Comparison of environmental DNA and SCUBA diving methods to survey keystone rockfish species on the Central Coast of British Columbia, Canada
Date
2024
Authors
Acharya-Patel, Neha
Groenwold, Emma
Lemay, Matthew A.
Clemente-Carvalho, Rute
Morien, Evan
Dudas, Sarah
Rubidge, Emily
Yang, Cecilia Lingyu
Coombe, Lauren
Warren, René L.
Journal Title
Journal ISSN
Volume Title
Publisher
Ecological Indicators
Abstract
The 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.
Description
This 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.
Keywords
marine conservation, biodiversity monitoring, conservation, methods development, SCUBA diving, eDNA, unikseq, mtGrasp, full mitogenome-based eDNA assay design
Citation
Acharya-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