Brian Hunt

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
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Lotic organisms experience and have adapted to a high degree of spatio-temporal variability in their flowing environments. Streams play a key role in the lifecycle of Pacific salmon (genus Oncorhynchus), a group of species of high ecological, cultural, and economic importance. Conservation of salmon habitat in streams often centers on the management and restoration of physical components, such as geomorphic features and instream flows. Recent technological developments and years of government-led monitoring programs have equipped us with the tools and knowledge to further our understanding of the relationship between salmon and their flowing environments. In this thesis, I investigate the importance of variability in stream environments through the lens of both ecohydraulics and ecohydrology. In Chapter 2 (ecohydraulics), I used an observational field-study to demonstrate the importance of fine-scale turbulence and velocity gradients in mediating microhabitat selection by drift-foraging juvenile steelhead, challenging the averaged metrics traditionally used to describe and quantify fish habitat. In Chapter 3 (ecohydrology), I compiled a database of historical records of stream discharge and salmon production across British Columbia, Washington State, and Oregon, in order to explore key drivers in the relationship between interannual variation in flow conditions and juvenile salmon production across broader spatio-temporal scales in the region. Together, both chapters highlight the ecological importance of variability in the flowing environment for Pacific salmon across spatio-temporal scales, highlighting potential mechanisms driving this relationship in both the context of individual behaviour and population dynamics. Such information is especially important given that climate change is causing shifts in the global hydrological cycle, potentially impacting Pacific salmon populations. By exploring this topic through different lenses, this document provides useful insights in the integration of scientific disciplines which allows us to move towards more system-based approaches in resource management and species conservation.

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Scyphozoan jellyfish are important components of marine ecosystems as generalist feeders with complex trophic interactions. These interactions can be investigated using biomarkers, like stable isotope (SI) ratios and fatty acid (FA) profiles. However, the absence of reliable estimates for SI and FA turnover time and modification in jellyfish limits the accuracy of these approaches for investigation of jellyfish trophic ecology. In this thesis, I conducted a controlled feeding experiment for two scyphozoan predators (Aurelia aurita and Chrysaora pacifica) and two prey types (crustacean zooplankton and gelatinous A. aurita) to provide quantitative estimates for SI and FA turnover time and modification between trophic levels. I estimated SI trophic enrichment factors for jellyfish feeding on crustacean zooplankton (Δδ¹³C = 1.19‰ and Δδ¹⁵N = 2.09‰) and jellyfish feeding on interspecific jellyfish (Δδ¹³C = 1.59‰ and Δδ¹⁵N = 1.35‰). I found some similarities between both predators when consuming the same prey, which suggests some metabolic pathways that are conserved for jellyfish. Specifically, 18-carbon FAs decreased in proportion in the predators compared to their prey, while 20-carbon FAs increased, which implies a 2-carbon elongation pathway in jellyfish. By providing estimates for turnover time and modification of SIs and FAs for jellyfish, I have advanced the utility of SIs and FAs for investigating jellyfish trophic ecology. After establishing SI and FA turnover time and modification parameters, I applied these parameters to investigate the trophic ecology of Aurelia labiata in a temperate coastal food web. Using SIs and FAs for 152 jellyfish 19-225 mm in size, I documented a shift in diet, where the proportion of zooplankton in the diet of A. labiata increased as bell diameter increased. I also documented a size-based shift in the nutritional quality of A. labiata, where C:N decreased with size, arachidonic (ARA) and docosahexaenoic (DHA) acid increased with size, and eicosapentaenoic (EPA) acid was unaffected by size. Only changes in C:N and DHA were apparently related to changes in the diet. Marine food webs are highly size structured, so these size-specific results will have implications for the flow of energy and nutrients through jellyfish in marine food webs broadly.

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The cultural and ecological contributions of salmon cannot be understated, as these keystone species have underpinned coastal ecosystems and societies from time immemorial. Despite this millennia-long intimate relationship with Pacific salmon, returns of stocks have become unpredictable and difficult to manage from overfishing and multiple complex stressors. Research has shown that juvenile salmon feeding is a crucial factor for growth and recruitment, and the ocean conditions driving prey availability are tightly coupled with survival of salmon. Pink and chum are abundant co-migratory species of salmon that may exert competitive pressure for food resources during their vulnerable early marine phase. However, competition research on juvenile pink and chum salmon is limited, especially within the complex British Columbia coast. This research aimed to fill gaps in understanding of juvenile pink and chum foraging strategies and interactions in areas of good and poor foraging conditions during their coastal outmigration. In the Discovery Islands and Johnstone Strait regions, there were foraging deserts and oases, where juvenile salmon mean stomach fullness values ranged from 6% body weight. In good foraging conditions, juvenile pink and chum both consumed the same high-quality crustacean prey with limited competition, but under poor foraging scenarios, salmon diets differed. Chum salmon consistently consumed gelatinous prey and pink salmon relied more heavily on copepods and nearshore zooplankton, differing in niche in response to competitive interactions. There was a match between predators and prey in 2015, when salmon fed on larger prey, and were in healthier condition (K = 1.0). There was a potential mismatch in 2016, when small prey taxa may have caused poorer condition for juvenile salmon (K = 0.94). Chum salmon had a stronger relationship to prey size than pink, when larger chum successfully consumed the largest prey. These foraging strategies of opportunistic specialization may indeed provide salmon with resilience to face the challenges of shifting climates. Pink and chum salmon can be monitored as indicators for ecosystem health and zooplankton availability. Salmon reflect the health of socio-ecological systems and require our understanding and care to view them holistically as they migrate through diverse, challenging habitats.

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Salmon migrate thousands of kilometers through dynamic ecosystems of the North Pacific Ocean, however, their open ocean life phase is poorly understood with limited research comparing salmon trophic ecology across the entire basin. Understanding the marine trophic ecology of salmon has the potential to reveal information about ocean conditions, competition, prey abundance, as well as salmon health and survival. The first goal of this research was to build an open-access database to centralize Pacific salmon diet data using a standardized format (‘North Pacific Marine Salmon Diet Database’). This database was then populated with an initial data set that came from 62 sources identified through a systematic literature review, targeting peer reviewed and gray literature from time periods with high research activity: 1959–1969 and 1987–1997. The second goal was to examine spatial and interspecies differences in diet and trophic niche for chum, pink and sockeye salmon across the North Pacific between 1959 and 1969, a period during a negative phase of the Pacific Decadal Oscillation and prior to significant hatchery enhancement. In the Western Subarctic, all species tended to consume zooplankton and prey availability was higher than the Eastern Subarctic. In the Gulf of Alaska and Eastern Subarctic, interspecies differences in diet were most apparent with chum and sockeye specializing on zooplankton and micronekton, respectively, while pink ate a mixture of zooplankton and micronekton. In the Bering Sea chum ate zooplankton while sockeye and pink alternated between zooplankton and micronekton. In addition to the large-scale trophic patterns, these data revealed novel fine-scale spatial trophic patterns, including latitudinal, onshore-offshore, and cross-gyre gradients. These results showed that pink were more generalist consumers, and their diets may be a better reflection of overall prey presence and abundance in the environment. Conversely, chum and sockeye were more specialist consumers, and their diets may be a better reflection of interspecies dynamics and/or specific prey presence and abundance of zooplankton and micronekton, respectively. Overall, this research provides an open-access database that can help address gaps in ecological understanding of the North Pacific, as well as complementary data analyses to further understanding of salmon marine ecology.

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