The whole mitochondrial genome sequences from specimens of ancient Siberian Tagar and Pazyryk cultures vanished in the first century BC: implications to their origin and medical history
The genetic replacement of the Mesolithic populations during the Neolithic in Europe and Asia is not yet well elucidated. The Tagar (upper reaches of Yenisei river) and Pazyryk (Altai) cultures both flourished during the Scythian period of Siberia history (first millennium BC) and became exceptional in livestock breeding, metal production and arts. Both bronze and iron casting have been mastered for production of tools and weapons. As others in southern Siberia, they had a highly developed artistic culture of Scythian-Siberian animalistic style. Interestingly, trepanning is one of the oldest surgical procedures which has archaeological evidence, and, among other places, ancient trepanned sculls have been discovered in Pazyryk culture sites.
We extracted DNA from two ancient tooth specimens (one of Tagar culture individual and one of Pazyryk culture subject with trepanned scull) and prepared deep sequencing libraries using modified single-stranded DNA protocol to increase the highly degraded DNA yield and to exclude contamination with modern samples. Using deep sequencing with Illumina HiSeq 2500, we generated short read sequencing data and reconstructed whole mitochondrial genome sequences for Pazyryk and Tagar samples. The authenticity of DNA was confirmed by the observed specific ancient DNA signatures: short DNA fragments and elevated rates of C->T substitutions towards fragment ends. The potential contamination of modern DNA was estimated by Schmutzi program testing of 256 Eurasian population haplotypes. After excluding potential minor contamination with modern DNA (1-3%), we reconstructed almost complete mitochondrial genome sequences and identified haplogroups for both samples.
We found haplogroup F1b1b for the Tagar subject and U5b2b for the Pazyryk subject. These haplotypes are presented in both Asian and European populations. The F1b is relatively frequent as a fraction of total F in northern parts of East Asia and Central Asia and frequent in Tai peoples. The U5b has been found in remains dating from prehistoric times in Europe. Therefore, the common view is that ancient European mitochondrial haplogroup, U5, arose in Europe. The coalescence time is ~20–24 ky (thousand years) for U5b haplotype. The frequency of U5 haplotypes in Neolithic and present day populations (1-8 %), is lower than in Mesolithic (except Saami populations). Previously, unexpectedly widespread presence of U5b was noted for ancient Mesolitic samples across Europe. We showed the finding of this haplotype in ancient Siberian culture with elements of early advanced medical history. The data show surprisingly uniform presence of U5b in ancient human populations extended from Europe to Asian Siberia. The data suggest the origin of widespread ancient human populations from small number of founders with U5 haplotype expanded to vast historical time-span and geographic areas.