The upper reaches of the Yangtze River section from Yibin to Jiangjin are located in the upper reaches of the Yangtze River Rare and Endemic Fish National Nature Reserve (hereinafter referred to as “the Reserve”), which is a key protection area for rare and endemic fishes in China. With the successive development of hydropower stations at the lower reaches of the Jinsha River and the implementation of the “10-year fishing ban” policy, the structure and diversity of rare and endemic fish communities in this section of the river are expected to change. Therefore, conducting a comprehensive survey and assessment of rare and endemic fishes in this section of the river is necessary. In this study, we analyzed the inter-annual changes in the community structure of rare and endemic fishes in this section of the river based on the fish resources survey data from 2007 to 2021. We evaluated the diversity of rare and endemic fishes in this section of the river at different periods (before impoundment in Jinsha River Phase I, after impoundment, and early after the fishing ban) using eight indices in three dimensions: species diversity, taxonomic diversity, and functional diversity. The results showed that 29 species of rare and endemic fish belonging to three orders, six families, and 23 genera were identified during the 15 consecutive years of monitoring. Regarding ecological types, the rare and endemic fishes in this section of the river were mainly omnivorous or carnivorous fishes inhabiting the bottom, laying drifting eggs, and preferring flowing water habitats. Cluster analysis and non-metric multidimensional scale analysis (NMDS) showed that the rare and endemic fish communities for the different years could be divided into four groups with stress=0.09＜0.1 when the similarity level was 70%, and the ranking result was good.
The One-way ANOSIM test showed no significant difference in the community composition of rare and endemic fishes between the before-and after-impoundment periods, whereas significant differences were observed in community composition between the early fishing ban period and the before-and the after-impoundment periods (P˂0.05). The results of species diversity analysis showed that the Shannon-Wiener, Simpson, Margalef, and Pielou indices had different interannual trends, with ranges of 1.709–2.506, 0.729–0.906, 1.719–3.147, and 0.647–0.867, respectively. The mean taxonomic difference index (Δ+) and categorical difference variance index (Λ+) both showed that the early fishing ban > before the impoundment > after the impoundment. Functional diversity in different dimensions, such as motor, reproduction and feeding, showed some differences in different periods, with locomotion functional richness being higher at the early fishing ban, feeding function richness being higher after impoundment, and reproduction function richness being higher before impoundment. The uniformity of locomotion functional richness was significantly higher during the early fishing ban than that before and after impoundment. No significant difference was observed in the uniformity of feeding and reproduction functions in different periods. The dispersion of the functions was significantly higher at the beginning of the fishing ban than that before and after impoundment. Dispersion was significantly higher during the early fishing ban than before and after the impoundment. The results showed that the community structure and diversity of rare and endemic fish in the upper reaches of the Yangtze River are evidently affected by environmental factors such as hydropower development and fishing ban policy, and the relationship between diversity indices in different dimensions is complex, reflecting the adaptation and adjustment of fish communities under the changes of ecological environment. This study reveals the dynamic evolution law of the diversity of rare and endemic fish, which provides a powerful scientific basis for protecting and restoring the diversity of rare and endemic fish in this section and promotes the healthy and sustainable development of the Yangtze River ecosystem.