Towards improved metabarcoding
FishCARD was designed to improve effectiveness of metabarcoding of California Current marine fishes. To further improve and expand the taxonomic coverage of the database, we generated a website that identifies species needing 12S reference barcodes and provides the research community targets for additional barcoding efforts (https://github.com/zjgold/FishCARD). The ability to update and expand FishCARD will be especially important as climate change leads to range expansions of sub-tropical species that may become resident within the California Current Large Marine Ecosystem (Gentemann, Fewings, & García‐Reyes, 2017; Harvell et al., 2019; Sanford, Sones, García-Reyes, Goddard, & Largier, 2019). The importance of expanding the database is highlighted by our detection of Finescale triggerfish, Balistes polylepis, in the eDNA samples, a species that has only recently become more common off Santa Cruz Island and La Jolla since the 2014-2016 marine heatwave (B. Frable & S. McMillan, personal communication).
Additionally while the MiFish Teleost and Elasmobranch 12S loci are important targets for current marine metabarcoding studies, future efforts and different applications of marine metabarcoding will likely rely on additional barcoding targets. Recent efforts have found success multiplexing CO1 and 16S loci simultaneously, providing more species-level identifications than either marker alone and demonstrating complimentary genetic loci can improve metabarcoding assignments (Duke & Burton, 2020). Future efforts to develop rapid and affordable multi-loci barcoding and mitogenomic tools will provide greater resources for marine metabarcoding and population genomic efforts (Coissac, Hollingsworth, Lavergne, & Taberlet, 2016). As these new barcode loci are developed (e.g. Sebastes -specific barcodes), FishCARD can be expanded to include these loci. Additionally, resources like the SIO Marine Vertebrates Collection will continue to provide important voucher specimens for advancing marine molecular ecology resources as they accession new material.
Here we demonstrate that FishCARD provides an important genetic resource for California Current marine metabarcoding efforts, improving the accuracy and effectiveness of this important and growing research tool. The development of robust and complete reference databases dramatically improves the accuracy of species-level taxonomic assignments, in turn enhancing the efficacy and applicability of these tools for marine biomonitoring. This tool dramatically improves fish eDNA metabarcoding efforts in the California Current Large Marine Ecosystem and provides marine resource managers and researchers an important tool for surveying and monitoring marine fish communities using eDNA.