High altitude adaptation in Daghestani populations from the Caucasus

Abstract

We have surveyed 15 high-altitude adaptation candidate genes for signals of positive selection in North Caucasian highlanders using targeted re-sequencing. A total of 49 unrelated Daghestani from three ethnic groups (Avars, Kubachians, and Laks) living in ancient villages located at around 2,000 m above sea level were chosen as the study population. Caucasian (Adygei living at sea level, N = 20) and CEU (CEPH Utah residents with ancestry from northern and western Europe; N = 20) were used as controls. Candidate genes were compared with 20 putatively neutral control regions resequenced in the same individuals. The regions of interest were amplified by long-PCR, pooled according to individual, indexed by adding an eight-nucleotide tag, and sequenced using the Illumina GAII platform. 1,066 SNPs were called using false discovery and false negative thresholds of ~6%. The neutral regions provided an empirical null distribution to compare with the candidate genes for signals of selection. Two genes stood out. In Laks, a non-synonymous variant within HIF1A already known to be associated with improvement in oxygen metabolism was rediscovered, and in Kubachians a cluster of 13 SNPs located in a conserved intronic region within EGLN1 showing high population differentiation was found. These variants illustrate both the common pathways of adaptation to high altitude in different populations and features specific to the Daghestani populations, showing how even a mildly hypoxic environment can lead to genetic adaptation.

Fig. 1

False discovery and missingness rates using a range of filtering thresholds

Fig. 2

Principal components analysis (PCA). The Daghestani populations form a sub-cluster within the European/Caucasian cluster

Fig. 3

F _ST outlier SNPs in EGLN1 from the three high-altitude populations. The customized UCSC track shows the genomic location of all the SNPs called in this study from the EGLN1 genic region (black) and the outlier SNPs for the F _ST statistic in Avars (blue), Kubachians (red) and Laks (brown). Below the SNPs is the gene structure, some relevant histone modifications, the conservation of the region and all the SNPs reported in the dbSNP(130) database. The Kubachian 13-SNP cluster is seen in the left half of the plot, spanning the 229580000 coordinate

Fig. 4

F _ST outlier SNPs in HIF1A from the three high-altitude populations. The customized UCSC track shows the genomic location of all the SNPs called in this study in the HIF1A genic region (black) and the outlier SNPs for the F _ST statistic in Avars (blue), Kubachians (red) and Laks (brown). Below the SNP position is the gene structure, some relevant histone modifications, the conservation of the region and all the SNPs reported in the dbSNP(130) database. The non-synonymous SNP rs11549465 is identifiable as the only outlier in the Laks track

Fig. 5

a Neutrality tests for EGLN1. The y axis shows the fold above the neutral region maximum, chosen as the empirical threshold for deviation from neutrality. b Network of EGLN1 haplotypes. Circles represent haplotypes, with area proportional to frequency (smallest = 1) and are coloured according to the population of origin as in A. Lines represent mutational steps separating the haplotypes, with the number of steps indicated in red