The Y-chromosome haplogroup Q-M242 forms the basis of the gene pool of the Native Americans, and in Eurasia it reaches the highest frequencies in populations of Central and Southern Siberia. Genotyping with an extensive panel of SNP markers, highlighting about 60 branches within haplogroup Q, allowed us to perform an in-depth phylogeographic analysis in populations of Southern Siberia and adjacent regions. The study of six populations of Tuvans and Tozhu people revealed three branches of haplogroup Q, ascending to one root, YP1102. The most frequent of them, the YP1691 lineage, reaches a maximum in the gene pool of northeastern Tozhu Tuvans (51%), decreasing in frequency from east to west to 4%. The distribution of the YP1102* basal lineage follows a similar trend. The third BZ99* lineage is rare in Tuvans (2%), but is noticeable in the Khakas gene pool (9%). Phylogenetic analysis of STR haplotypes showed the distribution of the same clusters not only in different groups of Tuvans but also among the surrounding populations. The structure of the main cluster indicates an increase in the number of carriers of the YP1691 lineage during the Late Iron Age. The frequency map of the YP1691 lineage reflects the consequences of active migration processes during the Common Era within the territory of Southern and Western Siberia. Among the ancient populations of Siberia, the YP1102* variant was found in five individuals: four representatives of the Bronze Age of the Baikal region and one representative of the Scythian-Siberian type culture at the border of Mongolia and Tuva. Ancient DNA data and a higher genetic diversity in the population of Southern Siberia suggest the origin of haplogroup Q-YP1102 in this region and its further penetration to the west and north of Siberia, possibly including with the ancestors of populations of the Yenisei language family. [ABSTRACT FROM AUTHOR]