Reference Database Comparisons
To compare the effectiveness of the three reference databases, we examined the total number of ASVs and taxonomic ranks identified using each database. We also investigated differences in taxonomic assignment between single direction ASVs (comprised of forward- and reverse-only sequence reads) and merged ASVs (merged paired-end sequence reads). Specifically, we compared the CRUX-12S database to the combined database to determine how the inclusion of additional region-specific reference barcodes improved taxonomic assignment of California Current fish species from eDNA samples. Next, we compared taxonomic assignments between the FishCARD California Current-specific 12S reference database and the combined reference database to determine whether a curated metabarcoding reference database specific to a regional fauna performs better than a database that uses all available 12Sreference barcodes.