The Genetic Landscape of Kyrgyzstan: admixture and genetic history of a population from Central Asia

Kyrgyzstan is a Central Asia country, inhabited mainly by a Turkic ethnic group, the Kyrgyz people. It was once crossed by the ancient Silk Road, being a melting point of cultures, languages, and genes. After the decline of the Silk Road trade, the region fell under the domination of different populations, like the Mongols and Russians. This complex history may have resulted in a puzzling pattern of admixture events. Untangling the genetic history and the genetic structure of Kyrgyzstan is essential for understanding the genetic landscape of this region. To achieve it, 184 Kyrgyz genotype data were analyzed through Principal Component Analysis (PCA), Runs of homozygosity (ROH), and linkage disequilibrium pattern to describe the level of population structure and level of inbreeding. To estimate the level of present and past gene flow from neighboring regions, allele frequency-based methods were performed. Then we estimate the effective population size (Ne) through time using IBDNe, identifying bottlenecks and expansions. Considering the level of admixture and the possible different ancestries present in Kyrgyz’s genomes it was also used AS-IBDNe to estimate the ancestry-specific effective population size. Finally, signatures of local adaptation were searched using haplotype-based scans to detect positive selection in the Kyrgyzstan population.