Autosomal and uniparental portraits of the native populations of Sakha (Yakutia): implications for the peopling of Northeast Eurasia

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and of the analysis of more than 500,000 autosomal SNPs of 758 individuals from 55 populations, including 40 previously unpublished samples from Siberia.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.

Figure 1

The phylogenetic relationships of mtDNA haplogroups and their distribution among the native populations of Siberia. Populations are coded as follows: CY = Central Yakuts, VY = Vilyuy Yakuts, NY = Northern Yakuts, EK = Evenks, EN = Evens, YK = Yukaghirs, DL = Dolgans. *Dolgan samples from Sakha and Taymyr were pooled together.

Figure 2

The phylogenetic relationships of Y-chromosome haplogroups and their distribution among the native populations of Siberia. The defining SNP markers are shown on the branches. Populations are coded as in Figure 1. *Dolgan samples from Sakha and Taymyr were pooled together.

Figure 3

Phylogenetic network of the Y-chromosome haplogroup N1c. Median joining network of N1c haplotypes was constructed based on data of five STRs (DYS19, DYS390, DYS391, DYS392 and DYS393) in 398 individuals by using the program Network 4.6.1.0. Circles represent microsatellite haplotypes, the areas of the circles and sectors are proportional to haplotype frequencies according to the data presented in Additional file 6. Populations from Sakha and the linguistic affiliations of the rest of the samples are indicated by color.

Figure 4

Heatmap plot of F_ST distances. Only populations with N≥4 are included (see Additional file 10 for list of samples).

Figure 5

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

Figure 6

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.

Figure 7

Map of Sakha, with sampling locations. Numbers correspond to the sampling locations: 1 – Kangalassky district, 2 – Megino-Kangalassky district, 3 – Amginsky district, 4 – Churapchinsky district, 5 – Ust-Maysky district, 6 – Tattinsky district, 7 – Ust-Aldansky district, 8 – Namsky district, 9 – Vilyuysky district, 10 – Verkhnevilyuysky district, 11 – Nyurbinsky district, 12 – Suntarsky district, 13 – Oleneksky district, 14 – Zhigansky district, 15 – Eveno-Bytantaysky National district, 16 – Verkhoyansky district, 17 – Momsky district, 18 – Verkhnekolymsky district, 19 – Srednekolymsky district, 20 – Nizhnekolymsky district, 21 – Anabarsky district, 22 – Volochanka, 23 – Ust-Avam, 24 – Dudinka.