New eDNA based tool applied to the specific detection and monitoring of the endangered European eel

European eel (Anguilla anguilla) populations have declined drastically over the last decades and it has been included in the IUCN red list of endangered species as critically endangered since 2007. Thus, continuous population monitoring is crucial in order to warrant the conservation of this emblematic species. Environmental DNA (eDNA) has been recently implemented as a powerful method for the detection and monitoring of freshwater species, particularly for endangered species, where eDNA methods have shown to be less invasive than other methods (e.g. electrofishing). In this study, we developed and validated, under controlled conditions, a new species-specific tool for detecting A. anguilla from water samples by means of eDNA. Furthermore, we applied a semi-quantitative approach for monitoring of glass eel at different depths (surface and bottom) during different seasons in two rivers of northern Spain (Nalón and Sella rivers). We detected a significantly higher proportion of positive DNA amplifications in bottom than surface samples. Moreover, the proportion of replicas with positive amplification varied along the estuaries sections examined, and especially in the different sampling months. The temporal detection trends found in this study were compatible with the known upstream migration pattern of this species. Altogether, this study contributes to the establishment of a simple, easy and cheap system based on eDNA, that could be routinely applied in conservation research and management programs to monitoring wild populations of endangered species.