Application of eDNA metabarcoding for monitoring the fish diversity of the Jiangjin to Fuling section of the upper reaches of the Yangtze River

The fish communities in the Yangtze River (YR) basin is in a degraded state due to the influence of human factors. Here, we used environmental DNA (eDNA) metabarcoding technology to conduct a survey on the fish diversity in the upper reaches of the YR from Jiangjin to Fuling to search for better monitoring methods. We set up 12 sampling sites in this river section, collected 36 environmental samples, and obtained 5,067,423 valid sequences. After conducting an annotated comparative analysis utilizing the NCBI public database, a total of 104 freshwater fish species were identified, belonging to 8 orders, 24 families, and 72 genera. This included six nationally protected fish species, as well as endemic, introduced, and previously unrecorded species within this basin. The results of this survey indicate a trend toward miniaturization of species and a decline in endemic fish species as well as an increase in exotic fish species in the region, which implied the fish communities in the upper YR region remains in a degraded state. However, the species composition at the family level has remained relatively stable over the past decade. Furthermore, the diversity analysis revealed that fish composition and diversity exhibit variability across different locations.