Detection of diadromous fish using environmental DNA: prospects for its use in conservation of endangered species occurring in Portugal

Abstract The high economic value and cultural relevance of diadromous fish make them primary targets for traditional fisheries, that need effective management to ensure the long-term survival of their populations. In Portugal, these species are experiencing a marked decline, primarily due to habitat loss and fragmentation, alongside pollution and overfishing. Accurate monitoring is therefore essential to strengthen the management of diadromous fish within Portuguese ecosystems. Advancements in monitoring methodologies could benefit from more sensitive approaches, such as environmental DNA (eDNA) analysis, which is increasingly recognized as a valuable complement to conventional fish monitoring. However, eDNA-based tools remain largely absent and untested in Portugal’s monitoring and management of diadromous fish. This study reviews literature on eDNA-based detection of diadromous fish species and discusses key methodological aspects influencing the detection efficiency, including sample processing (e.g., water filtration), DNA extraction methods, marker regions and primers, approach and platforms. A particular focus is placed on diadromous fishes occurring in Portugal, which includes several endangered species, and the prospects of using eDNA to monitor them. We also report a pilot study comparing specific assays and DNA metabarcoding in eDNA-based detection of sea lamprey in the Minho River watershed. By consolidating current literature, this work underscores the potential of eDNA to strengthen diadromous fish conservation in Portugal and offers insights to support the integration of eDNA-based tools into national monitoring frameworks. Although our study focuses on Portuguese species, the approaches and insights discussed are broadly applicable and can inform conservation efforts in other regions facing similar challenges. Graphical Abstract