On the genetic prehistory of the Greater Caucasus (Wang et al. 2018 preprint)

Finally, the focus shifts to the Eneolithic/Bronze Age North Caucasus. In a new manuscript at bioRxiv, Wang et al. present new genome-wide SNP data from 45 prehistoric individuals from the region along a 3000-year temporal transect (see here). From the preprint (emphasis is mine):

Based on PCA and ADMIXTURE plots we observe two distinct genetic clusters: one cluster falls with previously published ancient individuals from the West Eurasian steppe (hence termed ‘Steppe’), and the second clusters with present-day southern Caucasian populations and ancient Bronze Age individuals from today’s Armenia (henceforth called ‘Caucasus’), while a few individuals take on intermediate positions between the two. The stark distinction seen in our temporal transect is also visible in the Y-chromosome haplogroup distribution, with R1/R1b1 and Q1a2 types in the Steppe and L, J, and G2 types in the Caucasus cluster (Fig. 3A, Supplementary Data 1). In contrast, the mitochondrial haplogroup distribution is more diverse and almost identical in both groups (Fig. 3B, Supplementary Data 1).

Thus, the most important “Indo-European” Y-haplogroups today, R1a-M417 and R1b-M269, did not arrive in Europe from the Caucasus or Near East. They’re native to Europe. Hence, it appears that Bronze Age Eastern Europeans mostly acquired their Near Eastern-related ancestry via female exogamy from populations in the Caucasus. That’s basically what I’ve been arguing for a few years now. It feels good to be vindicated, especially considering how much unfair criticism I was subjected to here and elsewhere because of expressing this opinion (for instance, see here).
However, as far as I can see, based on the samples in this preprint, neither the Caucasus Maykop nor steppe Maykop appear to be unambiguous sources of this southern admixture in ancient Eastern Europe. For one, the Caucasus Maykop mtDNA profile does look somewhat off in this context, and, secondly, steppe Maykop includes West Siberian forager-related genome-wide ancestry that is practically absent in the Yamnaya and all other closely related peoples.
In any case, please note the happy coincidence that academia has finally caught up to this blog and managed to find European farmer-derived ancestry in Yamnaya:

Importantly, our results show a subtle contribution of both Anatolian farmer-related ancestry and WHG-related ancestry (Fig.4; Supplementary Tables 13 and 14), which was likely contributed through Middle and Late Neolithic farming groups from adjacent regions in the West. A direct source of Anatolian farmer-related ancestry can be ruled out (Supplementary Table 15). At present, due to the limits of our resolution, we cannot identify a single best source population. However, geographically proximal and contemporaneous groups such as Globular Amphora and Eneolithic groups from the Black Sea area (Ukraine and Bulgaria), which represent all four distal sources (CHG, EHG, WHG, and Anatolian_Neolithic) are among the best supported candidates (Fig. 4; Supplementary Tables 13,14 and 15).

Check out what I had to say about this issue exactly two years ago: Yamnaya = Khvalynsk + extra CHG + maybe something else. Not bragging, just making a point that I do know what I’m doing here, most of the time anyway.
Wang et al. conclude their preprint with, unfortunately I have to say, some downright bizarre comments in regards to the Proto-Indo-European (PIE) homeland debate. But I’ll get back to that later, when the ancient data from this and forthcoming related papers are released online.
Wang et al., The genetic prehistory of the Greater Caucasus, bioRxiv, posted May 16, 2018, doi: https://doi.org/10.1101/322347
See also…
Late PIE ground zero now obvious; location of PIE homeland still uncertain, but…

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