Advances in the Creation of a DNA Barcoding Reference Library for Freshwater Fishes of Western Ecuador with Emphasis on Metabarcoding Applications

This research provides a DNA reference library for the freshwater fish species of Western Ecuador, emphasizing endemic species of the Guayas River Basin and southwestern, lowland areas. Western Ecuador is currently grappling with severe overexploitation of its endemic freshwater fishes across many drainage basins, compounded by habitat destruction, pollution from commercial and agricultural activities, and the looming threat of climate change, notably in the form of coastal incursion events. Methods for rapid-surveying biodiversity at community levels is urgently needed. This reference library is particularly designed for metabarcoding applications, providing a non-invasive method for surveying aquatic biodiversity in vulnerable areas using environmental DNA (eDNA). The use of all three genetic loci commonly used for DNA barcoding fishes (12S, 16S, and COI) is an integral component of this research for minimizing species misidentification and maximizing detection rates. This genetic reference library provides a total of 78-12S sequences, 78-16S sequences, and 76-COI sequences representing 42 species across 21 taxonomic families of which, 50-COI sequences, 62-12S sequences, and 57-16S sequences are novel species contributions to Genbank. Prior to this study, coverage of Western Ecuador’s freshwater fishes were at 15.67%, 23.13%, and 20.90% for 12S, 16S, and COI, respectively. Coverage for the loci post-study is now at 45.52% (12S), 54.48% (16S), and 52.24% (COI).