Genetic Variation in Central Asia: An Examination of Population History and Structure

Abstract

The population structure of Central Asia and the effects of population history on that structure have not been well studied. To address this gap, 4,169 mtDNA control region sequences from Central Asia and the surrounding areas (Caucasus, East Asia, East Europe, and northern and southern Asia) sourced from GenBank were analyzed. MtDNA sequences were aligned using MAFFT version 7 and haplogroups were assigned with HaploGrep 2.0. Arlequin 3.5.2 was used to calculate the haplotype diversity, nucleotide diversity, and the mean number of pairwise differences, and to perform an AMOVA. Additionally, genetic distances were calculated between all populations and used in PCA to visualize the distribution of genetic diversity. Lastly, the percentages of mtDNA haplogroups in each population were estimated and used in PCA to examine clustering patterns. The results of this study show that Central Asian populations have a high degree of genetic variation as evidenced by high haplogroup, haplotype, and nucleotide diversities. This genetic variation has been shaped by admixture with populations from East and West Eurasia, and indigenous groups from North and South Asia. Most of the haplogroups in Central Asia have an East or West Eurasian origin, with a small percentage of haplogroups from India. Two haplogroups, D4c and G2a, that may have their origins in Central Asia were also identified. A small, but significant portion of the variation in Central Asia can be accounted for by geographic region. This geographic structure is most consistent with an isolation by distance model. Finally, the history of population interactions within Central Asia has greatly influenced the distribution of genetic variation there. This includes not only recent interactions resulting from the policies of the Soviet Empire, but also those like the movement of Mongol groups into Central Asia beginning thousands of years ago. This study has situated Central Asia in global models of human variation and has provided a framework with which hypotheses regarding the origin and dispersal of humans, Middle and Late Pleistocene hominin interactions, and the geographic extent of Neandertals can be tested.