Y-chromosome variation in Altaian Kazakhs reveals a common paternal gene pool for Kazakhs and the influence of Mongolian expansions

Abstract

Kazakh populations have traditionally lived as nomadic pastoralists that seasonally migrate across the steppe and surrounding mountain ranges in Kazakhstan and southern Siberia. To clarify their population history from a paternal perspective, we analyzed the non-recombining portion of the Y-chromosome from Kazakh populations living in southern Altai Republic, Russia, using a high-resolution analysis of 60 biallelic markers and 17 STRs. We noted distinct differences in the patterns of genetic variation between maternal and paternal genetic systems in the Altaian Kazakhs. While they possess a variety of East and West Eurasian mtDNA haplogroups, only three East Eurasian paternal haplogroups appear at significant frequencies (C3*, C3c and O3a3c*). In addition, the Y-STR data revealed low genetic diversity within these lineages. Analysis of the combined biallelic and STR data also demonstrated genetic differences among Kazakh populations from across Central Asia. The observed differences between Altaian Kazakhs and indigenous Kazakhs were not the result of admixture between Altaian Kazakhs and indigenous Altaians. Overall, the shared paternal ancestry of Kazakhs differentiates them from other Central Asian populations. In addition, all of them showed evidence of genetic influence by the 13(th) century CE Mongol Empire. Ultimately, the social and cultural traditions of the Kazakhs shaped their current pattern of genetic variation.

Figure 1. Kazakh populations analyzed in this study.

The asterisks (*) denote the locations of Altaian Kazakh populations sampled for this study. The locations of comparative Kazakh populations are shown with each corresponding number: Altaian Kazakh [this study], Kazakh1 , , Kazakh2 , Kazakh3 , Kazakh4 , and Kazakh5 . Kazakh1 represents samples that were collected from four locations , .

Figure 2. Reduced median-median joining network of Altaian Kazakhs using 14-STR haplotypes.

Figure 3. Reduced median-median joining network of Altaian and Indigenous Kazakh populations using 5-STR haplotypes.

Figure 4. Principal component analysis plot of genetic distances based on Y-chromosome haplogroup frequencies in Central Asian and Mongolian populations.

Figure 5. Multidimensional scaling plot of R_ST values estimated from Y-STR haplotypes in Central Asian and Mongolian populations.