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Thread: Reconstructing Prehistoric African Population Structure

  1. #41
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    Quote Originally Posted by Chad Rohlfsen View Post
    Awale, do you also have Levant_N and Anatolia for your runs?
    They're in the Global-10 PCA but no, I don't use them for my runs. They tend to be totally edged out once Natufians are present:

    distance%=0.5928 / distance=0.005928

    Somali

    Dinka 54.05
    Natufian 36.45
    Levant_BA 7.35
    Mota 2.15
    Levant_N 0.00
    Barcin_N 0.00


    And using Levant_N instead of Natufians makes the fits a lot worse (would make the above one jump up to about 1.3 or so) so I just avoid throwing them in and use Natufians instead.

    Quote Originally Posted by Chad
    They might help your fits with regards to Eurasian ancestry in Horners. Also, the broadly Eurasian affinity of Mota shouldn't be a big concern. Considering the introgression of E and the dates of those branches, it may be older than Ust_Ishim, in regards to the type of Eurasian ancestry. There's even a chance it is Basal to all, including Basal Eurasian, so it can't choose between Natufian, WHG, and Onge. One thing about using WHG is that they are so inbred, they are going to be hard to fit in anywhere that doesn't have a sizeable contribution from them.
    Hmm, I personally think this Eurasian affinity has something more to do with sharing descent from pre-historic East-Africans with Eurasians, but who knows. It doesn't shock me too much either. Interesting point about WHGs, though. I'll be waiting on those qpGraph runs of yours. I wanna see some good qpGraphs for Africans big time.

    Quote Originally Posted by Michalis Moriopoulos View Post
    Are the Hadza supposed to be direct descendants of Mota? Descendants of a closely-related side-branch? They certainly share a lot of alleles with Mota, but I'm curious if their exact relationship with the sample has been resolved to anyone's satisfaction...
    Welcome back, co-founder. Arash-meng has told me much about you. Anyway, Hadzas are not descendants of Mota. Probably descended from pre-historics in Southeast Africa who were rather similar to him on a basal level like the Malawi samples (existing along the "East-South cline"), though. And they definitely seem to have some Horn-African admixture as well but more along the Erythraeaic (Cushitic) speaking pastoralist variety than the Mota-like variety.
    Last edited by Awale; 11-20-2017 at 11:50 PM.

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  3. #42
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    Thanks for the explanation, Awale. I've seen a few African populations modeled in qpGraph, but only in very specific contexts (i.e., pastoralist geneflow into South Africa). It would be nice to see a more inclusive project where all the major players were included. That's why I'm excited for Chad's project.

    We need all the ancient SSA DNA we can get. One wonders if the most famous fossils from the region are just too damaged to test. I'm talking about Hofmeyr, Jebel Sahaba, Iwo Eleru, and Asselar. If I worked for an academic genomics lab, those would be among the first fossils I'd want to check out.
    "By all means, get married: if you find a good wife, you'll be happy; if not, you'll become a philosopher." - Socrates, 5th Century BCE
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  5. #43
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    Quote Originally Posted by Michalis Moriopoulos View Post
    We need all the ancient SSA DNA we can get. One wonders if the most famous fossils from the region are just too damaged to test. I'm talking about Hofmeyr, Jebel Sahaba, Iwo Eleru, and Asselar. If I worked for an academic genomics lab, those would be among the first fossils I'd want to check out.
    In the case of Jebel-Sahaba, the Nataruk remains samples might be a good stand-in for Mesolithic Nubia/Jebel-Sahaba site considering the presence of pottery at the massacre site as well as previous finds of wavy-line pottery at Lake Turkana.
    Last edited by blackflash16; 11-22-2017 at 02:23 PM.

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