Unraveling fish diversity and assembly patterns by eDNA metabarcoding in a highly dynamic freshwater ecosystem with diverse rare and endemic fish species

Fish diversity is often challenging due to its labor-intensive and time-consuming, particularly when it comes to detecting rare and endemic fishes in fast-flowing waters. Environmental DNA metabarcoding has emerged as a powerful tool that enables a comprehensive understanding of freshwater biodiversity. In this study, we applied eDNA metabarcoding to assess fish diversity and assembly patterns in a highly dynamic and complex freshwater ecosystem characterized by diverse rare and endemic fish species. Specifically, three extensive surveys were performed to characterize the structure and spatial variation of fish communities within the Yangtze River Upstream Nature Reserve of Rare and Endemic Fishes. A total of 166 fish species, spanning8 orders, 25 families and 99 genera, were identified. Seasonal variations in alpha diversity were found to be significant. Changes in species composition across different sample sites were primarily associated with the species turnover rather than nestedness across the three seasons. This finding suggested that the conservation efforts should be applied to the whole Nature Reserve rather than a specific area. Endemic fishes were found to be concentrated in the core areas of the reserve, which serve as critical habitats for rare and endemic fish species. Therefore, stronger protection measures should be implemented in these core areas. This study also demonstrated the feasibility of using eDNA technology to evaluate fish diversity in fast-flowing rivers, particularly when conducting large-scale, rapid monitoring over extensive spatial areas. • eDNA can effectively detect rare and endemic fishes in fast-flowing waters. • The reserve exhibited a high fish diversity especially in the rare and endemic fish. • Endemic fishes were found to be concentrated in the core areas. • Conservation efforts for fish diversity should focus on the entire Nature Reserve.