Unusual occurrences of fishes in the Southern California Current System during the warm water period of 2014–2018

Walker, H. J.; Hastings, Philip A.; Hyde, John R.; Lea, Robert N.; Snodgrass, Owyn E.; Bellquist, Lyall

doi:10.1016/j.ecss.2020.106634

Cited by 31 publications

(39 citation statements)

References 29 publications

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“…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 (Zack Gold, 2020). The ability to update and expand the regional reference database 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 et al, 2017;Harvell et al, 2019;Sanford et al, 2019;Walker et al, 2020 32 metabarcoding efforts, it allowed us to more easily and rapidly sequence and generate barcodes for our intended purpose. Furthermore, recent efforts have found success multiplexing CO1 and 16S loci simultaneously provides more species-level identifications than either marker alone, demonstrating complimentary genetic loci can improve metabarcoding assignments (Duke & Burton, 2020).…”

Section: Towards Improved Metabarcoding 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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Section: Towards Improved Metabarcoding 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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“…West Coast fisheries are known for their intrinsic fluctuations, yet there are signs that this variability may be increasing across the California Current (Black et al., 2014; Sydeman et al., 2013). Alongside anomalous oceanographic conditions observed in 2004–2006 (Peterson et al., 2006) and 2014–2016 (Bond et al., 2015; Jacox et al., 2016), numerous changes to ecosystem structure and function have been reported (Cavole et al., 2016; Lindley et al., 2009; Sanford et al., 2019; Walker et al., 2020). Despite landings trending positively in the early 2000s, West Coast salmon fisheries were severely restricted during the 2008–2009 and 2016–2017 fishing seasons amidst poor run strength and increasingly variable escapement associated with drought, warm ocean temperatures and limited food availability (Richerson & Holland, 2017; Satterthwaite et al., 2019).…”

Section: Discussionmentioning

confidence: 99%

Changes to the structure and function of an albacore fishery reveal shifting social‐ecological realities for Pacific Northwest fishermen

et al. 2020

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Marine fisheries around the globe are increasingly exposed to external drivers of social and ecological change. Though diversification and flexibility have historically helped marine resource users negotiate risk and adversity, much of modern fisheries management treats fishermen as specialists using specific gear types to target specific species. Here, we describe the evolution of harvest portfolios amongst Pacific Northwest fishermen over 35+ years with explicit attention to changes in the structure and function of the albacore (Thunnus alalunga, Scombridae) troll and pole‐and‐line fishery. Our analysis indicates that recent social–ecological changes have had heterogenous impacts upon the livelihood strategies favoured by different segments of regional fishing fleets. As ecological change and regulatory reform have restricted access to a number of fisheries, many of the regional small (<45 ft) and medium (45–60 ft) boat fishermen who continue to pursue diverse livelihood strategies have increasingly relied upon the ability to opportunistically target albacore in coastal waters while retaining more of the value generated by such catch. In contrast, large vessels (>60 ft) targeting albacore are more specialized now than previously observed, even as participation in multiple fisheries has become increasingly common for this size class. In describing divergent trajectories associated with the albacore fishery, one of the US West Coast's last open‐access fisheries, we highlight the diverse strategies and mechanisms utilized to sustain fisheries livelihoods in the modern era while arguing that alternative approaches to management and licensing may be required to maintain the viability of small‐scale fishing operations worldwide moving forward.

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“…Islas Coronados (Walker et al 2020) to Bahía Banderas, Jalisco, Mexico (Thomson et al 1979) Jordan, 1888. Broomtail Grouper.…”

Section: Alphestes Immaculatusmentioning

confidence: 99%

“…Not always correctly distinguished from Coryphaena hippurus Linnaeus, 1758, and the larger sizes reported likely are from that species. Circumglobal; western Pacific Ocean north to Sea of Japan (Parin 2003); 43 Fathom Bank, southern California (about 32°39.3'N, 117°58.3'W) (Walker et al 2020) to at least Ecuador , including south-western Gulf of California (Robertson and Allen 2002). Depth: Surface to 50 m (164 ft) (min.…”

Section: Family Coryphaenidae-dolphinfishesmentioning

confidence: 99%

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Checklist of marine and estuarine fishes from the Alaska–Yukon Border, Beaufort Sea, to Cabo San Lucas, Mexico

Love

Bizzarro

Cornthwaite

et al. 2021

Zootaxa

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This paper is a checklist of the fishes that have been documented, through both published and unpublished sources, in marine and estuarine waters, and out 200 miles, from the United States-Canadian border on the Beaufort Sea to Cabo San Lucas, Mexico. A minimum of 241 families and 1,644 species are known within this range, including both native and nonnative species. For each of these species, we include maximum size, geographic and depth ranges, whether it is native or nonnative, as well as a brief mention of any taxonomic issues.

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Unusual occurrences of fishes in the Southern California Current System during the warm water period of 2014–2018

Cited by 31 publications

References 29 publications

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

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

Changes to the structure and function of an albacore fishery reveal shifting social‐ecological realities for Pacific Northwest fishermen

Checklist of marine and estuarine fishes from the Alaska–Yukon Border, Beaufort Sea, to Cabo San Lucas, Mexico

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