Assessing drivers of rocky reef fish biomass density from the Southern California Bight

Pondella, Daniel J.; Piacenza, Susan E.; Claisse, Jeremy T.; Williams, Chelsea M.; Williams, Jonathan P.; Zellmer, Amanda J.; Caselle, Jennifer E.

doi:10.3354/meps13103

Cited by 11 publications

(9 citation statements)

References 68 publications

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“…Historically, sunflower sea stars were prevalent in the colder waters of the western islands and uncommon in the eastern NCI (Bonaviri et al ), so we restricted our study area to the western portion of the region. Restricting the study area to the western islands also allowed us to better control for environmental conditions (e.g., sea temperature, productivity; see Hamilton et al b , Pondella et al , ). All MPAs used for this study are no‐take state marine reserves where all forms of fishing are banned.…”

Section: Methodsmentioning

confidence: 99%

Trophic redundancy and predator size class structure drive differences in kelp forest ecosystem dynamics

Eisaguirre

Davis

et al. 2020

Ecology

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Ecosystems are changing at alarming rates because of climate change and a wide variety of other anthropogenic stressors. These stressors have the potential to cause phase shifts to less productive ecosystems. A major challenge for ecologists is to identify ecosystem attributes that enhance resilience and can buffer systems from shifts to less desirable alternative states. In this study, we used the Northern Channel Islands, California, as a model kelp forest ecosystem that had been perturbed from the loss of an important sea star predator due to a sea star wasting disease. To determine the mechanisms that prevent phase shifts from productive kelp forests to less productive urchin barrens, we compared pre-and postdisease predator assemblages as predictors of purple urchin densities. We found that prior to the onset of the disease outbreak, the sunflower sea star exerted strong predation pressures and was able to suppress purple urchin populations effectively. After the disease outbreak, which functionally extirpated the sunflower star, we found that the ecosystem response-urchin and algal abundances-depended on the abundance and/or size of remaining predator species. Inside Marine Protected Areas (MPAs), the large numbers and sizes of other urchin predators suppressed purple urchin populations resulting in kelp and understory algal growth. Outside of the MPAs, where these alternative urchin predators are fished, less abundant, and smaller, urchin populations grew dramatically in the absence of sunflower stars resulting in less kelp at these locations. Our results demonstrate that protected trophic redundancy inside MPAs creates a net of stability that could limit kelp forest ecosystem phase shifts to less desirable, alternative states when perturbed. This highlights the importance of harboring diversity and managing predator guilds.

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Section: Methodsmentioning

confidence: 99%

Trophic redundancy and predator size class structure drive differences in kelp forest ecosystem dynamics

Eisaguirre

Davis

et al. 2020

Ecology

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“…Further, there is now a 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 Large Marine Ecosystem between 1951-2019 (only missing Showy Bristlemouth Cyclothone signata and White 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, our barcoding efforts represents an important genetic resource for coastal California marine metabarcoding monitoring efforts.…”

Section: Limitations Of Barcoding Effortsmentioning

confidence: 99%

“…Despite these limitations, however, the current regional California Cyclothone signata and White 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 et al, 2019). As such, our barcoding efforts represents an important genetic resource for coastal California marine metabarcoding monitoring efforts.…”

Section: Limitations Of Barcoding Effortsmentioning

confidence: 99%

Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem

Gold

Curd

Goodwin

et al. 2021

Molecular Ecology Resources

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DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. Specifically, we use a taxonomy cross‐validation by identity framework to compare classification performance between a global database comprised of all available sequences and a curated database that only includes sequences of fishes from the California Current Large Marine Ecosystem. We demonstrate that the regional database provides higher assignment accuracy than the comprehensive global database. We also document a tradeoff between accuracy and misclassification across a range of taxonomic cutoff scores, highlighting the importance of parameter selection for taxonomic classification. Furthermore, we compared assignment accuracy with and without the inclusion of additionally generated reference sequences. To this end, we sequenced tissue from 597 species using the MiFish 12S primers, adding 252 species to GenBank's existing 550 California Current Large Marine Ecosystem fish sequences. We then compared species and reads identified from seawater environmental DNA samples using global databases with and without our generated references, and the regional database. The addition of new references allowed for the identification of 16 additional native taxa representing 17.0% of total reads from eDNA samples, including species with vast ecological and economic value. Together these results demonstrate the importance of comprehensive and curated reference databases for effective metabarcoding and the need for locus‐specific validation efforts.

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“…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.…”

Section: Limitations Of Fishcardmentioning

confidence: 99%

FishCARD: Fish 12S California Current Specific Reference Database for Enhanced Metabarcoding Efforts

Gold

Choi

Kacev

et al. 2020

Preprint

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DNA metabarcoding is an important tool for molecular ecology. However, metabarcoding effectiveness hinges on the quality of reference databases for taxa and loci of interest. This limitation is true for metabarcoding of marine fishes in the California Current Large Marine Ecosystem where there is a paucity of reference 12S barcodes. Here we present FishCARD, a California Current-specific fish 12S-specific reference barcode database. We barcoded 612 species using the MiFish metabarcoding primers; an addition of 258 species to the 459 California Current fish species with existing 12S barcodes from GenBank. The resulting FishCARD database covers 82.7% of California Current fishes, and it includes virtually all fishes sampled by large marine monitoring programs such as the Partnership for Interdisciplinary Studies of Coastal Oceans and California Cooperative Oceanic Fisheries Investigation. To demonstrate the importance of complete reference databases for eDNA metabarcoding, we compared species and reads identified from three 1L seawater samples collected off Santa Cruz Island, CA using GenBank sequences with and without our generated barcodes, as well as the FishCARD database curated here. The inclusion of our generated barcodes allowed the additional identification of 15 native taxa and 21.8% of total reads from eDNA samples. However, we found that half of all amplicon sequence variants (ASVs) generated by MiFish 12S primers were of non-vertebrate 16S origin, demonstrating a clear limitation of a widely employed fish metabarcoding primers. Despite these limitations, FishCARD provides an important genetic resource to enhance the effectiveness of marine metabarcoding efforts in the California Current Large Marine Ecosystem.

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Assessing drivers of rocky reef fish biomass density from the Southern California Bight

Cited by 11 publications

References 68 publications

Trophic redundancy and predator size class structure drive differences in kelp forest ecosystem dynamics

Trophic redundancy and predator size class structure drive differences in kelp forest ecosystem dynamics

Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem

FishCARD: Fish 12S California Current Specific Reference Database for Enhanced Metabarcoding Efforts

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