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

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500,000 autosomal SNPs of 758 individuals from 55 populations, including 40 previously unpublished samples from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.