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Thread: New K12 Ancient Calculator

  1. #1
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    New K12 Ancient Calculator

    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.


    Before I go on to describe the various components in this calculator I would like to mention that the results from this calculator take precedence over results from other calculators I have out there.


    My dataset for this calculator includes imputed diploid ancient genomes which were published in Martiniano et al, 2017 (http://journals.plos.org/plosgenetic...l.pgen.1006852).


    My dataset included genotype information for about 1.5 million SNPs, out of which I was able to extract a subset of markers with lower allele frequencies, which are more informative to direct associations between populations vs common alleles which are more informative to more general associations via common distant ancestors.


    The improvements over my previous K11 include:



    1. A higher number of overlapping alleles with commercial testing companies;
    2. A less ambiguous African component, which has been parsed into separate E and W African components. For example, W Asians score non-negligible amounts of this E African component, which represents diffusion of genetic material from E Africa into the Middle East over the past couple of thousand years via possibly the Horn of Africa, the Sinai, and the slave trade. In calculators based on modern references this cryptic E African gene flow is hidden inside the SW Asian component.
    3. A more robust Karasuk component, described in below. The Karasuk percentage should be interpreted as diffusion of DNA from Eastern Steppe populations post Bronze Age via Turkic expansions, Scythians, as well as more subtle diffusions via NE Caucasus populations.
    4. A SE Eurasian component that can be thought of as a hybrid ASI/SE Asian component.



    The references for the various components are as follows:



    1. Yamnaya-Afansievo: Yamnaya Samara, Yamnaya Kalmykia, Poltavka, and Afanasievo;
    2. Andronovo-Srubnaya: 3 Andronovo and 2 Srubnaya samples
    3. E-European Farmer: Neolithic genomes from Turkey, Greece, and other parts of SE Europe.
    4. W-European Farmer: Neolithic genomes from Portugal, and Chalcolithic genomes from Spain.
    5. SE Eurasian: Jarawa, S Indian tribals, Brunei tribals, and Burmese.
    6. Karasuk: 5 genomes from the Karasuk culture, supplemented with 2 IA Eastern Scythian samples.
    7. WHG-SHG: 8 genomes from continental Europe and Sweden.
    8. ENA; Papuans and Aboriginal Australians.
    9. IRAN-N/CHG: Includes Iran-N, and imputed Kotias and Satsurbila genomes.
    10. W African: Yoruba, Gambian, and Esan modern samples;
    11. E African: Masai, Luhya, and Hadza modern samples.
    12. Levant N/BA: The higher coverage 4 samples



    Some sample results in a couple of hours.
    Last edited by Kurd; 08-13-2017 at 12:30 AM.
    EurasianDNA.com - A study of the population history of West & South Asia.

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  3. #2
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    Some samples. More in a few minutes

    COMPONENT Kurd-Kurmanji-Iraq Kurd-Feyli-Iraq Zephyrous-Assyrian Jesus-SW Iranian Turkish Turkish Khana Punjabi-Rajput
    ID001 ID001 ID001 ID001 Kayseri-23271 Balikesir-16653 ID001 ID001
    FARMER 63.22% 64.99% 81.24% 63.72% 71.56% 59.81% 39.87% 33.65%
    E-European-Farmer 24.61% 33.68% 31.16% 22.38% 30.42% 22.79% 13.02% 11.86%
    W-European-Farmer 12.43% 3.16% 17.85% 13.18% 17.06% 17.35% 0.00% 0.18%
    Levant N/BA 10.97% 7.59% 12.32% 10.25% 6.73% 7.40% 9.13% 4.35%
    Iran N/CHG 15.21% 20.56% 19.91% 17.92% 17.35% 12.27% 17.72% 17.27%
    STEPPE 27.88% 24.98% 13.25% 17.67% 25.02% 30.18% 35.16% 29.74%
    Andronovo-Srubnaya 10.90% 8.86% 1.99% 5.56% 6.78% 0.00% 7.95% 9.15%
    Yamnaya-Poltavka-Afanasievo 5.65% 10.93% 7.50% 5.26% 8.56% 4.63% 12.34% 11.43%
    Karasuk 11.33% 5.18% 3.76% 6.85% 9.69% 25.54% 14.87% 9.16%
    WHG-SHG 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 0.00% 3.19%
    SE Eurasian 3.71% 6.25% 1.87% 8.13% 2.42% 5.78% 22.88% 27.14%
    AFRICAN 4.85% 3.36% 3.49% 8.82% 0.73% 3.92% 0.40% 2.79%

    E-African 4.85% 0.00% 3.48% 6.53% 0.73% 3.92% 0.40% 2.79%

    W-African 0.00% 3.36% 0.00% 2.29% 0.00% 0.00% 0.00% 0.00%
    ENA 0.34% 0.43% 0.16% 1.66% 0.28% 0.31% 1.69% 3.48%
    EurasianDNA.com - A study of the population history of West & South Asia.

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    COMPONENT Ruhka-Tajik/Pashtun Reza-Bengali Passa-N-Italian Helegenes-Normandy Copt 1- Egypt
    ID000 ID001 ID001 ID001 ID001
    FARMER 41.04% 18.52% 76.91% 57.73% 82.09%
    E-European-Farmer 18.10% 0.99% 32.42% 21.43% 34.01%
    W-European-Farmer 1.71% 1.67% 32.38% 25.20% 22.55%
    Levant N/BA 3.24% 3.11% 5.16% 7.55% 14.05%
    Iran N/CHG 17.99% 12.75% 6.96% 3.55% 11.47%
    STEPPE 39.91% 24.96% 21.11% 30.41% 0.00%
    Andronovo-Srubnaya 12.70% 2.94% 4.62% 10.82% 0.00%
    Yamnaya-Poltavka-Afanasievo 10.34% 7.65% 5.93% 10.38% 0.00%
    Karasuk 16.87% 14.37% 10.56% 9.20% 0.00%
    WHG-SHG 2.95% 4.06% 0.00% 11.86% 0.00%
    SE Eurasian 13.57% 48.16% 0.00% 0.00% 2.43%
    AFRICAN 1.11% 2.32% 1.42% 0.00% 15.48%

    E-African 0.00% 2.32% 0.00% 0.00% 15.48%

    W-African 1.11% 0.00% 1.42% 0.00% 0.00%
    ENA 1.42% 1.97% 0.56% 0.00% 0.00%
    EurasianDNA.com - A study of the population history of West & South Asia.

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    Can't wait to get my hands on it Kurd
    Paper trail ancestry to the best of my knowledge:
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  9. #5
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    279 of my direct ancestors recorded. 277 appear SE English. 2,400+ names in my kid's joint family tree.
    Hidden Content .

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    Egypt
    I had thought E-European farmer meant Eastern European farmer & I was confused, but I see its actually Neolithic farmer genomes from Anatolia/SE Europe & the result makes far more sense now.

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    Is this going to be on GEDMatch also or no?

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    When will it be available on geneplaza, thank you

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    Quote Originally Posted by Sikeliot View Post
    Is this going to be on GEDMatch also or no?
    No, unfortunately my algorithm is not compatible with-the DIYDodecad program.
    EurasianDNA.com - A study of the population history of West & South Asia.

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    Quote Originally Posted by jortita View Post
    When will it be available on geneplaza, thank you
    I'm hoping within a week...
    EurasianDNA.com - A study of the population history of West & South Asia.

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