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Thread: Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry

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    Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry

    https://www.biorxiv.org/content/early/2018/09/20/423079

    Abstract:

    The earliest ancient DNA data of modern humans from Europe dates to ~40 thousand years ago, but that from the Caucasus and the Near East to only ~14 thousand years ago, from populations who lived long after the Last Glacial Maximum (LGM) ~26.5-19 thousand years ago. To address this imbalance and to better understand the relationship of Europeans and Near Easterners, we report genome-wide data from two ~26 thousand year old individuals from Dzudzuana Cave in Georgia in the Caucasus from around the beginning of the LGM. Surprisingly, the Dzudzuana population was more closely related to early agriculturalists from western Anatolia ~8 thousand years ago than to the hunter-gatherers of the Caucasus from the same region of western Georgia of ~13-10 thousand years ago. Most of the Dzudzuana population's ancestry was deeply related to the post-glacial western European hunter-gatherers of the 'Villabruna cluster', but it also had ancestry from a lineage that had separated from the great majority of non-African populations before they separated from each other, proving that such 'Basal Eurasians' were present in West Eurasia twice as early as previously recorded. We document major population turnover in the Near East after the time of Dzudzuana, showing that the highly differentiated Holocene populations of the region were formed by 'Ancient North Eurasian' admixture into the Caucasus and Iran and North African admixture into the Natufians of the Levant. We finally show that the Dzudzuana population contributed the majority of the ancestry of post-Ice Age people in the Near East, North Africa, and even parts of Europe, thereby becoming the largest single contributor of ancestry of all present-day West Eurasians.
    First thought: Whatever is the cause of ME affinity in WHG really is old. Also, good to see Ofer Bar-Yosef in this as he once suggested back migrations from Europa to the Levant to account for the Levantine Aurignacian. Together with the Anatolian Epipaleolithic sample stuff to digest.

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    From the paper:

    In qpAdm modeling, a deeply divergent hunter-gatherer lineage that contributed in relatively unmixed form to the much later hunter-gatherers of the Villabruna cluster is specified as contributing to earlier hunter-gatherer groups (Gravettian Vestonice16: 35.711.3% and Magdalenian ElMiron: 60.611.3%) and to populations of the Caucasus (Dzudzuana: 72.5 3.7%, virtually identical to that inferred using ADMIXTUREGRAPH). In Europe, descendants of this lineage admixed with pre-existing hunter-gatherers related to Sunghir3 from Russia for the Gravettians and GoyetQ116-1 from Belgium for the Magdalenians, while in the Near East it did so with Basal Eurasians. Later Europeans prior to the arrival of agriculture were the product of re-settlement of this lineage after ~15kya in mainland Europe, while in eastern Europe they admixed with Siberian hunter-gatherers forming the WHG-ANE cline of ancestry (Fig. 1c).
    So, if that UHG lineage admixted into Magdalenians, into Gravettians and into the M.E., where did it come from?

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    "Our co-modeling of Epipaleolithic Natufians and Ibero-Maurusians from Taforalt confirms that the Taforalt population was mixed11, but instead of specifying gene flow from the ancestors of Natufians into the ancestors of Taforalt as originally reported, we infer gene flow in the reverse direction (into Natufians). The Neolithic population from Morocco, closely related to Taforalt17 is also consistent with being descended from the source of this gene flow, and appears to have no admixture from the Levantine Neolithic (Supplementary Information section 3). If our model is correct, Epipaleolithic Natufians trace part of their ancestry to North Africa, consistent with morphological and archaeological studies that indicate a spread of morphological features22 and artifacts from North Africa into the Near East. Such a scenario would also explain the presence of Y-chromosome haplogroup E in the Natufians and Levantine farmers6, a common link between the Levant and Africa. Moreover, our model predicts that West Africans (represented by Yoruba) had 12.51.1% ancestry from a Taforalt related group rather than Taforalt having ancestry from an unknown Sub-Saharan African source11; this may have mediated the limited Neanderthal admixture present in West Africans23. An advantage of our model is that it allows for a local North African component in the ancestry of Taforalt, rather than deriving them exclusively from Levantine and Sub-Saharan sources."

    Odds are that Paleolithic data from Northeast Africa will confirm this model.
    ᾽Άλλο δέ τοι ἐρέω, σὺ δ᾽ ἐνὶ φρεσὶ βάλλεο σῇσιν:
    κρύβδην, μηδ᾽ ἀναφανδά, φίλην ἐς πατρίδα γαῖαν
    νῆα κατισχέμεναι: ἐπεὶ οὐκέτι πιστὰ γυναιξίν.


    -Αγαμέμνων; H Οδύσσεια, Ραψωδία λ

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    This paper could prove to be rather revolutionary to ancient genomes, if I'm grokking it correctly. A Taforalt source without SSA inputting ancestry into SSA? That's new...
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    Quote Originally Posted by epoch View Post
    https://www.biorxiv.org/content/early/2018/09/20/423079

    Abstract:



    First thought: Whatever is the cause of ME affinity in WHG really is old. Also, good to see Ofer Bar-Yosef in this as he once suggested back migrations from Europa to the Levant to account for the Levantine Aurignacian. Together with the Anatolian Epipaleolithic sample stuff to digest.

    page 44:

    Table S3.5: Feasible models of 2-way mixtures (N=2) using the AllAfrican set.
    Mixture Proportions Std. Errors
    Test S1 S2 P-value S1 S2 S1 S2
    Anatolia_N Dzudzuana Natufian 0.070 0.859 0.141 0.029 0.029
    Natufian Dzudzuana Taforalt 0.405 0.863 0.137 0.019 0.019
    PPNB Dzudzuana Natufian 0.910 0.409 0.591 0.042 0.042
    PPNB Villabruna Natufian 0.187 0.163 0.837 0.024 0.024
    Taforalt could not be modeled as any 2-way mixture. The best model involving Natufians and an African
    population (Yoruba) could still be strongly rejected (p=2.7e-13). Taforalt could also not be modeled as a
    3-way mixture. However, Natufians could be convincingly modeled as a 2-way mixture of ~86%
    Dzudzuana and ~14% Taforalt
    (p=0.405)
    with small standard errors of 1.9%. Thus the affinity between
    Natufians and Taforalt described in ref.15 may have come about by admixture from a North
    African/Taforalt-related population into Natufians, rather than by admixture in the opposite direction.


    page 45: in supplemets
    Neolithic Anatolians fit as ~86% Dzudzuana and ~14% Natufians. This does not disprove that Neolithic
    Anatolians are approximately a clade with Dzudzuana, since Natufians trace ~86-89% of their ancestry to
    Dzudzuana (Tables S3.2, 5), and thus Neolithic Anatolians trace >98% of their ancestry from Dzudzuana,
    also in agreement with the 2-way models of Table S3.2.
    This does not mean that there was gene flow
    from the Levant into western Anatolia, as the (unsampled) hunter-gatherer precursors of Neolithic
    Anatolians may not have been identical to Dzudzuana.
    Finally, PPNB can be modeled as a mixture of ~41% Dzudzuana and ~59% Natufians, consistent with
    them tracing a large part of their ancestry to pre-farming populations of the Levant


    12. Again, we should
    not necessarily interpret these admixture proportions as signifying admixture into the Levant from the
    north during the formation of early Neolithic populations, as PPNB could be descended from a Levantine
    population that was not identical to the sampled Natufians

    Conclusions
    page 46 in supplementry information
    We summarize our main conclusions from this section:

    • “Western” Near Eastern populations, including Dzudzuana from the Caucasus, belonged to a
    cline of decreasing Villabruna/increasing deep ancestry: Villabruna → Dzudzuana/Anatolia_N →
    PPNB → Natufian → Taforalt

    • “Eastern” Near Eastern populations, including Caucasus hunter-gatherers (CHG) and Neolithic
    Iranians (Iran_N) traced most of their ancestry from populations of this cline, but also had
    additional Ancient North Eurasian/Eastern non-African (ANE/ENA) admixture.

    • Similar ANE/ENA admixture was represented in Eastern European hunter-gatherers (EHG) from
    Karelia; both Europe and the Near East was impacted by this eastern influence.

    • Within the main Villabruna/Basal Eurasian cline, we can determine that there was both
    Dzudzuana/Villabruna-like influence in North Africa (Taforalt), but also Taforalt-like admixture
    in the Levant

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    We clarify that in this section we are using the term .Deep ancestry. to represent any type of ancestry that separated from the main group of Eurasians before they differentiated from each other. This type of ancestry includes the "Basal Eurasian" lineage that was previously shown to have admixed into Near Easterners and that is inferred to have descended from same founder event/bottleneck that gave rise to the main ancestry in all non-Africans. However, our “deep ancestry” definition also includes deeper splitting lineages as well, some of whose ancestors may not have experienced this bottleneck. Indeed, in what follows we show that “Deep Ancestry” in West Eurasians is comprised not only of Basal Eurasian ancestry but also some more deeply splitting lineages.
    This also is really surprising. So now we have *two* Basal Eurasian lineages. One that did go through the bottleneck and one pre-bottleneck. This doesn't really simplify things, to put it mildly. What are the current theories on what that bottleneck was? Mount Toba? Anything else? When was it again?
    Last edited by epoch; 09-21-2018 at 12:59 PM.

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    I have pushed a theory a while ago - mind you, I am a mere amateur so my pushing of theories should be taken slightly tongue in cheek - that the M.E.-affinity in Villabruna is the result of a very old proto-Aurignacian European ancestry that up to now hasn't been sampled yet, that back migrated to the ME. This obviously isn't my idea, I got it from this article:

    http://www.patrimoniocultural.gov.pt...ogia/45/20.pdf

    The Levantine Aurignacian is not clearly understood today, because there are unresolved, competing ideas about what it represents. Researchers of this subject can be divided into two camps. On one side of the debate, the most outspoken members are Ofer Bar-Yosef and Anna Belfer-Cohen, who have maintained Dorothy Garrod’s original definition and conception of the Levantine Aurignacian. Like Garrod, they believe that the Levantine Aurignacian represents a cultural migration or diffusion, or a “social network” that spread to the Levant from its European homeland (Bar-Yosef and Belfer-Cohen, 1988, p. 36). In this scenario, the Levantine
    Aurignacian should share a striking similarity to the French Aurignacian, with specific typological markers such as an elaborate bone/antler tool industry, nosed and shouldered scrapers, thick keeled scrapers, and blades with Aurignacian retouch.
    Ofer Bar-Yosef, who came to this conclusion because the Levantine Aurignacian is dated *later* than the onset of French Aurignacian, contributed to this paper so maybe he feels vindicated.

    The other position in the debate is stretching up the definition of Levantine Aurignacian:

    Their framework expanded the definition, geographic scope, and temporal scale of the Levantine Aurignacian. The definition was expanded to include assemblages that did not meet all of the typological requirements of the classic perspective, and the Levantine Aurignacian was expanded spatially, to the steppe/desert areas, and temporally, to the terminal Upper Paleolithic.
    But that has been rejected later:

    http://www.patrimoniocultural.gov.pt...ogia/45/19.pdf

    Indeed by adhering to the original definitions of the Aurignacian in the Levant we can more readily observe the fascinating phenomenon of the appearance of a geographically (and chronologically?) limited cluster of assemblages of the classic Aurignacian variety. These are so similar to assemblages from southwest France at the other end of the Mediterranean, that one is tempted to view them literally as well as figuratively having just disembarked from the boat! They appear, “out-of-the-blue”, in the midst of other, endemic, Upper Paleolithic lineages (e.g. the Ahmarian) with few, if any, obvious ties to the preceding and succeeding Levantine industries.
    Last edited by epoch; 09-21-2018 at 01:36 PM.

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    Quote Originally Posted by epoch View Post
    This also is really surprising. So now we have *two* Basal Eurasian lineages. One that did go through the bottleneck and one pre-bottleneck. This doesn't really simplify things, to put it mildly. What are the current theories on what that bottleneck was? Mount Toba? Anything else? When was it again?
    Pre-bottleneck could simply mean post OOA African populations migrating into the Middle East according to the authors:

    Europeans are differentiated by an excess of
    227 up to ~20% Villabruna-related ancestry relative to non-European populations and also by a
    228 relative lack of extra ‘Deep’ ancestry compared to the Near East and North Africa, a type of
    229 ancestry that may only partially be explained by the Basal Eurasian ancestry of ancient West
    230 Eurasian populations and must also trace to Africa
    More than that, although the authors seem to disagree, I don't see why Basal Eurasian itself should not be seen as additional post OOA African migration into the Near East:

    The detection
    of this type of ancestry, twice as early as previously documented5,6
    148 and at the northern edge
    149 of the Near East, lends weight to the hypothesis that it represents a deep Near Eastern lineage
    rather than a recent arrival from Africa6
    150 .
    Last edited by Mansamusa; 09-21-2018 at 01:48 PM.

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    Harvard does it again! I'm starting to read the paper now, but it's clear from the abstract and commentary that this is a paper of great import. Reich, Lazaridis, et al are legends.
    Ελευθερία ή θάνατος.

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