Evaluating mtDNA metabarcoding markers to identify zooplankton and ichthyoplankton in the Salish Sea

Zooplankton and ichthyoplankton community assessments depend on species diagnostics, yet morphological identifications are time consuming, require taxonomic expertise, and often are stymied by lack of diagnostic characters - particularly at larval stages. Rare, cryptic and/or invasive species may be missed, thwarting management decisions. Metabarcoding can yield accurate species/taxon identifications, yet often is hit-or-miss across phylogenetic groups, with resolution varying among markers, gene regions, and reference sequence databases. In this study, we evaluate five published metabarcode mitochondrial (mt)DNA markers for (a) cytochrome oxidase I (LrCOI), (b) cytochrome b (FishCytb), (c) 16S rDNA (Cop16S, Mol16S) and (d) 12S rDNA (MiFish12S) gene regions to determine which best resolve zooplankton and ichthyoplankton species/taxa, using DNA extracted from net tows in the Salish Sea. We additionally compare molecular species detection to morphological identifications, as well as sequence relative abundance to biomass estimates.