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Thread: 1st Look at Damgaard et al 2018 C Asian Samples

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    Lightbulb 1st Look at Damgaard et al 2018 C Asian Samples

    It's great to have the recently sequenced samples from Damgaard et al and the Narasimhan et al 2018 to fill the void in our understanding of the demography of Eurasia. I will of course use the samples in an exhaustive analysis over the coming months to better our understanding of Eurasian population history. Everything from f3 and f4s for shared drift analyses on an individual level to using proprietary techniques I have developed for relatedness of the various aDNA samples to modern individuals will be performed over the coming months.

    To start out a PCA with some samples from both papers along with a few project members. I would have liked to include more pops and members on a single PCA but as you can see from the legend on the right they did not fit.

    A couple of general comments about PCAs.:

    1- PC1 - PC2 project maximum variation but not all variation. You would have to check PC3-PC4 and PC5-PC6 also for a more complete picture
    2- PCA gives general clustering of pops, however they should not be used to infer admixture from the various pops, or relatedness on an individual to a particular pop. For example, distance of a W Asian individual from a Scythian sample should not be used to infer Scythian geneflow into the W Asian individual, because other pops on the PCA such ENF are pulling that individual away from Scythians because W Asians have substantial ENF. If I were to remove ENF from the PCA, the W Asian individual would suddenly move much closer to the Scythian.

    Some interesting observations:

    1- E Eurasian admixture in the various Scythian samples varies quite a bit, see for ex placement of various Tien Shan or E Scythians (prior study).
    2- Hungarian Scythians appear to have substantial ENF based on the pull in that direction
    3- Ottoman samples unexpectedly higher E Eurasian admixture
    4- Affinity between Botai and Siberian-HG vs Okunevo


    Feel free to post any interesting observations you see. Other analyses results to be posted tonight.


    [IMG][/IMG]
    EurasianDNA.com - A study of the population history of West & South Asia.

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    Members: Jesus & Dluffy are on the PCA but their tags didn't fit.
    EurasianDNA.com - A study of the population history of West & South Asia.

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    It seems that Andronovo is very close to Scythians Sarmatians and Hajji_Firuz_BA is close to Kumyks.

    Also it is interesting to see that Hajji_Firuz_BA is closer to some steppe populations than it is to Hajji_Firuz_C on this plot.

    Kurd, I am really curious where modern European populations would be plotted e.g. Orcadians, Lithuanians, Sardinians etc.
    Last edited by michal3141; 05-11-2018 at 05:10 PM.
    For K25 and other calculators by me you can send me you raw data to my email: Hidden Content

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    Also notice the very close placement of Iran-Chl to Turan, indicating that Chalcolithic W Iranian farmers are substantially ancestral to Turan and BMAC populations

    EHG appears to be on a WHG-Siberian-HG/ MA-1 cline (the blue dot is MA1, didnt have space to put a separate label) but closer to MA1 than WHG
    EurasianDNA.com - A study of the population history of West & South Asia.

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    Quote Originally Posted by michal3141 View Post
    It seems that Andronovo is very close to Scythians Sarmatians and Hajji_Firuz_BA is close to Kumyks.

    Also it is interesting to see that Hajji_Firuz_BA is closer to some steppe populations than it is to Hajji_Firuz_C on this plot.

    Kurd, I am really curious where modern European populations would be plotted e.g. Orcadians, Lithuanians, Sardinians etc.
    I can only fit so many labels, Ill do one later with Europeans and leave out project members. Europeans will for sure be included in subsequent analysis with rare alleles, ADMIXTURE, f3 f4, etc
    EurasianDNA.com - A study of the population history of West & South Asia.

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    Hi Kurd,
    If you plan on doing f3 and f4 on these new samples I take it that means you'll have converted them to eigenstrat format? If so could you share the samples so others can work on them too?
    PM me for d-stats. If I have the samples I will run them. Also, here is a collection of 14,000. Part 1: Hidden Content Part 2: Hidden Content Part 3: Hidden Content

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    Quote Originally Posted by Kurd View Post
    I can only fit so many labels, Ill do one later with Europeans and leave out project members. Europeans will for sure be included in subsequent analysis with rare alleles, ADMIXTURE, f3 f4, etc
    Perfect. This is what I was about to suggest. Just add 4-5 modern European populations instead of project members for the next plot please.
    Last edited by michal3141; 05-11-2018 at 05:50 PM.
    For K25 and other calculators by me you can send me you raw data to my email: Hidden Content

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    Does ottoman samples have YDNA?

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    Quote Originally Posted by michal3141 View Post
    It seems that Andronovo is very close to Scythians Sarmatians and Hajji_Firuz_BA is close to Kumyks.

    Also it is interesting to see that Hajji_Firuz_BA is closer to some steppe populations than it is to Hajji_Firuz_C on this plot.

    Kurd, I am really curious where modern European populations would be plotted e.g. Orcadians, Lithuanians, Sardinians etc.
    Better with Norwegians than Orcadians

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    Quote Originally Posted by Anabasis View Post
    Does ottoman samples have YDNA?
    I think Onur is on to something when he mentioned in another thread that these are likely Seljuk era samples rather than Ottoman (the DNA profile seems too eastern for Ottoman times).. As they are not carbon dated..

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