Convergent genomic signatures of high-altitude adaptation among domestic mammals

Abstract

Abundant and diverse domestic mammals living on the Tibetan Plateau provide useful materials for investigating adaptive evolution and genetic convergence. Here, we used 327 genomes from horses, sheep, goats, cattle, pigs and dogs living at both high and low altitudes, including 73 genomes generated for this study, to disentangle the genetic mechanisms underlying local adaptation of domestic mammals. Although molecular convergence is comparatively rare at the DNA sequence level, we found convergent signature of positive selection at the gene level, particularly the EPAS1 gene in these Tibetan domestic mammals. We also reported a potential function in response to hypoxia for the gene C10orf67, which underwent positive selection in three of the domestic mammals. Our data provide an insight into adaptive evolution of high-altitude domestic mammals, and should facilitate the search for additional novel genes involved in the hypoxia response pathway.

Keywords: Tibetan Plateau; convergent evolution; domestic animals; genome; high altitude.

Figure 1.

Frequent shared targets of positive selection in Tibetan domestic mammals. (A) Distribution of the numbers of simulated shared positively selected genes. Observed number of shared positively selected genes was 43 (O = 43). Namely, 43 protein coding genes evolved under positive selection in at least two Tibetan domestic mammals (in the top 1% ranking). (B) Distribution of the numbers of simulated shared positively selected genes based on one-to-one orthologous genes. We further investigated evidence of convergent signature of positive selection in 10 103 one-to-one orthologous genes. The number of genes observed to potentially evolve under positive selection (in the top 5% ranking) in at least three mammals is 30 (O = 30) (Supplementary Fig. S2). (C) Observed and simulated ratios of gene–gene interactions among positively selected genes within species and between positively selected genes of different species. Lower red circled boxes present the simulated ratios, and above blue boxes are observed ratios (×10⁻³).

Figure 2.

Rapid evolution of hypoxia response genes in six Tibetan domestic mammals. Significantly higher values of XP-EHH (cross population extended haplotype homozygosity), F_ST and ΔDAF (the difference of the derived allele frequencies) were observed for SNPs found in genes known to be involved in hypoxia response than in other genome-wide genes or randomly selected genes. Columns A (compared with genome-wide genes) and B (compared with random genes) represent the –log10 transformed P values calculated using Mann–Whitney U tests. The hypoxia response genes were retrieved from a previous study [35]. Numbers on the nodes of the phylogenetic tree are the divergence times from present (millions of years) and their confidence intervals. Dates are from a previous study [67].

Figure 3.

Functional analysis of C10orf67. (A) Relative mRNA expression levels of mC10orf67 in NIH-3T3 cells stably expressing two independent shRNAs compared with scramble-control shRNA. *P < 0.05. (B) Suppression of apoptosis by depleting C10orf67 expression in NIH-3T3 cells under 1% O₂ hypoxic conditions. (C) After 72 h treatment under hypoxic conditions, NIH-3T3 cells were stained with annexin V/PI, and the percentage of apoptotic cells was assessed by flow cytometry. The scramble-control shRNA stable cell line served as a control. SC, C1 and C2 indicate cells treated by control shRNA, shRNA #1 and shRNA#2, respectively. *P < 0.05, ^**P < 0.001. (D) Comparison of gene expression with scramble-control and C10orf67 knockdown by RNA-seq under normoxic (left panel) and hypoxic (right panel) conditions. A summary dot plot is shown, with blue dots representing down-regulated and yellow dots representing up-regulated genes (n = 3 samples for each, at least 2-fold difference and P-corrected < 0.05). (E) List of GO (gene ontology) terms related to hypoxia and apoptosis that were significantly enriched among the differentially expressed genes between the scramble-control and C10orf67 knockdown cells under normoxic conditions by RNA-seq. The x-axis shows the –log10 transformed FDR corrected P values. The number of enriched genes in each GO is also presented.