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

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 underwa...

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Bibliographic Details
Published in:Ecological Indicators
Main Authors: Neha Acharya-Patel, Emma Groenwold, Matthew A. Lemay, Rute Clemente-Carvalho, Evan Morien, Sarah Dudas, Emily Rubidge, Cecilia Lingyu Yang, Lauren Coombe, René L. Warren, Alejandro Frid, Inanc Birol, Caren C. Helbing
Format: Article in Journal/Newspaper
Language:English
Published: Elsevier 2024
Subjects:
Marine conservation
Biodiversity monitoring
Conservation
Methods development
SCUBA diving
eDNA
Ecology
QH540-549.5
First Nations
Online Access:https://doi.org/10.1016/j.ecolind.2024.111830
https://doaj.org/article/820766ab9dff489eb3299e9e43fed28c
Description
Summary: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.

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