Limitations of FishCARD
The FishCARD database did not include barcodes for all California
Current marine fishes due to a combination of limited resources,
difficulties amplifying vouchered tissue samples, and a lack of some
vouchered reference material within the Marine Vertebrates Collection of
the Scripps Institution of Oceanography. Of the 149 (17.2%) California
Current fishes absent from FishCARD, 44.0% (n=66) are rare in the
California Current, 14.7% (n=22) are common but not coastal species,
and 2.0% (n=3) were introduced estuarine species; only, 18.0% (n=27)
were common coastal species (Supplemental Table 7). As such, FishCARD
provides coverage for the vast majority of California Current marine
fishes, making it an important tool for metabarcoding studies, despite
these missing taxa.
The one major shortcoming of FishCARD is that 20.8% (n=31) of the
missing taxa are in the Genus Sebastes, and rockfish are
ecologically important (Hyde & Vetter, 2007), form the basis of many
commercial and recreational fisheries (Lea, McAllister, & VenTresca,
1999; Williams, Levin, & Palsson, 2010), and declines in rockfish
stocks led to the establishment of the largest marine protected areas in
southern California, the Cowcod Conservation Areas (Thompson et al.,
2017). Unfortunately, this shortcoming cannot be easily overcome through
additional 12S barcoding. This is because rockfish are a recent
and diverse radiation comprised of 110 species (Ingram & Kai, 2014) and12S fails to resolve most Sebastes to species-level (Hyde
& Vetter, 2007; Yamamoto et al., 2017). Thus effective metabarcoding ofSebastes will require designing novel Sebastes- specific
metabarcoding primers that target a more rapidly evolving region of the
mitochondrial genome (e.g. CytB ) (Thompson et al., 2017).
However, FishCARD includes 100% of all non-Sebastes nearshore
species monitored by the Channel Islands National Kelp Forest Monitoring
Program (n=80, Sprague et al., 2013), as well as by PISCO, the
Partnership
for Interdisciplinary Studies of Coastal Oceans (n=76; (Caselle,
Rassweiler, Hamilton, & Warner, 2015; Pondella et al., 2015). Further,
there is now 12S reference sequence for 98 of the 100 most
abundant ichthyoplankton species collected by the
California
Cooperative Oceanic Fisheries Investigation (CalCOFI) from the
California Current between 1951-2019 (only Showy bristlemouthCyclothone signata and Spotted barracudina Arctozenus
risso ) (Moser, 1993). Moreover, in real world application, this
reference barcode database assigned taxonomy to over 90% of vertebrate
ASVs detecting a broad range of ecologically and commercially important
nearshore rocky reef species (Pondella II et al., 2019). As such,
FishCARD represents an important genetic resource for coastal California
marine metabarcoding monitoring efforts.