The early marine period for juvenile salmon is a critical life history stage for growth and survival. The health of near-shore ecosystems where juvenile salmon spend their early marine life, and the capacity of these habitats to provide prey are thus important for overall salmon returns. While near-shore habitat is generally accepted as being of critical importance, few studies have examined how juvenile salmon use this habitat during their early marine life. Understanding the trophic dynamics in these ecosystems and the characteristics of these habitats that are important for food provision will help us gauge the value of near-shore areas to the early marine phase of juvenile salmon. The importance of this avenue of research is underscored by declined rates of early marine survival of salmon, and suggestions that the rapid development of the shoreline is contributing to this decreased survival. My project investigates the role that near-shore habitat plays in promoting growth and survival of juvenile salmon by evaluating eelgrass as foraging grounds for juvenile salmon in the Comox Estuary, British Columbia. In 2015, we compared juvenile Chum salmon diets to prey availability in zooplankton tows and in epifaunal and infaunal eelgrass samples across a gradient of eelgrass shoot density. We complemented diet analysis with the use of stable isotope ratios of carbon (δ13C) and nitrogen (δ13N) to examine the relative contribution of zooplankton, eelgrass, and terrestrial invertebrates to juvenile Chum salmon diet. In 2016, we collected additional eelgrass samples to cover a wider range of eelgrass density, and compared juvenile Chinook salmon diets to prey availability in eelgrass. Prey invertebrates, such as polychaete worms, harpacticoid copepods, and amphipods, increased with eelgrass shoot density. Juvenile Chum salmon and juvenile Chinook salmon assessed in this study fed primarily on benthic species, specifically on harpacticoid copepods, which were only abundant in epifaunal eelgrass samples. The abundance of prey invertebrates in eelgrass beds and the benthic diet of juvenile salmon in the Comox Estuary leads us to conclude that the presence of eelgrass is an important habitat feature for juvenile salmon. / Graduate

Factors affecting energy transfer to higher trophic levels can determine the survival and production of commercially important species and thus the success of fisheries management regimes. Juvenile salmon experience particularly high mortality during their early marine residence, but the root causes of this mortality remain uncertain. One potential contributing factor is the food quality encountered at this critical time. The nutritionally vital essential fatty acids (EFA) docosahexaenoic acid (DHA, 22:6n-3) and eicosapentaenoic acid (EPA, 20:5n-3) are essential to all marine heterotrophs, and their availability has the potential to affect energy transfer through a limitation-driven food quality effect. Assessing variability in DHA and EPA in an ecologically important prey species of juvenile salmon could give insight into the prevalence and severity of food quality effects. On the west coast of Vancouver Island (WCVI), one such species is the calanoid copepod Calanus marshallae. This omnivorous species possesses a high grazing capacity and the ability to store large amounts of lipids. As it is also an important prey item for a diverse array of predators, including juvenile Pacific salmon, C. marshallae plays a key role in energy transfer from phytoplankton to high-trophic iv consumers. This study quantified spatiotemporal variability in the quality of C. marshallae as prey for higher trophic levels using three polyunsaturated fatty acid indicators: DHA:EPA, %EFA and PUFA:SFA (polyunsaturated fatty acids to saturated fatty acids). Samples were collected on the WCVI in May and September of 2010 and May 2011. The environmental parameters included in the analysis were the phase of the Pacific Decadal Oscillation (PDO), sea surface temperature (SST), latitude, station depth, and season (spring versus late summer). Despite a phase shift in the PDO from positive to negative, overall means of the fatty acid indicators did not vary between May 2010 and May 2011. Same-station %EFA values rarely fluctuated more than 5%. DHA:EPA ratios were more variable but without a discernable pattern, while PUFA:SFA ratios decreased in shelf stations and increased offshore. Contrary to expectations, fatty acid indicators showed a weak positive correlation or no relationship with SST, nor was there a relationship with latitude. The narrow temperature range observed across all stations suggests that temperature may not play a significant role in PUFA availability off the WCVI. There were, however, significant relationships between the fatty acid indicators and bottom depth and season. Shelf and slope stations showed significantly higher %EFA and PUFA:SFA than did offshore stations (depth >800 m), with this gradient appearing stronger in May than September. While the food quality represented by C. marshallae was consistent across all shelf stations, the lower food quality observed offshore could potentially affect juvenile salmon growth along the WCVI where the shelf narrows to less than 5 km. / Graduate / dpbevan@uvic.ca

Cumulative effects from multiple anthropogenic stressors over the past three centuries have severely impacted estuarine and coastal habitats, with cascading effects on the species that rely upon them. Pacific salmon (Oncorhynchus sp.) are migratory species that use estuaries as juveniles and as adults and deliver critical nutrients to coastal ecosystems as they move between fresh and marine waters. Many once abundant salmon populations have been extirpated or are in severe decline relative to historic levels, yet the strength of the relationship between habitat loss and population productivity has been challenged. In this dissertation, I applied field studies, otolith analyses, and conservation decision science tools to investigate the relative importance of estuarine habitat to salmon populations, with the aim of advancing effective management solutions for these species and their habitats. First, I conducted a two-year field survey of fish communities in the Fraser River estuary, British Columbia, Canada comparing the species richness and relative catch amongst three distinct habitats. I found that this impacted estuary still supported a rich community of migratory marine and anadromous fishes, as well as resident estuarine fish species. Each habitat supported some unique fish assemblages, with eelgrass supporting the highest catch and diversity of fishes overall but brackish marsh supporting the highest and most consistent catch of salmonids. Next, I used otolith analyses to quantify the residency and growth of juvenile Chinook salmon in the estuary. I found that for one of the only two remaining Chinook salmon stocks abundant enough to still support limited harvest in the Fraser River, the estuary provides vital rearing habitat, with juveniles residing in the estuary for an average of 6 weeks, during which time they had mean daily growth rates of 0.57 mm fork length, approximating growth in healthier estuarine systems. The use of these habitats by juvenile Chinook salmon had not been quantified previously, so these findings directly inform management of this population, which was recently designated as Threatened by the Committee on the Status of Endangered Wildlife in Canada. Finally, I applied Priority Threat Management, a conservation decision science framework, to predict the future status of Pacific salmon in the lower Fraser River and identify the most cost-effective conservation solutions out of a suite of alternative management strategies. On our current trajectory none of these populations were predicted to be assessed as ‘green’ or healthy status at the end of 25 years. In contrast, implementation of broad scale habitat restoration, protection, and watershed management could considerably improve the viability of the lower Fraser to support these salmon, such that many (14/19) of these populations would have a >50% likelihood of being assessed as healthy. Together, this research provides novel evidence of active and selective use of estuarine habitats by juvenile salmon, reliance on estuarine habitat for early marine growth by juvenile Chinook salmon, and a direct link between habitat health and population status for lower Fraser River salmon populations. / Graduate / 2023-04-13