Seasonal Differences in Fish Community Structure in the Upper Yangtze River Based on eDNA Metabarcoding: A Multi-Dimensional Analysis

This study used environmental DNA (eDNA) metabarcoding to monitor fish communities at 14 sites along the upper Yangtze River across four seasons, aiming to understand seasonal variations in community structure. This study reflects on the current status of fish community structure in the region by leveraging an analytical discussion on the composition of fish species and functional groups, the application of 16 multidimensional diversity indices, and the relationships between fish communities and environmental variables. A total of 120 fish species were detected. The communities predominantly consisted of species that produce sticky eggs, are sedentary, and have omnivorous diets. However, the sequence reads of species producing drifting eggs, migratory, and carnivore fish groups were higher in autumn and winter compared to spring and summer. Except for the functional evenness index (FEve), all other functional diversity indices, as well as α diversity, taxonomic diversity, and phylogenetic diversity indices, were higher in spring and summer compared to autumn and winter. This suggests that fish diversity is greater in spring and summer due to increased fish activity during the spawning season and higher eDNA shedding and detectability under warmer conditions; however, ecological niche overlap is more pronounced during these seasons. This study provides practical experience for fish monitoring based on eDNA metabarcoding technology.