Research on the driving factors of fish community structure and phylogenetic diversity in the Three Gorges Dam based on environmental DNA.

Environmental DNA (eDNA) technology enables rapid species identification through high-throughput sequencing, providing a critical technical tool for studies on regional biodiversity and species evolution. This study utilized eDNA technology, combined with taxonomic and phylogenetic diversity α and β diversity indices, to characterize fish community traits in the Three Gorges Dam (TGD) and investigate the influence of environmental factors on fish diversity. The results showed that eDNA detected a total of 87 fish species, with Cyprinidae (47 %) and Bagridae (12 %) being the dominant groups, among which 66 species (75.9 %) were still flowing species. The average taxonomic diversity (TD, 22 species) and phylogenetic diversity (PD, 3.19) during the impoundment period (IP) were significantly higher than those during the flood period (FP) (TD, 14; PD, 2.32), with environmental filtering dominating the fish community assemblages. Turnover dominated changes in TD, while nestedness dominated changes in PD, indicating that species replacement between different sampling sites occurred among closely related species. Using the locally weighted regression (LOESS) method, it was found that water physical variables such as water temperature, dissolved oxygen, specific conductance, total dissolved solids, and salinity are key factors influencing TD and PD. Overall, eDNA provides scientific support for fish diversity research in the TGD across multiple dimensions of biodiversity (TD and PD), offering new insights into fisheries conservation and management in the TGD and the mechanisms maintaining biodiversity in the Yangtze River basin.