Comparing eDNA Metabarcoding and Morphological Surveys Reveals Distinct Fish Community Patterns in the Gaya River

Assessing fish biodiversity is essential for freshwater ecosystem conservation. This study compares environmental DNA (eDNA) metabarcoding and traditional morphological surveys to investigate fish communities in the Gaya River, China. A total of 42 fish species were identified, with 13 detected only by eDNA, 7 exclusively by morphology, and 11 by both methods. A comparative analysis of species composition, functional diversity, and phylogenetic diversity revealed significant differences between the two approaches. Notably, eDNA data indicated higher phylogenetic diversity (PD), while morphological surveys captured greater functional evenness (FEve). Multivariate analyses indicated that total phosphorus (TP), total suspended solids (TSS), electrical conductivity (EC), temperature (T), and pH significantly influenced fish community composition, while dissolved oxygen (DO) was a key driver of species richness (SR), functional richness (FRic), and PD. These findings highlight the methodological differences and complementary strengths of eDNA and morphological approaches in biodiversity assessments. By providing comparative insights into fish diversity patterns, this study underscores the importance of using multi-method approaches to improve freshwater biodiversity monitoring and conservation strategies.