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People have traditionally relied on fish to supply their major food and healthcare needs all across the world. However, there has been little focus on the traditional dietary, cultural identity, and integrity of traditional food systems in many rural Himalayan populations. The current study looks into the use of fish in traditional food and foraging practices, as well as its role in local traditional medicine and cultural practices. Semi-structured interviews and group discussions were used to collect data in the years 2020–2021. The data were analyzed using various statistical indices such as the fidelity level (FL), rank order priority (ROP), and relative popularity level (RPL). The data were then classified through a heat map, and ordination techniques were used to refine them even further. The current study identified 20 fish species of five families, with Cyprinidae (70%) as the dominant family. Three unique traditional fish preservation techniques were documented, namely: (1) smoking, (2) sun drying, and (3) pickling. The smoked fish are locally called fari, sun-dried fish are known as hugaad, and pickled fish are gaad anchaar. As a result of rapid modernization, fish has become a symbol of social class in the valley. In total, 17 diseases were identified, with joint pain being treated by the greatest number of species (N = 10). Flesh (43%) was the most commonly used part to treat various diseases. The mode of application of various fishbody parts for treating a variety of diseases was most commonly peroral (65%), followed by topical (35%). Schizopyge niger demonstrated the highest level of fidelity (82%) for joint pain. Schizopygeniger, Schizothorax curvifrons, Catla catla, Schizothorax esocinus, Schizothorax labiatus, and Schizothorax plagiostomus were the most popular (relative popularity level = 1.0). The rank order priority of six species was above 55 (Schizothorax plagiostomus (59.18), Labeo dyocheilus (61.99) Schizothorax labiatus (64.28), Schizothorax esocinus (68.36), Schizothorax curvifrons (73.19), and Schizopyge niger (82)). Two principal groups of six ethno-zoological categories (medicine, food, black magic, poultry, agricultural, and recreational) were identified using cluster analysis. Fish are also important as a source of livelihood and are closely associated with a local ethnic group known as Hanji/Haanz, who have extensive knowledge of ecology of the local fish species. Our research will contribute to filling a knowledge gap in the Kashmir Himalayan region, with policy implications for the protection and preservation of high-quality traditional knowledge for future generations. The findings of this documentation study can be used as an ethnopharmacological foundation for selecting fish in future pharmaceutical research.

Schizothorax prenanti (S. prenanti) is mainly distributed in the upstream regions of the Yangtze River and its tributaries in China. This species is indigenous and commercially important. However, in recent years, wild populations and aquacultures have faced the serious challenges of germplasm variation loss and an increased susceptibility to a range of pathogens. Currently, the genetics and immune mechanisms of S. prenanti are unknown, partly due to a lack of genome and transcriptome information. Here, we sought to identify genes related to immune functions and to identify molecular markers to study the function of these genes and for trait mapping. To this end, the transcriptome from spleen tissues of S. prenanti was analyzed and sequenced. Using paired-end reads from the Illumina Hiseq2500 platform, 48,517 transcripts were isolated from the spleen transcriptome. These transcripts could be clustered into 37,785 unigenes with an N50 length of 2,539 bp. The majority of the unigenes (35,653, 94.4%) were successfully annotated using non-redundant nucleotide sequence analysis (nt), and the non-redundant protein (nr), Swiss-Prot, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. KEGG pathway assignment identified more than 500 immune-related genes. Furthermore, 7,545 putative simple sequence repeats (SSRs), 857,535 single nucleotide polymorphisms (SNPs), and 53,481 insertion/deletion (InDels) were detected from the transcriptome. This is the first reported high-throughput transcriptome analysis of S. prenanti, and it provides valuable genetic resources for the investigation of immune mechanisms, conservation of germplasm, and molecular marker-assisted breeding of S. prenanti.

Schizothorax prenanti is an endemic fish in the mountain rivers of southwestern China with unique protection value. To further explore the vortex motion of hydraulic habitats, which is closely related to the fish breeding process, the cross-sectional vorticity was used to evaluate the hydraulic conditions of the natural spawning habitat of S. prenanti. A coupled level-set and volume-of-fluid (CLSVOF) three-dimensional (3D) model was applied to simulate the hydraulic habitat of the Weimen reach, a typical natural spawning ground for S. prenanti in the upper Yangtze River. The model was used in conjunction with the Wilcoxon rank sum test to distinguish the distributions of vertical vorticity in spawning and non-spawning reaches. Statistical analysis revealed that the cross-sectional vorticity in spawning reaches was significantly greater than in non-spawning reaches, with likely biological significance in the spawning process. The range of cross-sectional mean values of vorticity was 0.17 s-1-0.35 s-1 in areas with concentrated fish sperm and eggs; the minimum value was 0.17 s-1, and the majority of values were greater than 0.26 s-1. Based on this study, a vague-set similarity model was used to assess the effectiveness of ecological restoration by evaluating the similarity of the cross-sectional vorticity of the natural spawning reach and rehabilitated spawning reach after implementing ecological restoration measures. The outcome might provide a theoretical basis for the recovery of damaged S. prenanti spawning grounds and act as an important complement for the assessment of recovery effectiveness and as a useful reference for the coordination of ecological water use with the demands of hydraulic and hydropower engineering.

Phenotypically diverse species from recently evolved groups always share allele/haplotype due to insufficient differentiation in the early process. In this study, we performed population genetics analyses using sequences from the mitochondrial cytochrome b gene, and two nuclear genes to investigate the genetic differentiation of the closely related Schizothorax species complex, comprising a group of alpine fish living in the Nujiang River. The results from both mtDNA and nDNA markers revealed relatively low but pronounced genetic differentiation among the three Schizothorax species, i.e., Schizothorax gongshanensis , S . lissolabiatus , and S . nukiangensis . However, haplotype sharing was frequently occurred among the three species. Divergence time estimation suggested the last glaciation on the Tibetan Plateau (0.075–0.01 Ma) might drive the divergence of the species complex. Gene flow might contribute to the haplotype sharing between S . gongshanensis and S . lissolabiatus , and between S . gongshanensis and S . nukiangensis , whereas retention of ancestral polymorphisms seemed to be a better explanation of the haplotype sharing between S . lissolabiatus and S . nukiangensis . In addition, S . lissolabiatus populations should obtain more protection in the future because of their low genetic diversity and habitat fragmentation. In summary, our study assesses genetic differentiation among the three closely related Schizothorax species and explores the possible driving forces for their differentiation.

PrenantE9s schizothoracin, Schizothorax prenanti, an endemic fish to China, has undergone a dramatic decline in numbers due to human impacts. We studied its genetic diversity in three tributaries of the Yangtze River: the Qingyi River, which has many hydropower dams, and the Dadu River and Muli River where many hydropower dams are being proposed. Using amplified fragment length polymorphism (AFLP), 621 loci were amplified with seven AFLP primer combinations in 45 individuals. The loci were highly polymorphic and heterozygous (87% polymorphism, 30% heterozygosity). The genetic distances within populations were large. The analysis of molecular variance demonstrated that most variation occurred within populations. The estimated fixation index ( Phi sub(st)) value averaged over all polymorphic loci across the three rivers was 0.0837, indicating a moderate genetic differentiation. The differentiations between populations were significant, and population structure was strong. The results suggested that China had wild populations of PrenantE9s schizothoracin with considerable genetic diversity in the Muli, Dadu and Qingyi rivers. The proposals to dam these rivers should take into account the importance of conserving their genetic quality.

Despite its wide presence in cold-water bodies of central Asian mountains,  Schizothorax plagiostomus  is highly neglected Himalayan ichthyofauna. Here we have performed de novo RNA-sequencing in adult  S. plagiostomus  gonads captured from natural habitat of Garhwal Himalaya [during three distinct maturational stages (pre-spawning, spawning and post-spawning) for both sexes] and compared the season and sex specific differential transcriptomic profiles. Functional analyses of KEGG pathway and GO enrichment demonstrated augmentation in cellular signaling for multiple growth factors, chemokines, cytokines, exosomes and vascular patterning in pre-spawning gonads, rise in t-RNA biosynthesis, chaperone cofactor dependent protein refolding, steroidogenic and calcium signaling network at spawning time, whereas elevated proteolysis, autophagy and apoptotic pathways were prevalent during regressing stages. Among differentially expressed genes (DEGs) distinct sexual dimorphic pattern of male specific  Dmrt1, Sox18, Amh, Wt1, GDNF receptor α  and female specific  Foxl 2 , Gdf9, Zar1,Cyp19a1a, Wntless  were observed.Collectively, this is the first comprehensive gonadal atlas of season dependent developmental transcriptome with respective gametogenic output in any Schizothoracine species. This data will potentially serve as a vital resource for future programs in conservation management and artificial breeding of schizothoracine fishes.

Fish invasions threaten native freshwater ecosystems worldwide, yet methods to map biodiversity in data-deficient regions are scarce. Rainbow trout ( Oncorhynchus mykiss ) and brown trout ( Salmo trutta fario ) have been introduced to the Himalayan ecoregion where they are sympatric with vulnerable native snow trout Schizothorax plagiostomus and Schizothorax richardsonii . We aim to evaluate potential habitat overlap among snow trout and non-native trout in the Indus and Ganges River basins, Himalayan ecoregion. We transferred maximum entropy (MaxEnt) models developed with spatially continuous freshwater-specific environmental variables to map the distribution of potentially suitable habitats for rainbow and brown trout in the Himalayas. We adopted a similar procedure to map suitable habitats for snow trout species. There were substantial habitat overlaps (up to 96%) among snow trout and non-native trout. Yet, the physiography of receiving basins could play a role minimizing the impacts of each non-native trout on native snow trout . We generate high-resolution classified stream suitability maps as decision support tools to help managers in habitat allocation and policy formation to balance recreational fisheries with conservation of snow trout. Our workflow can be transferred to other basins and species for mapping freshwater biodiversity patterns in species-rich yet data-poor regions of the world.

Background Schizothorax o’connori is an endemic fish distributed in the upper and lower reaches of the Yarlung Zangbo River in China. It has experienced a fourth round of whole gene replication events and is a good model for exploring the genetic differentiation and environmental adaptability of fish in the Qinghai-Tibet Plateau. The uplift of the Qinghai-Tibet Plateau has led to changes in the river system, thereby affecting gene exchange and population differentiation between fish populations. With the release of fish whole genome data, whole genome resequencing has been widely used in genetic evolutionary analysis and screening of selected genes in fish, which can better elucidate the genetic basis and molecular environmental adaptation mechanisms of fish. Therefore, our purpose of this study was to understand the population structure and adaptive characteristics of S. o’connori using the whole-genome resequencing method . Results The results showed that 23,602,746 SNPs were identified from seven populations, mostly distributed on chromosomes 2 and 23. There was no significant genetic differentiation between the populations, and the genetic diversity was relatively low. However, the Zangga population could be separated from the Bomi, Linzhi, and Milin populations in the cluster analysis. Based on historical dynamics analysis of the population, the size of the ancestral population of S. o’connori was affected by the late accelerated uplift of the Qinghai Tibet Plateau and the Fourth Glacial Age. The selected sites were mostly enriched in pathways related to DNA repair and energy metabolism. Conclusion Overall, the whole-genome resequencing analysis provides valuable insights into the population structure and adaptive characteristics of S. o’connori . There was no obvious genetic differentiation at the genome level between the S. o’connori populations upstream and downstream of the Yarlung Zangbo River. The current distribution pattern and genetic diversity are influenced by the late accelerated uplift of the Qinghai Tibet Plateau and the Fourth Ice Age. The selected sites of S. o’connori are enriched in the energy metabolism and DNA repair pathways to adapt to the low temperature and strong ultraviolet radiation environment at high altitude.