Complementary eDNA Markers Reveal Fish Biodiversity Patterns Across Environmental Gradients in a High-Andean River System

This study represents the first comprehensive characterization of fish biodiversity in the Sonche Canyon (northeastern Peru) using environmental DNA (eDNA), revealing a community of 19 taxa whose detection depended critically on a multi-marker approach. The analysis demonstrated that the use of both Metafish and Mifish-U PCR primer pairs generated a high complementarity index (0.53), allowing the capture of divergent biological signals; Metafish was essential for identifying characiformes; while Mifish-U revealed the presence of specific gymnotiformes and loricariids. The findings, supported by rarification curves confirming sampling saturation. Principal Component Analysis (PCA) revealed co-variation between the biodiversity “hotspot” in Tingorbamba and elevated nitrate concentration (6.1 mg/L), as well as the ubiquitous presence of the invasive species Oncorhynchus mykiss. In conclusion, the utility of the molecular markers and the observed co-variation between physicochemical variables and species distributions underscore the need for standardized protocols for the monitoring and conservation of fauna in the vulnerable lotic systems of the Peruvian Andes.