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Thread: New K12 Ancient Calculator

  1. #621
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    Quote Originally Posted by Nikiforov View Post
    Perhaps the ancient Finno-Ugrians and the Scythians were genetically related. As Kurd wrote earlier "The Finno-Ugric network has considerable Karasuk related flow".
    In a sense, but it is probably more complex than that. The Siberian admixture in Saami and relatedly in Finns is different from that of Russians. Scythians or Karasuk (or even Mongols but that is more dubious) may be a closer proxy for that admixture in Russians (and nearby Ugric peoples) but not so for Finns. See M. Myllylä's blog (terheninenmaa) and posts about rare allele sharing in Saami people. The blogger seems to maintain the Siberian admixture was in Finland when Saami and Finns, respectively, started moving in.

    I guess this means that Kurd's calculator cannot trace the eastern admixture in Finns as well as for Russians? :/

  2. #622
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    Quote Originally Posted by Pessipeikko View Post
    In a sense, but it is probably more complex than that. The Siberian admixture in Saami and relatedly in Finns is different from that of Russians. Scythians or Karasuk (or even Mongols but that is more dubious) may be a closer proxy for that admixture in Russians (and nearby Ugric peoples) but not so for Finns. See M. Myllylä's blog (terheninenmaa) and posts about rare allele sharing in Saami people. The blogger seems to maintain the Siberian admixture was in Finland when Saami and Finns, respectively, started moving in.

    I guess this means that Kurd's calculator cannot trace the eastern admixture in Finns as well as for Russians? :/
    Thanks Pessipeikko. An interesting and knowledgeable point.
    In any case, studies in recent years have shown that the Steppe proportion is high among the Finns. What do you think is the main source of it?
    Last edited by Nikiforov; Yesterday at 04:32 AM.

  3. #623
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    Quote Originally Posted by Kurd View Post
    The K12 Ancient Admixture Calculator


    After dozens of tests, I am getting ready to roll out a production K12 calculator to GenePlaza.com. I am pleased with this calculator and I believe it adequately describes genetic substructure in Eurasians, particularly those who are predominantly W Eurasian admixed. The reason it is more informative to predominantly W Eurasian admixed individuals is that most of the recovered ancient human remains have belonged to the W Eurasian clade. There are exceptions, such as the Bronze Age Karasuk remains, and the Eastern Scythian Iron Age skeletons, which I have also utilized to source allele frequencies for the “Karasuk” component, which represents gene flow into Eurasians from the eastern Eurasian steppe. There are of course a couple of E Eurasian - E/W Eurasian components based on moderns as well.
    Kurd, apologies in advance if you have answered this earlier in the thread but could you describe the differences between the steppe sub-components in more detail?

    What differentiated the steppe components from each other, and what was the ancestry common to all of them? Cheers

  4. #624
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    Quote Originally Posted by bmoney View Post
    Kurd, apologies in advance if you have answered this earlier in the thread but could you describe the differences between the steppe sub-components in more detail?

    What differentiated the steppe components from each other, and what was the ancestry common to all of them? Cheers
    Subtle differences in the grand scheme of things, especially between the Yamna and Andronovo comps. The W steppe 2 pops are in a broad sense Caucasus/Near Eastern/W Siberian(EHG) derived, along with some E Asian input into the Karasuk comp, thus the Indo-Europeans who contributed to both S & W Asia and Europe can arguably be defined as Caucasian-Near Eastern-W Siberian. The actual vectors for this geneflow varied based on geography and time.
    Last edited by Kurd; Yesterday at 12:17 PM. Reason: Emphasis added
    EurasianDNA.com - A study of the population history of West & South Asia.

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  6. #625
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    Quote Originally Posted by Pessipeikko View Post
    In a sense, but it is probably more complex than that. The Siberian admixture in Saami and relatedly in Finns is different from that of Russians. Scythians or Karasuk (or even Mongols but that is more dubious) may be a closer proxy for that admixture in Russians (and nearby Ugric peoples) but not so for Finns. See M. Myllylä's blog (terheninenmaa) and posts about rare allele sharing in Saami people. The blogger seems to maintain the Siberian admixture was in Finland when Saami and Finns, respectively, started moving in.

    I guess this means that Kurd's calculator cannot trace the eastern admixture in Finns as well as for Russians? :/
    Your interrogations are congruent with my own interrogations about my maternal grand-mother's mother. Shortly: my grand-mother is born in Belgium from a dutch frisian father. Her mother's father was a german frisian, but her mother's mother is unknown. The only thing we know about her ( after nearly two years of researches, including by professional genealogists in Belgium) is her mitochondrial haplogroup: K1c1c. This haplo is nearly absent elsewhere than in Finland and north-Russia. Furthermore, my father, one of his brothers, myself, a first cousin on this line, and some individuals more, have an unusually high number of finnish relatives. In addition, many of those relatives are rather close ( around 4 gen to MRCA), with long shared segments ( up to 15 cM). For example, each update of my own list of matches with ftdna provides me at least one new finnish. Last but not least, and supplementary reason why I post on this thread: the Karasuk amount of my father: 18.5%!
    When, two years ago or so ( long before Kurd's K12), when I and my paternal family reviewed the elements of the problem, there was no doubt for us about the fact that Finland was the craddle of this genealogic line, and we started to search. How many dozens of mails written, how many scenarios developed? Dont know. Results: nothing.
    We just had forgotten a very tiny thing ( or perhaps did'nt want to take it into account): the presence on the relatives' lists of Russians, with the same segments as the finnish, and closer than them. Important precision: those close russians are 100% erzya or mordovians with all the calculators.

    Now, it's time to autosomal genetics.
    First, with qpAdm. The reference spreadsheet is MinoenMycenean/Reich 2017 merged with some populations from Pagani/Estonian BioCenter ( Mordvins, Maris, Chuvashes, Chukchis, Nganasans, Forest and Tundra Nenets),and my father (23&me V4 imputed), around 1.000.000 snps. The reference model is one that gives a very good adjustment for him: scandinavian Battle-Axe and central Europe mid-neolithic ( Salzmünde, Esperstedt, Baalberge):

    left pops:
    dad
    Battle-Axe
    Europe_MNChL1

    right pops:
     
    Mota
    Ust_Ishim
    Kostenki14
    GoyetQ116-1
    Vestonice16
    MA1
    AfontovaGora3
    ElMiron
    Villabruna
    WHG
    EHG
    CHG
    Iran_N
    Natufian
    Levant_N
    Barcin
    Nganasans
    Chukchis



    best coefficients: 0.774 0.226

    chisq tail prob
    10.434 0.84298
    ************************************************** ********

    The question was: how will this model respond to the introduction of an uralic population? First, with Nenets:

    left pops:
    dad
    Battle-Axe
    Europe_MNChL1
    forest_nenets

    best coefficients: 0.734 0.247 0.019

    chisq tail prob
    10.008 0.819205

    ************************************************** *******
    left pops:
    dad
    Battle-Axe
    Europe_MNChL1
    tundra_nenets

    best coefficients: 0.731 0.249 0.020

    chisq tail prob
    9.995 0.820052
    ************************************************** **********
    Conclusion: the coefficient of the Nenets is too weak to be significant, and furthermore the tail_prob has decreased (2%). Now I'll try with Mordvins ( the closest to Erzya):


    left pops:
    dad
    Battle-Axe
    Europe_MNChL1
    Mordvins

    best coefficients: 0.566 0.246 0.188
    chisq tail prob
    9.438 0.85353
    ************************************************** ************
    The adjustment has increased ( 1%, it's not huge, but it is), and the coefficient of the Mordvins is indeed significant (18.8%)


    With Global10 and nMonte2.
    Spreadsheet:
     
    ,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10
    Nordic_LN:RISE97,0.0159,0.026,-0.002,-0.0373,-0.0074,0.0186,0.0237,-0.0055,-0.0046,-0.0019
    Nordic_LN:RISE98,0.0169,0.0237,0.0011,-0.0469,-0.0069,0.0189,0.0318,0.0007,-0.0041,-0.0004
    BattleAxe_Sweden:RISE94,0.0157,0.0231,0.0015,-0.0366,-0.0049,0.0074,0.0303,0.0063,0.0017,-0.003
    Nordic_LN:RISE71,0.0147,0.025,0,-0.0381,-0.0078,0.0162,0.0241,-0.0038,-0.0008,0.0012
    Megalithic:Ballynahatty,0.0164,0.0317,0.0017,-0.0011,-0.0019,0.0605,0.0063,-0.0078,-0.0183,0.006
    Salzmuende_MN:I0551,0.0172,0.0351,-0.0045,0.0005,0.0001,0.061,0.0047,0.0017,-0.0126,0.0005
    Baalberge_MN:I0559,0.0177,0.0351,-0.0033,-0.0033,-0.0051,0.0557,0.0043,-0.0056,-0.0155,0.0032
    Baalberge_MN:I0560,0.0179,0.0325,-0.001,-0.001,-0.0027,0.0531,0.0079,-0.0057,-0.0185,0.0016
    Esperstedt_MN:I0172,0.0176,0.0333,-0.0026,-0.0002,-0.0022,0.0595,0.0037,-0.0085,-0.0071,0.004
    Megalithic:I0405,0.0178,0.0312,0.0004,-0.0041,-0.0038,0.0614,0.0061,-0.0104,-0.0249,0.0056
    Megalithic:I0406,0.0174,0.0304,-0.0002,-0.0042,-0.0019,0.0543,0.0056,-0.0046,-0.0217,0.0065
    Megalithic:I0407,0.0171,0.0305,-0.002,-0.0034,-0.0032,0.0573,0.0113,-0.0095,-0.0202,0.0046
    Megalithic:I0408,0.0176,0.0325,0.0004,-0.0046,-0.0025,0.0615,0.0071,-0.0025,-0.0222,0.0054
    Mari,0.01624,-0.006,0.01446,-0.05524,-0.01444,0.00162,-0.0062,0.00352,-0.00454,-0.00272
    Mordovian,0.01868,0.01828,0.00508,-0.04602,-0.009,0.01386,0.02432,0,-0.00288,-0.0026
    Chuvash,0.01718,0.00148,0.01252,-0.04848,-0.01178,0.00508,0.00178,0.00252,-0.00224,-0.00328
    Nenets,0.01316,-0.04646,0.03056,-0.06832,-0.0255,-0.01658,-0.0677,0.01142,-0.00628,-0.00096
    Nenets_Forest,0.0139,-0.0459,0.0332,-0.0695,-0.0245,-0.0183,-0.0682,0.007,-0.0083,-0.0011
    Nganasan,0.01116,-0.06922,0.04114,-0.0641,-0.02772,-0.01596,-0.10372,0.01248,-0.00556,0.00258


    [1] "distance%=0.5516 / distance=0.005516"

    anglesqueville:dad
    "Nordic_LN:RISE97" 65.3
    "Esperstedt_MN:I0172" 13.35
    "Mordovian" 21.35

    Of course, as the methods are very different, one cannot expect to find the same results, but the percentages of nMonte are at least close with the coefficients of qpAdm, in particular for the Mordvins ( 18.8% vs 21.35%).

    For comparison the Finnish average gets this model:

    [1] "distance%=0.8569 / distance=0.008569"

    Finnish
    "Nordic_LN:RISE98" 90.75
    "Nenets_Forest" 6.8
    "Mari" 2.45

    I'm afraid that the finnish track was likely a wrong track for my g-g-mother. Afraid and sorry, because I like so much your country. But truth is truth. I likely have to remove the finnish flag under my avatar , as my unknown K1c1c ancestor was more likely a russian woman (mordovian,erzya, mari, perhaps even chuvach despite the fact that qpAdm and the D-stats give the best results with Mordvins). How did this girl land in Germany or the Netherlands in the XIXth or XVIIIth century? That is an enigma, and will remain so, because I am tired of genealogy.
    Last edited by anglesqueville; Yesterday at 03:36 PM.
    En North alom, de North venom
    En North fum naiz, en North manom

    (Roman de Rou, Wace, 1160-1170)

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