Assessing Japanese Eel Populations in a River System Using eDNA: Seasonal Variation and Modest Effectiveness of Stocking Where Natural Recruitment Is Restricted

ABSTRACT Japanese eel, Anguilla japonica , is a highly endangered species in the Western Pacific region despite its high commercial value in fisheries. To enhance fisheries resources of this catadromous fish, eel stocking programs are conducted annually in many rivers across Japan. These programs involve capturing naturally recruited glass eels at river mouths, farming them in artificial ponds and releasing them into rivers. However, the impact of these stocking efforts on eel populations remains unclear. Recently, environmental DNA (eDNA) has emerged as an effective tool for assessing the biomass of target species in aquatic environments. This study aims to evaluate the spatiotemporal changes in Japanese eel population over 3 years and the effect of stocking using species‐specific eDNA marker in the Shigenobu River system in western Japan, where numerous sediment‐control dams and weirs are present, and eel stocking is conducted both upstream and downstream of these barriers. Our results show that eDNA concentration was significantly correlated with both the density and biomass of captured eels, confirming the effectiveness of eDNA assays for eel stock assessment. eDNA concentrations, as well as captured density and biomass, were higher downstream than upstream. After stocking, eDNA concentrations increased and remained elevated at upstream stocking sites where natural recruitment was blocked by sediment‐control dams. Seasonal variation in eDNA concentrations was most pronounced downstream, where natural recruitment occurs. These findings suggest that stocking enhances eel populations in areas where natural recruitment is restricted, but the effect is modest compared to natural recruitment. Therefore, ecosystem‐based habitat management, including habitat restoration and connectivity, should be prioritized for eel conservation.