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Thread: From East to West, who is more Yamna culture? G25

  1. #11
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    Quote Originally Posted by JMcB View Post
    Here are my runs:


    JMcB_scaled
    Pen 0.001
    1000 cycles
    500 batches

    Fit: 5.4936

    EEF: 50.6
    SHG: 21.6
    EHG: 18.8
    CHG: 8.6
    Iran_N: 0.4


    & Pen 0

    JMcB_scaled

    Fit 5.3433

    EEF: 50
    EHG: 25.6,
    SHG: 15.4
    CHG: 9
    Strange that it didn't work? Why there is no Yamna culture?

  2. #12
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    Quote Originally Posted by poi View Post
    Did you run this from the online freeform runner? If so, you are missing Yamna, which could mean that your "Step1" has "contains header"... if so, change to "no header" so that the tool can use the Yamna row.
    There you go, that’s the ticket! Thanks!

    JMcB_scaled (default)
    1000 cycles
    500 batches

    Fit: 4.0674

    EEF: 44
    Yamnaya_Samara: 39
    SHG: 17




    & Pen 0


    JMcB_scaled

    Fit:4.0217

    EEF: 45.2
    Yamnaya_Samara: 36
    SHG: 18.8
    Last edited by JMcB; 04-06-2019 at 07:38 PM.
    Paper Trail: 43.8% English, 29.7% Scottish, 12.5% Irish, 6.25% German, 6.25% Italian & 1.5% French. Or: 86% British Isles, 6.25% German, 6.25% Italian & 1.5% French.
    LDNA(c): 86.3% British Isles (48.6% English, 37.7% Scottish & Irish), 7.8% NW Germanic, 5.9% Europe South (Aegian 3.4%, Tuscany 1.3%, Sardinia 1.1%)
    BigY 700: I1-Z140 >I-F2642 >Y1966 >Y3649 >A13241 >Y3647 >A13248 (circa 620 AD) >A13242/YSEQ (circa 765 AD) >FT80854 (circa 1650 AD).

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  4. #13
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    Quote Originally Posted by AlexRus View Post
    Strange that it didn't work? Why there is no Yamna culture?

    See Poi’s comment and my results above
    Paper Trail: 43.8% English, 29.7% Scottish, 12.5% Irish, 6.25% German, 6.25% Italian & 1.5% French. Or: 86% British Isles, 6.25% German, 6.25% Italian & 1.5% French.
    LDNA(c): 86.3% British Isles (48.6% English, 37.7% Scottish & Irish), 7.8% NW Germanic, 5.9% Europe South (Aegian 3.4%, Tuscany 1.3%, Sardinia 1.1%)
    BigY 700: I1-Z140 >I-F2642 >Y1966 >Y3649 >A13241 >Y3647 >A13248 (circa 620 AD) >A13242/YSEQ (circa 765 AD) >FT80854 (circa 1650 AD).

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  6. #14
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    Quote Originally Posted by AlexRus View Post
    This topic became of interest to me after reading this article.
    http://xn--c1acc6aafa1c.xn--p1ai/?page_id=30338

    Conclusion - the gradient of Yamna culture decreases from the East of Europe to the West.
    For autosomal DNA, you can't really tell with that model.

    In different countries, steppe pastoralists interacted with farmers of different admixtures. Like in Poland, the GAC were already hunter gatherer admixed, but still farmers culturally. In other countries, the farmers were purer. In some parts hunter gatherers survived better too. That's why if you want to understand the Yamna or steppe contribution in the locals, then you need to create local models. Otherwise, you risk attributing the hunter gatherer admixture from farmers to Yamna.



    Like for example, if I'm not mistaken Bell Beakers are a mix of Yamna and GAC. So this should work for Northwestern Euros and maybe Northeastern Euros.


    For Southeastern Europe, the farmer ought to get replaced for someone local, who would be less hunter gatherer admixed.


    So it looks like autosomally the Yamna component is the highest in the Northwest. Y-DNA too, but that's another topic
    Last edited by Dorkymon; 04-06-2019 at 07:46 PM.

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  8. #15
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    Could you please run for me?

    ,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
    TG_scaled,0.117238,0.108662,0.003017,-0.016473,0.004308,-0.011713,0.004935,0.002308,-0.008181,0.00492,-0.000487,0.002997,0.004311,0.000413,-0.009365,0.013657,0.02021,0,-0.001383,0.003877,-0.010606,0.000742,0.001602,-0.001446,0.001676

    ,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
    TG,0.0103,0.0107,0.0008,-0.0051,0.0014,-0.0042,0.0021,0.001,-0.004,0.0027,-0.0003,0.002,0.0029,0.0003,-0.0069,0.0103,0.0155,0,-0.0011,0.0031,-0.0085,0.0006,0.0013,-0.0012,0.0014

    Thanks

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  10. #16
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    Quote Originally Posted by zuzu14 View Post
    Could you please run for me?

    ,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
    TG_scaled,0.117238,0.108662,0.003017,-0.016473,0.004308,-0.011713,0.004935,0.002308,-0.008181,0.00492,-0.000487,0.002997,0.004311,0.000413,-0.009365,0.013657,0.02021,0,-0.001383,0.003877,-0.010606,0.000742,0.001602,-0.001446,0.001676

    ,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
    TG,0.0103,0.0107,0.0008,-0.0051,0.0014,-0.0042,0.0021,0.001,-0.004,0.0027,-0.0003,0.002,0.0029,0.0003,-0.0069,0.0103,0.0155,0,-0.0011,0.0031,-0.0085,0.0006,0.0013,-0.0012,0.0014

    Thanks
    [1] "distance%=3.1885"

    TG_scaled

    EEF,46
    Yamnaya_Samara,30.6
    Iran_N,10.2
    Natufian,5.2
    CHG,4.2
    Nganassan,3.8

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  12. #17
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    My fit is awful, since there's no AASI or AA, but I get 0% Yamnaya on 0 penalty.

    Pen = 0.001

    "sample": "Test1:Kulin",
    "fit": 9.0467,
    "Iran_N": 30,
    "EEF": 15,
    "Nganassan": 15,
    "Natufian": 11.67,
    "Yamnaya_Samara": 8.33,
    "Yoruba": 7.5,
    "SHG": 6.67,
    "EHG": 5.83,
    "CHG": 0


    Pen = 0
    "sample": "Test1:Kulin",
    "fit": 8.5858,
    "Iran_N": 28.33,
    "EEF": 22.5,
    "EHG": 16.67,
    "Nganassan": 15.83,
    "Yoruba": 10.83,
    "Natufian": 5,
    "SHG": 0.83,
    "CHG": 0,
    "Yamnaya_Samara": 0


    Any run me with a better fit?

    ,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
    Kulin_scaled,0.042115,-0.106631,-0.128221,0.091086,-0.044008,0.055499,-0.00282,0.008307,0.037632,0.017495,-0.002598,0,0.004311,0.001651,-0.004343,-0.005038,-0.002608,0.00114,0.005154,-0.000875,-0.002995,0.001855,-0.003574,0.000361,0.002994

    ,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
    Kulin,0.0037,-0.0105,-0.034,0.0282,-0.0143,0.0199,-0.0012,0.0036,0.0184,0.0096,-0.0016,0,0.0029,0.0012,-0.0032,-0.0038,-0.002,0.0009,0.0041,-0.0007,-0.0024,0.0015,-0.0029,0.0003,0.0025
    Last edited by Kulin; 04-06-2019 at 08:13 PM.

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  14. #18
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    global 25 is not a calculator to model such kind of ancient ancestry. This was already discussed here various times. North East Euros were historically a small population and have specific drift. North West Europeans dont have more steppe ancestry than East Europeans
    Y-DNA: R1a> R-M417> R-Z645> R-Z93> R-Z94> R-Y3 (Sredny Stog)> R-L657> R-Y4 (Andronovo)> R-Y6> R-Y5> R-Y920* (Pashtun/Indo-Aryan)

    mtDNA: H28 (Globular Amphora, Bronze Age Latvia) > H28a (Ruthenian)

    mtDNA (Wife): H1b (found in Globular Amphora, EBA Poland, Bronze Age Latvia) > H1b5 (found in Viking-Age Gotland) > H1b5 (Russian)

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  16. #19
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    http://eurogenes.blogspot.com/2017/0...-invasion.html

    qpadm gives a better estimate and is not so much effected by genetic drift.
    Y-DNA: R1a> R-M417> R-Z645> R-Z93> R-Z94> R-Y3 (Sredny Stog)> R-L657> R-Y4 (Andronovo)> R-Y6> R-Y5> R-Y920* (Pashtun/Indo-Aryan)

    mtDNA: H28 (Globular Amphora, Bronze Age Latvia) > H28a (Ruthenian)

    mtDNA (Wife): H1b (found in Globular Amphora, EBA Poland, Bronze Age Latvia) > H1b5 (found in Viking-Age Gotland) > H1b5 (Russian)

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  18. #20
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    Quote Originally Posted by Dorkymon View Post
    For autosomal DNA, you can't really tell with that model.

    In different countries, steppe pastoralists interacted with farmers of different admixtures. Like in Poland, the GAC were already hunter gatherer admixed, but still farmers culturally. In other countries, the farmers were purer. In some parts hunter gatherers survived better too. That's why if you want to understand the Yamna or steppe contribution in the locals, then you need to create local models. Otherwise, you risk attributing the hunter gatherer admixture from farmers to Yamna.
    Like for example, if I'm not mistaken Bell Beakers are a mix of Yamna and GAC. So this should work for Northwestern Euros and maybe Northeastern Euros.
    Model Globular Amphora+Yamna culture is successful for the Irish. Since Globular Amphora collects a lot of EEF. This can be seen from the distance. For the Eastern Slavs it doesn't work. The Irish and the Eastern Slavs are not one region. So I suggested to use the pure ancient European components + Yamna culture. This is how we see that the Eastern Slavs and North-Western Europeans have almost equal amounts of Yamna culture.

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