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Thread: Genetic analysis of the 34000 years old Salkhit Skull from Mongolia

  1. #31
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    The main argument was modern diversity, but ancient diversity has revealed other options besides SEAsia.
    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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  3. #32
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    J1c7a*

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    # Summary Statistics per sample
    # SampleName: Name of the sample as given by the user
    # TotalSites: Total number of sites in the given Snp file (before transition filtering)
    # NonMissingCalls: Total number of sites output with a non-Missing call (before transition filtering)
    # avgRawReads: mean coverage of raw pileup input data across total sites (incl. missing sites)
    # avgDamageCleanedReads: mean coverage of pileup after single-stranded damage removal
    # avgSampledFrom: mean coverage of pileup after removing reads with tri-allelic alleles
    SampleName TotalSites NonMissingCalls avgRawReads avgDamageCleanedReads avgSampledFrom
    Salkhit1 1233013 1082065 4.545784188812283 4.545784188812283 4.531609155783435
    https://www.mediafire.com/file/fzjyk...khit1.zip/file
    Both BED and Eigenstrat.

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  5. #33
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    Davidski posted these:
    Salkhit_scaled,0.021626,-0.158423,-0.027907,0.053618,0.015387,-0.018128,-0.00235,-0.009692,0.025361,0.009841,-0.001624,3e-04,0.005352,-0.002752,-0.002714,0.005834,0.008605,0.001014,0.00088,0.0186 34,0.008111,0.009892,-0.008874,-0.012291,0.004431

    Salkhit,0.0019,-0.0156,-0.0074,0.0166,0.005,-0.0065,-0.001,-0.0042,0.0124,0.0054,-0.001,0.0002,0.0036,-0.002,-0.002,0.0044,0.0066,0.0008,0.0007,0.0149,0.0065,0. 008,-0.0072,-0.0102,0.0037

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  7. #34
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    Our friend Salkhit is quite interesting...
    F4: Salkhit Tianyuan AR33K = z -3.07
    There's a unique connection with Tianyuan. First thought for qpadm then, Salkhit = Tianyuan + Yana... no go, not even close.
    Ran some f3 outgroup stats to get a general picture of what's going on...

    Turns out in general Salkhit isn't really interested in being part of the whole Tianyuan / AR33K group.
    F4: Mbuti.DG Salkhit AR33K AR(everybody later) ~= 0
    Unlike...
    F4: Mbuti.DG Tianyuan AR33K AR(everybody later) = z scores of -10 to -12

    It also turns out Salkhit is a lot closer to Near-Eastern populations than it 'should be'. The exemplar of that...
    F4: Iran_GanjDareh_N Yana_UP.SG Salkhit = z -0.49
    Which is odd given the I guess 'null' hypothesis that Salkhit is a pretty even split between Yana and Tianyuan because...
    F4: Iran_GanjDareh_N Yana_UP.SG Tianyuan / AR33K = both around z -5
    But interestingly...
    F4: Iran_GanjDareh_N Yana_UP.SG post-LGM-EastAsians = ~0

    So my proposition is that Salkhit represents a mixture of Yana and an early representative of the population who would later replace Tianyuan/AR33K types post-LGM throughout East Asia (with the caveat of perhaps having a small amount of Tianyuan-specific ancestry also).

    So with that in mind returning to qpadm...
    Yana_UP.SG: 43.7% +/- 3.4%
    AR13_10K (as an example post-LGM East Asian): 56.3% +/- 3.4%
    right = c('Mbuti.DG', 'ZlatyKun.SG', 'Ust_Ishim.DG', 'BachoKiro_IUP', 'Gravettian', 'Kostenki14', 'Sunghir.SG', 'GoyetQ116_1', 'MA1.SG', 'Iran_GanjDareh_N', 'CHG.SG', 'Onge.DG', 'AR33K')
    Tail prob: 0.21
    Putting Tianyuan in the right drops the tail to 0.02, I think that supports the caveat of Salkhit having at least some actual Tianyuan ancestry.
    Last edited by Kale; 06-24-2021 at 07:14 AM.
    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. #35
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    Quote Originally Posted by Kristiina View Post
    According to Derenko et al (https://journals.plos.org/plosone/ar...l.pone.0015214), the respective ages of different D subclades are the following (complete genome rate) + reference to the ancient sample record:
    D4b 28.44 ky (Neolithic Mongolia, Transbaikal and Yakutia, Neolithic Ust’Belaya), D3/D4b1* 23.88 ky (Belkachi Yakutia)
    D4j 16.21 ky/ D4j1 22.83 ky (Neolithic Mongolia, Baikal Eneolithic)
    D4c 21.62 ky (Ang’angxi culture Heilongjiang)
    D4m 20.45 ky (Neolithic Devil’s Gate Cave)
    D4g 20.35 ky/ D4g2 21.89 ky (Early Yangshao)
    D4e 20,28 ky (Baikal Eneolithic, Boisman Middle Neolithic), D2/D4e1* 15.37 ky (Neolithic Transbaikal, Saqqaq Paleo-Eskimo D2a1)
    D4h 20.06 ky (Neolithic Mongolia) (Anzick, 12707–12556 years BP, D4h3a!)
    D4k'o'p 18.75 ky (Boisman Middle Neolithic)
    D4l 16.17 ky (Boisman Middle Neolithic)
    D4f 13.93 ky
    D4i 10.61 ky (Qinghai Neolithic)
    D4a 10.5 ky
    D4q 8.79 ky
    D4n 5.66 ky

    It now occurred to me that the oldest D4 is Anzick! Moreover Saqqaq is D2a1. According to the Derenko paper, D4b is the oldest subclade. It has been detected among the northernmost populations. Ancient American data and the distribution of D4b indicate that D4 started expanding from a relatively northern location.
    D4a had recently been found in two of the ancient DNA samples from Guangxi in the paper "Maternal genetic history of southern East Asians over the past 12,000 years". Some of the downstream of D4a like D4a1 had been found in Yaoyi, Mongol, and Heishui_Mohe_EarlyMedieval. Lineages like D4a5 had also been found in the Zibo_Linzi_Houli site (Zhou) where D4a3 and D4a6 had been found in DaCaoZi (East Han) and DA43 Xiongnu (could possibly be a Han soldier as well). Unfortunately, the oldest D4a sample found was HL-M84 at the Zibo_Linzi_Houli site (Zhou), which was only 2950 years ago.

  10. #36
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    Quote Originally Posted by Norfern-Ostrobothnian View Post
    # Summary Statistics per sample
    # SampleName: Name of the sample as given by the user
    # TotalSites: Total number of sites in the given Snp file (before transition filtering)
    # NonMissingCalls: Total number of sites output with a non-Missing call (before transition filtering)
    # avgRawReads: mean coverage of raw pileup input data across total sites (incl. missing sites)
    # avgDamageCleanedReads: mean coverage of pileup after single-stranded damage removal
    # avgSampledFrom: mean coverage of pileup after removing reads with tri-allelic alleles
    SampleName TotalSites NonMissingCalls avgRawReads avgDamageCleanedReads avgSampledFrom
    Salkhit1 1233013 1082065 4.545784188812283 4.545784188812283 4.531609155783435
    https://www.mediafire.com/file/fzjyk...khit1.zip/file
    Both BED and Eigenstrat.
    Hmmm. Upon further examination I believe this version of Salkhit is heavily contaminated.
    F3 outgroup nmonte with columns...
    ,Anatolia_Barcin_N,Levant_N,Iran_GanjDareh_N,CHG.S G,Taforalt,ONG.SG,Tianyuan,Vanuatu_ancient,Primors kyKrai_Boisman_MN,Peru_Laramate_900BP,Karelia_HG,I ronGates_Meso1,Yamnaya_Samara,Ust_Ishim.DG

    This looks legit.
    "SongnenPlain_33KBP" 38.7
    "Yana_UP.SG" 16.55

    But contamination from a European.
    "Czech.DG" 14.7
    "Polish.DG" 5.7

    And someone from Southeast Asia (Indonesia, Phillipines? Don't have anyone from there in my dataset)
    "Cambodian.DG" 17.45
    "Kharia.DG" 6.9

    The fit for this model is quite tight also, no outlying columns at all.
    Last edited by Kale; 07-02-2021 at 06:06 AM.
    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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