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Thread: PCA G25_scaled - Africans only (Users & Ancients/Modern Avgs)

  1. #511
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    Quote Originally Posted by Angoliga View Post
    Here's a close-up:
     


    There seems to be two Fulani clusters around the Cameroonian, and Burkina Faso avg:








    All Africans:






    I prefer sticking with averages for a cleaner macrolevel view of these populations, it also keeps the PCA more visually balanced.

    Some pops only have 1 or 2 samples, whereas others like these BFA_Fulani have over 50. Keeping the sample plots to a minimum also gives more visibility to users (X); I'd like to think it encourages more African participants.

    For future sample data, I can post similar screenshots with all samples plotted but I think it'd be more visually democratic to keep the averages on actual saved PCAs:

    3D PCA: https://plot.ly/~Angoliga/3/
    2D PCA: https://plot.ly/~Angoliga/4/

    What are your thoughts?
    Thanks for that.
    Yes, I too would love it nice and clear. So, guess what you did by adding that screenshot for closer look on individual samples is excellent. I'm down on using averages on all groups.
    Keep up the good work!
    Last edited by Espoir; 10-16-2020 at 05:11 AM.

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  3. #512
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    Quote Originally Posted by gihanga.rwanda View Post
    Side note: The Toubou do resemble Sudanese Arabs/Nubians - and vaguely Horners - but to me they appear a lot more “gracile” (probably due to them being pastoralists) and a lot less admixed than the former. It obviously various from tribe to tribe and individual to individual, but I think recent Arabian admixture is pretty evident in the phenotype of many Sudanese Arabs (case in point: Sadiq al-Mahdi).
    One thing that's really interesting about many Sudani Arab nomadic groups is their cultural similarity to Cushitic speaking nomads. I was bloody startled when I noticed the Baggara of Chad and Sudan, named such for the fact that they often favor cattle over camels, straight-up use the typical domed mat-tents of Cushites that were even used and spread by South-Cushites:

     
    The Baggara:





    Bejas:




    Afars:




    Somalis:




    The Khoekhoe of Southern Africa:




    Even their early modern attire tended to look like an extension of what was traditionally worn by Bejas and Horners that I once displayed here. A style of attire that honestly reminds me of ancient Nile Valley attire to some extent. They're probably significantly descended from the same early pastoralists of the region as Horners, other admixtures from further west and the MENA region being obviously present or no. The mat-tent is no joke. It's a staple of Cushitic nomads' material culture, as much so as Yurts/Gers are for Turkic and Mongolic nomads in the steppes and goat-hair tents are for MENA nomads like the Bedouin.

     
    What startled me even more than any of the above, by the way, is that domed mat-tents are actually found all over the Sahel, even among the Fulani. It's inspired a whole new interest in me and I recently started reading this and becoming quite interested in Chadic speakers in particular and whether or not they're responsible for the spreading of these cultural implements.

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  5. #513
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    Quote Originally Posted by Angoliga View Post
    Here's a close-up:
     


    There seems to be two Fulani clusters around the Cameroonian, and Burkina Faso avg:








    All Africans:








    Some pops only have 1 or 2 samples, whereas others like these BFA_Fulani have over 50. Keeping the sample plots to a minimum also gives more visibility to users (X); I'd like to think it encourages more African participants.

    3D PCA: https://plot.ly/~Angoliga/3/
    2D PCA: https://plot.ly/~Angoliga/4/
    20201016_232004.jpg

    *Peul1 is Fulanis in French
    Who knew an old study on Dermatoglyphics would produce similar results as one about DNA

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  7. #514
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    Quote Originally Posted by Ajeje Brazorf View Post
    Why is Masai:NA21425 so isolated from the rest of Africans or even the Masai? This is a sample that I used to use to make models, but not anymore.

    I haven't checked for this sample, but there are two Maasai outliers in the MKK dataset with some % Indian from India.

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    Quote Originally Posted by NetNomad View Post
    I haven't checked for this sample, but there are two Maasai outliers in the MKK dataset with some % Indian from India.
    Masai from G25 don't, that sample happens to be just more distant to other samples.

    Distance to: Masai:NA21425
    0.04812520 Masai:NA21514
    0.04945788 Masai:NA21648
    0.05113311 Masai:NA21581
    0.05263755 Masai:NA21400
    0.05547148 KEN_Pastoral_IA:I12379
    0.05840407 KEN_Pastoral_IA:I12381
    0.06465938 Ogiek:T_Ogiek-1.DG
    0.06497603 Datog:GOR067
    0.06696871 Elmolo:T_Elmolo-1.DG
    0.07063016 Masai:NA21487

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  10. #516
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    Quote Originally Posted by Ajeje Brazorf View Post
    Masai from G25 don't, that sample happens to be just more distant to other samples.

    Distance to: Masai:NA21425
    0.04812520 Masai:NA21514
    0.04945788 Masai:NA21648
    0.05113311 Masai:NA21581
    0.05263755 Masai:NA21400
    0.05547148 KEN_Pastoral_IA:I12379
    0.05840407 KEN_Pastoral_IA:I12381
    0.06465938 Ogiek:T_Ogiek-1.DG
    0.06497603 Datog:GOR067
    0.06696871 Elmolo:T_Elmolo-1.DG
    0.07063016 Masai:NA21487
    Probably filtered out, but I was kind of surprised to find Indian in two of them while I was playing with HapMap data since this population come from a small village.

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    Quote Originally Posted by NetNomad View Post
    Probably filtered out, but I was kind of surprised to find Indian in two of them while I was playing with HapMap data since this population come from a small village.
    Yes it does happen though, I personally know a bunch and I mean a buncha folks from different ethnic groups in Kenya from tiny villages/towns that harbor some South Asian ancestry and I'm not talking about anwhere near the coast. I know of a Kikuyu family, 2 Kalenjin/Nandi families, a bunch of Kisii families and of course some Luos/Luhyas that all have distant Indian ancestry. What's crazy is that they're not from any where near the cities. When it comes to Maasai, I know two branches of a family that are interrelated - 1 side almost entirely South Asian and the other side almost entirely Maa. Giriama/Chonyi/Meru/Taita/Kamba also heard the same but don't know any personally.
    Last edited by ThaYamamoto; 10-17-2020 at 06:50 PM.

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  13. #518
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    Quote Originally Posted by Mnemonics View Post
    Can you try replacing Dinka with Sudanese7. I think it is the most pristinely AEA sample.
    Is that based on your observations using fstats? Please share, I'm curious

    Quote Originally Posted by ThaYamamoto View Post
    Yes it does happen though, I personally know a bunch and I mean a buncha folks from different ethnic groups in Kenya from tiny villages/towns that harbor some South Asian ancestry and I'm not talking about anwhere near the coast. I know of a Kikuyu family, 2 Kalenjin/Nandi families, a bunch of Kisii families and of course some Luos/Luhyas that all have distant Indian ancestry. What's crazy is that they're not from any where near the cities. When it comes to Maasai, I know two branches of a family that are interrelated - 1 side almost entirely South Asian and the other side almost entirely Maa. Giriama/Chonyi/Meru/Taita/Kamba also heard the same but don't know any personally.
    Interesting! I wonder if some of their ancestry is derived from the colonial period (*presumably as British subjects during Railway construction?).
    There's quite a few families in and around removed towns in NW-Uganda; some going back >6 generations from the latter end of the 19th century.

    It can seem shocking at times hearing them speak our local dialects perfectly : )
    Last edited by Angoliga; 10-22-2020 at 10:25 PM. Reason: *presumably as British subjects during Railway construction?
    .... .. I have spoken."

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    Quote Originally Posted by Angoliga View Post
    Is that based on your observations using fstats? Please share, I'm curious



    Interesting! I wonder if some of their ancestry is derived from the colonial period. There's quite a few families in and around removed towns in NW-Uganda; some going back >6 generations.
    It can seem shocking at times hearing them speak our local dialects perfectly : )
    I haven't tried out running formal stats on the Sudanese dataset because of poor overlap but in the nmonte models Sudanese7 seems to lack the excess West African affinity that is present in the Dinka from the G25 dataset and acts as a pretty good source for the AEA admixture in East/Northeast Africans. Try it out if you can.

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    Quote Originally Posted by Mnemonics View Post
    I haven't tried out running formal stats on the Sudanese dataset because of poor overlap but in the nmonte models Sudanese7 seems to lack the excess West African affinity that is present in the Dinka from the G25 dataset and acts as a pretty good source for the AEA admixture in East/Northeast Africans. Try it out if you can.
    The issue is the excess East-African HG affinity; Sudanese7 shows 6.4% ETH_4500BP, so it can't possibly be more pristinely AEA. The same goes for the Anuak samples. I recall these HG-Affinities getting eaten-up with runs on Central-Sudanic samples.

    *We could tinker with the Dinka individuals vs. the avg though, to cross-check the purest AEA sample.
    .... .. I have spoken."

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