Conclusion and perspectives
This study demonstrated that the dietary DNA metabarcoding of freshwater scavenger shrimps offers a comprehensive and reliable snapshot of fish assemblages in neotropical rivers. As the cost and speed of molecular analyses continue to decrease, the relative ease of sampling and processing makes this method particularly suitable for carrying out rapid biodiversity assessments. Crustacean-derived dDNA likely provides fine-scale, recent insights, making it a valuable tool for detecting the localized ecosystem impacts of anthropogenic disturbances, such as overfishing, gold mining, deforestation, or dam construction, on fish communities along river networks. However, this should be seen as a complement to traditional WFD approaches, as it does not provide data on fish abundance, biomass or condition, which remain essential for effective management. Additionally, the method’s ability to detect small and elusive species could make it particularly useful for early detection of invasive species or for monitoring rare native species that are difficult to capture using conventional methods.