The Yeniseian and Andronovo Substrates in the Gene Pools of the Indigenous Southern Siberian Populations Analyzed by Q and R1a Y-Haplogroups

Background/Objectives: Due to advances in paleogenetic research, a substantial amount of data has been accumulated on the Y-chromosome of the ancient Scytho-Siberian population that inhabited South Siberia and the adjacent territories of modern Mongolia and North-West China. It became possible to compare the Y-chromosomes of ancient men and modern Tuvans of various clans. Methods: We analyzed Y-SNPs and Y-STRs of ancient and modern samples. Results: During Tuvan ethnogenesis, the total frequency of the haplogroups Q and R1a dropped from 85% in Scytho-Siberian populations to 35% in modern Tuvans. Today, the gene pool of Tuvans is dominated by haplogroups N-P43, N-M178 and O-M175, which remain undetected in the samples from the Scytho-Siberian period. An analysis of the Y-STR phylogenetic networks that integrated data on Y-STR haplotypes and Y-SNPs of the Q and R1a haplogroup branches of both ancient and modern specimens provides findings that should be interpreted as broad phylogenetic affinities consistent with the paternal lineage continuity of haplogroups Q-YP1102 and R1a-Y39884. At the same time, the TMRCA estimate for the Y-STR cluster of the dominant branch of haplogroup Q in modern Tuvans, Q-YP1102-YP1691, is only 670 ± 130 YBP. Clusters of Y-STR haplotypes of the R1a-Y39884, R1a-YP1506, and R1a-YP1543 branches in modern Tuvans are also young and date back to between 1200 and 400 YBP. The Scytho-Siberian haplogroups R1a-YP1272, Q-BZ180, and N-Y147969 were not found in our sample set of modern Tuvans (n = 633). Conclusions: Haplogroups Q-YP1102 and R1a-Y39884 originated in Siberia and their branches are typical for the modern indigenous populations of South and West Siberia. Q-YP1102 marks the Yeniseian substrate and R1a-Y39884 was common in the ancient Siberian Andronovo culture. Overall, the gene pool of the Tuvan population was shaped (at least since the Scytho-Siberian period) by close interactions with the gene pools of Siberia and West Mongolia. However, the resolution of Y-SNP and Y-STR genotyping, as well as the limited sample size of ancient samples and their location in a limited area of the Eerbek River valley, do not allow us to conclude about the direct inheritance of modern Tuvan lineages from the ancient Scytho-Siberian population.