Environmental DNA Metabarcoding Reveals the Variations in Fish Diversity Across the Yangtze River Basin and the Effects of the Three Gorges Dam

It is imperative that freshwater fish biodiversity research incorporates diverse components, encompassing taxonomy, phylogeny and function, alongside multifaceted facets, including richness, divergence and regularity. This comprehensive approach is essential to facilitate a more profound comprehension of freshwater ecosystem functions, to elucidate the mechanisms underpinning fish community assembly, and to accurately assess the impacts of anthropogenic disturbance. Consequently, this scientific understanding can inform the development of effective fish conservation and ecosystem management strategies. This study utilized environmental DNA metabarcoding to assess the diversity of fish across the entire Yangtze River, encompassing the upper reach (Upper), the Three Gorges Reservoir area (RES_SX), and the downstream reach (Down). The results indicated that 150 distinct fish species were detected, with the RES_SX area exhibiting a significantly lower taxonomic diversity and fish detection rate in comparison to the other two regions. Conversely, phylogenetic and functional diversity exhibited stability post-normalization by taxonomic richness. Furthermore, investigation of the divergence facet of alpha-diversity demonstrated a reduction in clustering and an improvement of overdispersion on the phylogenetic and functional diversity, respectively, in the RES_SX and Down regions. Beta-diversity analysis further revealed lower taxonomic beta-diversity but higher phylogenetic and functional beta-diversity in the RES_SX area. A substantial degree of geographic distance-dependent similarity was identified for all three components of beta-diversity in the Upper Reach. Conversely, these components were found to be disrupted in the Down Reach. Finally, an analysis of the assembly mechanism revealed stochastic processes, dispersal limitation and drift as the dominant factors shaping the fish communities, with reduced dispersal limitation in the RES_SX area. This study provides novel insights into the multidimensional diversity of fish populations in response to dam construction, emphasizing the necessity of integrating multiple facets of diversity for accurate impact assessment and supporting evidence-based conservation of fish species in the Yangtze River.