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Thread: Ancient DNA from North Africa (this time with formal stats)

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    Quote Originally Posted by K33 View Post
    I think it's fairly clear that "Basal Eurasians" are this ghost population. They need to scan the Empty Quarter of Saudi Arabia for Paleolithic human remains, that's probably the best bet to find unadmixed BE DNA... Even Natufians are only 63% Basal Eurasian (as per this particular qpGraph). Interesting that as you note, Ryu, their qpgraph has the remaining 37% of Natufian's ancestry coming from a Euro HG clade immediately basal to WHG (which in turn makes Iberomaurusians 25% WHG-related).

    I think Agamemmon a while back was the first to speculate that the non-Basal ancestry of Natufians was derived from the Levantine Aurignician culture-bearers. That seems the most obvious working hypothesis at this point, given LA's archaeological link with Europe...
    I speculate that as well, with a back migration from Europe being the source. Cause or Trigger: Repopulation of the area touched by the Phlegraean eruption [1]. Remnants of the part that remained in Europe would then admix with other post-LGM remnants to produce the famed Middle-Eastern affinity of Villabruna cluster and - to a lesser degree - some of the Magdalenians. It would require a second, unknown Aurignacian population in Europe, related to GoyetQ116-1 but not the same. A ghost population, an UHG.

    The Levantine Aurignacian dates *later* than the European Aurignacian.

    [1] This also neatly explains the disappearance of the Oase type ancestry from Europe.
    Last edited by epoch; 03-16-2018 at 05:38 PM.

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    Quote Originally Posted by K33 View Post
    What's interesting is that the Fu et al 2016 Ice Age Paper associated the following genetic components temporally with the corresponding cultures:

    GoyetQ116: Aurignacian
    Vestonice Cluster: Gravettian
    Villabruna Cluster: Epigravettian

    The Levant had an Aurignacian cultural phase, yet not an Epigravettian one (AFAIK). Yet GoyetQ116 doesn't show the elevated affinity with Natufians that Villabruna does, despite ADMIXTUREGRAPH demonstrating GoyetQ116-1 derives from the same deep Euro HG line as WHG (as opposed to Vestonice Cluster which is more significantly derived from the more divergent "Kostenki" branch)

    Can anybody include GoyetQ116-1 in a gpGraph run with WHG, the Iberomaurusians and Natufians (among others)? I'm curious to see whether Goyet shows any link to their non-Basal ancestry ...

    Attachment 22131
    For what its worth, the authors included "Basal to WHG" admixture into Taforalt in all trees with Taforalt, but this admixture consistently comes out as 0%.

    Most likely whatever WHG the Iberomaurusians contain is that in Natufians.
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    Quote Originally Posted by epoch View Post
    I speculate that as well, with a back migration from Europe being the source. Cause or Trigger: Repopulation of the area touched by the Phlegraean eruption [1]. Remnants of the part that remained in Europe would then admix with other post-LGM remnants to produce the famed Middle-Eastern affinity of Villabruna cluster and - to a lesser degree - some of the Magdalenians. It would require a second, unknown Aurignacian population in Europe, related to GoyetQ116-1 but not the same. A ghost population, an UHG.

    The Levantine Aurignacian dates *later* than the European Aurignacian.

    [1] This also neatly explains the disappearance of the Oase type ancestry from Europe.
    I think the famed 'Middle'-Eastern affinity is a bit of a misnomer.
    Mbuti Iran_Neolithic Kostenki14 Villabruna 0.0137 2.493 716391
    716k snps a quite a bit, and though I would certainly say there is a link, this stat doesn't even technically reach the Z score of 3 or -3 required by most academic publications.
    I would consider it possible that affinity was entirely transmitted through mixture with their neighbors.
    Mbuti Anatolia_Neolithic Villabruna Kostenki14 -0.0449 -13.697 905480
    Mbuti Levant_Neolithic Kostenki14 Villabruna 0.0464 8.951 710555

    While there may be much more ancient links, the sharing of mtdna-k between SE Europe and Anatolia/Levant clearly indicates mingling 20,000 years ago. Same with y-hg I2 between Europe and Anatolia (Levant neolithic will probably turn some up with additional sampling, but that overwhelming E kind of subsumes all other lineages). I heard there were even C1a2-V86 clades that diverged about 20,000 years ago between Europe and modern Anatolia/Armenia?

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    Quote Originally Posted by Ryukendo View Post
    For what its worth, the authors included "Basal to WHG" admixture into Taforalt in all trees with Taforalt, but this admixture consistently comes out as 0%.

    Most likely whatever WHG the Iberomaurusians contain is that in Natufians.
    But is it certain the non-Basal portion of Natufian is most closely related to Villabruna, or could Goyet116 be a better approximation of this ghost population?

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    Quote Originally Posted by Kale View Post
    I think the famed 'Middle'-Eastern affinity is a bit of a misnomer.
    Mbuti Iran_Neolithic Kostenki14 Villabruna 0.0137 2.493 716391
    716k snps a quite a bit, and though I would certainly say there is a link, this stat doesn't even technically reach the Z score of 3 or -3 required by most academic publications.
    I would consider it possible that affinity was entirely transmitted through mixture with their neighbors.
    Mbuti Anatolia_Neolithic Villabruna Kostenki14 -0.0449 -13.697 905480
    Mbuti Levant_Neolithic Kostenki14 Villabruna 0.0464 8.951 710555
    That's the admixture I mentioned. And it's not there in Iran_N. Or at least not enough to make a difference. Interestingly enough this paper models Natufians as 30% WHG and 70% Basal and Iran as a mixture between EHG and Basal.

    Quote Originally Posted by Kale View Post
    While there may be much more ancient links, the sharing of mtdna-k between SE Europe and Anatolia/Levant clearly indicates mingling 20,000 years ago. Same with y-hg I2 between Europe and Anatolia (Levant neolithic will probably turn some up with additional sampling, but that overwhelming E kind of subsumes all other lineages). I heard there were even C1a2-V86 clades that diverged about 20,000 years ago between Europe and modern Anatolia/Armenia?
    And certainly there was neighbour mixture. Iain Mathieson said on twitter this:

    https://twitter.com/mathiesoniain/st...83881777070080

    I mean the evidence is D(Mbuti, Anatolia_Neolithic, WHG, Iron_Gates_HG)=+7 but I don't know what the direction is.
    But that isn't all of the admixture. Have a look:

    Mbuti Barcin_N WHG Iron_Gates_HG 0.0092 5.171 1140577
    Mbuti Natufian WHG Iron_Gates_HG 0.0056 2.222 502960

    There is no special affinity to Iron Gates in Natufian. But above we found that in Natufians there is affinity to the whole Villabruna cluster. So there must have been at least two admixture events.
    Last edited by epoch; 03-16-2018 at 07:32 PM.

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    Quote Originally Posted by Kale View Post
    I'm wondering how much of this ghost affinity to various African populations by Taforalt over the model of Natufian + Yoruba, is actually attributable to the poor sample quality of the Natufians.
    If poor sample quality (or a divergent ghost, or something) pulls Natufians away from everyone, that could also account for their apparent lack of any African admixture in f4, despite it seemingly appearing with other methods.

    Is there anythng else ruling out Natufians having a bit of this North African SSAish ghost? Geographically and considering the E-M35 it's a plausible thing for them to have.

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    people try by all force
    to make those natuffians as part africans autosomaly
    just because they carry a specific e-m35 branch
    if they did have something african autosomally speaking it would be horner east african /
    not west african like those ancients in morocco.
    ........


    The Iberomaurusians lived before the Natufians, but they were not their direct ancestors: The Natufians lack DNA from Africa, Krause says. This suggests that both groups inherited their shared DNA from a larger population that lived in North Africa or the Middle East more than 15,000 years ago, the team reports today in Science.

    As for the sub-Saharan DNA in the Iberomaurusian genome, the Iberomaurusians may have gotten it from migrants from the south who were their contemporaries. Or they may have inherited the DNA from much more ancient ancestors who brought it from the south but settled in North Africa where some of the earliest members of our species, Homo sapiens, have been found at Jebel Irhoud in Morocco.
    Last edited by kingjohn; 03-16-2018 at 09:15 PM.

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    Quote Originally Posted by Megalophias View Post
    If poor sample quality (or a divergent ghost, or something) pulls Natufians away from everyone, that could also account for their apparent lack of any African admixture in f4, despite it seemingly appearing with other methods.

    Is there anythng else ruling out Natufians having a bit of this North African SSAish ghost? Geographically and considering the E-M35 it's a plausible thing for them to have.
    To explain what exactly?

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    This kind of question (is it North African or not?) simply can't be profitably answered at this point. Whats even the point of this question? Say we have evidence that E-M35 mutated 1 km West of the Sinai vs 1 km East of it, what difference does it make?

    E-M35 is not a young clade like R-M417, for which you can (stretching it) still claim some kind of kinship and the marker is still phylogeographically informative about population movements, E-M35 age of formation is the same as Tianyuan, i.e. when the map of Eurasia was very scrambled genetically and phylogeographically it was nothing like what is was today, so this kind of speculation is really pointless.

    The most we can say given what we have now is that there seems to be some association between E-m35 and Natufian ancestry, since the natufian gene pool is not more than 20,000 years old (from simulations in Broushaski et al and also the age of the Villabruna cluster) and so far our E-M35's have been found with autosomes carrying such ancestry.
    Last edited by Ryukendo; 03-16-2018 at 10:22 PM.
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