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...
Published in: | Ecological Indicators |
---|---|
Main Authors: | , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Elsevier
2024
|
Subjects: | |
Online Access: | https://doi.org/10.1016/j.ecolind.2024.111830 https://doaj.org/article/820766ab9dff489eb3299e9e43fed28c |
id |
ftdoajarticles:oai:doaj.org/article:820766ab9dff489eb3299e9e43fed28c |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:820766ab9dff489eb3299e9e43fed28c 2024-09-15T18:06:46+00:00 Comparison of environmental DNA and SCUBA diving methods to survey keystone rockfish species on the Central Coast of British Columbia, Canada 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 2024-03-01T00:00:00Z https://doi.org/10.1016/j.ecolind.2024.111830 https://doaj.org/article/820766ab9dff489eb3299e9e43fed28c EN eng Elsevier http://www.sciencedirect.com/science/article/pii/S1470160X24002875 https://doaj.org/toc/1470-160X 1470-160X doi:10.1016/j.ecolind.2024.111830 https://doaj.org/article/820766ab9dff489eb3299e9e43fed28c Ecological Indicators, Vol 160, Iss , Pp 111830- (2024) Marine conservation Biodiversity monitoring Conservation Methods development SCUBA diving eDNA Ecology QH540-549.5 article 2024 ftdoajarticles https://doi.org/10.1016/j.ecolind.2024.111830 2024-08-05T17:49:38Z 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. Article in Journal/Newspaper First Nations Directory of Open Access Journals: DOAJ Articles Ecological Indicators 160 111830 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Marine conservation Biodiversity monitoring Conservation Methods development SCUBA diving eDNA Ecology QH540-549.5 |
spellingShingle |
Marine conservation Biodiversity monitoring Conservation Methods development SCUBA diving eDNA Ecology QH540-549.5 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 Comparison of environmental DNA and SCUBA diving methods to survey keystone rockfish species on the Central Coast of British Columbia, Canada |
topic_facet |
Marine conservation Biodiversity monitoring Conservation Methods development SCUBA diving eDNA Ecology QH540-549.5 |
description |
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. |
format |
Article in Journal/Newspaper |
author |
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 |
author_facet |
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 |
author_sort |
Neha Acharya-Patel |
title |
Comparison of environmental DNA and SCUBA diving methods to survey keystone rockfish species on the Central Coast of British Columbia, Canada |
title_short |
Comparison of environmental DNA and SCUBA diving methods to survey keystone rockfish species on the Central Coast of British Columbia, Canada |
title_full |
Comparison of environmental DNA and SCUBA diving methods to survey keystone rockfish species on the Central Coast of British Columbia, Canada |
title_fullStr |
Comparison of environmental DNA and SCUBA diving methods to survey keystone rockfish species on the Central Coast of British Columbia, Canada |
title_full_unstemmed |
Comparison of environmental DNA and SCUBA diving methods to survey keystone rockfish species on the Central Coast of British Columbia, Canada |
title_sort |
comparison of environmental dna and scuba diving methods to survey keystone rockfish species on the central coast of british columbia, canada |
publisher |
Elsevier |
publishDate |
2024 |
url |
https://doi.org/10.1016/j.ecolind.2024.111830 https://doaj.org/article/820766ab9dff489eb3299e9e43fed28c |
genre |
First Nations |
genre_facet |
First Nations |
op_source |
Ecological Indicators, Vol 160, Iss , Pp 111830- (2024) |
op_relation |
http://www.sciencedirect.com/science/article/pii/S1470160X24002875 https://doaj.org/toc/1470-160X 1470-160X doi:10.1016/j.ecolind.2024.111830 https://doaj.org/article/820766ab9dff489eb3299e9e43fed28c |
op_doi |
https://doi.org/10.1016/j.ecolind.2024.111830 |
container_title |
Ecological Indicators |
container_volume |
160 |
container_start_page |
111830 |
_version_ |
1810444142473379840 |