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. 2013;9(7):e1003634.
doi: 10.1371/journal.pgen.1003634. Epub 2013 Jul 18.

Genomic analysis of natural selection and phenotypic variation in high-altitude mongolians

Jinchuan Xing  1 , Tana Wuren, Tatum S Simonson, W Scott Watkins, David J Witherspoon, Wilfred Wu, Ga Qin, Chad D Huff, Lynn B Jorde, Ri-Li Ge
Affiliations

Genomic analysis of natural selection and phenotypic variation in high-altitude mongolians

Jinchuan Xing et al. PLoS Genet. 2013.

Abstract

Deedu (DU) Mongolians, who migrated from the Mongolian steppes to the Qinghai-Tibetan Plateau approximately 500 years ago, are challenged by environmental conditions similar to native Tibetan highlanders. Identification of adaptive genetic factors in this population could provide insight into coordinated physiological responses to this environment. Here we examine genomic and phenotypic variation in this unique population and present the first complete analysis of a Mongolian whole-genome sequence. High-density SNP array data demonstrate that DU Mongolians share genetic ancestry with other Mongolian as well as Tibetan populations, specifically in genomic regions related with adaptation to high altitude. Several selection candidate genes identified in DU Mongolians are shared with other Asian groups (e.g., EDAR), neighboring Tibetan populations (including high-altitude candidates EPAS1, PKLR, and CYP2E1), as well as genes previously hypothesized to be associated with metabolic adaptation (e.g., PPARG). Hemoglobin concentration, a trait associated with high-altitude adaptation in Tibetans, is at an intermediate level in DU Mongolians compared to Tibetans and Han Chinese at comparable altitude. Whole-genome sequence from a DU Mongolian (Tianjiao1) shows that about 2% of the genomic variants, including more than 300 protein-coding changes, are specific to this individual. Our analyses of DU Mongolians and the first Mongolian genome provide valuable insight into genetic adaptation to extreme environments.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. A) Northern Eurasian populations analyzed. The sampling location of each population is shown on the map, and the number of individuals in each population is shown at the bottom of the figure. B) Neighbor-joining tree for northern Eurasian populations based on the pairwise FST.
Figure 2
Figure 2. Principal components analysis of A) ten northern Eurasian populations; and B) six East Asian populations.
First two principal components are shown. Each individual is represented by one dot and the color label corresponding to their population. The percentage of variance explained by each PC is shown on the axis.
Figure 3
Figure 3. Genome-wide admixture of Eurasian individuals inferred by ADMIXTURE.
Results from K = 3 to K = 6 are shown. Each individual's genome is represented by a vertical bar composed of colored sections, where each section represents the proportion of an individual's ancestry derived from one of the K ancestral populations. Individuals are arrayed horizontally and grouped by population as indicated.
Figure 4
Figure 4. Comparison of DU Mongolian and HapMap CHB haplotypes at the EPAS1 genomic region.
Haplotype pattern at the EPAS1 genomic region in the 84 chromosomes of 42 DU Mongolian individuals and 84 randomly drawn chromosomes from 45 CHB individuals is shown. An asterisk at position 46490868 on chromosome 2 indicates the core SNP haplotype for the EPAS1 genomic region shown (chr2:46304028–46851921; 191 SNPs total); all haplotypes were sorted as previously described (Figure 1 of [20]).
Figure 5
Figure 5. A) Number of variants shared between Tianjiao1 and CGI54 panel individuals. CGI54 panel individuals were grouped by populations, and the mean number of shared variants and standard deviation for each population are shown. Population code: CHB: Han Chinese; JPT: Japanese; GIH: Gujarati; PUR: Puerto Rican; MXL: Mexican-American; TSI: Tuscan; CEU: Utah residents (CEPH) with Northern and Western European ancestry; MKK: Maasai; ASW: African-American; YRI: Yoruba; LWK: Luhya. B) Neighbor-joining tree of Tianjiao1 and the CGI54 panel individuals. The bootstrap value for each branch is shown.
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