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

  1. #11
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    Several points about their autosomal affinities. The great thing is, there are unanswered questions still in this paper, so now we can (potentially) contribute to clarification:

    1. Iberomaurusians are clearly admixed between Natufian Hunter-gatherers and some sort of Sub-Saharan African. On the other hand Natufian hunter-gatherers do not appear admixed:

    bGpR5R4.png

    Although the oldest Iberomaurusian microlithic bladelet technologies are found earlier in the Maghreb than their equivalents in northeastern Africa (Cyrenaica) and the earliest Natufian in the Levant, the complex sub-Saharan ancestry in Taforalt makes our individuals an unlikely proxy for the ancestral population of later Natufians who do not harbor sub-Saharan ancestry. An epicenter in the Maghreb is plausible only if the sub-Saharan African admixture into Taforalt either post-dated the expansion into the Levant or was a locally confined phenomenon. Alternatively, placing the epicenter in Cyrenaica or the Levant requires an additional explanation for the observed archaeological chronology.
    Also this quote from the authors in the press release:
    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.
    So the debate about KEB and the other N African genomes for which the other North African aDNA paper (Fregel et al) only included difficult-to-interpret fsts can finally be resolved.

    2. Eurasian ancestry in Iberomaurusians clearly Natufian, African ancestry in Iberomaurusians most strongly resemble present-day Yoruba and other West Africans:

    xbaeYao.png

    3. In simple tree with Yoruba as only African population, Iberomaurisians can be well-fitted as admixed between Yoruba and Natufian:

    VBHIeJu.png

    Affinity to Yoruba among Iberomaurusian can be accounted for in this way. Interestingly this should make Taforalt ~25% Villabruna as well.

    4. However, in complex trees this model fails. The Iberomaurusians have too much similarity to all other Africans to be completely a Yoruba+Natufian mix.

    bKaYVLX.png

    Turning the admixture to 100% Natufian and 0% Yoruba solves the problem for Mota, Dinka and Hadza, but makes the problem worse for Mbuti and Biaka (i.e. even further away) and does not substantially affect the problem for Ju_Hoan.

    A third admixture source with Mbuti, Hadza, or aSouthAfrica (Ju_Hoan-like) can be used in addition to Natufian and Yoruba. Of the three the Natufian+Yoruba+Hadza model works best, but in that model to account for similarity for Hadza the Yoruba % goes to 0 and Hadza takes over completely, and the resulting model is still too far away from Mbuti at a highly significant level (Z>5).

    r6gUpwq.png

    I.e., there is some weird "ghost" that is responsible for increased affinity between Hadza, Mbuti, plus ancient South Africans and Taforalt, that is neither of the three and not more divergent from the rest of humans than aSouthAfrican, that causes Taforalt to have increased affinity to all other Africans.

    The trees in their models do not include Mota, or genomes on the Mota-ancient South African cline discovered in Schlebusch et al; though they made passing reference to the results of that paper:

    Since f4 statistics are linear under admixture, we expect Taforalt not to be any closer to these outgroups than Yoruba or Natufians if the two-way admixture model is correct. However, we find instead that Taforalt is significantly closer to both outgroups (“aSouthAfrica” and “Mbuti”) than any combination of Yoruba and Natufians (Z ≥ 2.728 SE; Fig. 4). A similar pattern is observed for the East African outgroups Dinka, Mota and Hadza (table S11 and fig. S20). These results can only be explained by Taforalt harboring an ancestry that contains additional affinity with South, East and Central African outgroups. None of the present-day or ancient Holocene African groups serve as a good proxy for this unknown ancestry, because adding them as the third source is still insufficient to match the model to the Taforalt gene pool (table S12 and fig. S21). However, we can exclude any branch in human genetic diversity more basal than the deepest known one represented by aSouthAfrica (4) as the source of this signal: it would result in a negative affinity to aSouthAfrica, not a positive one as we find (Fig. 4). Both an unknown archaic hominin and the recently proposed deep West African lineage (4) belong to this category and therefore cannot explain the Taforalt gene pool.
    The qpGraphs in that paper differ from this one in that the presence of Mota and Yoruba together in a tree consistently force Yoruba to be an admixture of peri-Eurasian+basal human, the alternate model is Yoruba unadmixed and Mota as per-Eurasian and Basal Human. We should check what happens to the trees in this paper once we add Mota to the tree as well; does the Yoruba admixture now re-attach itself to one of the source populations of the Yoruba? Or does the pattern become even more complex than before?

    I think this problem may be related to the Mbuti-Mota-East African signal found in ADMIXTURE pointed out by, I think it was drobbah or Lank? There may be this same ghost pop that mediates sharing between Mota, Mbuti-Biaka and Taforalt, maybe a clue there... Maybe it is Mota admixed between peri-Eurasian and basal human, Yoruba unadmixed, then basal human to Mbuti, Biaka, Ju_Hoan, Mota and Taforalt to the exclusion of Yoruba (i.e. we reject the most parsimonious model in Schlebusch and accept the second-most parsimonious model, then using the ghost pop "basal human" in that to play with.) Either way a lot to chew over.
    Last edited by Ryukendo; 03-16-2018 at 12:59 AM.
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    Hmmm, fig S15 appears to have a mislabeled Y-axis that does not correspond to the caption. Someone can leave a comment on bioarXiv if they wish.
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    From the data presented thus far, can we infer anything in regards to how Basal Eurasian these samples are?

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    Quote Originally Posted by TuaMan View Post
    From the data presented thus far, can we infer anything in regards to how Basal Eurasian these samples are?
    .7 x .63 = 44% Basal Eurasian. These Iberomaurusians, and thus KEB likely as well, are ~63% Natufian.
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    Delete
    Last edited by Ryukendo; 03-16-2018 at 01:57 AM.
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    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. Demonstration of what differing sample quality does to stats with chimp as an outgroup
    Chimp Mbuti LBK_EN HungaryGamba_EN -0.0086 -3.477 13100 12877 353595

    Typically putting Mbuti as the outgroup instead gives nowhere for the garbage to dump, as misreads/decayed bases or what have you, will not make one closer to any particular modern.

    Chimp Yoruba Karitiana Ust_Ishim -0.0231 -5.858
    MbutiPygmy Yoruba Karitiana Ust'-Ishim -0.0019 -0.828

    But how do we do that when we are trying to discern African substructure and Mbuti may be a conflating factor?
    Last edited by Kale; 03-16-2018 at 04:18 AM.

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    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.
    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...

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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...
    That 63% would probably include not only basal, but Western Eurasian ancestry shared between Natufians and Iran Neolithic as well. I'm fairly confident that 30% basal should be accurate for Barcin Neolithic (I detailed why in some other post, I can find it on the 1% chance you care), and if that's the case, Natufians would be around 45%.

    There is the link of mt-dna K1 between Levant Neolithic and SE Europe mesolithic, that can only be about 20,000 years old. If K1 was derived from Levantine Aurignacian, as opposed to developing in Europe, we should expect something like:
    D: Mbuti Kostenki14/Vestonice16 Loschbour/Villabruna/KO1 Iron_Gates_HG
    ...to be significantly negative (I would expect it to be mildly negative due to Iron Gates extra EHG).
    If that stat is not significant (beyond excess EHG in Iron Gates) then K1 would probably be European, in which case Natufians (or Levant Neolithic, but the differences are minor) would have a decent chunk of WHG ancestry.

    Or...on second thought, much easier
    Mbuti Natufian Kostenki14 Vestonice16
    All WHG and Barcin Neolithic have significantly positive stats here, CHG and Iran Neolithic result is effectively 0. If Natufian has WHG this stat should be positive. Could try Taforalt there too when they become available.
    Last edited by Kale; 03-16-2018 at 04:40 AM.

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    Quote Originally Posted by Kale View Post
    There is the link of mt-dna K1 between Levant Neolithic and SE Europe mesolithic, that can only be about 20,000 years old. If K1 was derived from Levantine Aurignacian, as opposed to developing in Europe ...
    Phylogenetically, the ancestor of K1 is U8b'K. U8a has been detected in Magdaleniens in Europe: HohleFels Germany c. 15,5 kya, Brillenhohle Germany c. 15 kya and Burkhardtshohle Germany c. 15 kya, GoyetQ-2 Belgium c. 15 kya. However, the Magdalenien culture gave rise to U8a and K belongs to U8b. The oldest U8b is from the Near East: Levant_N ''Ain Ghazal Jordania I1709 c. 10 kya U8b1a. Moreover, U8 is clearly different from Europe-specific U5 as U8 goes back to U2'3'4'7'8'9. U2 is over 30 kya old in Europe and belongs to the Kostenki cluster, but the origin of U8 may be elsewhere and it may have arisen in Anatolia/Near East.
    Last edited by Kristiina; 03-16-2018 at 03:11 PM.

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    Quote Originally Posted by Kale View Post
    That 63% would probably include not only basal, but Western Eurasian ancestry shared between Natufians and Iran Neolithic as well. I'm fairly confident that 30% basal should be accurate for Barcin Neolithic (I detailed why in some other post, I can find it on the 1% chance you care), and if that's the case, Natufians would be around 45%.

    There is the link of mt-dna K1 between Levant Neolithic and SE Europe mesolithic, that can only be about 20,000 years old. If K1 was derived from Levantine Aurignacian, as opposed to developing in Europe, we should expect something like:
    D: Mbuti Kostenki14/Vestonice16 Loschbour/Villabruna/KO1 Iron_Gates_HG
    ...to be significantly negative (I would expect it to be mildly negative due to Iron Gates extra EHG).
    If that stat is not significant (beyond excess EHG in Iron Gates) then K1 would probably be European, in which case Natufians (or Levant Neolithic, but the differences are minor) would have a decent chunk of WHG ancestry.
    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 ...

    ice age europe.JPG
    Last edited by K33; 03-16-2018 at 03:28 PM.

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