Bioenergetics is the study of how energy flows through and transforms within organisms. Variables such as temperature and food availability have variable effects on growth and metabolism. There is an increasing interest in determining fish bioenergetics in conjunction with behavior and life-history traits to predict species-specific responses to climate change.The Sacramento-San Joaquin River Basin, California, USA, supports multiple species of anadromous fishes – Chinook salmon, green sturgeon, and white sturgeon – which return to these freshwater natal habitats to spawn. Many of the physical and ecological characteristics of this watershed have been impacted by physical modifications and climate change. Specifically, dams and channelization have led to changes in water temperature, flow, and altered food web dynamics. Early life stages of fish are particularly vulnerable, and declining recruitment is thought to contribute to precipitous population decline. Each chapter addresses an aspect of fish bioenergetics, using metabolism as a foundation due to its representation of the sum of biochemical processes used for energy intake and support for life functions. Chapter 2 examined the metabolic cost of digestion in juvenile Chinook salmon across a broad range of temperatures, finding that the digestive response largely retains its energy efficiency at all temperatures. Chapter 3 determined the scaling of metabolic rate and differences in developmental trajectories across early ontogeny of green sturgeon, finding that rearing in suboptimal cold temperature is metabolically costly and leads to large size-at-age delays. Chapter 4 investigated the relationship between metabolic rate and locomotory activity in juvenile white sturgeon under nutritional stress, finding that the relationship is context dependent, requiring sufficient exposure to nutritional stress. Collectively, my research investigated stage- and species-specific aspects of larval and juvenile fish bioenergetics that can help us understand how various environmental stressors may impact fish populations. The intersection of bioenergetics, behavior, and organismal performance is critical for continued insight on species- and ecosystem-wide responses to perturbations, because it illuminates the diversity of physiological and behavioral responses available to fish. By investigating these responses with respect to current and expected climate-induced conditions, we can better craft management strategies to conserve these commercially and culturally important native California fishes.

Physiological stress incurred upon transported and released animals may limit the efficacy of population supplementation - a commonly used conservation strategy designed to recover depleted populations. In a recently developed experimental supplementation program for the critically endangered delta smelt (Hypomesus transpacificus), combined stressors of handling, transport, and shifts in water chemistry are expected to elicit a considerable stress response. Acclimation enclosures have been developed in an attempt to facilitate stress recovery and allow delta smelt to acclimate to field conditions. Pertinent questions surrounding the use of enclosures include determining the optimal time of release from enclosures and ideal transport densities to minimize stress and maximize fish performance. To address these knowledge gaps, we quantified whole-body cortisol, glucose, lactate, and gill ionocyte morphology at 10 time points across 72 hours following transport to enclosures at high and low densities. We observed significant peaks in cortisol and glucose within 30 min of release into enclosures, followed by significant recovery of both parameters after 27 hours. Lactate was moderately affected, and we did not detect an effect of transport density on cortisol, glucose, or lactate. Gill ionocytes significantly increased in surface area following transport, and we observed gill ionocytes having up to three different types of microvilli, including two types that have never been reported. Changes in ionocyte morphology is correlated to elevated cortisol levels and suggests greater demand for ion-transport at the release site. This work provides agency managers with data to optimize delta smelt supplementation methodologies and expands our understanding of how fishes respond to targeted stressors.

Understanding the variations that exist between organisms, populations, and species can provide valuable insight into the evolutionary and environmental drivers relevant to organism fitness. Developing this understanding is critical in an era of rapid environmental change, where effective conservation and management efforts must predict the response of organisms to future, novel environmental conditions.Pacific salmonids are widely considered at-risk from anthropogenic and climatic changes. Additionally, Pacific salmonids exhibit a semelparous anadromous life-history strategy which limits gene-flow and promotes the formation of distinct populations. My first chapter reviews the literature on the thermal physiology of Chinook salmon (Oncorhynchus tshawytscha) from the Central Valley of California, which are the southernmost native populations in the world. I found very little prior research studying interpopulation in thermal physiology among Chinook salmon, despite a vast literature demonstrating the capacity for interaction between thermal physiology and a salmonid’s local environment. I propose a place-based management paradigm which combines both and organisms fundamental and ecological thermal physiology. My second and third chapters employed a common-garden experimental design and several physiological metrics to assess the thermal physiology and acclimation capacity of eight hatchery populations of Chinook salmon from the west coast of North America. All eight populations were reared at the same suite of acclimation temperatures (11, 16 and 20°C) and assessed using five physiological metrics, (growth rate, critical thermal maximum, routine and maximum metabolic rate and aerobic scope). The second chapter aimed to determine whether the thermal physiology and acclimation capacity of three seasonal runs of Chinook salmon in the Sacramento River watershed (CA) differed. I identified quantifiable population differences in CTM, growth, and metabolism among the studied populations and found compelling evidence that the critically endangered Sacramento River winter-run exhibits growth and metabolic capacities indicative of mal-adaptive physiological plasticity to warm temperatures. The final chapter studied six populations of fall-run Chinook salmon and assessed statistical associations between the five physiological traits and 15 environmental predictors to test hypotheses of local adaptation and countergradient variation. My results support local adaptation, wherein populations from warmer habitats exhibit higher critical thermal maxima and faster growth when acclimated to warm temperatures. Among metabolic traits I also found positive associations between migration distance and metabolic capability, indicating that populations with longer migrations may have higher metabolic capacity. Collectively, my research demonstrates that populations of Chinook salmon differ in their thermal physiology and that these differences can be associated with aspects of their environment consistent with hypotheses of local adaptation. With this understanding, one-size-fits-all management frameworks are poised to underserve unique or unusual populations. Instead, place-based population-specific strategies would best serve at-risk populations like the Sacramento River winter-run Chinook salmon.

The impacts of climate change and anthropogenic disturbance are pervasive throughout ecosystems. Yet particularly in aquatic and marine systems, animal responses to the resulting environmental changes can be difficult to determine, which inhibits appropriate management strategies. Conservation efforts are often based on research that examines the effect of stressors or human-induced impacts on a single species and/or scale. However, this approach can be too narrowly focused. Species do not exist in isolation, and there are many potential drivers of their survivorship and behavior that extend beyond the individual or population. Particularly for mobile species, such as many fishes, population dynamics can be strongly influenced by species interactions, individual movements within a habitat, or changes in habitat suitability. As a result, the impacts of environmental change can be highly complex or even counter-intuitive, particularly in locations where these changes are occurring rapidly.

Among these, California hosts a variety of aquatic and marine habitats that have been dramatically modified by human activity over the last century. These ecosystems now face further alteration due to a changing climate. Consequently, there is growing concern about how species will respond to additional stressors, such as increasing water temperatures. Our ability to forecast these effects is becoming increasingly important, because while many endemic fishes are already heavily managed, some populations are continuing to decline. The potential consequences of these declines can be dire, affecting ecological communities as well as human populations that rely on fish for sustenance. However, the mechanisms underlying patterns of fish presence and survival are multifaceted and remain undetermined in many cases, preventing a reevaluation of conservation efforts. To address this, my dissertation demonstrates the value of a more holistic perspective on organismal response to environmental change. Focusing on species that are threatened or data deficient in California waters, I use select case studies to examine fish responses to environmental changes at multiple scales, including fish physiology, behavior, and habitat use.

Chapter 1 is based in the Sacramento-San Joaquin River Delta of California’s Central Valley. Here, increased mortality of outmigrating juvenile salmon has been correlated to warming water temperature. It has been assumed that reduced survivorship is due to salmon thermal physiology. Yet emerging laboratory studies suggest that these salmon populations are relatively thermally robust. Instead, I test the hypothesis that decreases in salmon survivorship are due to increased activity of non-native predators. My results suggest that major predators of salmon in the Delta are more thermally adapted to warmer temperatures, increasing the possibility of their threat to juvenile salmon in light of global warming. This indicates that an understanding of fundamental thermal physiology can be useful in predicting predator-prey dynamics; however, I also show that such an approach is highly dependent on the physiological metric employed, and it is more effective for some species than others. Regardless, given that the Delta is a highly modified ecosystem, managers could hypothetically improve juvenile salmon survivorship by adjusting water flow, and therefore temperature, along primary outmigration routes based on predator thermal preferences.

Chapter 2 scales up to consider fish behavioral response to current flows in the San Francisco Bay Estuary. In estuarine habitats, seasonal and daily hydrological variance is affected by human activity, such as dredging and coastal wetland development, and rising sea levels due to global warming. However, assessing fish responses to hydrological patterns is logistically challenging, limiting our ability to predict how future changes will impact the behavior of local populations. In this chapter, I explore the use of hydrodynamic models for examining the influence of tidal flow in the San Francisco Bay Estuary on broadnose sevengill sharks (Notorynchus cepedianus). Combining acoustic tracking data with these models, I find evidence that sharks swim in and out of the bay with most of the ebb and flood tides, presumably to move in the most energetically efficient manner. However, this movement was not universal, nor was it dependent on the strength of the tide. This suggests that there may be other variables shaping sevengill shark behavior in this habitat, such as prey availability, which offsets the energetic cost of moving against the tide. Taken together, my results demonstrate that tidal movement is not the sole driver of sevengill shark behavior, but this species will likely be susceptible to potential hydrological changes in the future.

Chapter 3 examines environmental impacts at the largest scale, using a spatial modeling approach to determine population-level trends and habitat use in a large, highly migratory species: the basking shark. Historically targeted globally for their liver oil, fins, and meat, basking sharks were classified as globally endangered in 2019. While they seem to be responding well to protective measures in some parts of their range, there appears to be no sign of recovery in the Eastern North Pacific population. However, evaluating the status of this population is hindered by multiple data gaps. It has not been determined whether variation in shark sightings over time is due to changes in population size or the effect of environmental change on basking shark distribution. To fill these gaps, I compile recent and historical data to describe variation in basking shark sightings and school size over time in the California Current Ecosystem (CCE). I also build species distribution models using general additive mixed models to determine the environmental factors that may affect their distribution and sightings probability. My results suggest that the number and probability of sightings declined in the mid-1980s, as did the size of schools reported. Simultaneously, there was a shift in sighting seasonality, from fall and spring to summer starting in the 2000s. The species distribution models also revealed that sightings probability increased with low sea surface temperature and high chlorophyll a concentration, and was correlated with larger-scale climatic oscillations. Based on these analyses and previous studies, I conclude that the decline in sightings after the 1980s most likely emerged because of a decrease in the population following a century of culling and overfishing. This was perhaps exacerbated by an Allee effect based on the simultaneous decrease in group size. Furthermore, there is a high probability that the basking sharks that remain in the CCE will be affected by a combination of changing sea surface temperatures and shifting prey fields in the future, though the degree to which this will shift their spatial or temporal distribution is unknown. To better inform management of the CCE basking shark population, there should be more coordinated documentation of fisheries mortalities and sightings to inform population estimates and track potential changes in habitat use. I also advocate for improved monitoring of shark fin markets to ensure existing conservation regulations are being followed.

In conclusion, climate change and increasing anthropogenic activity are rapidly altering California’s aquatic and marine ecosystems, rendering conservation more difficult. My dissertation contributes to a large body of evidence highlighting numerous threats, from warming temperatures to habitat alteration, that are affecting species directly and ecosystem interactions more broadly. Together, these chapters show that species responses to potential threats will vary depending on environmental variables, animal behavior, and community interactions. It is critical to consider each of these levels of influence when predicting how populations will fare with environmental change. In turn, this broader understanding will improve dynamic management strategies for threatened species facing an uncertain future.

Salmon are socio-ecologically important fishes distributed across the Pacific rim, and multiple ecologically significant units are declining in the Sacramento-San Joaquin River Delta of California. Available data suggests that spring-run smolt survival from the upper river in San Joaquin River restoration area (>270 rkm) to the California Delta (<160 rkm) is consistently low. Additionally, limited information from previous acoustic telemetry studies suggest that Franks Tract, a 1429 ha flooded island, is a potential mortality hotspot for outmigrating smolts. During Winter/Spring 2020, we conducted a series of targeted acoustic telemetry and tethering experiments to better understand salmon entrainment into Franks Tract as well as overall survival patterns. Telemetry studies investigating broad scale emigration patterns involved surgical tagging and release of 796 juvenile spring-run Chinook Salmon (Oncorhynchus tshawytscha) with JSATs acoustic transmitters. Tagged fish were distributed between three releases: an upper (n = 350) and a lower river (n = 348) release in the San Joaquin River, and an additional 98 smolts released directly into Franks Tract. The third release was conducted to investigate survival and emigration potential from the area. Provisional telemetry results suggest poor outmigration survival from all three release groups (<1% to ocean entry), but at least some (n = 2) fish released in Franks Tract did survive to Pacific Ocean entry (Benicia Bridge, 52 rkm). We also conducted a series of tethering experiments to contextualize relative predation risk of smolts within different submerged aquatic vegetation (SAV) coverage, water depth, and tidal movement in Franks Tract. Tethering results suggest that relative predation risk was moderately high over the deployment time (10.5% over 2 hours). Further, high- versus low-vegetation coverage had no effect on relative predation risk, nor did water depth. Tidal movement did have an effect on relative predation risk, with a hazard ratio for predation of 4.96 during ebb tides. Combined, our data supports the hypothesis that Franks Tract is a mortality hotspot for juvenile salmon, at least during the period studied here. Future telemetry and tethering studies may be essential for disentangling the ecology of declining salmon runs and investigating effectiveness of various management activities aimed at increasing juvenile survivorship, especially within tidal lake habitats.

In late 2019, at multiple hatcheries in California’s Central Valley (CCV), offspring of recently spawned fall-run Chinook salmon (Oncorhynchus tshawytscha) exhibited abnormalities in swimming, lethargy, and high early life-stage mortality; the combination of these symptoms is commonly referred to as thiamine deficiency complex (TDC). The cause of thiamine deficiency in Pacific salmonids is hypothesized to be due to a lack of diet heterogeneity and reliance on northern anchovies (Engraulis mordax), containing high levels of thiaminase, a thiamine-cleaving enzyme. Of CCV’s four runs, the endangered Sacramento River winter-run Chinook salmon (WRCS) is perhaps the most vulnerable to thiamine deficiency as any additional stressor will exacerbate current threats to survival. The goal of this study was to evaluate the effect of thiamine supplementation in pre-spawn WRCS females on their offspring egg thiamine concentrations, survival, prevalence of TDC-related symptoms, and physiological performance and behavioral traits. Sixty female WRCS at Livingston Stone National Fish Hatchery were randomly administered either a thiamine injection (n=33; 500 mg/ml thiamine hydrochloride) at a dose of 50 mg/kg body weight or a sham injection (n=27; sterile saline solution) at a volume of 0.127 ml/kg body weight. After spawn, a subset of fertilized eggs from each female were analyzed for thiamine concentration. Eyed embryos were transferred to the University of California, Davis and kept for observations of TDC, survival, and to assess the effects of maternal thiamine treatments on offspring physiology and behavior. Upper thermal tolerance, routine metabolic rate, spontaneous swimming activity, boldness, and anti-predator responses were evaluated in swim-up fry. On average, total egg thiamine concentrations were 5.02 and 34.91 nmol/g for untreated (n=27) and thiamine treated (n=33) females, respectively. Mortality rate of offspring from untreated females averaged 32.97 ± 0.33 %, with rates ranging from 0 to 100%, while offspring from thiamine treated females had a mean mortality rate of less than 1%. Using a binomial logistic regression model, we predicted that a mean total egg thiamine concentration of ~5 nmol/g supports 95% survival within a family (EC95). There were no statistically significant effects of maternal treatment on any of the physiological or behavioral metrics assessed in this study. Overall, we recommend the administration of supplemental thiamine to increase thiamine concentrations past the threshold at which TDC symptoms are commonly observed; however, additional research should be conducted to further examine potential latent effects of thiamine deficiency in Pacific salmonids.

The wild abundance of Longfin smelt (Spirinchus thaleichthys, LFS) in the San Francisco Estuary (SFE) has declined to less than 1% of pre-1980’s numbers. As a result, they have been listed as “threatened” under the California Endangered Species Act since 2009. In an effort to avoid localized species extinction, a captive culture program was created for LFS through the Fish Conservation Culture Laboratory at the University of California, Davis. Larviculture methods for LFS are still being optimized to ensure a successful culture program. For my MS thesis, I tested the impacts of rearing temperature on early post-hatch LFS larvae from three different parental clutches to identify which rearing temperatures are best for successful development of these early life stages. I reared newly fertilized embryos and post-hatch, non-feeding yolk-sac larvae in freshwater (0 ppt) at 10, 12, or 15°C until 3 days post-hatch (dph). I measured larval morphometrics (total length, eye diameter, yolk sac area), and mortality for all groups. I was the first to evaluate the incidence and severity of jaw and spinal malformations for cultured LFS. Larvae reared at 15°C were smaller (mean ± SE; 0.52 ± 0.0040 mm), significantly younger at hatch (13.1 ± 0.1 days post-fertilization; dpf), and had slightly higher mortality and increased spinal malformations compared to other rearing temperatures. Embryos reared at 10 and 12°C were of similar size (10℃: 0.59 ± 0.0030 mm, 12℃: 0.56 ± 0.0030 mm), but 10°C larvae were significantly older at hatch (10℃: 18.4 ± 0.05 dpf, 12℃: 15.8 ± 0.1 dpf). Clutch had a much more variable impact on response metrics, markedly in size, suggesting that parentage may mediate developmental responses to unfavorable environmental conditions and change. No incidences of jaw malformation and a very small percentage of spinal malformations were observed amongst all treatment groups. Overall, the novel results described in this study suggest that parentage modifies the impacts of rearing temperature on larval development and survival. As a result, I make recommendations to broaden the impact of future LFS and other sensitive larval fish studies on conservation larviculture techniques. While our understanding of factors impeding LFS culture is limited, this study represents a significant step towards identifying more biologically efficient larviculture and conservation management techniques for this and other critically threatened fish species.