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UBC Theses and Dissertations

Environmental DNA (eDNA) approaches to monitoring outmigration dynamics of juvenile Pacific salmon Benoit, Natalie P.


During the outmigration of Pacific Salmon, the early marine phase is a critical period when high mortality can occur. Traditional sampling and monitoring of juvenile salmon migration can be limited by logistically intensive gear requirements, accessibility, and cost. Improved understanding of the early marine phase, e.g., migration duration and habitat use, requires innovative techniques that can improve the spatial and temporal coverage of monitoring. Environmental DNA (eDNA) are genetic fragments present in the environment that can be used as a proxy for organism presence and can be effectively and efficiently collected through water samples. Estimating fish abundance or biomass from eDNA concentration data would provide a valuable fisheries tool but remains challenging to calibrate. To quantify the relationship between eDNA abundance and fish biomass, I used a controlled mesocosm experiment, in which eDNA samples were collected from 15 aquaria (340 L) with varying densities (0, 5, 10, 20, and 30 – in triplicate) of juvenile Chinook salmon per tank. The concentration of eDNA obtained by qPCR scaled positively with fish biomass (ANOVA, p < 0.05). I then tested this relationship in a field study to calibrate the application of eDNA for species detection, abundance estimates, and assemblage assessments of juvenile salmon against a traditional method, purse seine sampling, during their outmigration through the Discovery Islands of BC, Canada. From May to July, sampling occurred twice a week. The eDNA samples were analyzed using qPCR and metabarcoding, providing DNA concentration values and proportional DNA reads, respectively. Across all sampling sites, seine catch, eDNA-qPCR, and eDNA-metabarcoding effectively detected pink salmon. In the case of Chinook salmon, qPCR was more effective at fish detection than the other methods. Metabarcoding of salmonid assemblage structure revealed similar composition to seine net catch in the in-seine eDNA samples. There was a positive relationship between the number of fish caught and DNA concentration in the pre-seine and in-seine samples which indicated that the eDNA reflected the relative abundance of juvenile salmon in situ. I discuss the above findings with respect to the application of eDNA methods for monitoring juvenile salmon outmigration.

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