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Thread: Deep Ancestry using qpAdm

  1. #11
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    I don't understand the population selection, here. Particularly the use of Chechens and Saudis.

    Why are you choosing admixed modern populations, which we can be abundantly certain didn't contribute to modern Iranians in any significant shape or form, when we have aDNA from West Asia in the form of Kotias and the Anatolian farmers?

    I can understand using modern surrogates as Davidski did for the West Asian-related ancestry in Pashtuns through Georgians in his old qpAdm runs to better furnish the match-ups, but this doesn't make much sense at all. It's no wonder the fits don't look particularly robust!

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  3. #12
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    Quote Originally Posted by DMXX View Post
    I don't understand the population selection, here. Particularly the use of Chechens and Saudis.
    I thought I had clearly explained this in my opening post here
    I have purposely kept the left pops and right pops the same for all members, so that the fixed path values (100% modeling) between the various members can be kept comparable. Although some members may not have gotten good fits, their fixed path values are nonetheless informative, and I may attempt a qpAdm based PCA and dendogram, as I believed I have figured out a way to do that


    I guess it wasn't clear enough. The goal here is not to obtain excellent fits for everyone, as that would take a very long time, certainly more time than I have to spare. Some were lucky and got excellent fits, with others, I spent a few hours trying to improve their fits but was not able to do so. It then struck me that I could take the fixed path results for everyone, and take a jab at creating probably the 1st PCA and dendogram ever based on the fixed paths (100% modeling) for everyone. To do so, the fixed paths for everyone would have to be directly comparable, meaning I would have to use the same set of pops for everyone.

    Whereas the fits for some are poor and uninformative, the fixed paths by contrast are informative in that they are a direct comparison of a member to a fixed set of genomes. Thus I can use the fixed path values as dimensions on a 5 dimensional PCA to see where everyone clusters, on a more 'ancestral' basis if you will. I will be able to plot this innovative qpAdm fixed path based PCA and dendogram in a couple of weeks once I have completed the majority of members.

    EDIT: After this project I may start something using ancients only (including the Fu et al genomes in my dataset)

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  5. #13
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    Quote Originally Posted by Kurd View Post
    Yes, and affinity seems to be there even with formal methods such as these that dig deeper in time. After all Saudi ancestors in general are probably a very likely admixing pop for Iranians
    Cool, so what about Pashtuns and the Indian, north euro and other admixture in them, Kurds don't have that in the same scale but we still get modeled fine with a mordern kurdish sample, help me understand that anomaly please, also regarding the ancestor: which ofc has to do with the haplo groups! If you model kandahari with some selected modern Indian pop from North (west) India or Iran instead of a Kurdish one do you think that will form a good fit?
    Last edited by surbakhunWeesste; 05-19-2016 at 09:29 PM.

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    Quote Originally Posted by surbakhunWeesste View Post
    Cool, so what about Pashtuns and the Indian, north euro and other admixture in them, Kurds don't have that in the same scale but we still get modeled fine with a mordern kurdish sample, help me understand that anomaly please, also regarding the ancestor: which ofc has to do with the haplo groups! If you model kandahari with some selected modern Indian pop from North (west) India or Iran instead of a Kurdish one do you think that will form a good fit?
    Contrary to what a couple of members have been advocating, I don't believe the fits will be nearly as good, but the proof will be in the result. Pick 2 NW Indian members or pops, and I will do it for you tonight. In other words, I will keep everything the same as your best run, except switch kurd with the 2 samples of your choice, and will post under the pashto thread tonight

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  9. #15
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    Quote Originally Posted by Kurd View Post
    Contrary to what a couple of members have been advocating, I don't believe the fits will be nearly as good, but the proof will be in the result. Pick 2 NW Indian members or pops, and I will do it for you tonight. In other words, I will keep everything the same as your best run, except switch kurd with the 2 samples of your choice, and will post under the pashto thread tonight
    Tashakur, my picks are:
    Humza
    Monkey d luffy
    Varun

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  11. #16
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    Quote Originally Posted by Kurd View Post
    I thought I had clearly explained this in my opening post here

    I guess it wasn't clear enough. The goal here is not to obtain excellent fits for everyone, as that would take a very long time, certainly more time than I have to spare. Some were lucky and got excellent fits, with others, I spent a few hours trying to improve their fits but was not able to do so. It then struck me that I could take the fixed path results for everyone, and take a jab at creating probably the 1st PCA and dendogram ever based on the fixed paths (100% modeling) for everyone. To do so, the fixed paths for everyone would have to be directly comparable, meaning I would have to use the same set of pops for everyone.

    Whereas the fits for some are poor and uninformative, the fixed paths by contrast are informative in that they are a direct comparison of a member to a fixed set of genomes. Thus I can use the fixed path values as dimensions on a 5 dimensional PCA to see where everyone clusters, on a more 'ancestral' basis if you will. I will be able to plot this innovative qpAdm fixed path based PCA and dendogram in a couple of weeks once I have completed the majority of members.

    EDIT: After this project I may start something using ancients only (including the Fu et al genomes in my dataset)
    Ah, so "everyone" referred to both Iranians and non-Iranians alike... That appears to be the source of the misunderstanding, as (in combination with the title) it gave the impression that you were modelling Iranians using "ideal" left-groups rather than the generic roster preserved from your earlier experimentation.

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  13. #17
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    Quote Originally Posted by surbakhunWeesste View Post
    Tashakur, my picks are:
    Humza
    Monkey d luffy
    Varun
    Might I suggest Jam (who is like my father) instead of myself, as he is less mixed? Considering Balq is my grandmother, using me, might skew things? But Jam and I are usually similar, so it may make no difference. Either way, I'll defer to your collective judgements.
    Last edited by khanabadoshi; 05-20-2016 at 01:34 AM.
    “Chahar chez est tohfay Multan, Gard-o- Garma, Gada-o- Goristan”.

    Four things are the gift of Multan: Dusty winds, hot seasons, beggars and graveyards.




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  15. #18
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    Quote Originally Posted by khanabadoshi View Post
    Might I suggest Jam (who is like my father) instead of myself, as he is less mixed? Considering Balq is my grandmother, using me, might skew things? But Jam and I are usually similar, so it may make no difference. Either way, I'll defer to your collective judgements.
    Ok unless surbakhun indicates otherwise will go with Jam as per your suggestion

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  17. #19
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    If Kurdwrora has time, I'd ask him to model K. against every possible data. I picked humza because he is a melting pot, monkey because he clearly has some central Asian stuff goin on and Varun because he is a South and an North Indian mix! This should help me understand certain pattern of the algorithmic functions that the program uses. That's all thanks.

    Ps: he should use jam, balqis and you
    Last edited by surbakhunWeesste; 05-20-2016 at 02:17 AM.

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    Quote Originally Posted by surbakhunWeesste View Post
    If Kurdwrora has time, I'd ask him to model K. against every possible data. I picked humza because he is a melting pot, monkey because he clearly has some central Asian stuff goin on and Varun because he is a South and an North Indian mix! This should help me understand certain pattern of the algorithmic functions that the program uses. That's all thanks.

    Ps: he should use jam, balqis and you
    If the point is the melting pot, then the order goes: me/Hanif > Jam > Balq > Sadia. So better use me then Kurd.
    “Chahar chez est tohfay Multan, Gard-o- Garma, Gada-o- Goristan”.

    Four things are the gift of Multan: Dusty winds, hot seasons, beggars and graveyards.




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