Environmental drivers of multidimensional fish diversity patterns in the Upper Yangtze River Basin revealed by eDNA metabarcoding

It is imperative to comprehend the diversity of fish species and the factors influencing fish diversity (richness at the sequence-variant level) within river ecosystems to ensure the long-term sustainability of these environments. Biodiversity encompasses multiple distinct yet interconnected facets, and their distribution patterns and underlying interactions are vital for adaptive management practices aimed at sustaining biodiversity under changing conditions. In this study, environmental DNA metabarcoding was employed to investigate the fish communities present in the Upper Yangtze River Basin (UYRB) across different seasons. A total of 162 fish species were identified, with Cyprinus carpio and Carassius sp. being detected in more than 90% of the samples. Four alpha diversity indices of fish communities, encompassing diverse facets such as sequence, taxonomy, phylogeny, and function, were calculated. The results indicated that all indices were significantly lower in spring compared to summer and winter. As indicated by the findings of numerous association analyses, pH was identified as the environmental variable most strongly associated with fish diversity, with water temperature and dissolved oxygen ranking second and third, respectively. The effects of these factors on the assembly of fish functional diversity were primarily indirect, operating through direct interactions with taxonomic and phylogenetic diversity. Moreover, the associations between functional diversity and other diversity facets exhibited a non-linear pattern, wherein a decline in functional diversity was observed subsequent to the attainment of critical values by other diversity metrics. The findings of this study provide insights into the assembly mechanisms of fish diversity and inform conservation strategies by linking multidimensional diversity patterns to overall ecosystem health.