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Thread: Signals of ghost admixture in Yoruba related populations

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    2 members found this post helpful.

    Signals of ghost admixture in Yoruba related populations

    See: Arun Durvasula et al
    "Recovering signals of ghost archaic admixture in the genomes of present-day Africans"

    https://www.biorxiv.org/content/bior...85734.full.pdf

    "Analyses of Neanderthal and Denisovan genomes have characterized multiple interbreeding events between archaic and modern human populations. While several studies have suggested the presence of deeply diverged lineages in present-day African populations, we lack methods to precisely characterize these introgression events without access to reference archaic genomes. We present a novel reference-free method that combines diverse population genetic summary statistics to identify segments of archaic ancestry in present-day individuals. Using this method, we find that ~7.97±0.6% of the genetic ancestry from the West African Yoruba population traces its origin to an unidentified, archaic population (FDR ≤20%). We find several loci that harbor archaic ancestry at elevated frequencies and that the archaic ancestry in the Yoruba is reduced near selectively constrained regions of the genome suggesting that archaic admixture has had a systematic impact on the fitness of modern human populations both within and outside of Africa."


    Given that he has always argued for this, I was wondering if Dienekes would come out of retirement and opine, and he has...

    http://dienekes.blogspot.com/2018/03...oafricans.html

    "
    This ~8% matches well the ~9% of "West Africa A" in Yoruba of the model of Skoglund et al. Figure 3D. If "West Africa A" corresponds to the Archaic Ghost of D+S, then the Mende have the most of it at ~13%.

    I have long maintained that the higher genetic diversity of extant Sub-Saharan Africans is the result of admixture between "Afrasians" (a population that spawned Eurasians and much of the ancestry of Sub-Saharans and which had "low" (Eurasian-level) of genetic diversity) and multiple layers of "Palaeoafricans". It would seem that one such layer has now been discovered.

    Where did the Afrasians live? Recent developments pushed back the presence of modern humans in both North Africa and the Middle East, making both regions highly competitive as the cradle of the Afrasians. The odds for Sub-Saharan Africa have greatly diminished also by the discovery of late non-sapiens H. naledi in South Africa (which was naively postulated as a cradle based on the presence there today of genetically diverse San Bushmen, but who are not descendants of even Late Pleistocene South Africans), as well as of the archaic component in the genomes of West Africans. These discoveries pile up on top of known archaic skulls of late provenance in both Central and West Africa.

    Remember though, that the archaic admixture in West Africans is "less archaic" (more closely related to H. sapiens) than the Neandertal/Denisovan ancestry which contributed to extant Eurasians. All Africans (modern or archaic) are a branch within the phylogeny of Eurasians, with Australoids (and now apparently East Asians too) having the deepest known strain of human ancestry inherited from the elusive Denisovans."





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    Interesting. The Yoruba are also much higher in rh negative blood than most Africans other than a population in Gambella, Ethiopia with around 20%:http://www.rhesusnegative.net/stayne...bela-ethiopia/

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    the first archaic population that comes to my mind are the Aterians, the descendants of the Irhoud skulls
    we don't have their DNA

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    This paper is actually free to read. Either I did not understand anything in it, or their calculation only tells us how much of Yoruba DNA is distinct from other populations. I don't see how they can tell if it's from a modern human lineage that has only survived in them, or from an archaic one.

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    Wow. That's a high percentage.

    And 13% in Mende perhaps too? That's a ton.

    Could "Afrasian" = Basal Eurasian?

    A bit disappointed that it's not truly archaic. I was hoping for Homo Erectus. That would be crazy.

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    Quote Originally Posted by holderlin View Post
    Wow. That's a high percentage.

    And 13% in Mende perhaps too? That's a ton.

    Could "Afrasian" = Basal Eurasian?

    A bit disappointed that it's not truly archaic. I was hoping for Homo Erectus. That would be crazy.

    It's not basal Eurasian. His idea is that modern homo sapiens actually evolved either in the Middle East or over a wide region including the Middle East and North Africa. He calls that groups Afrasian. Then they supposedly spread all over the world, mixing with local hominins.

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    D(Natufian, Bichon; Mota, Chimp) Z = -0.9
    D(Natufian, Bichon; Yoruba, Chimp) Z = 0.4
    D(Chimp, Mota; Han, Sardinian) Z = -0.2
    D(Chimp, Yoruba; Han, Sardinian) Z = 1.7
    D(Chimp, Esan; Han, Sardinian) Z = 0.7
    D(Chimp, Dinka; Han, Sardinian) Z = 0.2

    Here Africans are compared against pairs of Eurasians, one with little or no Basal Eurasian, the other with some or a lot of it. If Africans had Basal Eurasian we would expect the D stats to be positive, but the results are approximately zero.

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    Quote Originally Posted by Megalophias View Post
    D(Natufian, Bichon; Mota, Chimp) Z = -0.9
    D(Natufian, Bichon; Yoruba, Chimp) Z = 0.4
    D(Chimp, Mota; Han, Sardinian) Z = -0.2
    D(Chimp, Yoruba; Han, Sardinian) Z = 1.7
    D(Chimp, Esan; Han, Sardinian) Z = 0.7
    D(Chimp, Dinka; Han, Sardinian) Z = 0.2

    Here Africans are compared against pairs of Eurasians, one with little or no Basal Eurasian, the other with some or a lot of it. If Africans had Basal Eurasian we would expect the D stats to be positive, but the results are approximately zero.
    Yeah that's obvious. Didn't think much before posting that one.

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