Comparison of environmental DNA and SCUBA diving methods to survey keystone rockfish species on the Central Coast of British Columbia, Canada

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dc.contributor.authorAcharya-Patel, Neha
dc.contributor.authorGroenwold, Emma
dc.contributor.authorLemay, Matthew A.
dc.contributor.authorClemente-Carvalho, Rute
dc.contributor.authorMorien, Evan
dc.contributor.authorDudas, Sarah
dc.contributor.authorRubidge, Emily
dc.contributor.authorYang, Cecilia Lingyu
dc.contributor.authorCoombe, Lauren
dc.contributor.authorWarren, René L.
dc.contributor.authorFrid, Alejandro
dc.contributor.authorBirol, Inanc
dc.contributor.authorHelbing, Caren C.
dc.date.accessioned2024-03-28T15:08:38Z
dc.date.available2024-03-28T15:08:38Z
dc.date.issued2024
dc.descriptionThis project was an extensive collaborative effort. We are thankful for the invaluable sharing of territory knowledge from the Kitasoo/Xai’xais Stewardship Authority, particularly Chief Doug Neasloss, Medrick Robinson, Spencer Mason, Tony Robinson, and Brady Stjerneberg. We are very grateful for the extensive expertise of the dive team: Derek Van Maanen, Andrew McCurdy, Tristan Blaine, and Courtney Edwards, whose knowledge and field skills made this project feasible. We thank Dr. Greg Owens for providing rockfish mitogenome sequences prior to their public availability. We also thank Braeden Schiltroth and Jeremy Heywood from the Vancouver Aquarium for providing access to tank water, and Cassandra Konecny, Jacob Imbery, and Dr. Mark D. Louie Lopez for helpful discussions and technical assistance. The photographs used in this work were generously provided by Neha Acharya-Patel, Andrew McCurdy, Mike Byerley, Vicky Okimura, the Washington Department of Fish and Wildlife, and NOAA Alaska Fisheries Science Center.
dc.description.abstractThe rocky reefs of British Columbia’s (BC) coast are a productive ecosystem, home to 38 rockfish species (Genus: Sebastes) that are culturally and economically important. Quantitatively assessing rockfish populations is vital to support conservation and stock assessment needs. Self-contained underwater breathing apparatus (SCUBA) diving surveys are a commonly used monitoring method in BC. However, this resource-intensive approach is challenging, particularly for cryptic or deeper species. Herein, we compared environmental DNA (eDNA) detection methods with SCUBA diving surveys to capture overall rockfish biodiversity. We employed two eDNA methods: 1) a targeted quantitative real-time polymerase chain reaction (qPCR) approach to monitor species of particular importance to First Nations collaborators and decision makers, and 2) a metabarcoding approach for assessing community composition using the previously published MiSebastes assay. Both approaches are confounded by the little DNA sequence divergence among species and high sequence variation within species. Overcoming these challenges using a whole mitochondrial approach with the mtGrasp and unikseq pipelines, we generated highly useful eDNA tools. We found that eDNA methods were highly comparable to dive surveys, as both methods indicated a similar ecological reality, including species detections and distributions. Though there are certain species that cannot be distinguished by the MiSebastes assay, eDNA metabarcoding still detected more rockfish species overall. Both eDNA methods show potential for use alongside conventional methods for scalable incorporation into community-based monitoring programs.
dc.description.reviewstatusReviewed
dc.description.scholarlevelFaculty
dc.description.sponsorshipThis project was funded in part through a NSERC CGS-D grant and the Stephenson’s Exploration Advancement Grant from the Explorers Club to NAP. It was also funded in part through a MITACS accelerate fellowship and a Genome Canada, Genome British Columbia, and Genome Québec large scale applied research project #312ITD to CCH.
dc.identifier.citationAcharya-Patel, N., Groenwold, E., Lemay, M. A., Clemente-Carvalho, R., Morien, E., Dudas, S., ... Helbing, C. C. (2024). Comparison of environmental DNA and SCUBA diving methods to survey keystone rockfish species on the Central Coast of British Columbia, Canada. Ecological Indicators, 160, 111830. https://doi.org/10.1016/j.ecolind.2024.111830
dc.identifier.urihttps://doi.org/10.1016/j.ecolind.2024.111830
dc.identifier.urihttps://hdl.handle.net/1828/16320
dc.language.isoen
dc.publisherEcological Indicators
dc.rightsAttribution-NonCommercial-NoDerivatives 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subjectmarine conservation
dc.subjectbiodiversity monitoring
dc.subjectconservation
dc.subjectmethods development
dc.subjectSCUBA diving
dc.subjecteDNA
dc.subjectunikseq
dc.subjectmtGrasp
dc.subjectfull mitogenome-based eDNA assay design
dc.subject.departmentDepartment of Microbiology and Biochemistry
dc.subject.departmentDepartment of Biochemistry and Microbiology
dc.subject.departmentDepartment of Biology
dc.titleComparison of environmental DNA and SCUBA diving methods to survey keystone rockfish species on the Central Coast of British Columbia, Canada
dc.typeArticle

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