.006194   21.490592
    details:           Morocco_EN       Iberomaurusian     0.026195   59.111918
    dscore:       Iberomaurusian f4:     0.000065 Z:     0.284975
    
    details:     Kenya_PastoralIA                 PPNB    -0.009356  -24.434080
    details:          EgyptianAnc                 PPNB     0.011182   36.271284
    details:           Morocco_EN                 PPNB     0.002564    6.495625
    dscore:                 PPNB f4:     0.000109 Z:     0.437978
    
    gendstat:      Cameroon_SMA.SG        Anatolia_N.SG     0.681
    gendstat:      Cameroon_SMA.SG Iran_TepeAbdulHosein_N.SG     0.101
    gendstat:      Cameroon_SMA.SG                  CHG     0.495
    gendstat:      Cameroon_SMA.SG                 Mota     0.580
    gendstat:      Cameroon_SMA.SG         DevilsGate_N     0.419
    gendstat:      Cameroon_SMA.SG            Iberia_HG     0.733
    gendstat:      Cameroon_SMA.SG       Lebanon_MBA.SG     0.618
    gendstat:      Cameroon_SMA.SG Russia_Afanasievo.SG    -0.164
    gendstat:      Cameroon_SMA.SG        Rome_Imperial     0.080
    gendstat:      Cameroon_SMA.SG Greece_Logkas_MBA.SG    -0.170
    gendstat:      Cameroon_SMA.SG       Iberomaurusian     0.285
    gendstat:      Cameroon_SMA.SG                 PPNB     0.438
    gendstat:        Anatolia_N.SG Iran_TepeAbdulHosein_N.SG    -0.705
    gendstat:        Anatolia_N.SG                  CHG    -0.197
    gendstat:        Anatolia_N.SG                 Mota    -0.140
    gendstat:        Anatolia_N.SG         DevilsGate_N    -0.345
    gendstat:        Anatolia_N.SG            Iberia_HG     0.087
    gendstat:        Anatolia_N.SG       Lebanon_MBA.SG    -0.182
    gendstat:        Anatolia_N.SG Russia_Afanasievo.SG    -1.088
    gendstat:        Anatolia_N.SG        Rome_Imperial    -1.118
    gendstat:        Anatolia_N.SG Greece_Logkas_MBA.SG    -1.142
    gendstat:        Anatolia_N.SG       Iberomaurusian    -0.511
    gendstat:        Anatolia_N.SG                 PPNB    -0.337
    gendstat: Iran_TepeAbdulHosein_N.SG                  CHG     0.515
    gendstat: Iran_TepeAbdulHosein_N.SG                 Mota     0.395
    gendstat: Iran_TepeAbdulHosein_N.SG         DevilsGate_N     0.354
    gendstat: Iran_TepeAbdulHosein_N.SG            Iberia_HG     0.747
    gendstat: Iran_TepeAbdulHosein_N.SG       Lebanon_MBA.SG     0.654
    gendstat: Iran_TepeAbdulHosein_N.SG Russia_Afanasievo.SG    -0.319
    gendstat: Iran_TepeAbdulHosein_N.SG        Rome_Imperial    -0.051
    gendstat: Iran_TepeAbdulHosein_N.SG Greece_Logkas_MBA.SG    -0.333
    gendstat: Iran_TepeAbdulHosein_N.SG       Iberomaurusian     0.179
    gendstat: Iran_TepeAbdulHosein_N.SG                 PPNB     0.410
    gendstat:                  CHG                 Mota     0.016
    gendstat:                  CHG         DevilsGate_N    -0.136
    gendstat:                  CHG            Iberia_HG     0.266
    gendstat:                  CHG       Lebanon_MBA.SG     0.062
    gendstat:                  CHG Russia_Afanasievo.SG    -0.844
    gendstat:                  CHG        Rome_Imperial    -0.666
    gendstat:                  CHG Greece_Logkas_MBA.SG    -0.801
    gendstat:                  CHG       Iberomaurusian    -0.282
    gendstat:                  CHG                 PPNB    -0.097
    gendstat:                 Mota         DevilsGate_N    -0.130
    gendstat:                 Mota            Iberia_HG     0.199
    gendstat:                 Mota       Lebanon_MBA.SG     0.029
    gendstat:                 Mota Russia_Afanasievo.SG    -0.664
    gendstat:                 Mota        Rome_Imperial    -0.496
    gendstat:                 Mota Greece_Logkas_MBA.SG    -0.635
    gendstat:                 Mota       Iberomaurusian    -0.277
    gendstat:                 Mota                 PPNB    -0.095
    gendstat:         DevilsGate_N            Iberia_HG     0.414
    gendstat:         DevilsGate_N       Lebanon_MBA.SG     0.225
    gendstat:         DevilsGate_N Russia_Afanasievo.SG    -0.661
    gendstat:         DevilsGate_N        Rome_Imperial    -0.487
    gendstat:         DevilsGate_N Greece_Logkas_MBA.SG    -0.664
    gendstat:         DevilsGate_N       Iberomaurusian    -0.159
    gendstat:         DevilsGate_N                 PPNB     0.045
    gendstat:            Iberia_HG       Lebanon_MBA.SG    -0.249
    gendstat:            Iberia_HG Russia_Afanasievo.SG    -1.078
    gendstat:            Iberia_HG        Rome_Imperial    -1.026
    gendstat:            Iberia_HG Greece_Logkas_MBA.SG    -1.101
    gendstat:            Iberia_HG       Iberomaurusian    -0.565
    gendstat:            Iberia_HG                 PPNB    -0.388
    gendstat:       Lebanon_MBA.SG Russia_Afanasievo.SG    -1.034
    gendstat:       Lebanon_MBA.SG        Rome_Imperial    -1.131
    gendstat:       Lebanon_MBA.SG Greece_Logkas_MBA.SG    -1.052
    gendstat:       Lebanon_MBA.SG       Iberomaurusian    -0.407
    gendstat:       Lebanon_MBA.SG                 PPNB    -0.186
    gendstat: Russia_Afanasievo.SG        Rome_Imperial     0.393
    gendstat: Russia_Afanasievo.SG Greece_Logkas_MBA.SG    -0.014
    gendstat: Russia_Afanasievo.SG       Iberomaurusian     0.490
    gendstat: Russia_Afanasievo.SG                 PPNB     0.733
    gendstat:        Rome_Imperial Greece_Logkas_MBA.SG    -0.408
    gendstat:        Rome_Imperial       Iberomaurusian     0.275
    gendstat:        Rome_Imperial                 PPNB     0.658
    gendstat: Greece_Logkas_MBA.SG       Iberomaurusian     0.497
    gendstat: Greece_Logkas_MBA.SG                 PPNB     0.763
    gendstat:       Iberomaurusian                 PPNB     0.212

  15. The Following 8 Users Say Thank You to Mnemonics For This Useful Post:

     Aben Aboo (11-27-2021),  altvred (11-27-2021),  Angoliga (11-27-2021),  drobbah (11-27-2021),  Megalophias (11-27-2021),  pegasus (11-27-2021),  Sabz (11-27-2021),  theplayer (11-27-2021)

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