Monitoring and predicting the presence and abundance of juvenile Atlantic salmon in tributaries according to habitat characteristics using environmental DNA

Conservation of the Atlantic salmon Salmo salar requires to monitor the spatial distribution and abundance of juveniles at a local scale in tributaries. However, tributaries are rarely accounted for in monitoring programs despite their importance for juvenile life stages. This is mainly because inventories of young salmon populations in tributaries can be technically challenging with traditional methods, as the number of tributaries in a watershed can be important and their access limited compared to the main stem. In this study, we tested the use of environmental DNA (eDNA) to quantify the abundance of juvenile Atlantic salmon in tributaries. We successfully detected eDNA of juvenile Atlantic salmon in 19 tributaries of three main rivers of the Gaspé Peninsula (Québec, Canada) using quantitative real-time PCR analyses. By comparing the eDNA approach with electrofishing surveys conducted in parallel to water sampling, we found that eDNA concentrations positively correlated with juvenile abundance, total biomass, and body surface area. The use of the allometrically scaled mass (ASM) instead of abundance improved the correlation. Furthermore, we demonstrated that the levels of eDNA molecules detected for juvenile Atlantic salmon were also correlated with water temperature and canopy cover measured in each tributary. Finally, we tested if eDNA concentrations measured in a tributary could be used as a reliable indicator of juvenile abundance or biomass in that tributary. We found that our models slightly better predicted juvenile biomass than juvenile abundance. The use of ASM did not improve model prediction, suggesting that further refinement would be required in the future. Our method will facilitate the implementation of conservation practices appropriate to the ecology of juvenile Atlantic salmon in tributaries.