Connectivity between and among ecosystems is a key feature of the marine environment, taking many forms, and affecting populations, food webs, and a wide range of ecosystem processes. In the kelp forest ecosystem, connectivity with adjacent habitats and with interacting human systems shapes communities and influences ecosystem functioning. However, the identity and strength of these important connections, and their key features and consequences are not well understood. One approach for incorporating various forms of connectivity into marine ecology is through the social-ecological systems framework. By characterizing a system as having both ecological and social components, both of which are affected by external forces and entities such as adjacent ecosystems, the presence and consequences of these connections become more clear. The purpose of this dissertation was to expand our knowledge of kelp forests by characterizing and quantifying two distinct forms of kelp forest connectivity. In Chapter 1, I explore kelp forest food webs through the lens of ecosystem connectivity with adjacent coastal pelagic habitats. I synthesize existing knowledge about relevant kelp forest consumers, data on the dynamics of open ocean organisms, and information on community responses to trophic subsidies to better understand kelp forest food webs. I then further assess the role of trophic subsidies from open ocean habitats by looking specifically at five species of kelp forest fishes in central California (Chapter 2). I use stable isotopes and traditional diet content analyses to evaluate the importance of pelagic-based energy for nearshore rockfishes, and to provide a better understanding of how the kelp forest fish assemblage accesses and uses energy sources from the open ocean. In Chapter 3, I turn to the connectivity between kelp forest ecosystems and associated social systems. The nearshore fishery is the primary commercial fishery operating in central California’s kelp forests. I use a social-ecological systems framework to characterize the nearshore fishery and create a social baseline from which to better understand the connections among fishermen, fishing operations, markets, and kelp forests where the target species reside. I use fishery-dependent landings data, archival sources, information gained from interviews, and long-term ecological monitoring data to inform the research. In Chapter 4, I dig more deeply into one component of social-ecological connectivity in the nearshore fishery, combining ecological and social data sources to shed light on factors influencing the species composition of fisheries landings, a key component of the nearshore fishery and kelp forest dynamics.

The study of ecosystem connectivity and social-ecological relationships is an interdisciplinary endeavor. In this dissertation, I use a mixed methods approach to add to our understanding of kelp forest trophic connectivity and the connections between humans and kelp forests. I draw on theory and literature from both the ecological and the social sciences, integrating ideas related to ecosystem connectivity and the human dimensions of natural resources management. I show that new and useful insights can be gained through interdisciplinary approaches that incorporate connectivity among marine habitats and with people into our concept of marine ecosystems.

California kelp forests are highly productive and species rich ecosystems. However, ecosystem-wide consequences of fishing higher tropic levels (fishes) and the effect of climate on primary producers such as the giant kelp, Macrocystis pyrifera, are not well understood. I develop and apply mass-balanced ecological network models, Ecopath with Ecosim, to explore separately how fishing and the dynamics of giant kelp influence ecosystem functions (e.g., species interactions, biomass dynamics), structure (e.g., the distribution of biomass density among species or species groups) and their dynamics. Faced with the difficulty of synthesizing information required to construct these models, I develop and apply an online database (http://kelpforest.ucsc.edu/) to facilitate the accessibility of such information. It is the first online database designed specifically to inform development of ecological network models.

To explore ecosystem-wide effects of fishing in giant kelp forests, I examine (i) the extent to which changes in species interactions and biomass of nodes caused by fishing extend across the ecological network, how these changes vary with (ii) levels of fishing mortality, (iii) fishing of six different species of fishes, and (iv) when all six species are fished simultaneously. Results suggest that fished species differ markedly in the extent to which species interactions and biomass densities are altered across the ecosystem and these responses vary with different levels of fishing mortality.

I also used the models to predict ecosystem-wide responses to different dynamics of giant kelp biomass. I test the hypotheses that different scenarios of dynamics of giant kelp biomass will influence (i) total network biomass, (ii) distribution of biomass density across nodes, (iii) temporal variation in biomass density of nodes, and (iv) how this variation differs among trophic levels. Results suggest that both the mean and the variability of giant kelp biomass alter the direction and magnitude of change in total network biomass. Variation is greater for lower trophic levels. Although all inferences of these models are based solely on trophic interactions, they illustrate the value of ecosystem models to generate hypotheses and predictions of ecosystem responses to one or more changes in kelp forests.

Understanding what drives the distribution, abundance, structure and dynamics of populations and communities, and how this knowledge can inform effective conservation and management, are among the most fundamental goals of basic and applied ecology. Approaches developed in the field of landscape ecology have much to offer for achieving these goals. For my dissertation, I first conducted an extensive review of the literature for different approaches to applying landscape ecology in advancing our understanding of attributes of populations, communities and ecosystems, and its application to spatial approaches to conservation and management. In Chapter 1, I applied some of these insights to determine the importance of environmental variables on the spatial and temporal persistence of stands of giant kelp (Macrocystis pyrifera) along the central coast of California. I also used that knowledge to create a model to predict geographic patterns of giant kelp persistence and tested the accuracy of those predictions with empirical data. This chapter revealed strong relationships between giant kelp persistence and several environmental variables, which contributed to a model that accurately predicted spatial patterns of kelp persistence. Chapter 2 used similar environmental variables to quantify the relationships between the density of seven species of nearshore fishes, as well as the structure of the fish assemblage, with geomorphic and oceanographic habitat attributes. Again, this chapter identified several environmental variables that explained and predicted variation in the density and diversity of nearshore fishes along the coast of central California. In Chapter 3, I used landscape ecology approaches to evaluate the design of a network of marine protected areas (MPAs) along the central coast of California. I tested how well habitat representation and replication was achieved in the design of the MPA network and found that across the network, these design criteria were well met, but shortfalls occurred for individual MPAs. This dissertation demonstrates how landscape ecology can be applied to the marine environment to understand what drives the distribution, abundance and dynamics of populations, the structure and diversity of the communities they constitute, and how this knowledge can be used in applications to conservation and management.

Generalist predators can alter or limit the survival of individuals and the dynamics of populations, especially for imperiled prey. The effects of predation can be further exacerbated if anthropogenic subsidies provide novel food sources to predators that decouple predator-prey dynamics and contribute to extinction risk of native prey. However, quantifying predation rates on rare prey is challenging; as is identifying shifts in predator diet and resource use over time. For my research, I developed new approaches and integrated existing methods to quantify predation and evaluate the impact of predation risk of a generalist avian predator (Western Gull, Larus occidentalis) on threatened populations of steelhead (Oncorhynchus mykiss) in central California (USA), and document temporal shifts in anthropogenic resource use by gulls and the effect on predation risk for steelhead.

This dissertation focuses on three key components to disentangle the relationship between generalist gull predators, threatened steelhead prey, and the role of anthropogenic subsidies in impacting predator-prey dynamics. In Chapter 1, I quantified predation by Western Gulls on imperiled steelhead populations through a novel Bayesian integration of fish tag recoveries, an experiment to quantify tag transportation rates, and monitoring to quantify tag loss. Together, these analyses provide the most robust estimates of avian predation on these imperiled fishes to date, and I found that predation rates are extremely high (median probability of per capita predation ≥ 0.306 per year). In Chapter 2, I compared individual traits of juvenile steelhead that influence survival to maturity and predation risk by generalist gulls through analyses of over nine years of PIT (passive integrated transponder) tag recapture data. I discovered that large and wild-origin juvenile steelhead were more than 20 times more likely to survive the marine ecosystem than small hatchery individuals, and gull predators preferably consumed wild-origin steelhead, regardless of size class. Based on these data, I estimated that gull predation provides an additive source of mortality and reduces the total population of returning adults by approximately 24%. In Chapter 3, I used stable isotope analysis of δ¹³C and δ¹⁵N to conduct a 100-year retrospective analysis to identify changes in resource use by Western Gulls and implications for threatened steelhead populations. Results from this study suggest gulls have become increasingly reliant on anthropogenic food sources which likely contribute to wider gull niche width and increased predation risk to native steelhead.

Together, these dissertation chapters demonstrate that even opportunistic predation from a generalist predator (i.e., Western Gulls) can provide a significant source of additive mortality to imperiled prey (i.e., juvenile steelhead). Furthermore, my research highlights the role of humans in contributing to the degradation of coastal ecosystems. By providing new food sources from landfills, humans indirectly enhance abundance of opportunistic generalist predators such as gulls and contribute to steelhead population decline.

Thermal refuges, patches of habitat that provide physiological refuge from stressful temperatures, form increasingly important habitat in the face of rising ambient temperatures caused by large-scale habitat alteration and climate change. Thermal refuges in river ecosystems are highly heterogeneous, and habitat heterogeneity offers mobile consumers a choice of disparate habitats, allowing them to balance trade-offs between critical resources (e.g., temperature, food availability). Understanding how individuals negotiate fine-scale spatio-temporal heterogeneity in the thermal and prey resource landscape at thermal refuges may help shed light on the potential trade-offs associated with refuge use.

For this dissertation, I developed innovative methods to quantify the probability of thermal refuge use by juvenile salmonids (steelhead, Oncorhynchus mykiss; Chinook salmon, O. tshawytscha) at fine spatial and temporal scales in the Klamath River in northern California (USA), and determine how variability in the thermal and trophic landscapes at refuge sites influenced salmonid diet and thermal habitat use. In Chapter 1, I used temperature-sensitive radio tagging studies to quantify how spatio-temporal variability in abiotic (temperature, flow, time of day) and biotic (body size) variables influenced juvenile steelhead use of thermal refuges. This study represents the most in-depth analysis of spatio-temporal variation in steelhead thermal refuge use to date. I found that mainstem temperature, time of day, and body size were the main drivers of refuge use (>80% of juvenile steelhead moved into refuges when mainstem temperatures reached 22-23°C, and all fish moved in by 25°C). In Chapter 2, I used a combination of radio tagging studies and isotopic diet analyses to quantify how spatial variability in thermal and trophic resources at thermal refuges mediate the foraging behavior and thermal habitat use of juvenile steelhead and Chinook salmon. I found that juvenile salmonids using thermal refuges obtained the majority (~75-95%) of their diet from mainstem prey sources, and that fish thermal habitat use was significantly cooler than diet-inferred fish foraging temperatures, indicating that while fish seek cooler habitat for physiological benefits, they still rely primarily on mainstem prey resources. In Chapter 3, I used lab experiments on internally tagged juvenile steelhead to determine how variation in water temperature and body size affects the amount of time it takes for Lotek temperature-sensitive radio tags to acclimate to a new ambient temperature. I found that tag temperature response time depended on the magnitude and direction (heating vs. cooling) of water temperature change and fish body size (fork length and weight); these experiments determined the sub-sampling interval for data collected in Chapters 1 and 2.

This dissertation demonstrates that fine-scale variability in the temperature and prey landscape mediate how juvenile salmonids use thermal refuges. Moreover, this research highlights the importance of habitat heterogeneity and connectivity for thermal refuges, as refuges may allow fish to more effectively exploit adjacent (and likely more abundant) non-refuge habitat (i.e. mainstem river) by providing temporary thermal respite; this could be a critical and currently under-valued benefit of maintaining refuges.

Empirical evaluations of the ecological processes that enhance or dampen the likelihood of shifts between top-down (i.e., predator-driven) and bottom-up (i.e., resource-driven) forcing are essential to understanding the potential for cascading effects that can underpin community functioning, productivity, and stability. This suite of research used an extraordinary herbivore-outbreak in kelp forests along the central coast of California as a natural field setting to disentangle: (1) how alternations in the foraging behavior of a primary consumer drives patch state transition dynamics, (2) whether predation or resource abundance are the predominant drivers of community regulation, and (3) community-wide consequences to the formation of alternative ecosystem states. This dissertation was motived by a rapid and dramatic decline in the abundance of a sea star predator (Pycnopodia helianthoides) of sea urchins, and a decline of a primary producer (Macrocystis pyrifera, ‘kelp’) that initiated a fundamental change in purple sea urchin (Strongylocentrotus purpuratus) foraging behavior and condition, resulting in a spatial mosaic of remnant kelp forests interspersed with patches of sea urchin barrens. In Chapter 1, I demonstrate the important role of grazer behavior in mediating switching among patch states. I show that the 2014 sea urchin outbreak along the Monterey Peninsula, California, USA is explicable by a shift in sea urchin grazing behavior, not by a demographic (i.e., recruitment or survivorship) response. During this six-year study, kelp forests recovered to an area that was once an expansive sea urchin barren. I show that this remarkable recovery of kelp forests in 2019 to an area in deep water was evidenced by sea urchin movement to shallow water. These results highlight the role of grazer behavior in facilitating patch transition dynamics. In Chapter 2, I demonstrate how the behavioral response of an apex predator to changes in prey behavior and condition can dramatically alter the role and relative contribution of top-down forcing, depending on the spatial organization of ecosystem states. I show that the mosaic of adjacent alternative ecosystem states led to an increase in the number of sea otters (Enhydra lutris nereis) specializing on urchin prey, a population-level increase in urchin consumption, and an increase in sea otter survivorship. I further show that the spatial distribution of sea otter foraging effort for urchin prey was not directly linked to high prey density, but rather was predicted by energetically profitable prey patches. Finally, in Chapter 3 I examine whether the spatial mosaic of sea urchin barrens interspersed with remnant patches of kelp forest resulted in a departure of community structure from the long-standing configuration that proceeded the formation of the mosaic. I found that beginning in 2013, many sites across the study region departed from a common multivariate (“forested”) state, which had persisted for the previous six-years, and drifted into a new multivariate configuration (“urchin barrens”). Although sites trended toward a common reconfiguration, community trajectories were highly variable, and sites exhibited regional cohesion in their trajectories (Carmel, Monterey Bay). These results suggest that outbreaks of grazers associated with punctuated environmental (e.g., marine heatwaves) and biotic (loss of predators, sea urchin outbreaks) perturbations can drive apparently stable kelp forest communities to alternative potentially stable states. Collectively, the results of this dissertation highlight how patch dynamics, behavioral responses, and biotic and environmental perturbations underpin the structure and stability of ecosystems.

Individuals of the same species can vary dramatically in their size, physiology or behavior, thereby influencing their movement, growth and survival. Through influencing demographics individual variation is important to population resilience in the face of environmental change in space and time. Understanding the ecological consequences of individual and population variation is timely considering the dramatic rates of extinction and anthropogenic alterations we are witnessing including global climate change. Coastal rainbow trout (Oncorhynchus mykiss) express a dizzying range of variability in movement and growth rate. I used acoustic telemetry to determine the diversity of O. mykiss movement patterns in an altered river. Movement distance and frequency ranged widely from no movement over the 218d study period to traveling 170km to the Pacific Ocean in 14d. However, most individuals did not move more than 0.5km. Movement correlated with size, season and location. Mortality correlated with the number of moves rather than distance moved suggesting movement regardless of scale influenced survival. In laboratory experiments I found more northerly O. mykiss populations had growth optimals at colder temperatures than more southerly populations. However, temperature-dependent growth varied among populations at very local scales. Temperatures previously experienced did not affect temperature-dependent growth which is beneficial for a species that may experience dramatic fluctuations in temperature through space and time. I used a diet-switch experiment and model fitting to quantify the nitrogen isotope tissue turnover rate and discrimination factor for seven O. mykiss tissues. Among seven tissues, diet-tissue δ15N discrimination factors ranged from 1.3 to 3.4 /. Model supported tissue turnover half-lives ranged from 9.0 to 27.7 days. Using parameter estimates and their uncertainty, I developed stable isotope clocks to estimate the time since resource-shifts. A greater understanding of the extent and importance of individual and population-level variation in fundamental demographic (i.e. growth and survival) and life history (i.e. anadromy and thermal optima) parameters is key to the management and conservation of threatened species. This research revealed that O. mykiss populations vary in these fundamental parameters, implying the importance of local-scale management and conservation practices that ensure the continued diversity of these parameters within and among populations.

Marine fishes' intolerance to global change conditions can affect the abundance and distribution of ecologically and economically important species, reshape the structure of trophic webs, and profoundly impact the human communities that rely on fished species for their livelihood and culture. Only by understanding the vulnerability of fished species and fishing communities to global change can we take effective adaptive action and implement climate-ready fisheries management. In this dissertation, I investigate the vulnerability of eight commercially important fished species and one fishing community to global change in the Northeastern Pacific Ocean. In chapter one, I expose Lingcod (Ophiodon elongatus), a benthic egg layer,to temperature, oxygen, and pH conditions we expect to see in the Central California Current System (CCS) by the year 2050 and 2100. I examine both the lethal and sublethal effects of these two multistressor climate change scenarios by measuring differences in metabolic rate, hatching success, and larval quality between treatments. In chapter two, I use a species distribution modeling approach to evaluate how historical (1982-2019) and projected (2030 through end-of-century) warming in the Eastern Bering Sea (EBS), Alaska, affects predator-prey interactions for some of the most commercially valuable fisheries in the U.S. These species include: 1) Pacific Cod (Gadus macrocephalus), 2) Pacific Halibut (Hippoglossus stenolepis), 3) Arrowtooth Flounder, 4) Walleye Pollock (Gadus chalcogrammus), 5) Tanner Crab (Chionoecetes bairdi), 6) Snow Crab (Chionoecetes opilio), and 7) Alaskan Pink Shrimp (Pandalus eous). In chapter three, I use social network analyses to depict the resilience and adaptability of the California Market Squid fishery (Doryteuthis opalescens), the most valuable in the state, to climate perturbations and project changes in habitat suitability by the year 2100 in the CCS. By using all of these vulnerability assessment tools, we can begin to prepare U.S. west coast fisheries for global environmental change.

Marine fish population fluctuations are pervasive. A primary driver of marine fish population fluctuation is annual recruitment variability. For over a century, fisheries oceanographers have tried to attribute cause to observed recruitment variability with varying degrees of success. While several hypotheses of recruitment variability can be found in the literature, most can be grouped into either food web- or transport-dependent mechanisms. The mechanistic basis of food web-dependent drivers is that larval survival, and eventual recruitment, is determined by starvation or predation mortality. Transport-dependent drivers are related to advective processes that disperse larvae into or out of habitat favorable for recruitment. In this dissertation I address these two mechanisms of recruitment variability for Shortbelly Rockfish, a highly abundant and ecologically important fish species of the California Current System. In Chapter 1, I develop and apply a bioenergetics growth model to understand how spatial variation in ocean conditions determines growth potential. I find that spatial patterns of early life stage-specific growth potential correspond with important early life history events. In Chapter 2, I introduce interannual variability in ocean conditions to the growth model and find that hotspots of spatial growth potential explain 78.6% of Shortbelly recruitment variability. This result supports the hypothesis that food web-dependent processes are important for recruitment strength. In Chapter 3, I introduce transport-dependent processes to the model framework and find that the relative importance of food limitation and transport on recruitment are dependent on interannual climate cycles (El Niño Southern Oscillation). The preponderance of recruitment drivers being context dependent amongst a backdrop of differing climate conditions may explain why understanding recruitment mechanisms has been so challenging.

Large brown algae in the class Phaeophyceae (Heterokontophyta) form the structural and energetic foundation of temperate and subtropical nearshore marine forests of high productivity and ecological diversity. This dissertation examines the carbon uptake and transport physiology of large brown algae with a particular focus on the plastic or adaptive responses of these physiological traits to their abiotic environment. Chapter 1 takes an anatomical and modeling approach to investigate the structure and function of photosynthate transport networks (analogous to phloem) in diverse members of the Laminariales. To evaluate the existence of scaling and optimization of the kelp vascular system, a model of optimized transport anatomy was developed and tested with a diverse suite of kelp species in the Laminariales. Results revealed a surprising lack of universal scaling in the kelps and the presence of optimized transport anatomy in the giant kelp (Macrocystis pyrifera) only. Chapter 2 focuses on the dynamics of carbon uptake in M. pyrifera, which can acquire both carbon dioxide and bicarbonate as carbon substrates for photosynthesis. To evaluate whether the proportion of carbon dioxide and bicarbonate utilized by M. pyrifera is constant or a variable function of their fluctuating environment, oxygen evolution experiments were carried out on entire blades from several targeted populations in the Monterey Bay. Results indicated that M. pyrifera possesses a plastic carbon uptake physiology in which proportionally more bicarbonate is used in high irradiance and high flow conditions, but that local populations have not yet developed fixed genetic differences. Chapter 3 investigates the mechanism and patterns of carbon stable isotope discrimination in M. pyrifera. Results of a dual field and laboratory incubation approach indicate that 13C discrimination patterns are determined by a complex interaction of light intensity, dissolved inorganic carbon limitation, and fractionation occurring during transport of polysaccharides. Overall, this dissertation informs patterns and mechanisms of carbon uptake and transport in kelps, and highlights the many ways in which kelps may impact and structure their ecosystems.