Siberia and Western Russia are home to over 40 culturally and linguistically diverse indigenous ethnic groups. Yet, genetic variation of peoples from this region is largely uncharacterized. We present whole-genome sequencing data from 28 individuals belonging to 14 distinct indigenous populations from that region. We combine these datasets with additional 32 modern-day and 15 ancient human genomes to build and compare autosomal, Y-DNA and mtDNA trees. Our results provide new links between modern and ancient inhabitants of Eurasia. Siberians share 38% of ancestry with descendants of the 45,000-year-old Ust-Ishim people, who were previously believed to have no modern-day descendants. Western Siberians trace 57% of their ancestry to the Ancient North Eurasians, represented by the 24,000-year-old Siberian Malta boy. In addition, Siberians admixtures are present in lineages represented by Eastern European hunter-gatherers from Samara, Karelia, Hungary and Sweden (from 8,000-6,600 years ago), as well as Yamnaya culture people (5,300-4,700 years ago) and modern-day northeastern Europeans. These results provide new evidence of ancient gene flow from Siberia into Europe.Valouey et al., "Reconstructing Genetic History of Siberian and Northeastern European Populations" (2015).
Eurogenes has noted that while there is a close correspondence between Malta-like ancestry and Eastern European Hunter-Gatherer genetics, that there is not a good correspondence between this autosomal component and the Y-DNA N1c1 commonly found in Uralic and Scandinavian populations. This maker may instead distinguish circumpolar from non-circumpolar populations.
Time depth is a tricky issue in Siberian populations. There appear to have been multiple populations sweeps from East to West and then back from West to East again across the region, even in historical times, and this area was completely depopulated during the LGM with less clarity than in some other places about where the refugia from which it was repopulated were located.
There are Paleo-Siberian layers (pre-modern Siberian), modern indigenous Siberian layers (pre-Uralic), Uralic layers (ca. 35th to 25th centuries BCE), Proto-Indo-European layers (Tocharians ca. 20th century BCE to ca. 6th century CE), Turkic migrations (1st to 6th centuries CE), Islamic expansions (West to East starting in the 7th century CE), Mongolian migrations (East to West ca. 13th-14th centuries CE), and Russian migrations (West to East starting in the 17th century or so CE). It is possible that instances of Y-DNA C in Europe in ancient DNA may represent traces of old East to West migration, but they are outliers and it is hard to say why they turn out. This list is illustrative only and surely contains mistakes and overlooks nuances.
Honestly, the extent to which Siberian ancestry is Paleolithic is remarkably high and probably reflects the fact that the region is largely ill suited to intense farming. It isn't clear to what extent "Ust-Ishim ancestry" and "Malta ancestry" overlap from my initial glance at the paper. But, it does appear that modern Siberia is more eastern influenced than western influenced. It also isn't clear to which extent the chosen populations minimize some of the migrations known to have occurred historically.