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Natural hybridization plays an important role in species evolution, and its heterosis also provides inspiration for breeding. The present study is to compare the genetic diversity and muscle nutritional quality of Schizothorax waltoni , Schizothorax o’connori , and their natural hybrids that are naturally distributed in the Yarlung Zangbo River. Based on the cluster analysis, the genetic relationship between 13 hybrids (namely S. w. ♀ hybrid) and S. waltoni was found to be closely related, whereas 24 hybrids (namely S. o. ♀ hybrid) were closely related to S. o’connori . The haplotype polymorphisms across the four populations varied between 0.847 and 0.936, while the nucleotide polymorphisms were 0.00305–0.00418. The genetic diversity of the two hybrids was higher than that of S. waltoni and S. o’connori . The crude fat content of the two natural hybrids is significantly higher than that of S. waltoni and S. o’connori . The total amino acid (TAA), essential amino acid (EAA), and delicious amino acid (DAA) contents and the EAA index (EAAI) in the two hybrids were greater than those in S. waltoni and S. o’connori . Compare to S. waltoni (22) and S. o’connori (18), the two natural hybrids (both 24) showed the richer types of fatty acids. The highest contents of polyunsaturated fatty acids (PUFAs), ω ‐3 PUFAs, and ω ‐6 PUFAs were observed in S. waltoni , and ω ‐6 PUFA within the two hybrids possessed intermediate characteristics. In conclusion, the hybrids of S. waltoni and S. o’connori showed advantages of growth rate, genetic diversity, and nutrition quality, therefore appearing to have a potential of breeding for further development and utilization.

The morphological variation in Schizothorax oconnori, Schizothorax waltoni, and their natural hybrids was examined using conventional and image‐based analysis approaches. In total, 38 specimens of S. oconnori, 35 of S. waltoni, and 37 natural hybrids were collected from the Shigatse to the Lhasa section of the Yarlung Zangbo River during June and July 2021. A total of 21 morphometric, 4 meristic, and 27 truss variables were employed for the classification of S. oconnori, S. waltoni, and natural hybrids. Principal component analysis (PCA) and factor analysis (FA), as well as discriminant function analysis (DFA) and cluster analysis (CA), were conducted to identify differences based on traditional and truss measurements. Four principal components explained 75.92% of the variation among the morphometric characters, while five principal components accounted for 79.69% of the variation among the truss distances. FA results showed that factor 1 was associated with head shape, and factor 2 was associated with fins based on morphometric characters. Among the truss characters, factor 1 was related to head shape, and factor 2 was related to chest shape. In DFA, morphometric measurements achieved higher accuracy (100%) compared to truss distances (94.55%). The head morphology of hybrids exhibited intermediate traits between S. oconnori and S. waltoni. Both morphometry‐based and truss‐based clustering indicated that the morphology of natural hybrids leaned toward S. oconnori. In conclusion, the combination of morphometric and truss analysis is beneficial for classifying S. oconnori, S. waltoni, and their natural hybrids. The presence of natural hybrids could be considered an evolutionary response to the differentiation of nutritional and spatial niches in the middle Yarlung Zangbo River. The combination of morphometric and truss analysis is beneficial for classifying Schizothorax oconnori, Schizothorax waltoni, and their natural hybrids. The presence of natural hybrids could be considered an evolutionary response to the differentiation of nutritional and spatial niches in the middle Yarlung Zangbo River.

The phylogeography of Schizothorax waltoni , an endemic and endangered tetraploid schizothoracine fish in the Yarlung Tsangpo River (YLTR) on southern margin of Qinghai-Tibet Plateau (QTP), was investigated using two mitochondrial DNA regions and eleven microsatellite loci. Analyses of concatenated sequences of cytochrome b (1141 bp) and the control region (712 bp) revealed high haplotype diversity and moderate nucleotide diversity. High genetic diversity was observed based on microsatellite variation. Both mtDNA and microsatellite analyses revealed significant genetic differentiation between the eastern population (Mainling) and the other four populations to the west, and non-significant genetic differentiation amongst the three central populations in the west. Significant genetic differentiation was observed between the western population (Shigatse) and the three central populations based on microsatellite analyses alone. Bayesian skyline plot analyses showed that S. waltoni experienced a pronounced population expansion 0.05 to 0.10 Ma. Hierarchical structure analyses of microsatellite data indicated that S. waltoni could be split into three groups (western, central and eastern YLTR). The results indicate that three management units should be considered for S. waltoni . Our findings highlight the need for the conservation and effective management of S. waltoni , which is a key member of the endemic and highly threatened fishes of the QTP.

Schizothorax spp. has experienced a rapid decline in wild population size. Evaluating its genetic diversity and population genetic structure is of critical importance. We developed ten microsatelittes for S. macropogon, S. oconnori, and S. waltoni, which will be useful for genetic analysis. The expected heterozygosity (H), observed heterozygosity (H), Shannon-Weiner diversity indices (H'), and polymorphic information content (PIC) for these 10 microsatellites varied within the ranges of 0.834 to 0.942, 0.643 to 0.899, 1.35 to 1.66, and 0.655 to 0.799, respectively. The 10 microsatellites in this study have shown high allelic polymorphism, suggesting that these markers will compensate for the lack of genetic tools available for the three Schizothorax species.

To help fish to bypass dams and other human-made barriers, some fishways have ingeniously incorporated extended tunnel sections. This innovative design not only optimizes the overall structure of the fishway but also significantly reduces disturbances to the surrounding ecosystem. However, the potential challenges posed by long tunnel sections to fish upstream migration remain insufficiently studied and poorly understood. This study conducted in situ experiments utilizing a passive-integrated-transponder (PIT) system to quantitatively assess the effects of dark and natural light environments on the upstream migration behavior of plateau-endemic fishes (Schizothorax macropogon, Schizothorax waltoni, and Schizothorax oconnori) in a vertical-slot fishway. A 655 m section of the fishway was selected for the experiment, with shading cloth used to simulate the dark environment (DE) of tunnel sections, and its removal serving as the natural light environment (NE). The results showed that in the DE, the upstream behaviors of S. macropogon, S. waltoni, and S. oconnori were not hindered. The entry efficiency at the experimental segment (Ee) of all three species exceeded 65% in the DE, which was higher than that in the NE. The passage efficiency (Ep) of S. macropogon and S. waltoni showed no significant difference between the DE and NE, whereas S. oconnori exhibited a significant difference, with an overall Ep of 0% in the NE and 75.0% in the DE. Additionally, the DE caused a temporary disruption to the diel migration rhythms of the three species. The transit speeds (St) of S. macropogon and S. waltoni were both elevated in the DE, with S. waltoni showing a particularly significant increase; its average St in the DE (0.080 m/s) was much higher than in the NE (0.021 m/s). Ridge regression analysis further indicated that the DE was the primary factor influencing the St and had a positive effect on upstream behavior. Moreover, differences in the upstream migration performances of different species under varying light conditions highlighted species-specific sensitivity to light. This study offers key insights for fish passage design in canyon hydropower projects and highlights the potential of tunnel-type fishways in restoring river connectivity.

As a vulnerable species in the Red List of China’s Vertebrates , Schizothorax waltoni ( S. waltoni ) is mainly distributed in the middle reaches of Yarlung Tsangpo River in Tibet. Due to its delicate meat and delicious taste, S. waltoni is the main economic fish in the producing area. But recently, it has undergone a drastic population decline due to the overfishing of fishery resources, the invasion of foreign species, environmental pollution and other factors. Therefore, it is extremely urgent to protect germplasm resource of S. wa ltoni. In this study, we used Illumina Hiseq 4000 sequencing to develop single nucleotide polymorphism (SNP) markers in S. waltoni. Based on a large number of transcriptome sequences and candidate SNP loci obtained by previous transcriptome studies, 63 SNPs were randomly selected from immune-related genes and 36 loci exhibited significant polymorphisms in genotyping by Sequenom MassARRAY. The observed heterozygosity and expected heterozygosity varied from 0.0789 to 0.9577 and 0.0763 to 0.5033, respectively. There is only 5 SNP loci accord with Hardy–Weinberg equilibrium ( p  > 0.05) and no linkage disequilibria. These polymorphic SNP markers could be used for conservation genetics research in S. waltoni , and may provide new insights into future conservation strategies.