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Wang Y.,CAS Wuhan Institute of Hydrobiology | Wang Y.,University of Chinese Academy of Sciences | Yang L.,CAS Wuhan Institute of Hydrobiology | Yang L.,University of Chinese Academy of Sciences | And 4 more authors.
Genome Biology and Evolution | Year: 2015

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. © The Author(s) 2015.

Zhang Y.P.,Gansu Fishers Research Institute | Du Y.Y.,Gansu Fishers Research Institute | Wang T.,Gansu Fishers Research Institute | Hu Y.B.,Gansu Fishers Research Institute | And 2 more authors.
Shengtai Xuebao/ Acta Ecologica Sinica | Year: 2014

Brachymystax lenok tsinlingensis is one of an endemic fishes distributing in Qinling mountains scatteredly. Due to environmental depravation and overfishing, its population size was sharply decreased. To establish a scientific basis to conserve this species, studies on the population genetic structure and phylogeography are necessary. In this study, the population genetic variations and phylogeographical patterns of 112 Brachymystax lenok tsinlingensis collected from six sites of the Wei River basin were investigated. An 891bp control region partial sequence of mtDNA was amplified in each sample, and 42 variable sites were detected, including 39 parsim-info sites and 3 singleton sites, with 26 haplotypes. The contents of cytosine, thymine, adenine and guanine were 23.1%, 30.8%, 31.7%, and 14.5%, respectively. Total haplotype diversity and nucleotide diversity were 0.883 and 0.00799, respectively. The genetic diversity of the Malu River population was the highest among these six populations, while the population of Zhang River was the lowest with only one haplotype H2. Of the 26 haplotypes, H2 was detected in 35 samples (31%) from 5 populations except the Malu River population. The result of AMOVA showed that 39.95% molecular variation was among populations and 60.05% within populations. The pairwise fixation index (Fst) revealed significant differences except between the Zhang River population and the Nabuda River population. Phylogenetic tree with Hucho taimen as outgroup showed that three geographic populations from the middle reach of Wei River including 16 haplotypes formed a big branch, and the rest haplotypes formed several small branches. The minimum spanning network for Brachymystax lenok tsinlingensis showed that the haplotypes of six geographical populations formed two big groups: the upper reach group and the middle reach group of the Wei River. The haplotype H2 was inner branch haplotype, it tend to be more widely as the ancestors haplotype, thus Brachymystax lenok tsinlingensis may have originated in the haplotype H2. Mismatch distribution analysis map showed a peak type, and Tajima’s D value (-0.18715) of neutrality test is negative, but no significant difference, which indicates that Brachymystax lenok tsinlingensis in this research hadn’t experience population expansion. Maybe due to climate change, the remaining individuals do not adapt to the living environment, the population don’t carry out expansion. The haplotype H2 derives to the other haplotype in the different environmental, Wei River was cut off by a large number of water-shore projects, the migratory route is blocked, it was distributed with dots along the Wei River basin, lacked gene exchange between among populations. Due to the low level of genetic variation of three populations in the Wei River upper reach, more attentions should be paid to protect Brachymystax lenok tsinlingensis as a whole population. © 2014, Science Press. All rights reserved.

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