Graduation Date
Fall 2022
Document Type
Thesis
Program
Master of Science degree with a major in Natural Resources, option Fisheries
Committee Chair Name
Dr. Andre Buchheister
Committee Chair Affiliation
HSU Faculty or Staff
Second Committee Member Name
Dr. Andrew P. Kinziger
Second Committee Member Affiliation
HSU Faculty or Staff
Third Committee Member Name
Dr. Eric P. Bjorkstedt
Third Committee Member Affiliation
HSU Faculty or Staff
Fourth Committee Member Name
Dr. Darren Ward
Fourth Committee Member Affiliation
HSU Faculty or Staff
Subject Categories
Fisheries
Abstract
Environmental DNA (eDNA) has developed into a useful tool for determining the distribution of rare aquatic species, but relatively few studies have directly compared the detection probabilities of this method with other conventional survey techniques. These comparisons can inform which method may be better suited to address study objectives. In this study, the overall goal was to compare the ability of eDNA and underwater visual count (UVC) surveys to detect juvenile coho salmon (Oncorhynchus kisutch), a species of conservation concern at the southern extent of its geographic range. Specifically, I address two objectives: (1) compare the ability of eDNA and UVC surveys to detect coho salmon and the influence of environmental covariates on detectability and (2) evaluate the utility of eDNA concentrations and habitat covariates to predict the count of coho salmon within small pools. Water samples for eDNA analysis and snorkel surveys were conducted at 96 pools across 25 stream reaches in the Smith River basin, California. I used multi-scale occupancy models to estimate method-specific detection probabilities (p) and the effect of habitat covariates, including basin area (as a proxy for discharge), residual pool depth, and large woody debris. Results showed that eDNA and UVC surveys had a high degree of agreement in detecting the presence of coho salmon at both the pool scale (93% agreement) and reach scale (80% agreement), however there were several occasions where only one method detected coho salmon. The top occupancy model, identified using Akaike’s information criterion, indicated that the detection probabilities were best predicted by method, basin area, residual pool depth, and an interaction between method and basin area. Under median habitat conditions, detection probabilities were similar and high for both methods (peDNA=91%, pUVC=89%). Residual pool depth had a slight positive effect on peDNA and pUVC. Detection probabilities for both methods were affected negatively by increasing basin size, but p declined more substantially for eDNA; at the highest basin areas, peDNA =40% compared to pUVC=78%. Finally, eDNA concentrations were a poor predictor of coho salmon count in small pools. The absence of a relationship between eDNA concentrations and fish counts is contrary to other studies and may have resulted as a consequence of the relatively small differences in counts observed between pools, which ranged from 0 to 210 individuals. Overall, this study illustrates that eDNA methods were as sensitive as UVC surveys for detecting coho presence under most conditions but could not be used to produce reliable estimates of the average observed count of the target species in this system. Therefore, these findings support the use of eDNA methods for monitoring the distributions of a rare species but indicate that implementation should be guided by study objectives and local environmental conditions.
Citation Style
American Fisheries Society
Recommended Citation
Shaffer, Jason T., "Comparison of environmental DNA and underwater visual count surveys for detecting juvenile coho salmon (Oncorhynchus kisutch) in rivers" (2022). Cal Poly Humboldt theses and projects. 602.
https://digitalcommons.humboldt.edu/etd/602