Natural selection on EPAS1 (HIF2alpha) associated with low hemoglobin concentration in Tibetan highlanders

Abstract

By impairing both function and survival, the severe reduction in oxygen availability associated with high-altitude environments is likely to act as an agent of natural selection. We used genomic and candidate gene approaches to search for evidence of such genetic selection. First, a genome-wide allelic differentiation scan (GWADS) comparing indigenous highlanders of the Tibetan Plateau (3,200-3,500 m) with closely related lowland Han revealed a genome-wide significant divergence across eight SNPs located near EPAS1. This gene encodes the transcription factor HIF2alpha, which stimulates production of red blood cells and thus increases the concentration of hemoglobin in blood. Second, in a separate cohort of Tibetans residing at 4,200 m, we identified 31 EPAS1 SNPs in high linkage disequilibrium that correlated significantly with hemoglobin concentration. The sex-adjusted hemoglobin concentration was, on average, 0.8 g/dL lower in the major allele homozygotes compared with the heterozygotes. These findings were replicated in a third cohort of Tibetans residing at 4,300 m. The alleles associating with lower hemoglobin concentrations were correlated with the signal from the GWADS study and were observed at greatly elevated frequencies in the Tibetan cohorts compared with the Han. High hemoglobin concentrations are a cardinal feature of chronic mountain sickness offering one plausible mechanism for selection. Alternatively, as EPAS1 is pleiotropic in its effects, selection may have operated on some other aspect of the phenotype. Whichever of these explanations is correct, the evidence for genetic selection at the EPAS1 locus from the GWADS study is supported by the replicated studies associating function with the allelic variants.

Fig. 1.

A genome-wide allelic differentiation scan that compares Tibetan residents at 3,200–3,500 m in Yunnan Province, China with HapMap Han samples. Eight SNPs near one another and EPAS1 have genome-wide significance. The horizontal axis is genomic position with colors indicating chromosomes. The vertical axis is the negative log of SNP-by-SNP P values generated from the Yunnan Tibetan vs. HapMap Han comparison. The red line indicates the threshold for genome-wide significance used (P = 5 × 10⁻⁷). Values are shown after correction for background population stratification using genomic control.

Fig. 2.

Sex-adjusted hemoglobin concentrations and allelic variation in EPAS1 SNPs in a Tibetan sample from Mag Xiang (4,200 m), Tibet Autonomous Region, China. Values were, on average, 0.8 g/dL lower for individuals who were homozygous for the major alleles compared with those who were heterozygous. (Top) The results of testing variants at 49 SNPs with a minor allele frequency ≥5% for genotypic association with sex-adjusted hemoglobin concentration. (Middle) The estimated hemoglobin concentration difference (mean ± 95% confidence interval) between the major allele homozygote and heterozygote genotypes at each SNP. Filled circles represent SNPs detected as having a significant association with hemoglobin concentration, with the false discovery rate controlled at <0.05 across the EPAS1 locus. Open diamonds represent SNPs without significant association. (Bottom) The pairwise linkage disequilibrium measured as r² between SNPs.

Fig. 3.

Sex-adjusted hemoglobin concentrations and allelic variation in EPAS1 SNPs in a Tibetan sample from Zhaxizong Xiang (4,300 m), Tibet Autonomous Region, China. Values were, on average, 1.0 g/dL lower for individuals who were homozygous for the major alleles compared with those who were heterozygous (Top) The results of testing variants at 45 SNPs with a minor allele frequency ≥5% for genotypic association with sex-adjusted hemoglobin concentration. (Middle) The estimated hemoglobin concentration difference (mean ± 95% confidence interval) between the major allele homozygote and heterozygote genotypes at each SNP. Filled circles represent SNP detected as having a significant association with hemoglobin concentration with the false discovery rate controlled at <0.05 across the EPAS1 locus. Open diamonds represent SNP without significant association. (Bottom) The pairwise linkage disequilibrium measured as r² between SNPs.

Fig. 4.

Differences in allelic frequency at SNPs within EPAS1 between the HapMap Han, Mag Xiang and Zhaxizong Xiang cohorts. The horizontal axis is SNP position according to build 36.1. The vertical axis is allelic frequency, with the allele selected for display as the one occurring most frequently in the Mag Xiang cohort. Squares denote data for HapMap Han; circles denote data for Mag Xiang Tibetans; triangles denote data for Zhaxizong Xiang Tibetans. Filled symbols denote those SNPs having significant associations with hemoglobin in both Mag Xiang and Zhaxizong Xiang cohorts; open symbols denote those SNPs without both such associations.