Genome-wide analysis of cold adaptation in indigenous Siberian populations

Alexia Cardona, Luca Pagani, Tiago Antao, Daniel J Lawson, Christina A Eichstaedt, Bryndis Yngvadottir, Ma Than Than Shwe, Joseph Wee, Irene Gallego Romero, Srilakshmi Raj, Mait Metspalu, Richard Villems, Eske Willerslev, Chris Tyler-Smith, Boris A Malyarchuk, Miroslava V Derenko, Toomas Kivisild

Research output: Contribution to journalArticle (Academic Journal)peer-review

74 Citations (Scopus)

Abstract

Following the dispersal out of Africa, where hominins evolved in warm environments for millions of years, our species has colonised different climate zones of the world, including high latitudes and cold environments. The extent to which human habitation in (sub-)Arctic regions has been enabled by cultural buffering, short-term acclimatization and genetic adaptations is not clearly understood. Present day indigenous populations of Siberia show a number of phenotypic features, such as increased basal metabolic rate, low serum lipid levels and increased blood pressure that have been attributed to adaptation to the extreme cold climate. In this study we introduce a dataset of 200 individuals from ten indigenous Siberian populations that were genotyped for 730,525 SNPs across the genome to identify genes and non-coding regions that have undergone unusually rapid allele frequency and long-range haplotype homozygosity change in the recent past. At least three distinct population clusters could be identified among the Siberians, each of which showed a number of unique signals of selection. A region on chromosome 11 (chr11:66-69 Mb) contained the largest amount of clustering of significant signals and also the strongest signals in all the different selection tests performed. We present a list of candidate cold adaption genes that showed significant signals of positive selection with our strongest signals associated with genes involved in energy regulation and metabolism (CPT1A, LRP5, THADA) and vascular smooth muscle contraction (PRKG1). By employing a new method that paints phased chromosome chunks by their ancestry we distinguish local Siberian-specific long-range haplotype signals from those introduced by admixture.

Original languageEnglish
Pages (from-to)e98076
JournalPLoS ONE
Volume9
Issue number5
DOIs
Publication statusPublished - 2014

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