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

  1. #1
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    PCA G25_scaled - Africans only (Users & Ancients/Modern Avgs)

    PCA G25_scaled - Africans only
    Users & Ancients/Modern Avgs
    (09/22/2019)





    Ancients = ◇
    Active Users = x
    Modern Samples = •





    Inviting all native Africans to participate, we can update these PCAs as we get more African users and additional Ancient/Modern samples. For the few African users found who've already posted their G25 cords on the forum, I've had them plotted as "x" on the PCAs. To get added on these PCAs, either PM me or post your G25 cords on this thread.

    If you don't already have G25 cords, here's how to get them (from AncestryDNA, FTDNA, LivingDNA, MyHeritage or 23andMe) and how to run PCAs on your own (it's fairly simple):

     

    How to get your G25 cords:

    • "send your request and autosomal genotype data (from AncestryDNA, FTDNA, LivingDNA, MyHeritage or 23andMe) to [email protected] and money via PayPal to the same e-mail" (current prices are $12 USD)
    • Here's an explanation of G25 cords along with instructions on how to run these PCAs for free (link)
    • The PAST data files when running the PCAs are here; I'll update them as we get more samples







    Sub-Regional PCAs


    North-Africans:

     


    Tropical-Africans:

     


    South-Africans:

     



    It might've been ideal to have separate threads for these sub-regions but seeing as we're a limited bunch on the forum, one central-thread might suffice. For better resolution, sub-regional PCAs can be updated concurrently as more samples are added.



    *Feel free to discuss any observations*
    Last edited by Angoliga; 09-23-2019 at 05:12 AM.
    .... .. I have spoken."

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  3. #2
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    "SM_blackflash16" user added:

     


    Tropical-Africa








    Africa

    Last edited by Angoliga; 09-24-2019 at 06:06 AM.
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  5. #3
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    Here's an update with Mbuti added:

     

    *Mbuti wasn't initially included because Davidski (creator of G25) had them removed from datasheets; I happened to grab this Mbuti_avg from an old file.
    Anyhow, I've reached out for confirmation, if there's nothing fundamentally faulty with the Mbuti sample data, there'd be value in keeping it plotted.





    Tropical-Africa
















    Africa





    Regarding the Ugandan Nilo-Saharans pulling towards African-Archaics, this likely reflects absorption of indigenous Great-Lake HGs. Here's an nMonte run of the UG_ARN samples showing MWI forager, KEN_LSA and Mbuti affinities:

     





    Malawi forager ancestry circled in red, illustrating the split of Hadza/Mbuti/South-African-like affinities:





    Fig 1) Skoglund, 17








    Excerpt relating to Ugandan Central-Sudanic and GL-HGs...




    (A New History of Tanzania, Kimambo 17')


    If taken as a literal reflection of GL-HGs, the extra Mbuti-affinity might reflect a prehistoric West>East cline of this Mbuti affinity emanating from the adjacent Congo-basin. Perhaps this gradient also decreased south/eastward to these Malawi HGs with lower Mbuti-affinities.
    Last edited by Angoliga; 09-24-2019 at 07:04 PM. Reason: *West>East cline
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    Isn't Kongo multiethnic?

  8. #5
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    Quote Originally Posted by Bealfire View Post
    Isn't Kongo multiethnic?
    By Kongo, I think this means the Bantu ethnic group of Kikongo speakers along the Atlantic coast of modern day Congo and Angola.

    This is opposed to "Congo" the nation, as in the Democratic Republic of Congo -- I also didn't catch this at first
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  10. #6
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    "EGY_COPT_lifeisdandy" user added:




     
    North-Africa














    Africa



    .... .. I have spoken."

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  12. #7
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    Those Somali samples are definitely Borana admixed

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  14. #8
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    Quote Originally Posted by drobbah View Post
    Those Somali samples are definitely Borana admixed
    Good catch! I think the modern average file I obtained had Ayodo's Kenyan Somalis mixed with Somalis proper.

    They're actually distinguished on the individual sample description, this is where they plot:

     










    I've now updated the PCAs and split the two with separate avgs (KEN_Somali, SM_Somali):

     
    Last edited by Angoliga; 09-24-2019 at 06:04 PM.
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    "SM_NetNomad" user added:

     






    Africa PCA (updated)

     

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    Nilotic peoples (Sudanese and the Nilotic Ethiopians like Mursi) plot very similar to West Africans and Bantu peoples. Is this what we would have expected?

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