eDNA-based monitoring metrics for migratory and resident fish following full and partial removal of river barriers

The fragmentation of river systems by artificial barriers is contributing to the global decline of migratory fish species. In response, many barriers are now being considered for removal or mitigation to restore connectivity, but the effectiveness of such interventions is unclear due to a lack of monitoring before and after mitigation. We used two complementary monitoring methods based on environmental DNA (eDNA) analysis, detection (determined by number of positive qPCRs) and abundance (based on the analysis of copy numbers), to assess the response of two migratory fish (the European eel, Anguilla anguilla, and the Atlantic salmon Salmo salar ) as well as the (predominantly) potadromous brown trout ( Salmo trutta ) to the partial or full removal of twelve barriers in five Welsh rivers. We observed species-specific responses, and differences based on the assessment method (detection or abundance) and mitigation type (easement or removal). Trout detection and abundance increased following barrier mitigation, while salmon and eel detection declined, with salmon abundance remaining the same. Analysis using the number of copies offered higher resolution than relying on qPCR positives alone, indicating that eDNA monitoring which relies solely on detection may obscure subtle changes in populations following barrier mitigation. Our abundance estimates comparing the removal and easement of small weirs indicate that full barrier removal leads to an increase in trout abundance one year after mitigation when compared to easement, but even small mitigation interventions of in-stream barriers influence both migratory and resident fish populations, which may benefit from increasing habitat availability and connectivity. • The response to barrier mitigation is highly species-specific after one year. • Using absolute abundance for eDNA is more likely to identify subtle changes. • In weirs, barrier removal leads to an increase in abundance compared with easement. • Long-term monitoring is vital before and after all river barrier mitigation projects.