Scott Hinch

Pacific salmon are now experiencing temperatures in freshwater that can reach or exceed their upper thermal limits. The aims of this thesis are to evaluate the role of acclimation on the Upper Thermal Tolerance (UTL) in stream-type juvenile Chinook salmon (Oncorhynchus tshawytscha), to evaluate how different methods in measuring UTL affect the measured outcome, and determine how acclimation temperature affects post-swim mortality. Both parr and fry life stages were acclimated for two weeks at temperatures spanning present and expected future summer levels (15°C, 18°C, 20°C, 24°C). Using fish from each acclimation temperature, we measured post-swim mortality following an endurance trial (Eswim), whereby swimming fish were exposed to increasing speeds at each temperature, and subsequently returned to their initial acclimation trough and monitored for 48 hours. The effect of acclimation temperature on critical thermal maximum (CTmax) was measured by two means: stationary (CTmax stat) and swimming (CTmax swim). CTmax stat was determined by water evenly heated at 0.3°C/min in a stationary bath, with loss of equilibrium (LOE) as the indicator of CTmax stat. CTmax swim was determined using a swim flume heated at 1°C/30min with fish swimming at a fixed speed of 4 BL/s, and cessation of swimming as the endpoint. Fish acclimated to higher temperatures generally exhibited higher thermal tolerance until 24°C, where fish were not able to acclimate to higher temperatures. Based on CTmax stat trials, parr showed a consistent increase in acclimation up to 24°C, with increasing CTmax temperatures, though in CTmax swim trials, there was a distinct thermal ceiling at that temperature. Fry exhibited a greater sensitivity to increased temperatures, with a drop in CTmax at 24°C for both stationery and swimming trials. There was high post-swim mortality following the 24°C acclimation groups in the Eswim trials in both parr and fry, indicating an upper thermal limit where impaired recovery. This work highlights the need for varied metrics in studying thermal tolerance and the influence that such metrics have on the measured outcome. Warm temperatures exceeding 20°C are now routinely occurring in the study population region, so we expect increasing mortality rates of fish in coming year.

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Habitat fragmentation has been implicated in broad declines of Pacific salmon and trout populations in the Pacific Northwest of North America. Dams are often considered to be the largest driver of fragmentation. However, small-scale barriers like floodgates, weirs and culverts can have significant negative impacts on stream habitat. In British Columbia (BC), Canada, an estimated 135,000 - 200,000 culverts act as barriers to fish passage, making them a major issue for salmonids and a target for restoration. Despite barrier culverts being one of the leading anthropogenic causes of stream fragmentation globally and a frequent target of restoration efforts, the efficacy of these interventions and their conformance with best practices has rarely been examined. Effective planning of these restoration efforts is often hindered by incomplete barrier inventories and uncertainty about where best to perform restoration. I addressed these issues by performing two complementary studies. I first performed a 'post-treatment' audit of culvert barrier remediations in southcentral BC through an examination of current physical attributes at 15 retrofit and 15 replacement sites and scored sites based on the BC culvert fish passage assessment and on best practice guidelines for stream crossings in BC. I then used two modelling approaches to evaluate historical habitat availability, how barriers potentially prevent Chinook and Coho salmon migrations, and the role of barrier remediation in enhancing habitat accessibility in the South Thompson watershed of BC. At barrier remediation sites, 80% of retrofits and 20% of replacements were classified as fish passage barriers, and conformance with best practices was at most 80% at any site. I modelled that Chinook and Coho salmon historically had access to 3600 km and 3400 km of stream length, and these habitats are currently impacted by 1955 barriers. These results show that fragmentation of salmon habitat is a widespread issue, potentially exacerbated by predicted barriers, and that poor conformance may be hindering the effectiveness of remediation actions.

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Urban streams are under constant assault from pollutants, including highly damaging heavy metals. Zinc is a common and nearly ubiquitous contaminant in urban streams and water bodies with a myriad of sources including mining, agriculture, commercial industry, and stormwater runoff. At high levels, zinc is known to cause physical damage and death to olfactory cells in fish, resulting in a loss of smell. This is highly concerning, as fish use their sense of smell for foraging, communication, migration, mating, and defence. This is particularly true for salmonid species like coho, that lack other methods of predator defence. While most urban streams do not contain high levels of zinc contamination, zinc is often present at lower concentrations. The influence of zinc on olfaction at low levels is not well understood and could have significant impacts on survival. In the present study, juvenile coho were exposed to environmentally relevant levels of zinc (30 - 120 µg/L for 3 hours) and were then challenged with a con-specific chemical alarm cue, which was intended to reflect a nearby predation event. Coho that were not exposed to zinc immediately reduced their activity and demonstrated classic anti-predator behaviours such as sinking, shoaling, and freezing in place. The coho exposed to any of the three levels of zinc failed to react to the alarm cue and showed little to no expected alarm behaviours. This suggests that the current acceptable limit of 33 µg/L of zinc outlined in the BC water quality guidelines is not protective for coho juveniles. The inhibition of successful olfaction and reaction to an alarm cue shows that zinc exposed fish are compromised by low level zinc contamination and fail to respond to their chemosensory environment appropriately. This could have large impacts on predator avoidance and, ultimately, survival through the freshwater phase.

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Evaluations of habitat use and the functions of specific habitats in an organism’s life history can help identify potential survival bottlenecks and guide the development of habitat-based conservation measures. Using acoustic telemetry, I investigated the effect of biological and environmental factors on the residence of sub-yearling Chinook Salmon Oncorhynchus tshawytscha in a fjord estuary in British Columbia. Wild Chinook Salmon (n=49; 67-95 mm) were experimentally released into the estuary of which 36 exited successfully. The median residence duration for the fish I released was 11.2 days (95% CI 6.5 -15.5). Using model selection and time-to-event analysis, I found tide direction and salinity to be important factors influencing when fish left the estuary. While in the estuary, fish displayed either direct or indirect migration patterns. Binomial generalized linear models were used to evaluate the association between intrinsic factors and the probability of a fish making direct movements. In this analysis, faster freshwater growth increased the probability of a fish making direct movements out of the estuary. This study indicates this estuary to be a stop-over habitat for larger sub-yearlings. The results of this study also suggest migration phenology and habitat use are both partially shaped by intrinsic factors in sub-yearling Chinook Salmon.In a second experiment, I modelled the spatial distribution of juvenile salmon (O. kisutch, O. keta, O. tshawytscha) and flatfish (Platichthys stellatus) in a fjord estuary as a function of habitat conditions. Fish were captured bi-weekly in channel and beach habitats (n=20) at the North end of Howe Sound. A spatial generalized linear model (sdmTMB) was used to elucidate associations between catch and habitat factors. Both environmental and structural habitat factors were included as predictors. I found most associations between catch and the variables included in the analysis to be weak. The results of the two studies in this thesis indicate environmental conditions to have weak and uncertain effects on the residence duration and distribution of juvenile salmon in the fjord estuary studied, which suggests juvenile salmon are able to exploit a range of habitats and tolerate variable environmental conditions.

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Freshwater habitat loss is a major threat to the persistence of salmonid (Oncorhynchus spp.) populations in the Pacific Northwest of North America. To better inform where and when to preserve this critical habitat, information on its extent and quality is required over spatial scales fish use for various life stages. Further, current and accurate habitat associations are required to make location-specific conservation recommendations. Given the limitations of fine-scale analysis due to sampling logistics and that land conversion activities and climate change affect stream salmonids on extremely large spatial scales, approaches to extend small-scale fish-habitat assessments accurately and cost-effectively to the watershed level are needed. To address this challenge, I investigated the habitat associations of juvenile rainbow trout (Oncorhynchus mykiss) and Dolly Varden char (Salvelinus malma) in the Nahmint watershed on Vancouver Island, British Columbia, during summer 2019. I also assessed whether 3-D Airborne laser scanning (ALS) derived measurements of small stream characteristics provided similar explanatory power in establishing habitat associations with physical characteristics as conventional field-based surveys. I surveyed 200 m of habitat across varying tributary stream sizes (5.1 m to 10.6 m) and implemented mark-recapture fish sampling using minnow traps and passive integrated transponder tags to establish habitat associations and characterize movement. The density of both species was significantly higher in pool habitats than in glides and riffles. Generally, restricted movement was observed by both species, with some Dolly Varden char moving in a primarily downstream direction. Further, ALS-measured and field-measured variables produced similar habitat associations, with fish presence and density associated with pool habitats classified by the ALS data. Overall, these results highlight the importance of habitat quality (such as abundant pools) and connectivity in small streams, while also illustrating the utility of using ALS -derived measures of small stream habitat to establish fine-scale habitat associations of juvenile salmonids within a watershed. Moreover, ALS has the potential to be used as a predictive tool to assess juvenile salmonid distributions at a broad scale in a timely and cost-effective way.

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To facilitate the movement and processing of timber in some regions of the Pacific Northwest, bundles of logs are tied together to form large rectangular rafts (also known as booms) which are transported and stored in aquatic environments. In the lower Fraser River, some reaches have > 50% of their shoreline with adjacent log booms, yet our understanding of the effects of log storage on aquatic habitats and biota is very limited. The objectives of my thesis were to examine key environmental characteristics that may be affected by log storage activities in the lower Fraser River and estuary. I sampled water and sediment at control, current log storage sites, and former log storage sites and investigated: metal contaminant concentrations, water quality (pH, temperature, turbidity, total dissolved solids, and oxygen concentrations and saturation), invertebrate diversity, biomass and abundance, vegetation coverage, and sediment compaction. I found that at most sites with current log storage, they had compacted sediments and reduced vegetation coverage, effects that are likely caused by logs ‘grounding’ onto the benthic environment due to tidally influenced changes in water level. I found that bottom water pH was lower, and surface temperatures cooler, at current log storage sites, but found no other differences in water quality or in metal contaminants, among log storage categories. Median abundance of total benthic invertebrates was 4.26 times lower at current log storage sites relative to control sites, potentially attributed to log grounding and poorer water quality in their benthic habitats. Diptera were most abundant and Haplotaxida least abundant at control sites. Unfortunately, lack of reliable data on when logs were moved onto and off of sites made it impossible to confirm the ‘time since fallow’ for former log storage sites. Thus, interpreting results from former sites was difficult, and assessing the potential ‘recovery’ from log storage was not possible. While the presence of log booms on nearshore environments may have some effects on water quality, the largest effects seem to come from logs grounding on the substrate which changes the physical habitat. The fact that log booms are coming into contact with, or resting on the substrate, is in direct contradiction with known best management practices for log storage which state that at no time should logs and substrate come into contact.

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Aquatic systems are warming and exceeding upper thermal limits (UTL) of Pacific salmon (Oncorhynchus spp), yet quantifying UTL and understanding how they inform resilience to climate change is challenging. This thesis focuses on quantifying upper thermal tolerance limits in Pacific salmon with specific reference to Kokanee salmon (O. nerka).I conducted a systematic review involving 168 papers investigating UTL in five Pacific salmon species and found considerable variation among species, within species, and across life stages -largely due to different methodological approaches (e.g. CTmax/UILT, Aerobic/Cardiac Scope, Thermal Migration Barriers, Rearing Mortality, Thermal Preference/Avoidance). Each method displayed strengths and weaknesses owing to logistics, time scale, and ecological realism, I recommend reporting an ‘UTL range’ instead of single UTL values, to reflect inherent and methodology-based variation. Comparing studies with similar experimental design showed that within species, UTL was higher for populations that historically encountered higher temperatures suggesting local thermal adaptation. Within populations, UTL differed across the lifecycle -highest in fry for some populations and in migrating adults for others. UTL has not been assessed for spawning fish and few studies examined estuarine and marine stages, limiting life history perspectives. My analysis suggests pink salmon are most resilient to warming due to their exceptional aerobic capacity, high straying rates, short generation time and limited exposure to high temperatures.In an additional experiment, I conducted thermal tolerance trials using two commonly employed methodologies: The Critical Thermal Maximum (CTmax) and Thermal Performance Curves for Aerobic Scope (AS). Juvenile and spawning adult fish were held overnight at a range of experimental temperatures (12˚, 17˚, 20˚, 22˚ and 24˚C).. In CTmax trials water temperatures were increased at a constant temperature (0.3˚Cmin⁻¹) until fish lost equilibrium. CTmax values ranged on average from 28.7˚C – 29.7˚C and differed significantly between life stages. Absolute AS – the difference between maximal and standard metabolic rates – were found to differ significantly between male and female adults, however Optimal (Topt) and functional temperature limits (Tpejus) occurred at similar temperatures (Topt: ~15˚C, Tpejus: ~20˚C). The large degree of variation in upper thermal tolerance metrics highlights the need for careful selection of values when conducting vulnerability assessments.

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Telemetry tracking of Fraser River Sockeye salmon (Oncorhynchus nerka) smolts from Chilko Lake to the open ocean has revealed relatively high mortality through some coastal areas of British Columbia, and that coastal migratory routes may influence survival. Acoustic arrays were strategically deployed through the Discovery Islands region to track tagged smolts across all possible migratory routes, including three major entrances: Discovery Passage (DP), Sutil Channel (SC), and Desolation Sound (DS). A total of 465 smolts were tagged and released at Chilko Lake in 2017 (n = 315) and in the Northern Strait of Georgia in 2018 (n = 150) using a combination of VEMCO V4, V5 and V7 transmitters. Smolts were observed using all three routes with SC (n = 101), the most central, having the greatest proportion of use, followed by DP (n = 44) and DS (n = 13). Survival of the 2018 smolts was estimated using a Cormack Jolly Seber framework adjusted to account for variable distances of the major migratory routes. Highest survival was in DS (84% /100 km, 95% CI: 46 - 97%), followed by DP (71%, 95% CI: 39 - 90%), and lastly SC (48%, 95% CI: 37 - 60%). Each route presents variable environmental conditions that may influence smolt survival likely through variable exposure to predators. Smolts migrated through DP with mean travel rates of 36 km.d⁻¹ (SE ± 1.8) which was 1.7 timesfaster than through SC (mean travel rates of 21.5 km.d⁻¹ (SE ± 1.8) and 2.4 times faster than through DS (mean travel rates of 15 km.d⁻¹ (SE ± 2.9 ). Extreme tidal currents present with DPprovide rapid transport of smolts through the route, while other routes provide beneficial currents further along their migration path. Survival and travel rates did not appear to be linked as survival was poorest through SC which had the ‘intermediate’ travel rate. This study provides the most detailed picture of behaviour and mortality of Pacific salmon smolt migrations in marine coastal areas to date and highlights the potential of spatiotemporal variability of migration to impact survival in early marine migrations of smolts.

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Sockeye salmon (Oncorhynchus nerka) is a key species to nearly every community existing within the Skeena River Watershed. Spawning enhancement programs within the Babine sub-watershed have enabled two sockeye populations at Pinkut Creek and Fulton River to increase in abundance over several decades and now comprise the majority (> 75%) of the Skeena River sockeye aggregate stock, amidst a long-term decline for wild populations. Mixed-stock harvests without means to differentiate wild from enhanced populations have contributed to overexploitation of wild sockeye populations. This study used a microwave energy meter (Distell Fat Meter, Model FFM 692) to examine if populations could be differentiated based on energy reserves. At a full-span, salmon counting fence located along the migration route of Lake Babine sockeye populations, I externally tagged and assessed energy status of 2,056 sockeye, using tag recoveries (n = 252) on spawning grounds to infer population identification. I found that the energy meter was able to differentiate enhanced Babine sockeye (pooled between the two enhanced populations) from wild Babine sockeye (all wild populations pooled; Mann-Whitney U-test; P
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Understanding a species’ life history and habitat requirements are fundamental to conservation and successful resource management. Sockeye Salmon Oncorhynchus nerka are a highly valued fish species that exhibit astonishing life history variability; yet, despite their management importance and diversity, there are wide declines in productivity and many populations are at risk. Within Alouette Lake, British Columbia, are two ecotypes of O. nerka (the anadromous form, herein Sockeye Salmon; and the nonanadromous form, Kokanee), and both spawn anomalously deep within the lake. The objective of my thesis was to study the reproductive behaviour and habitats of deep spawning Sockeye Salmon and Kokanee, including reviewing potential habitat availability within Alouette Lake to support Sockeye Salmon restoration objectives. Using repeated gill net and remote operated vehicle surveys focused on the more abundant form, Kokanee (assuming Sockeye Salmon would behave similarly), I found that spawning behaviour was similar to other populations; this included protandry, large-scale movement patterns in males, some early arriving females, and nest excavation in a variety of lake bed types. Notable exceptions were the spawning depths (10-105 m), extended spawning period (2-3 months), and lack of floating carcasses that occurs in other deep spawning populations. Location data from Kokanee gill net surveys and Sockeye Salmon telemetry studies were combined with topographic and substrate information to develop Maxent habitat suitability models tested over a range of settings. Models predicted that suitable spawning habitat was available throughout the Alouette Lake at a magnitude that should not limit Sockeye Salmon restoration. Models for both ecotypes predicted stronger links to topographic variables than to substrate, but substrate was more important for predicting Kokanee spawning habitat. Moreover, ecological niche similarity tests showed significant differentiation between the two ecotypes. Innate differences between Sockeye Salmon and Kokanee and their mating preferences, as well as interactions between ground water and surface water movement that was detected (via a data logger mooring) may be associated with the variability in observed habitat use and model predictions. Together, these findings further our understanding of reproductive behaviour and habitats in deep spawning O. nerka populations and have important management implications.

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The migrations of animals between discrete locations frequently generate a range of ecological side effects. While many of the consequences of migrations are well understood, migratory coupling – the movements of predators over large spatial scales in response to migrant prey – has received little attention. I sought to describe a potential occurrence of migratory coupling in the Chilko Lake system, British Columbia, where bull trout (Salvelinus confluentus) aggregate near the lake outlet during the annual migration of anadromous sockeye salmon smolts (Oncorhynchus nerka), presumably to consume migrant smolts. To characterize the influence of the smolt migration on the spatial distribution of bull trout, I surgically implanted acoustic transmitters into 20 bull trout and tracked their movements throughout the Chilko system for one year. Because bull trout generally become increasingly piscivorous with size and age, I also combined acoustic telemetry with age estimates and length measurements to determine whether bull trout size, age, or growth influences their behavioural response to the smolt migration. Bull trout travelled substantial distances and 47% returned to the lake outlet during the smolt migration in consecutive years, suggesting that a portion of the population may be responding to the migrant smolts. However, bull trout returned to the outlet up to three months prior to the arrival of smolts at the outlet, thus their spatial distribution may also be influenced by other factors such as site fidelity. Furthermore, if bull trout are responding to the smolt migration, it remains unclear whether they are anticipating the arrival of smolts at the lake outlet or are following the diffusion of smolts from the lake. There was no detectable difference in age, size, or growth ratio among bull trout that returned to the outlet in consecutive years and those that did not; however, my inability to detect a difference may be a result of my small sample size and narrow range of ages and sizes. Through collecting these data, I also provided the estimates of size-structure, age-structure, and spatial distribution for Chilko bull trout, which has been identified as critical information for the management of bull trout in BC.

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The role of infectious diseases in the declining productivity of wild Chinook salmon (Oncorhynchus tshawytscha) in BC is poorly understood. In wild populations, it is difficult to study the effects of infectious diseases because they interact with environmentally induced stress and diseased fish are not often observed as many are likely predated upon or die out of view. The early marine life of Pacific salmon (Oncorhynchus spp.) is believed to be one of the key components of the declining populations. More focus on understanding the potential role of infectious agents during this life period is needed. My study assessed how infectious agents are associated with the physiology of migrating juvenile Chinook salmon upon their entry to marine waters by linking ancillary data, physiological responses and histopathological lesions with infectious agent detection. It is one of the first to study infectious agents carried by wild salmon through combining molecular, protein, and cellular levels of fish physiology information. Among 46 assayed infectious agent taxa, 26 were detected, including viruses, bacteria, and parasites. Fish from Columbia River system were found to have significantly higher infection burden than those derived from five other regional groups. I discovered and reported the associations between fish physiological conditions and five infectious agents, including Ichthyophonus hoferi, ‘Candidatus Branchiomonas cysticola’, Parvicapsula minibicornis, Ceratonova shasta, and Piscine orthoreovirus (PRV). PRV, particularly, was recently reported in many salmon farms in BC as the suspected causal agent of two related diseases in both Atlantic and Chinook salmon, and has potential to be exchanged between farmed and wild populations. I further provided one of the first lines of evidence of potential impacts of PRV both on host genes and histopathology in the wild juvenile Chinook salmon. Understanding the relationships between infectious agents and salmon can help inform conservation and management practices.

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For anadromous steelhead smolts (Oncorhynchus mykiss), physiological condition and spatiotemporal variability in movement patterns, such as routes, have the potential to influence survival, but these aspects of the migration are poorly understood. To investigate route-specific movements and survival during outmigration, I implanted acoustic tags into 243 hatchery steelhead smolts and tracked their migration through coastal British Columbia for up to ~400 km. Two release groups (marine and freshwater) were used to assess survival through the first marine inlet. To better understand how smolt condition influences migration fate, I combined acoustic telemetry with non-lethal gill biopsies and used high-throughput quantitative polymerase chain reaction to assess how infectious agents and host gene expression profiles influence smolt migration fate. Poorest survival was in the river and marine inlet first encountered by smolts. Survival rates in all other migratory segments did not differ between release groups, suggesting the near-shore marine environment is associated with particularly poor survival for outmigrant steelhead. I present rare evidence of route-specific survival for a migratory species, which was detected though a series of channels ~200 km from release. The westernmost route here was associated with significantly higher survival and was more travelled. A portion of smolts exhibited ‘milling patterns’ including reversals in migration direction or lateral movements along acoustic subarrays. Redundancy analyses of gene expression, infectious agent loads, and body condition highlighted gene expression profiles indicative of migratory fate. Smolts that were never detected in the river clustered together, far from other groups in ordination space. Smolts that did not make it from the river to the estuary had significantly elevated expression of the immune genes Il-17D and RPL6, and lower expression of the osmoregulatory gene NKA α1b relative to other individuals. Two infectious agents were detected in tagged smolts (Flavobacterium psychrophilum and 'Candidatus Branchiomonas cysticola'), neither of which had an influence on survival. My results identify potentially important, yet understudied regions affecting survival of salmonids smolts. I also demonstrate some of the first evidence of gene expression profiles predicting individual migration fate in juvenile salmonids, and highlight potential mechanisms influencing freshwater and early marine survival for steelhead smolts.

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Sockeye salmon (Oncorhynchus nerka) smolts typically experience high mortality during outmigration through freshwater and into the marine environment, yet factors influencing survival remain poorly understood. Telemetry studies investigating migration survival have largely focused on tracking large hatchery smolts or larger individuals within wild populations, which may not be representative of the majority of migrants. I used recently developed miniaturized acoustic transmitters (VEMCO V4) to track age-1 sockeye smolts (n = 200) for the first time over ~950 km from Chilko Lake, British Columbia, Canada through the coastal marine environment using large-scale receiver arrays. I compared their survival with concomitantly tagged and tracked age-2 smolts (n = 100). I paired acoustic telemetry with non-lethal gill biopsies and used high-throughput quantitative polymerase chain reaction to assess how infectious agents and host gene expression profiles influence smolt migration survival. Cumulative freshwater survival of age-1 smolts was double that of age-2 survival (56% vs 28%), potentially due to higher proportional tag burdens of age-2 smolts. Although survival between the age classes differed, trends in landscape-specific survival were similar, with the poorest survival occurring the in the upper river tributaries (76% and 53% for age-1 and age-2 smolts respectively over the first 14 km from release), and after ocean entry for age-1 smolts (36%). Three infectious agents (Flavobacterium psychrophilum, ‘Candidatus Branchiomonas cysticola’, and infectious hematopoietic necrosis virus) were most prevalent in tagged smolts, and F. psychrophilum was related to migration survival. Gene expression profiles differed between age groups and were strongly associated with migration survival. Smolts that died earlier in the river had a significantly higher expression of inflammatory (IL-11 and IL-17D) and stress (HSC70 and JUN) response genes than smolts that survived migration. These genes were also more highly expressed in age-2 smolts than age-1 smolts. My work highlights the importance of expanding research to include smaller age-1 smolts and provides important survival estimates for an indicator population of Fraser River sockeye salmon. My work also provides important and novel links between infectious agents and gene expression profiles with migration survival of age-1 and co-migrating age-2 smolts for the first time, highlighting mechanisms contributing to sockeye smolt mortality during migration.

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Upriver migrating adult Pacific salmon home to natal sites following natal water cues while also undergoing a suite of physiological changes to prepare for spawning. Migrants can encounter myriad environmental conditions that are physiologically and energetically challenging throughout these journeys. Many freshwater migration corridors have also been converted into hydroelectric systems (hydrosystems) that can change the composition of flows such that the availability and concentration of natal water cues can vary substantially. How such flow composition changes affect migration behaviour has rarely been examined, while the cumulative effects of environmental and physiological factors on the fate of migrating adult salmon in regulated rivers are not well understood. Using the Seton hydrosystem in British Columbia and two populations of sockeye salmon as a model, I conducted a field radio-tagging study that examined how physiology, temperature, and natal water concentration affected the behaviour and fate of adult salmon migrating through a regulated river while enroute to natal spawning sites. Most tagged migrants (89%) delayed in the outlet of the Seton powerhouse that discharges strong concentrations of natal water, and subsequently wandered in the mainstem Fraser River before continuing their upstream migration into the Seton River, where natal water cues can also vary. I found few associations between physiological stress and reproductive hormone levels with powerhouse delays and wandering, although fish with higher energy content were generally slower migrating through the whole hydrosystem. Higher temperatures and elevated natal water concentrations were associated with shorter delays at the powerhouse and less wandering, but only among late-run migrants. I found little evidence that the cumulative effects of physiology and environmental conditions during hydrosystem passage were related to survival to natal sites, suggesting that other factors aside from those encountered during hydrosystem passage (e.g. environmental factors prior to reaching the hydrosystem) may have played a role in influencing survival post dam-passage. My thesis provides the first detailed account of how varying natal water concentrations affects the homing behaviour of wild migrating adult salmon and how the cumulative effects of physiology and environmental conditions experienced during passage through a regulated migration corridor influences survival to natal sites.

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Water temperature affects every aspect of the physiology of ectothermic fishes. Heterothermic stenotherms, like Pacific salmon, use behavioural thermoregulation to swim into more optimal water temperatures and out of less optimal ones. The range of preferred temperatures can coincide with the thermal optima of important physiological processes. During the reproductive migration, adult Pacific salmon partition limited endogenous energy and aerobic scope for activity to multiple activities, including swimming, recovery from physiological stress, maturation, and immune function. Although much is known about the effect of temperature on aspects of salmonid physiology from laboratory experiments, how free-swimming fish use thermal habitats to manipulate physiological processes is not well understood.Radio telemetry, archival temperature loggers, blood biopsy, and spawning assessments were used to evaluate the relative importance of physiology and migratory experience to thermal behaviour and metrics of fitness in the Gates Creek population of sockeye salmon in the Fraser River, British Columbia. A framework was developed, using relationships between temperature and routine oxygen consumption and aerobic scope for activity, to determine whether the thermal experience of tagged fish reflected minimization of energetic cost or maximization of aerobic scope. Nearly all male and female fish preferred temperatures several degrees below the optimum for aerobic scope (ToptAS; i.e. 16.4 ºC), but two groups of fish benefitted from use of temperatures near ToptAS. Later migrants used these temperatures, where the cost of transport is minimized, to swim quickly through one lake, and female sockeye salmon that spent a greater proportion of the migration within a ToptAS window (13.4-19.5 ºC) lived longer on spawning grounds and had a lower probability of egg retention at death. In contrast, migrants that spent longer in the lakes occupied the cool water temperatures that I hypothesized would limit energy expenditure. Temperature preference was also related to the flow dynamics and water temperature that fish experienced during passage at the Seton Dam, which suggests that migrants use thermal habitats for recovery from anaerobic swimming.Future research can use existing relationships between temperature and physiological processes for greater insight into the ecological importance of fish temperature selection in thermally heterogeneous environments.

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Fish that are released from fisheries capture exhibit physiological and behavioural changes that can result in mortality. The ability to release fish that do not experience subsequent fitness consequences is fundamental to fisheries conservation and management tools that mandate live release. Thus, researchers have evaluated methods that fishers can use to reduce the potential for negative capture-related effects. Indeed, modifying capture and landing practices can limit the severity of the physiological and behavioural impairments. Moreover, release techniques that enhance the metabolic recovery process essential for mitigating capture-related physiological changes may help to enhance survival. Because this essential recovery process requires oxygen consumption that exceeds basal metabolic needs, I evaluated a ventilation assistance technique that forced a high flow of water over the fish’s gills in an attempt to provide additional oxygen. This assisted ventilation technique mimics manual recovery attempts that are recommended by fisheries managers and often employed by recreational anglers. The physiological, behavioural and survival responses of adult migrating Fraser River sockeye salmon (Oncorhynchus nerka) to capture and release, with and without ventilation assistance, were assessed in laboratory and field experiments. A simulation of capture and release consisting of 3 minutes of strenuous exercise and 1 minute of air exposure resulted in significant physiological impairment in the laboratory experiment. In a field experiment, this simulation resulted in an approximate 30% overall reduction in post-release survival to reach natal spawning grounds. Female fish exposed to simulated capture and release exhibited poorer survival relative to control females and males of all treatments in both of these experiments. The 1-minute assisted ventilation technique did not enhance survival. In fact, further reductions in survival were observed in the laboratory experiment for females subjected to ventilation assistance before release from capture. Capture and release can result in delayed mortality and it appears that a recovery technique recommended by fisheries managers to recreational fishers does not help to reduce capture-related mortality. Mitigating negative capture-and-release effects by disseminating capture and landing best practices, while incorporating scientifically-defensible post-capture mortality rates into management plans, may be the best approach to meeting conservation and management objectives.

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Juvenile Pacific salmon make large-scale migrations from natal freshwater rearing grounds to the Northern Pacific Ocean. To properly manage these species an understanding of their migration patterns and survival is necessary. Acoustic telemetry is an ideal tool used to study the migratory survival and behavior of juvenile salmonids. However, the assumption that tagged individuals behave similarly to non-tagged conspecifics in the freshwater and saltwater phases of their outmigration need to be validated as part of large-scale telemetry studies. Consequently, a laboratory-based experiment was carried out to evaluate intracoelomic tagging effects on juvenile sockeye salmon (Oncorhynchus nerka) swimming performance, growth, post-surgical wound healing and survival in both freshwater and saltwater. A sub-set of fish were tagged with three differently sized tags and the response of the fish to tagging was compared to both a sham surgery and non-tagged treatment group. Fish with tag burdens greater than 6 – 8% body weight (BW; tag weighed in water) resulted in some freshwater mortality and decreased freshwater prolonged swimming performance. Fish implanted with larger tags had decreased survival in saltwater and poorer post-surgical wound healing than fish implanted with smaller tags. To minimize the negative effects of intracoelomic tagging, this research suggests that tag burdens should not exceed 6 – 8% BW in juvenile, hatchery-reared sockeye salmon.Oxygen consumption rates were measured during the transition from freshwater to saltwater to investigate the hypothesis that intracoelomic tagging affects metabolic rate in juvenile salmonids during this period. Respirometer experiments during periods of rest and recovery post-swimming were used to assess metabolic rate in freshwater and saltwater for both tagged and non-tagged treatment groups. There was no effect of intracoelomic tagging on recovery metabolic rate post-swimming. However, tagging and salinity had an affect on resting metabolic rate; when fish transitioned from freshwater to 9 ppt saltwater, resting metabolic rate significantly increased. Resting metabolic rate at 9 ppt was elevated in comparison to the lowest resting metabolic rate recorded in saltwater at 28 ppt. However, both non-tagged and tagged fish were able to recover metabolically after transitioning to saltwater, indicated by similar metabolic rate values in saltwater as in freshwater.

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Pacific salmon experience intense fishing pressure as they commence their freshwater spawning migration, frequently encountering commercial net fisheries and recreational hook and line gear. Untold numbers of fish escape by their own volition or are released by fishers at a range of water temperatures, including those above metabolic and physiological optimums. This thesis focuses on the mortality and sublethal consequences of escape or release from fishing gears by migrating adult Pacific salmon, with a specific focus on how temperature mediates those effects. The role of temperature in the capture and release of fish was investigated in a comprehensive literature review. This revealed that 70% of studies examining mortality or sublethal effects at various temperatures found both to be magnified at warmer temperatures. Collectively, the results suggest that capture-release mortality increases at temperatures within, rather than above, species-specific thermal preferenda. Notably, there were no studies examining temperature effects on capture-release for adult migrating Pacific salmon. In two experiments, migrating adult sockeye salmon were intercepted during the early part of their freshwater migration held in a laboratory at three temperatures corresponding with the range of temperatures spanning the historic, current and predicted future migration conditions experienced by their run-timing group (13°C, 19°C, 21°C for summer-run fish in 2009, and 13°C, 16°C, 19°C for late-run fish in 2008). Fish were exposed to a simulated capture treatment including three minutes of burst exercise ± 60 seconds of air exposure. In both experiments, simulated capture treatments resulted in elevations of plasma lactate concentrations, most markedly after air exposure. The highest mortality was seen in the late-run females at 19°C. Late-run fish who died within 24 hours of capture treatment were characterized by higher hematocrit, plasma lactate and cortisol, and lower glucose, sodium and chloride concentrations than survivors. Air exposure and warm temperatures were associated with longer equilibrium loss and slower ventilation rates post-treatment, which significantly predicted 24-hour survival in late-run fish. Collectively, these results indicate that released or escaped sockeye salmon may be at higher mortality risk when river temperatures are exceedingly high, and that reducing or eliminating air exposure may result in greater survival.

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Populations of Pacific salmon are genetically and morphologically distinct across large watersheds, and these differences may reflect long-term adaptation to environmental factors such as temperature. While climate warming is predicted to affect sockeye salmon, it is likely that such impacts will happen differentially across life stages and populations. Given that selective pressures during early development plays an important role in lifetime fitness, and that elevated water temperatures can critically affect embryo success, this thesis focuses on inter-population differences in offspring response to supra-optimal temperatures during incubation. Variation in embryonic thermal tolerance was explored among populations of sockeye salmon using a common garden approach. The gametes of 15-20 families per population (N = 9) were incubated at water temperatures of 10°, 14°, and 16°C. Survival from fertilization to hatch varied significantly by temperature and population, and crossing reaction norms showed an interaction of genotype (population) and environment (incubation temperature). Thermal tolerance within the study was related to historical temperatures during early development in nature. From this correlation it seems that population thermal adaptation may exist, and be driven by elevated spawning ground temperatures.The same fertilization experiment was used to evaluate differences in egg size among populations, and to test the effect of temperature, population, and egg size on offspring size and hatching characteristics. Egg size varied among groups and was not related to hatch timing variation, but was tightly correlated to alevin size. Alevin length but not mass was significantly related to incubation temperature, perhaps due to a theoretical tradeoff between development rate and metabolic rate at high temperatures. Most embryos seemed to compensate for increased growth rates at high temperatures by requiring more thermal units to hatch than at lower temperatures. Overall, I found that populations of sockeye salmon responded differently to thermal stress during embryo development, and populations responded best to temperatures that reflected their historical natal thermal regime. In the context of climate change, these results show that inter-population thermal tolerance may influence future selection among populations, and additionally, that this intraspecific thermal adaptation will be important in ensuring population, and therefore species, persistence. 

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Pacific salmon experience intense selection pressures during their early development, and offspring survivorship and fitness traits are influenced by both parental and environmental influences. Given that elevated water temperature can critically impact early development, this thesis focuses on how individual spawners within a population influence the variation in offspring responses to thermal stress. The importance of parentage in assessing temperature effects on fish early life history was first examined in a comprehensive literature review. Only 20% of search-identified studies relating to incubation temperature assessed parental influences, but over 90% of those studies reported significant parentally mediated thermal responses. Research gaps in this area included a paucity of studies on offspring physiological traits (11% of studies), performance traits (2%), and on offspring responses beyond endogenous feeding stages (21%), providing impetus for future experiments. A review of the research on intergenerational temperature effects from adult thermal holding studies was also examined. Sockeye salmon were used in a cross-fertilization experiment to test the hypothesis that significant variation in offspring responses to embryonic temperature stress could be explained by parental identity. Using gametes from Weaver Creek spawners, 10 offspring families were replicated and incubated at 12, 14, and 16ºC from fertilization to hatch. Offspring families had substantially different survival responses across the thermal gradient (crossing reaction norms), and post-treatment mortality and offspring size reflected persistent temperature and parental influences. Within temperature treatments, substantial variation in embryonic survival, alevin mass, time-to-hatch, and hatch duration was attributable to family identity, and most traits exhibited significant temperature-family interactions. The same families were reared for three weeks after emergence then subjected to a second experiment assessing swim performance. Swim performance was reduced in fish exposed to the elevated incubation treatments and offspring parentage was found to have a significant effect on fry burst swim time; findings previously undocumented in salmon. Significant temperature-by-family interactions provide further evidence that parental and temperature influences cannot be examined in isolation. In the context of climate change, these findings collectively highlight the importance of family-level variation in influencing future selection within salmonid populations exposed to elevated thermal regimes.

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