Evidence for Adaptation to the Tibetan Plateau Inferred from Tibetan Loach Transcriptomes

Abstract

Triplophysa fishes are the primary component of the fish fauna on the Tibetan Plateau and are well adapted to the high-altitude environment. Despite the importance of Triplophysa fishes on the plateau, the genetic mechanisms of the adaptations of these fishes to this high-altitude environment remain poorly understood. In this study, we generated the transcriptome sequences for three Triplophysa fishes, that is, Triplophysa siluroides, Triplophysa scleroptera, and Triplophysa dalaica, and used these and the previously available transcriptome and genome sequences from fishes living at low altitudes to identify potential genetic mechanisms for the high-altitude adaptations in Triplophysa fishes. An analysis of 2,269 orthologous genes among cave fish (Astyanax mexicanus), zebrafish (Danio rerio), large-scale loach (Paramisgurnus dabryanus), and Triplophysa fishes revealed that each of the terminal branches of the Triplophysa fishes had a significantly higher ratio of nonsynonymous to synonymous substitutions than that of the branches of the fishes from low altitudes, which provided consistent evidence for genome-wide rapid evolution in the Triplophysa genus. Many of the GO (Gene Ontology) categories associated with energy metabolism and hypoxia response exhibited accelerated evolution in the Triplophysa fishes compared with the large-scale loach. The genes that exhibited signs of positive selection and rapid evolution in the Triplophysa fishes were also significantly enriched in energy metabolism and hypoxia response categories. Our analysis identified widespread Triplophysa-specific nonsynonymous mutations in the fast evolving genes and positively selected genes. Moreover, we detected significant evidence of positive selection in the HIF (hypoxia-inducible factor)-1A and HIF-2B genes in Triplophysa fishes and found that the Triplophysa-specific nonsynonymous mutations in the HIF-1A and HIF-2B genes were associated with functional changes. Overall, our study provides new insights into the adaptations and evolution of fishes in the high-altitude environment of the Tibetan Plateau and complements previous findings on the adaptations of mammals and birds to high altitudes.

Keywords: Tibetan Plateau; Triplophysa fishes; accelerated evolution; adaptation; transcriptome.

Fig. 1.—

Phylogenetic tree used in this study (A) and the Ka/Ks ratios for the terminal branches obtained from each ortholog (B), concatenated alignments constructed from all orthologs (C), and 1,000 concatenated alignments constructed from ten randomly chosen orthologs (D). The blue line in (A) represents the Triplophysa fishes, which are highlighted in light blue. Tda, T. dalaica; Tsc, T. scleroptera; Tsi, T. siluroides; Pda, P. dabryanus; Dre, D. rerio; Ame, A. mexicanus.

Fig. 2.—

Mean Ka/Ks ratios for each GO category with more than ten orthologs in each of the Triplophysa fishes and P. dabryanus (A–C, Tda, T. dalaica; Tsc, T. scleroptera; Tsi, T. siluroides). GO categories with statistically significantly higher Ka/Ks ratios in Triplophysa fish (red) and P. dabryanus (blue) are highlighted. Points with light red and light blue represent GO categories with higher but statistically not significant Ka/Ks ratios in each of the Triplophysa fishes and P. dabryanus.

Fig. 3.—

Analysis of Triplophysa lineage-specific nonsynonymous mutations. (A) Percentage of genes having Triplophysa lineage-specific nonsynonymous mutations. “All” represents all the orthologous genes. “Overlap” represents a subset of genes that are both FEGs and PSGs. (B) Number of Triplophysa lineage-specific nonsynonymous mutations among FEGs and non-FEGs, PSGs and non-PSGs, and overlap and nonoverlap of FEGs and PSGs. Significant differences are indicated by asterisks, based on chi-square test (A) and Wilcoxon rank-sum test (B), **P < 0.01.

Fig. 4.—

Evolutionary analysis and sequence alignments of Triplophysa lineage-specific nonsynonymous mutations across representative fishes based on positively selected HIF-1A gene (A) and HIF-2B gene (B). The protein coordinates of HIF-1A and HIF-2B referred to the Ensembl ID ENSDARP00000044281 and ENSDARP00000074832, respectively. (C) Structure model of the PAC domain. The mutated site S329N in the PAC domain is indicated and was predicted to decrease the thermodynamic stability of the domain (ΔΔG = 1.42). (D) Structure model of the C-TAD domain of HIF-1A and three mutated sites S710P, L712I, and L746Y in the C-TAD domain are marked and are predicted to decrease the thermodynamic stability of the domain (ΔΔG = 0.96 kcal/mol).