Andean Fish inventories using an eDNA metabarcoding approach

Fish diversity inventories often rely on capture-based methods, which are typically lethal and may have long-term impacts on fish populations. A promising alternative is environmental DNA (eDNA) metabarcoding —a non-invasive technique that uses molecular DNA barcodes to identify fish species. Implementing eDNA methods for fish inventories in the Andean region offers a sustainable solution for long-term monitoring programs. In this study, eDNA analyses were conducted using water samples collected from dammed rivers, where continuous monitoring of impacted areas is essential. The objectives were to compare the effectiveness of eDNA metabarcoding and traditional sampling methods for tracking fish communities in a reservoir of the Porce River, located in northwestern Colombia, and to develop a standardized, replicable protocol for long-term monitoring of Andean fish diversity. A range of sampling, molecular, and bioinformatic techniques were tested across different ecosystems, including rivers, reservoirs, and streams. Novel primer pairs targeting the mitochondrial COX1 and 12S genes were designed and evaluated through in silico simulations. Among the markers tested, the 12S gene showed the highest performance in our field-cllected samples, detecting 23 taxa —compared to only 6 taxa identified by COX1 and 14 species recorded through traditional fishing methods. When COX1 and 12S were combined, eDNA metabarcoding demonstrated greater sensitivity and cost-effectiveness than traditional approaches. This research establishes a foundational protocol for enhancing the detection of fish species in Andean aquatic ecosystems. Critical factors—including primer selection, the quality and taxonomic coverage of reference databases, and bioinformatic parameters—substantially influence the results and should be carefully considered in future studies.