May 18, 2014

Siberian genetics with focus on Yakutia

Informative study on the populations of Sakha Republic (Yakutia) and Siberia in general:

Sardana A. Fedorova et al., Autosomal and uniparental portraits of the native populations of Sakha (Yakutia): implications for the peopling of Northeast Eurasia. BMC Evolutionary Biology 2014. Open accessLINK [doi:10.1186/1471-2148-13-127]

Abstract

Background

Sakha – an area connecting South and Northeast Siberia – is significant for understanding the history of peopling of Northeast Eurasia and the Americas. Previous studies have shown a genetic contiguity between Siberia and East Asia and the key role of South Siberia in the colonization of Siberia.

Results

We report the results of a high-resolution phylogenetic analysis of 701 mtDNAs and 318 Y chromosomes from five native populations of Sakha (Yakuts, Evenks, Evens, Yukaghirs and Dolgans) and of the analysis of more than 500,000 autosomal SNPs of 758 individuals from 55 populations, including 40 previously unpublished samples from Siberia. Phylogenetically terminal clades of East Asian mtDNA haplogroups C and D and Y-chromosome haplogroups N1c, N1b and C3, constituting the core of the gene pool of the native populations from Sakha, connect Sakha and South Siberia. Analysis of autosomal SNP data confirms the genetic continuity between Sakha and South Siberia. Maternal lineages D5a2a2, C4a1c, C4a2, C5b1b and the Yakut-specific STR sub-clade of Y-chromosome haplogroup N1c can be linked to a migration of Yakut ancestors, while the paternal lineage C3c was most likely carried to Sakha by the expansion of the Tungusic people. MtDNA haplogroups Z1a1b and Z1a3, present in Yukaghirs, Evens and Dolgans, show traces of different and probably more ancient migration(s). Analysis of both haploid loci and autosomal SNP data revealed only minor genetic components shared between Sakha and the extreme Northeast Siberia. Although the major part of West Eurasian maternal and paternal lineages in Sakha could originate from recent admixture with East Europeans, mtDNA haplogroups H8, H20a and HV1a1a, as well as Y-chromosome haplogroup J, more probably reflect an ancient gene flow from West Eurasia through Central Asia and South Siberia.

Conclusions

Our high-resolution phylogenetic dissection of mtDNA and Y-chromosome haplogroups as well as analysis of autosomal SNP data suggests that Sakha was colonized by repeated expansions from South Siberia with minor gene flow from the Lower Amur/Southern Okhotsk region and/or Kamchatka. The minor West Eurasian component in Sakha attests to both recent and ongoing admixture with East Europeans and an ancient gene flow from West Eurasia.

The matrilineal mitochondrial DNA pool is dominated by  C4, C5, D4 and D5, with some instances of other lineages (see fig. 1). All these and most of the rest are common Siberian lineages of East Asian roots. 

In the odd zone, the extremely rare haplogroup R3 has been found among North Yuhaghirs in this study (previously only in Jordan that I know with any certainty). They mention that R3 and R1 are derived from the same root, sharing two coding region mutations, and therefore they proceed to rename R3 as R1b. R1 is an also rare Indian matrilineage. 

The patrilineal Y-DNA pool (see fig. 2) is massively dominated by N1c, which also dominates most Uralic-speaking peoples. This is unusual for a Turkic-speaking population but it was known since long ago. Other still important lineages are C2 (former C3, typical of NE Asia and some North American populations), N1b and R1a. Some instances of I, E1b1b1, J, O, F and L are also reported. C2 is more important among the Northern (non-Turkic) populations of Sakha Republic, reaching to 30-40%.

On the autosomal DNA pool, the heatmat (fig. 4) shows that among all sampled populations the Selkup are particularly isolated. Koryaks and Chukchis from the far NE Siberia form a small cluster of their own and so do Shors and Kets (West Siberians). Native American populations also show great individual isolation in comparison with most Eurasians.

Otherwise there are three major clusters: West/South/Central Eurasians, East Asians and Siberians, who generally also cluster with East Asians.

Some of this is also apparent in the PCA (fig. 5) although not as neatly:

PCA of the native populations of Sakha in the context of other Eurasian and American populations.

Maybe more illustrative is the ADMIXTURE analysis:

ADMIXTURE plots. Ancestry proportions of the 758 individuals studied (from 55 populations) as revealed by the ADMIXTURE software at K = 3, K = 4, K = 6, K = 8, and K = 13.
The analysis reveals, from K=6 upwards, the following clusters: West Eurasian (dark blue), South Asian (green), East Asian (orange, also light green at K=13) and several Siberian and Native American specific clusters (yellow, light and dark brown, red, etc.)

The persistance of the blue West Eurasian component in Aleutians and Greenlanders should raise some eyebrows. However, Greenlanders do not really cluster with West Eurasians in the heatmap, so this is almost certainly an artifact that indicates that a much greater K-depth should be achieved in order to properly classify this most diverse human sample. Thirteen clusters are obviously not enough.

6 comments:

  1. The tricky issue is to find out how long the region was East Asian in population genetics as it appeared to oscillate over deep history.

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    1. Not sure what kind of time depth you're thinking about but Yakutia is one of the coldest areas on Earth and my understanding of the proto-NA migration is that it probably went through Mongolia rather than North of Lake Baikal, moving northwards only after reaching the more favorable coast probably. In any case around the LGM it was surely a very hostile environment and hence unhinabited (see Don's Maps). I would discard any significant habitation of this area before the Late UP, a period that already brought East Asian type genetics to all Siberia (notably Uralic-like N1 Y-DNA lineages and also C2, which dominate Yakutia).

      In my interpretation, before the Late UP there were only P lineages in Siberia, mostly Q (but as we saw in Mal'ta also some R*), arrived from West or South Asia via Altai. In those times the contact area of Western and Eastern populations would be rather around Mongolia and Manchuria.

      It seems true that parts of Yakutia were ice-free in the LGM but much as the dry parts of Antarctica are, being in fact too cold and hostile for (meaningful?) human settlement. Notice that:

      At the Last Glacial Maximum, continuous permafrost covered a much greater area than it does today, covering all of ice-free Europe south to about Szeged (southeastern Hungary) and the Sea of Azov (then dry land) and East Asia south to present-day Changchun and Abashiri. (Wikipedia: "Permafrost")

      Even middle altitude areas in places as sunny as Valencia were permafrosted at some point, forcing the evacuation of some caves. In the Northern Eurasian belt the LGM definitely had an impact hostile to human inhabitation, although it is true that we do not know with certainty if small pockets survived here or there: Moravia and Ukraine seem confirmed, Beringia is speculated based on plant evidence but still no direct human one, but with great certainty Yakutia was way too hostile.

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  2. Maju wrote,

    "The persistance of the blue West Eurasian component in Aleutians and Greenlanders should raise some eyebrows."

    This does not reflect "persistence" of a West Eurasian component in Aleuts and Greenland Eskimos so much as it reflects recent European admixture in those populations. The Aleutians in particular have been devastated by European predation, and the sparse remnants of the native population are nearly all descended from Europeans in the male line. Actually, the modern "Aleut" population may be considered as a colonial European-derived population with a certain amount (approx. 1/3) of non-European, indigenous ancestry.

    Please do not make the mistake of assuming that all individuals in published samples of minority ethnic groups are 100% genetically descended from ancestors who also belonged to that ethnic group. For example, one of the three individuals in this sample of Nivkhs is obviously half Russian (or some other European) by descent. The two other Nivkhs more closely retain what was presumably the genetic profile of pre-colonial Nivkhs.

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    Replies
    1. My argument is based on how Greenlanders cluster in the heatmap, where they form a separate cluster with no particular relationship with any other group than themselves (West and East Greenlanders). However in the ADMIXTURE graph, they show up as heavily influenced by Europeans, almost as much as Aleuts, so my conclusion is (must be) that Greenlanders' apparent Euro-mix (as in ADMIXTURE) is not such but an artifact (as shown in the heatmap).

      Aleuts are not represented in the heatmap, so it's possible that they are still admixed to some important extent with Europeans but, extrapolating from the Greenlander case, it seems quite apparent that at least part of that blue component is probably an artifact.

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    2. Reich et al 2012 had to masque 55% and 38% of its Greenlandic samples due to European admixture, and the Aleutian numbers were so high that they were excluded from the study completely. So I don't think it's just an artifact. There's been a lot of contact between Europeans and locals in the far north over the years. The Norse got to Greenland before the Inuit did after all (though I doubt the Norse were responsible for much if any of this admixture). Whalers, fishers and fur trades like the Hudson's Bay Company would have had a huge presence over the years. Most of the modern day Inuit settlements in Canada actually formed around Hudson's Bay Company trading posts, or were put there by force by the Canadian government. :( I would think the Danish would have had a similar practice in Greenland. The great irony of course is that despite this huge amount of admixture, Inuit languages and culture are still overwhelmingly predominant in the Canadian High Arctic and Greenland. In any event, I think that "European" result for Greenland is real, though poorly studied.

      The Inuit's Thule culture expansion only started around 1,000 AD, and the Eskimo-Aleut breakup was only around 4,000 BC, so some earlier similarities aren't totally out of the question I'd think.

      From the earliest records of contact to about 100 years ago reports of "Blonde Eskimos" was a thing btw. I don't it's been settle whether or not these reports were factual or not though.

      Yupik samples would have been nice as an intermediate population.

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    3. Does someone know if this study also masked the Greenlanders? Because if, even one of the samples shows general appearance of Euro-admixture, both samples perform similarly in the heat map. If it's real Euro-admixture, then they would have shown some clustering with Europeans but they do not (only very weakly with some Central Asian populations like Uyghurs).

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