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.