Comparing Diversity and Structure of Freshwater Fish Assemblages Using Environmental DNA and Gillnetting Methods: A Case Study of a Large Deep Reservoir in East China

Abstract

Environmental DNA (eDNA) technology, as an alternative to traditional gillnet surveys, has attracted widespread attention. However, comparisons between eDNA technology and traditional methods in terms of biodiversity and structure have not yet been fully elucidated. The results showed that eDNA technology exhibits higher taxonomic resolution and detection rates, and significantly larger species diversity and richness indices compared with traditional gillnetting methods. Using abundance or biomass datasets from gillnets revealed significant differences in fish community composition between gillnetting and eDNA survey methods. Gillnet abundance was dominated by small-sized fish species, while gillnet biomass was dominated by larger-sized ones, and the species detected in eDNA reads included the dominant species from gillnet abundance and biomass, as well as a medium-sized alien invasive fish (Lepomis macrochirus). Non-metric multidimensional scaling (NMDS) showed that the spatial distribution in abundance of fish species sampled by gillnetting was more dispersed than that using eDNA technology. The explanatory power with the gillnet abundance and biomass together as predictor variables of the eDNA reads increased to some extent compared with taking them separately, and the fitting degree of quadratic functions was also improved to a certain extent compared to linear equations when using biomass to predict eDNA reads. Furthermore, the key environmental factors affecting fish communities differed between the two methods. Present research indicates that eDNA technology has advantages over gillnets in detecting fish species diversity, and it is recommended to combine it with traditional sampling methods. Under natural aquatic ecosystem conditions, the eDNA reads may comprehensively reflect the biomass and abundance information obtained by gillnetting, but their relationship is complex and requires further research. This study will provide guidance for biodiversity monitoring.

Keywords: eDNA, Gillnet, Freshwater fish diversity, Qiandao Lake