Dam removal is considered an effective measure to solve the adverse ecological effects caused by dam construction and has started to be considered in China. The sediment migration and habitat restoration of river ecosystems after dam removal have been extensively studied abroad but are still in the exploratory stage in China. However, there are few studies on the ecological response of fishes at different growth stages. Considering the different habitat preferences of Schizothorax prenanti (S. prenanti) in the spawning and juvenile periods, this study coupled field survey data and a two-dimensional hydrodynamic model to explore the changes in river morphology at different scales and the impact of changes in hydrodynamic conditions on fish habitat suitability in the short term. The results show that after the dam is removed, in the upstream of the dam, the riverbed is eroded and cut down and the riverbed material coarsens. With the increase in flow velocity and the decrease in flow area, the weighted usable area (WUA) in the spawning and juvenile periods decreases by 5.52% and 16.36%, respectively. In the downstream of the dam, the riverbed is markedly silted and the bottom material becomes fine. With the increase in water depth and flow velocity, the WUA increases by 79.91% in the spawning period and decreases by 67.90% in the juvenile period, which is conducive to adult fish spawning but not to juvenile fish growth. The changes in physical habitat structure over a short time period caused by dam removal have different effects on different fish development periods, which are not all positive. The restoration of stream continuity increases adult fish spawning potential while limiting juvenile growth. Thus, although fish can spawn successfully, self-recruitment of fish stocks can still be affected if juvenile fish do not grow successfully. This study provides a research basis for habitat assessment after dam removal and a new perspective for the subsequent adaptive management strategy of the project.

A multi-mesh trammel net has been developed and used for sampling freshwater fishes. However, little is known about the catch efficiency of the net. This research investigated the catch efficiency of a multi-mesh trammel net (nominal mesh size; 10.0, 30.0, 50.0, and 70.0 mm) for fish sampling in the Yangtze River of China. Catch composition and factors affecting catch per unit effort based on fish number (CPUE_N), weight (CPUE_W), and species number (CPUE_S) were analyzed. The results showed that the net was capable of capturing a wide range of fish sizes (total length, 5.5 to 121.0 cm) and species (n = 50). Increasing soak time from 9.4 to 24.0 h resulted in a decrease in CPUE_N and CPUE_W while a longer soak time increased CPUE_S. CPUE_N, CPUE_W, and CPUE_S varied significantly with fishing locations. The net provides a potential complement to the current fish sampling techniques used in freshwater ecosystems (e.g., large rivers, lakes, and reservoirs). The findings of this research help to improve our understanding of the catch efficiency of the multi-mesh trammel net and provides insight into better designs for gears and methods for sampling diverse fish sizes and species.

Cascade hydropower development in the upper Yangtze River has substantially altered riverine habitat conditions. However, quantitative information on fish substrate preferences remains limited. Based on field surveys, six representative substrate types were identified in the Yibin and Jiangjin reaches, and substrate selection patterns of Leptobotia elongata were quantified under controlled flume conditions. This study examined sex-specific and population-level differences in substrate preference. A total of 50 samples were analyzed using one-way ANOVA and the Kolmogorov–Smirnov test. The results are summarized as follows: (1) Substrates of 40–20 mm: Individual female L. elongata exhibited the longest residence time on the 40 mm substrate (1640 s), while individual males also spent the longest time on the 40 mm substrate (1549 s). Within this substrate range, males showed a preference only for the 40 mm substrate (PR = 739), whereas females preferred three substrate types, with the strongest preference for the 40 mm substrate (PR = 7543). (2) Substrates of 10–2.5 mm: Female individuals spent the longest time on the 10 mm substrate (1468 s), and male individuals likewise showed the longest residence time on the 10 mm substrate (1568 s). In this range, males did not show a significant preference for any substrate (PR = −907), whereas females preferred three substrate types, with the 2.5 mm substrate exhibiting the highest preference intensity (PR = 2059). (3) Population-level patterns for 40–20 mm substrates: The population spent the longest time on the 40 mm substrate (1799 s) and preferred three substrate types, among which the 20 mm substrate had the highest preference ratio relative to the other preferred substrates (PR = 4750). (4) Population-level patterns for 10–2.5 mm substrates: The longest residence time was observed on the 10 mm substrate (1762 s). The population preferred three substrate types, with the 10 mm substrate showing the highest preference ratio (PR = 5709). Overall, L. elongata showed a general tendency to prefer larger-sized substrates. This preference is likely associated with enhanced habitat complexity, improved foraging opportunities, and the formation of low-velocity refuges. Our results suggest that maintaining or restoring coarse substrate patches in regulated reaches may improve habitat suitability for L. elongata and potentially benefit other benthic fishes with similar ecological requirements.

Different viruses are abundant in aquatic ecosystems. There has been limited research on the viral communities in the upper reaches of the Yangtze River. Yellow catfish (Pelteobagrus fulvidraco), an important economic fish that is widely distributed in the upper reaches of the Yangtze River, was selected as the research object. Using RNA sequencing, we identified 11 viruses belonging to the Adintoviridae, Tombusviridae, Caudovirales, Microviridae, Picornavirales, and other bacteriophage families. The predominant viral families/order in Luzhou (LZ), Fuling (FL), and Wanzhou (WZ) were Caudovirales, Adinoviridae, and Microviridae, respectively. The virome from WZ had a unique community composition, with a high abundance of Picornavirales compared with LZ and FL. In LZ, the predominant double-stranded RNA virus family was Siphoviridae. Phylogenetic analyses showed that viruses presented high genetic diversity. Phylogenetically, Wenling pleuronectiformes picornavirus was close to the family Caliciviridae, which includes yellow catfish calicivirus (YcCV), responsible for the massive mortality of yellow catfish in 2020. This study provides insights into the viral community composition in yellow catfish in the upper reaches of the Yangtze River, revealing a diverse and unique river water virome and providing clues for future research on the origin of viral pathogens.

Environmental DNA (eDNA) metabarcoding has emerged as a powerful tool for biodiversity monitoring, yet its accuracy is fundamentally constrained by the completeness and taxonomic reliability of reference sequence databases. For the Three Gorges Reservoir (TGR), no integrated multi-marker eDNA reference library exists, hampering standardized fish conservation monitoring under the Yangtze River Ten-Year Fishing Ban. Here, we constructed a comprehensive, multi-marker eDNA reference database for the fish fauna of the TGR, encompassing mitochondrial 12S rRNA, 16S rRNA, and cytochrome c oxidase subunit I (COI) gene sequences from 173 specimens (120 species) collected between 2021 and 2024. After integrating publicly available sequences, the final database comprised 161 species. Then, we quantitatively compared species annotation performance between this local database and public repositories. Results showed that while public databases achieved higher nominal species coverage (94.67%), they exhibited critical deficiencies in annotation accuracy, correctly annotating only 77.97% (12S rRNA), 75.00% (16S rRNA), and 38.14% (COI) of sequences from shared species under controlled conditions. In contrast, the local database exhibited 92.37%, 93.10% and 100% annotation accuracy for the respective markers. Optimal interspecific Kimura 2-parameter (K2P) thresholds for species delimitation were 0.00448 (12S rRNA), 0.00531 (16S rRNA), and 0.00734 (COI). In addition, 15, 0, and 4 species pairs exhibited zero interspecific distance for 12S rRNA, 16S rRNA, and COI, respectively. These limitations reinforce the need for cautious interpretation of eDNA metabarcoding results and the integration of multiple markers or complementary nuclear loci. This study provides preliminary evidence that regionally curated, multi-marker reference libraries could improve taxonomic assignment reliability in eDNA metabarcoding compared to uncurated public repositories, providing a foundational resource for biodiversity conservation.

The genus Triplophysa (Nemacheilidae), a dominant component of the Qinghai–Tibet Plateau (QTP) fish fauna, remains poorly understood in its evolutionary relationships and phylogeography. We integrated mitochondrial phylogenomics and population genetics (COI and cytb) with MaxEnt modeling across four time periods—the present, the Last Interglacial (LIG), the Last Glacial Maximum (LGM), and the Mid-Holocene Optimum (MHO)—to examine 12 Triplophysa species, ranging from widely distributed to narrowly endemic taxa. Phylogenetic analyses recovered a monophyletic Triplophysa with a clear split between cave- and non-cave-dwelling lineages. Six range-restricted species (T. stenura, T. dalaica, T. siluroides, T. obscura, T. hsutschouensis, and T. minxianensis) formed reciprocally monophyletic clades, whereas widespread species (T. leptosoma, T. stoliczkae, T. brevicauda, T. orientalis, and T. bleekeri) exhibited non-monophyletic patterns in mitochondrial gene trees, likely reflecting incomplete lineage sorting or mitochondrial capture, though distinguishing these processes requires nuclear data. A positive association between genetic diversity and range size was observed for COI nucleotide diversity when two bottleneck-affected species were excluded. Paleoclimatic reconstructions revealed that suitable habitats expanded to their maximum during the LGM and contracted during interglacials, highlighting two climatically stable refugia in the central Loess Plateau–northern Qinling foothills and the eastern QTP margin–northern Hengduan Mountains. Our results demonstrate a tight coupling between phylogenetic patterns and range dynamics, with narrowly distributed endemics exhibiting both monophyly and reduced genetic diversity. These findings identify genetically vulnerable species as conservation priorities and provide a scientific framework for safeguarding Triplophysa diversity in a warming world.