The Yangtze River is the longest river in China and is divided into upstream and mid‐downstream regions by the Three Gorges (the natural barriers of the Yangtze River), resulting in a complex distribution of fish. Dramatic changes to habitat environments may ultimately threaten fish survival; thus, it is necessary to evaluate the genetic diversity and propose protective measures. Species identification is the most significant task in many fields of biological research and in conservation efforts. DNA barcoding, which constitutes the analysis of a short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) sequence, has been widely used for species identification. In this study, we collected 561 COI barcode sequences from 35 fish from the midstream of the Yangtze River. The intraspecific distances of all species were below 2% (with the exception of Acheilognathus macropterus and Hemibarbus maculatus). Nevertheless, all species could be unambiguously identified from the trees, barcoding gaps and taxonomic resolution ratio values. Furthermore, the COI barcode diversity was found to be low (≤0.5%), with the exception of H. maculatus (0.87%), A. macropterus (2.02%) and Saurogobio dabryi (0.82%). No or few shared haplotypes were detected between the upstream and downstream populations for ten species with overall nucleotide diversities greater than 0.00%, which indicated the likelihood of significant population genetic structuring. Our analyses indicated that DNA barcoding is an effective tool for the identification of cyprinidae fish in the midstream of the Yangtze River. It is vital that some protective measures be taken immediately because of the low COI barcode diversity.

River–lake interaction is important for maintaining biodiversity, yet it is vulnerable to hydrological alteration. The connectivity of the channel connecting Poyang Lake and the Yangtze River not only ensures the regular migration of fish but also makes Poyang Lake a feeding and fattening ground for them. Unfortunately, human activities have dramatically changed the hydrodynamic conditions of Poyang Lake, which is experiencing severe drought due to the obvious decline in the water level in autumn and winter, especially since 2003. However, the possible impacts of the changes in the water level on the habitats of migratory fish remain unclear due to the limitation of traditional techniques in spatiotemporal analysis. Here, we combined a hydrodynamic model and habitat suitability model to simulate variations in the suitable habitat area and their connectivity under different water-level conditions. The conditions for the migration pathway of the target fish were obtained by a hydroacoustic survey using the Simrad EY60 echosounder. The results showed that the change in water level will significantly affect the spatiotemporal change in the suitable habitats and their connectivity. In particular, we found the existence of two thresholds that play a dominant role in illuminating the connectivity of effective suitable habitats (HC). Firstly, the maximum value of the weighted usable area (WUA) and HC can be achieved when the water level is more than 16 m. Secondly, when the water level is between 10 and 16 m, the changes in the HC are sensitive and rapid, and the area flooded at this stage is called the sensitive area. HC is a crucial element in fish migration and habitat conditions. Under the condition of continuous drought in the middle reaches of the Yangtze River, our research contributes to clarifying the influence of water level on key habitats for fish and optimizes the practice of river–lake ecological management.

In order to investigate the influence of the high-altitude aquatic environment on indigenous fish metabolites, metabolomics studies were applied in this study. Widespread throughout the main stem of the Nujiang River of Schizothorax nukiangensis, we established sampling sites at high (3890 m) and low (2100 m) altitudes and selected six S. nukiangensis at each location, each weighing approximately 150 g and looking healthy. Then, metabolomics analysis was performed to compare the various metabolites of the two groups. Low concentrations of amino acids, dipeptides, eicosapentaenoic acid, docosahexaenoic acid, pentadecanoic acid, Thioetheramide-PC, 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine, 1-Stearoyl-sn-glycerol-3-phosphocholine, 1-Myristoyl-sn-glycero-3-phosphocholine and 1-Palmitoyl-sn-glycero-3-phosphocholine, high concentrations in S-Methyl-5’-thioadenosine, creatine, D-mannose-6-phosphate, D-mannose-1-phosphate, oleic acid and myristoleic acid were found in high-altitude fish liver. These differentially accumulated metabolites were involved in oxidative stress, energy metabolism, carbohydrate metabolism and lipid metabolism. mTOR signaling pathway, apoptosis and lysosome were the KEGG pathways that were enriched between different groups to ensure energy supply and limit tissue damage of fish at high altitudes. All these results contributed to the understanding of the high-altitude adaptation of S. nukiangensis in the Nujiang River. Nicotine and methoprene, two organic pollutants, performed differently in fish at different altitudes. Overall, our findings advanced the fundamental understanding of fish responses to high-altitude environments, adaptive mechanisms and organic contaminants pollution in the Nujiang River.

This study aimed to determine the practical efficacy of passive eDNA samplers (PEDS) for monitoring fish diversity in riverine ecosystems. It investigated the utility of environmental DNA (eDNA) in accurately depicting fish composition and diversity within the Lancang River. Environmental DNA technology, particularly PEDS, may be used as a substitute for traditional water filtration techniques. However, its effectiveness in natural water ecosystems remains to be proven. The filter materials included mixed cellulose acetate and nitrate (MCE), nylon (NL), glass fiber (GF), and polyvinyl chloride filter membrane (PVC). This study used four different types of filters, each with identical pore sizes and dimensions but constructed from various materials, to assess eDNA capture under laboratory and field conditions in the water samples. The filter materials included mixed cellulose acetate and nitrate (MCE), nylon (NL), glass fiber (GF), and polyvinyl chloride filter membrane (PVC). Environmental DNA macrobarcoding was used to analyze fish biodiversity and to understand the environmental effects on species distribution. Our study identified 50 fish species inhabiting the Lancang River, with equal representation of exotic and native species. A comparative analysis of four filter-based environmental DNA samplers and traditional environmental DNA sampling methods demonstrated comparable species richness. Redundancy analysis indicated that environmental variables, elevation, electrical conductivity, salinity, and chlorophyll-a significantly influenced the distribution patterns of both non-native and native fish species in the river. This study highlights the significance of eDNA technology in evaluating fish diversity across diverse habitats, thereby establishing a theoretical framework for the sustained monitoring and management of fish biodiversity in protected areas.

The ecosystem and Pleistocene glaciations play important roles in population demography. The freshwater gudgeon, Gobiobotia filifer, is an endemic benthic fish in the Yangtze River and is a good model for ecological and evolutionary studies. This study aimed to decode the population structure of G. filifer in the Yangtze River and reveal whether divergence occurred before or after population radiation. A total of 292 specimens from eight locations in the upper and middle reaches of the Yangtze River were collected from 2014 to 2016 and analyzed via mitochondrial DNA Cyt b gene sequencing. A moderately high level of genetic diversity was found without structures among the population. However, phylogenetic and network topology showed two distinct haplotype groups, and each group contained a similar proportion of individuals from all sampled sites. This suggested the existence of two genetically divergent source populations in G. filifer. We deduced that a secondary contact of distinct glacial refugia was the main factor creating sympatric populations of G. filifer, and climate improvement promoted population expansion and colonization.