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Thread: Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria[

  1. #511
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    Quote Originally Posted by Kale View Post
    Post-CI Europe a continuum between Goyet and Sunghir related pops?
    Kind of what I have been thinking.

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    The question then becomes, who's the mixture? Goyet or Kostenki?

    So alot has been said about the relationship between Goyet and BachoKiro & Tianyuan, but it's a bit more than that.
    1 Mbuti.DG ZlatyKun.SG GoyetQ116_1 Kostenki14 -1.10e-3 7.38e-4 -1.49 1.37e-1 711295
    2 Mbuti.~ ZlatyKun.SG GoyetQ1~ Sunghir.SG -1.27e-3 5.99e-4 -2.12 3.43e-2 740224
    3 Mbuti.~ ZlatyKun.SG GoyetQ1~ Gravettian -8.87e-4 5.94e-4 -1.49 1.36e-1 690182
    4 Mbuti.~ BachoKiro_IUP GoyetQ1~ Kosten~ -3.07e-3 6.01e-4 -5.11 3.23e-7 679471
    5 Mbuti.~ BachoKiro_IUP GoyetQ1~ Sunghi~ -2.48e-3 4.85e-4 -5.12 3.11e-7 706672
    6 Mbuti.~ BachoKiro_IUP GoyetQ1~ Gravet~ -2.20e-3 4.96e-4 -4.44 8.91e-6 666695
    7 Mbuti.~ Ust_Ishim.DG GoyetQ1~ Kosten~ -1.32e-3 7.15e-4 -1.85 6.42e-2 721087
    8 Mbuti.~ Ust_Ishim.DG GoyetQ1~ Sunghi~ -1.75e-3 5.91e-4 -2.97 3.02e-3 750277
    9 Mbuti.~ Ust_Ishim.DG GoyetQ1~ Gravet~ -1.56e-3 5.87e-4 -2.65 8.01e-3 698617
    10 Mbuti.~ Tianyuan_AR33K GoyetQ1~ Kosten~ -2.79e-3 6.24e-4 -4.46 8.08e-6 705483
    11 Mbuti.~ Tianyuan_AR3~ GoyetQ1~ Sunghi~ -2.31e-3 5.12e-4 -4.52 6.25e-6 732584
    12 Mbuti.~ Tianyuan_AR3~ GoyetQ1~ Gravet~ -2.05e-3 5.16e-4 -3.97 7.29e-5 691224
    13 Mbuti.~ Onge.DG GoyetQ1~ Kosten~ -1.25e-3 5.76e-4 -2.16 3.06e-2 722316
    14 Mbuti.~ Onge.DG GoyetQ1~ Sunghi~ -1.06e-3 4.87e-4 -2.17 2.97e-2 751546
    15 Mbuti.~ Onge.DG GoyetQ1~ Gravet~ -1.23e-3 4.98e-4 -2.47 1.37e-2 699823
    16 Mbuti.~ PrimorskyKrai_Boisman_MN GoyetQ1~ Kosten~ -1.63e-3 5.56e-4 -2.93 3.38e-3 710738
    17 Mbuti.~ PrimorskyKra~ GoyetQ1~ Sunghi~ -1.42e-3 4.52e-4 -3.15 1.63e-3 738344
    18 Mbuti.~ PrimorskyKra~ GoyetQ1~ Gravet~ -7.53e-4 4.72e-4 -1.59 1.11e-1 694063
    19 Mbuti.~ Yana_UP.SG GoyetQ1~ Kosten~ -1.07e-3 6.38e-4 -1.67 9.47e-2 722791
    20 Mbuti.~ Yana_UP.SG GoyetQ1~ Sunghi~ -1.37e-3 5.36e-4 -2.57 1.03e-2 752051
    21 Mbuti.~ Yana_UP.SG GoyetQ1~ Gravet~ -1.24e-3 5.49e-4 -2.27 2.33e-2 700309
    Now the ZlatyKun preference is not really significant, and you could say the East Eurasians are all mediated by BachoKiro, but what about Ust_Ishim? That's the one that's always stood out to me.

    Ust_Ishi~ ZlatyKun.~ GoyetQ11~ Kostenki14 1.71e-4 8.60e-4 0.199 0.842 721957
    Ust_Ishi~ ZlatyKun.~ GoyetQ11~ Sunghir.SG 5.02e-4 7.18e-4 0.698 0.485 751403
    Ust_Ishim~ ZlatyKun.SG GoyetQ11~ Gravettian 7.27e-4 7.53e-4 0.965 0.335 699932
    Ust_Ishi~ BachoKiro_IUP GoyetQ11~ Kosten~ -1.63e-3 7.86e-4 -2.08 0.0375 689384
    Ust_Ishi~ BachoKiro~ GoyetQ11~ Sunghi~ -6.10e-4 6.37e-4 -0.958 0.338 716974
    Ust_Ishim~ BachoKiro_~ GoyetQ11~ Gravett~ -5.61e-4 6.49e-4 -0.864 0.387 675989
    Ust_Ishi~ Tianyuan_~ GoyetQ11~ Kosten~ -1.47e-3 7.76e-4 -1.90 0.0577 715811
    Ust_Ishi~ Tianyuan_~ GoyetQ11~ Sunghi~ -5.33e-4 6.44e-4 -0.828 0.408 743269
    Ust_Ishim~ Tianyuan_AR33K GoyetQ11~ Gravett~ -4.17e-4 6.69e-4 -0.622 0.534 700963
    Ust_Ishi~ Onge.DG GoyetQ11~ Kosten~ 9.12e-5 7.18e-4 0.127 0.899 720626
    Ust_Ishi~ Onge.DG GoyetQ11~ Sunghi~ 7.02e-4 5.94e-4 1.18 0.237 749786
    Ust_Ishim~ Onge.DG GoyetQ11~ Gravett~ 3.36e-4 6.22e-4 0.540 0.589 698143
    Ust_Ishi~ Yana_UP.SG GoyetQ11~ Kosten~ 2.60e-4 7.85e-4 0.331 0.741 733840
    Ust_Ishi~ Yana_UP.SG GoyetQ11~ Sunghi~ 4.32e-4 6.61e-4 0.654 0.513 763659
    Ust_Ishim~ Yana_UP.SG GoyetQ11~ Gravett~ 3.34e-4 6.76e-4 0.493 0.622 710402
    'Control' for Ust_Ishim and the differences between Goyet and other paleo-Euros disappear.
    So what was the ol' term about populations who had less affinity to Ust_Ishim, basal was it?

    Now how about this for a doozy? Some qpadm...
    Sunghir.SG
    GoyetQ116_1: 55.4% +/- 6.53%
    Iran_GanjDareh_N: 44.6% +/- 6.53%
    Tail prob: 0.23
    right = c('Mbuti.DG', 'ZlatyKun.SG', 'Ust_Ishim.DG', 'BachoKiro_IUP', 'Onge.DG', 'Tianyuan_AR33K', 'PrimorskyKrai_Boisman_MN', 'Taforalt')

    Kostenki14
    GoyetQ116_1: 54.0% +/- 9.65%
    Iran_GanjDareh_N: 46.0% +/- 9.65%
    Tail prob: 0.03
    right = c('Mbuti.DG', 'ZlatyKun.SG', 'Ust_Ishim.DG', 'BachoKiro_IUP', 'Onge.DG', 'Tianyuan_AR33K', 'PrimorskyKrai_Boisman_MN', 'Taforalt')

    Gravettian
    GoyetQ116_1: 56.3% +/- 6.62%
    Iran_GanjDareh_N: 43.7% +/- 6.62%
    Tail prob: 0.46
    right = c('Mbuti.DG', 'ZlatyKun.SG', 'Ust_Ishim.DG', 'BachoKiro_IUP', 'Onge.DG', 'Tianyuan_AR33K', 'PrimorskyKrai_Boisman_MN')
    Didn't work with the same set of right pops as Sunghir/Kostenki, but dropping Taforalt fixed it considerably.
    I suspect Taforalt may have some Gravettian related ancestry as even in a more mundane model of Gravettians as BK1653 + Sunghir, adding Taforalt to the right breaks it.

    BK1653
    GoyetQ116_1: 57.7% +/- 8.43%
    Iran_GanjDareh_N: 41.0% +/- 8.39%
    Neanderthal_Altai.DG: 1.27% +/- 0.43%
    Tail prob: 0.23
    right = c('Mbuti.DG', 'ZlatyKun.SG', 'Ust_Ishim.DG', 'BachoKiro_IUP', 'Onge.DG', 'Tianyuan_AR33K', 'PrimorskyKrai_Boisman_MN', 'Denisova.DG')

    I'm guessing Goyet is a holdout, and if we find a hundred more Goyets and/or samples from pre-CI eruption Europe, not one will be y-hg IJ or mt-U (caveat... unless Goyet is not the baseline, e.g. we find something more extreme)
    That is what this Iran_N is representing here, the post-CI migration into Europe. Mark my words until the next curveball comes out and breaks it, where are you Dzudzuana!
    Last edited by Kale; 06-18-2021 at 07:51 AM.
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  4. #513
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    Quote Originally Posted by Kale View Post
    Mark my words until the next curveball comes out and breaks it, where are you Dzudzuana!
    Us, who like the old fogeys, have learned to live with shattered pet theories the hard way.

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    It's more fun when a pet theory is wrong, if you are right... now what? If you are wrong, you get to have fun crafting another pet! What's more fun, a fat old lazy dog or a brand new puppy?
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  7. #515
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    Quote Originally Posted by Kale View Post
    It's more fun when a pet theory is wrong, if you are right... now what? If you are wrong, you get to have fun crafting another pet! What's more fun, a fat old lazy dog or a brand new puppy?
    What is your full pet theory regarding these populations, which side of the Eurasian split they are on and what lineages are associated with them?

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    I guess this...
    1) Goyet is a thing, probably a mix of Ust-Ishim and BachoKiro.
    2) Iran_N (minus the ANE) was probably the general Near-Eastern population around 40kbp
    3) Kostenki/Sunghir a mix of Goyet and post-CI migrants from Near East (y-hg IJ, mt-U, the mt-pre-N1b in Burankaya also)
    4) The Near-Eastern population is probably a mix of 'basal' and an Onge-like population (whether that happens before or after the migration into Europe idk)
    5) That specific Onge-like pop mixes with Tianyuan to form East Asians
    6) ANE is a mixture of paleo-Euros and that same Onge-like pop
    7) Yana is ANE plus some bidirectional flow with Salkhit
    8) Taforalt is ANA + something probably related to the Goyet-input into Gravettians, rather than Anatolian_HG.
    9) Anatolia_HG = Iran_N-like + WHG + small amount of Taforalt
    10) CHG = intermediate between Iran-N + Anatolia_HG + a bit of ANE/EHG
    11) WHG = Gravettian baseline with various amounts of Goyet, ANE, and para-CHG ancestry

    Supporting stats for 4,5,6
     

    Mbuti.DG Iran_GanjDareh_N Tianyuan_AR33K Ust_Ishim.DG -9.25e-4 4.64e-4 -1.99 0.0462 9.66e5
    Mbuti.~ Iran_Ganj~ Ust_Ishi~ Onge.DG 1.28e-3 4.58e-4 2.80 0.00511 1.03e6
    Iran is a bit East Eurasian, we knew that...

    Mbuti.~ Iran_Ganj~ Tianyuan~ Onge.DG 4.65e-4 3.74e-4 1.24 0.214 9.67e5
    Not leaning any particular way along the two major branches...

    Mbuti.DG Iran_GanjDareh_N Tianyuan_AR33K Japan_Jomon 2.10e-3 3.86e-4 5.45 5.08e- 8 885120
    Mbuti.~ Iran_Ganj~ Tianyua~ PrimorskyKrai_Boisman_MN 2.00e-3 3.25e-4 6.15 7.82e-10 936630
    Mbuti.~ Iran_Ganj~ Onge.DG Japan_Jomon 1.61e-3 3.72e-4 4.34 1.42e- 5 913328
    Mbuti.~ Iran_Ganj~ Onge.DG PrimorskyKr~ 1.64e-3 3.21e-4 5.09 3.54e- 7 980455
    But very East Asian proper.

    Same things to a slightly lesser degree (the z stats are lower because of lower snp count but the d-value (first number) is quite close)
    Mbuti.~ MA1.SG Tianyua~ Japan_Jomon 1.66e-3 5.72e-4 2.90 3.70e-3 647952
    Mbuti.~ MA1.SG Tianyua~ PrimorskyKr~ 1.67e-3 4.83e-4 3.45 5.66e-4 686893
    Mbuti.~ MA1.SG Tianyua~ Onge.DG 4.53e-4 5.59e-4 0.810 4.18e-1 715224
    Mbuti.~ MA1.SG Onge.DG Japan_Jomon 1.36e-3 5.49e-4 2.48 1.32e-2 670639
    Mbuti.~ MA1.SG Onge.DG PrimorskyKr~ 1.33e-3 4.59e-4 2.90 3.73e-3 723875
    Mbuti.~ MA1.SG Onge.DG Tianyuan_AR~ -4.53e-4 5.59e-4 -0.810 4.18e-1 715224


    Supporting stats for 8
     

    1 Mbuti.DG Taforalt GoyetQ116_1 Bichon~ 1.05e-4 4.93e-4 0.212 8.32e-1 746807
    2 Mbuti.~ Taforalt GoyetQ~ Sunghir.SG -1.42e-3 4.02e-4 -3.53 4.18e-4 747760
    3 Mbuti.~ Taforalt Gravetian Bichon~ -2.91e-4 3.75e-4 -0.776 4.38e-1 906683
    4 Mbuti.~ Taforalt Gravet~ Sunghi~ -1.76e-3 2.90e-4 -6.05 1.49e-9 908036
    5 Mbuti.~ Anatolia_Epipaleolithic GoyetQ~ Bichon~ 3.86e-3 6.97e-4 5.54 3.07e-8 618889
    6 Mbuti.~ Anatolia_Epi~ GoyetQ~ Sunghi~ -5.42e-4 5.81e-4 -0.932 3.51e-1 619540
    7 Mbuti.~ Anatolia_Epi~ Gravet~ Bichon~ 3.38e-3 5.54e-4 6.09 1.12e-9 733904
    8 Mbuti.~ Anatolia_Epi~ Gravet~ Sunghi~ -1.08e-3 4.17e-4 -2.59 9.50e-3 734772


    Supporting qpadm for 11
     

    Gravettian ElMiron Steppe_Piedmont_Eneolithic Tail
    Bichon.SG 41.2 +/- 4.87 26.0 +/- 5.48 32.8 +/- 2.79 0.53
    Italy_GrottaContinenza_Meso.SG 45.4 +/- 4.11 24.1 +/- 4.76 30.5 +/- 2.31 0.16
    LaBrana_HG 25.5 +/- 4.39 51.8 +/- 5.23 22.7 +/- 2.62 0.13
    right = c('Mbuti.DG', 'ZlatyKun.SG', 'Ust_Ishim.DG', 'BachoKiro_IUP', 'Kostenki14', 'Sunghir.SG', 'GoyetQ116_1', 'Yana_UP.SG', 'MA1.SG', 'Iran_GanjDareh_N', 'CHG.SG', 'Onge.DG', 'Tianyuan_AR33K', 'PrimorskyKrai_Boisman_MN')

    Latvia_HG 18.7 +/- 2.85 22.7 +/- 2.98 25.1 +/- 3.06 (plus Karelia_HG 33.5 +/- 4.03) 0.17
    Last edited by Kale; 06-18-2021 at 07:38 PM.
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    Quote Originally Posted by Kale View Post
    I guess this...
    1) Goyet is a thing, probably a mix of Ust-Ishim and BachoKiro.
    2) Iran_N (minus the ANE) was probably the general Near-Eastern population around 40kbp
    3) Kostenki/Sunghir a mix of Goyet and post-CI migrants from Near East (y-hg IJ, mt-U, the mt-pre-N1b in Burankaya also)
    4) The Near-Eastern population is probably a mix of 'basal' and an Onge-like population (whether that happens before or after the migration into Europe idk)
    5) That specific Onge-like pop mixes with Tianyuan to form East Asians
    6) ANE is a mixture of paleo-Euros and that same Onge-like pop
    7) Yana is ANE plus some bidirectional flow with Salkhit
    8) Taforalt is ANA + something probably related to the Goyet-input into Gravettians, rather than Anatolian_HG.
    9) Anatolia_HG = Iran_N-like + WHG + small amount of Taforalt
    10) CHG = intermediate between Iran-N + Anatolia_HG + a bit of ANE/EHG
    11) WHG = Gravettian baseline with various amounts of Goyet, ANE, and para-CHG ancestry

    Supporting stats for 4,5,6
     

    Mbuti.DG Iran_GanjDareh_N Tianyuan_AR33K Ust_Ishim.DG -9.25e-4 4.64e-4 -1.99 0.0462 9.66e5
    Mbuti.~ Iran_Ganj~ Ust_Ishi~ Onge.DG 1.28e-3 4.58e-4 2.80 0.00511 1.03e6
    Iran is a bit East Eurasian, we knew that...

    Mbuti.~ Iran_Ganj~ Tianyuan~ Onge.DG 4.65e-4 3.74e-4 1.24 0.214 9.67e5
    Not leaning any particular way along the two major branches...

    Mbuti.DG Iran_GanjDareh_N Tianyuan_AR33K Japan_Jomon 2.10e-3 3.86e-4 5.45 5.08e- 8 885120
    Mbuti.~ Iran_Ganj~ Tianyua~ PrimorskyKrai_Boisman_MN 2.00e-3 3.25e-4 6.15 7.82e-10 936630
    Mbuti.~ Iran_Ganj~ Onge.DG Japan_Jomon 1.61e-3 3.72e-4 4.34 1.42e- 5 913328
    Mbuti.~ Iran_Ganj~ Onge.DG PrimorskyKr~ 1.64e-3 3.21e-4 5.09 3.54e- 7 980455
    But very East Asian proper.

    Same things to a slightly lesser degree (the z stats are lower because of lower snp count but the d-value (first number) is quite close)
    Mbuti.~ MA1.SG Tianyua~ Japan_Jomon 1.66e-3 5.72e-4 2.90 3.70e-3 647952
    Mbuti.~ MA1.SG Tianyua~ PrimorskyKr~ 1.67e-3 4.83e-4 3.45 5.66e-4 686893
    Mbuti.~ MA1.SG Tianyua~ Onge.DG 4.53e-4 5.59e-4 0.810 4.18e-1 715224
    Mbuti.~ MA1.SG Onge.DG Japan_Jomon 1.36e-3 5.49e-4 2.48 1.32e-2 670639
    Mbuti.~ MA1.SG Onge.DG PrimorskyKr~ 1.33e-3 4.59e-4 2.90 3.73e-3 723875
    Mbuti.~ MA1.SG Onge.DG Tianyuan_AR~ -4.53e-4 5.59e-4 -0.810 4.18e-1 715224


    Supporting stats for 8
     

    1 Mbuti.DG Taforalt GoyetQ116_1 Bichon~ 1.05e-4 4.93e-4 0.212 8.32e-1 746807
    2 Mbuti.~ Taforalt GoyetQ~ Sunghir.SG -1.42e-3 4.02e-4 -3.53 4.18e-4 747760
    3 Mbuti.~ Taforalt Gravetian Bichon~ -2.91e-4 3.75e-4 -0.776 4.38e-1 906683
    4 Mbuti.~ Taforalt Gravet~ Sunghi~ -1.76e-3 2.90e-4 -6.05 1.49e-9 908036
    5 Mbuti.~ Anatolia_Epipaleolithic GoyetQ~ Bichon~ 3.86e-3 6.97e-4 5.54 3.07e-8 618889
    6 Mbuti.~ Anatolia_Epi~ GoyetQ~ Sunghi~ -5.42e-4 5.81e-4 -0.932 3.51e-1 619540
    7 Mbuti.~ Anatolia_Epi~ Gravet~ Bichon~ 3.38e-3 5.54e-4 6.09 1.12e-9 733904
    8 Mbuti.~ Anatolia_Epi~ Gravet~ Sunghi~ -1.08e-3 4.17e-4 -2.59 9.50e-3 734772
    Excellent resumèè. Two things I would be curious/ cautious
    Near east population around 40kbp will turn out to be mostly basal with only a tad west eurasian. early west eurasian could be a migration from north africa IMHO
    I would be cautious to rule out the presence of IJ already in the Goyet cluster.
    Also I think Anatolia HG will turn out to be made of the same component of Taforalt ( obviously without ANA)
    Last edited by etrusco; 06-18-2021 at 07:24 PM.

  11. #518
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    In that setup there's not really a distinction between 'West' and 'Basal'.
    Regarding IJ and Goyet, sometimes you have to take a bold stance to get your point across , sure Goyet might not be the terminal end of that cline and could have some post-CI Near Eastern ancestry.
    Taforalt as part Anatolian_HG does work in qpgraph/qpadm but's it's such a delicate balance. It has to underfit Taforalt to Goyet & Gravettian almost to the point of significance and overfit Taforalt to WHG almost to the point of significance. I'm more inclined to go with a paleo-Euro source. The clincher will be if we find mt-M1 in paleolithic Europe, unfortunately we have U6 in both paleolithic Europe and Dzudzuana so that doesn't help discern things.
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    I’m guessing Salkhit is a mixture of Paleo-Euros and Tianyuan, and Tianyuan is Ust-Ishim+Bacho Kiro IUP. So ANE is more or less Paleo-Euro + Tianyuan (Bacho Kiro IUP + Ust-Ishim) + Onge-like? Also is there ANA in ANF due to the Taforalt in AHG?

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    Quote Originally Posted by Jack Johnson View Post
    I’m guessing Salkhit is a mixture of Paleo-Euros and Tianyuan, and Tianyuan is Ust-Ishim+Bacho Kiro IUP. So ANE is more or less Paleo-Euro + Tianyuan (Bacho Kiro IUP + Ust-Ishim) + Onge-like? Also is there ANA in ANF due to the Taforalt in AHG?
    I am not sure if Onge's or Onge like populations are needed for anything but AASI, they seem to just be a bit older branch of Eastern non-African.
    Onge-Amur-Australia.png
    PCA with ANE and West Eurasians.png

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