Assessing the Potential of Environmental DNA for Monitoring Nature‐Like Bypasses: Erroneous Surveillance Owing to DNA Flow‐Through

ABSTRACT Nature‐like bypasses refer to fishways that simulate natural streams. Apart from facilitating fish migrations, bypasses possess the capacity to enhance biodiversity in dammed rivers. Feasibility of environmental DNA (eDNA) as a tool for bypass assessments is unknown. This study investigated fish eDNA in 10 bypasses and their main channels. Initially, the relative DNA flow‐through was estimated in bypasses. Subsequently, the impact of environmental factors and bypasses on fish assemblages was evaluated, and the robustness of the eDNA and electrofishing methods was assessed pertaining to bypass monitoring. The eDNA flow‐through was computed using an equation to estimate the residual DNA at specified distances downstream of the source site. The relative DNA flow‐through was lowest in the longest bypass with low flow rate and highest in the shortest bypass with higher flow rate and was dependent on the DNA decay rate coefficient used. The redundancy analysis revealed significant effects of spatial location, agriculture, catchment area, and bypass length on the species composition. The within‐river analyses indicated significant and nonsignificant bypass effects on species composition and total species richness, respectively. Higher richness and DNA abundance of migratory and threatened species were observed in the bypasses than in the main channels. The eDNA samples displayed higher species richness compared to electrofishing. The species composition of the bypass eDNA samples was intermediate between that of the main channel eDNA and bypass electrofishing samples, which further corroborated performance of eDNA flow‐through in bypasses. Therefore, bypass eDNA samples represented variable mixtures of local and main channel assemblages, indicating relatively low robustness of eDNA for quantitative and spatially accurate bypass assessments. Nevertheless, these results demonstrate practical applicability of eDNA in surveying the presence of desired species and evidence of the benefits of bypasses in supporting biodiversity and species threatened by damming.