title: Genetic Adaptation of Schizothoracine Fish to the Phased Uplifting of the Qinghai-Tibetan Plateau.
abstract: Many species of Schizothoracine, a subfamily of Cyprinidae, are highly endemic to the Qinghai-Tibetan Plateau (QTP). To characterize the adaptive changes associated with the Schizothoracine expansion at high altitudes, we sequenced tissue transcriptomes of two highland and two subhighland Schizothoracines and analyzed gene evolution patterns by comparing with lowland cyprinids. Phylogenetic tree reconstruction and divergence time estimation indicated that the common ancestor of Schizothoracine fish lived ∼32.7 million years ago (MYA), coinciding with the timing of the first phase of QTP uplifting. Both high- and subhigh-Schizothoracines demonstrated elevated dN/dSratios in the protein-coding genes compared to lowland cyprinids, from which some biological processes implicated in altitude adaptation were commonly identified. On the other hand, the highland and subhighland lineages presented drastically divergent landscapes of positively selected genes (PSGs), enriched with very different gene ontology (GO) profiles, including those in "sensory organ morphogenesis," "regulation of protein ubiquitination," "blood circulation," and "blood vessel development." These results indicated different selection pressures imposed on the highland and subhighland lineages of the Schizothoracine subfamily, with a higher number of genes in the high-altitude species involved in adaptations such as sensory perception, blood circulation, and protein metabolism. Our study indicated divergent genetic adaptations in the aquatic species facing the phased uplifting of QTP.
authors.affiliation: Key Laboratory of Aquaculture Resources and Utilization, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, China.
authors.forename: Dongsheng
authors.initials: D
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Aquaculture Resources and Utilization, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, China.
authors.forename: Mengchao
authors.initials: M
authors.lastname: Yu
authors.affiliation: Key Laboratory of Aquaculture Resources and Utilization, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Hu
authors.affiliation: Key Laboratory of Aquaculture Resources and Utilization, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, China.
authors.forename: Sihua
authors.initials: S
authors.lastname: Peng
authors.affiliation: Key Laboratory of Aquaculture Resources and Utilization, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, China.
authors.forename: Yimeng
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, China.
authors.forename: Weiwen
authors.initials: W
authors.lastname: Li
authors.affiliation: Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, China.
authors.forename: Congcong
authors.initials: C
authors.lastname: Wang
authors.affiliation: The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
authors.forename: Shunping
authors.initials: S
authors.lastname: He
authors.affiliation: Key Laboratory of Aquaculture Resources and Utilization, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, China.
authors.forename: Wanying
authors.initials: W
authors.lastname: Zhai
authors.affiliation: Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, China qhxu@shou.edu.cn lbchen@shou.edu.cn.
authors.forename: Qianghua
authors.initials: Q
authors.lastname: Xu
authors.affiliation: Key Laboratory of Aquaculture Resources and Utilization, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, China qhxu@shou.edu.cn lbchen@shou.edu.cn.|Marine Biology and Biotechnology Laboratory, Qingdao National Laboratory for Marine Science and Technology, China.
authors.forename: Liangbiao
authors.initials: L
authors.lastname: Chen
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000531:Altitude; D000818:Animals; D003530:Cyprinidae / Q000235:genetics* / Q000502:physiology*; D017753:Ecosystem; D014644:Genetic Variation; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D060066:Protein Interaction Maps / Q000235:genetics; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D018609:Tibet; D059467:Transcriptome / Q000235:genetics
keywords: GenPred; Genomic Selection; Qinghai-Tibetan Plateau; Schizothoracine fish; Shared Data Resources; adaptive evolution; hypoxia