The Caucasus revisited (Yunusbayev et al. 2011)

This is another treasure trove of a paper, and together with Balanovsky et al. (2011) we now have a very clear picture of genetic variation in this most interesting of world regions.

Here is the ADMIXTURE analysis:

The authors also post results up to K=10 in the supplementary material, which show Druze/Bedouin/Basque-centered component. It is actually possible to push the analysis higher than K=7 without such problem components appearing, by retaining non-closely related individuals (using --genome in PLINK and then iteratively removing individuals from pairs with PI_HAT greater than some value).

Nonetheless, the components emerging from this analysis will be familiar to followers of the Dodecad Project. In terms of Dodecad v3:

• light yellow "North East Asian"
• orange "South East Asian"
• brown "Neo African" or "Sub_Saharan", as there are no African hunter-gatherers
• dark blue "North European", as there is no split of east/west Europe at this level
• middle blue "West Asian"
• light blue "Southwest Asian"
• green "South Asian", but anchored on Sindhi, a population from Pakistan, due to the lack of more southern populations from India

The labels of new populations sampled in this study can be seen in brown. I particularly hope that the substantial new autosomal data will become publicly available, so that I can use them in the Dodecad Project. It will be an invaluable new resource, filling some "holes" in the Eurasian landscape (e.g., east of the Caspian; Bulgarians; several new Caucasus populations) in the Li et al. (HGDP), and Behar et al. data.

(to be continued)

UPDATE I (Y-chromosomes):

Some observations:

• C has a concentration in the Turkic Nogays
• The presence of D this far west is very surprising, again in the Nogays. This haplogroup has a relic distribution, with particular concentrations in Tibet, Mongolia, Japan, and Andaman Islanders. In all likelihood its presence here is linked to the Nogays' eastern origin
• E and its subclades occurs at a very low frequency here
• G2a has a clear West Caucasus (both north and south) concentration
• I seems to have a mainly West Caucasus distribution as well; this is a common European haplogroup; it has quite elevated frequencies among the Andis and Kara Nogays. It would be interesting to discover some historical correlate for the presence of I in Kara Nogays but not Kuban Nogays and in Andis but not in most of the NE Caucasus
• J1 has the expected Northeast Caucasus nexus. This haplogroup is bimodal, with a mode in Arabians and a secondary mode in NE Caucasus. Note the paucity of J1e-P58, the reverse of the situation of Arabians; I've noted before the likely association of the P58 clade with Semitic languages.
• The extreme concentration of J2 in Chechens and Ingush are probably associated with low variance. Apart from these atypical populations, a substantial presence of this haplogroup can be found in the NW/S Caucasus in different populations and in the form of different subclades.
• The new LT mystery clade has its usual low-frequency wide distribution
• N occurs in Nogays as expected, and, like C, also in the NW Caucasus. This probably also represents an eastern influence, probably associated not only with the Nogays but also with various Tatar influences on the Caucasus.
• Q occurs widely in the NW Caucasus but only in 1 Nogay. Perhaps this is more of a Tatar marker, although a finer-scale resolution of this haplogroup is really necessary.
• R1a-related lineages occur less frequently here among eastern Slavs, a main reason for the disconnect between the Eastern European plain and the Caucasus. There does, however, appear to be good diversity here, with the presence of R1a*, R1a1-M198*, Note again how the Iranic Ossetians (both North and South) have almost no R1a1 compared to both their NW Caucasian and S Caucasian neighbors, again, suggesting that this may not have been an important Alan or steppe Iranian lineage, at least during the late antique time horizon. The occurrence of R1a1f-M458 may represent Slavic influence in the NW Caucasus.
• R1b-related lineages seem ubuiquitous in the Caucasus. R-M73 occurs substantially in Kara Nogays and Balkars, an apparent link with Central Asia where this haplogroup occurs frequently.

UPDATE II (Caucasus-Eastern Europe discontinuity)

The authors of this paper highlight the genetic discontinuity between the eastern European plain and the Caucasus. This was also apparent in the Balanovsky et al. (2011) paper, and was also a major conclusion of the Dodecad Project, with Caucasians exhibiting a high percentage of the "West Asian" component, while eastern Slavs low "West Asian" and high "East European".

The interpretation of this discontinuity is more difficult. There are surely parts of the Caucasus region that are mountainous and pose an ecological contrast to the flatlands of eastern Europe. That is consistent with a different type of population living in either region for a long time, despite the well-attested archaological contacts (e.g., Maikop or the settlement of steppe nomads such as Alans or Sarmatians).

On the other hand, the eastern Slavic population can, at least in part, have expanded more recently, in the medieval period, as part of the early Slavic dispersals, as well as the push to the north and east of the Russians. These appear to have partly displaced Turkic groups from the north Pontic region, with all of the above having displaced historical Scythian (Iranic) nomads, who, in turn, displaced the mysterious Cimmerians. If the discovery of east Eurasian mtDNA C in Neolithic and Bronze Age Ukraine stands up, there will be another layer of population replacement, as mtDNA C is quite rare in the broader region today. On the other hand, the Caucasus itself may have been affected from population movements from the Near East, as Balanovsky et al. suggest.

So, in conclusion, the discontinuity is a fact that emerges from different types of analyses, but its causes remain uncertain, and it is not clear when and how it was first established.

Mol Biol Evol (2011) doi: 10.1093/molbev/msr221

The Caucasus as an asymmetric semipermeable barrier to ancient human migrations

Bayazit Yunusbayev et al.

Abstract

The Caucasus, inhabited by modern humans since the Early Upper Paleolithic and known for its linguistic diversity, is considered to be important for understanding human dispersals and genetic diversity in Eurasia. We report a synthesis of autosomal, Y chromosome and mitochondrial DNA (mtDNA) variation in populations from all major subregions and linguistic phyla of the area. Autosomal genome variation in the Caucasus reveals significant genetic uniformity among its ethnically and linguistically diverse populations, and is consistent with predominantly Near/Middle Eastern origin of the Caucasians, with minor external impacts. In contrast to autosomal and mtDNA variation, signals of regional Y chromosome founder effects distinguish the eastern from western North Caucasians. Genetic discontinuity between the North Caucasus and the East European Plain contrasts with continuity through Anatolia and the Balkans, suggesting major routes of ancient gene flows and admixture.

Link