White abalone (Haliotis sorenseni) supported an intense commercial fishery in southern California during the 1970s, which closed in 1996. In 2001 white abalone was listed under the Endangered Species Act (ESA), and due to their high risk of extinction, National Oceanic Atmosphere Administration (NOAA) identified the species as a "Species in the Spotlight" in 2016. Efforts are underway to develop a conservation hatchery and outplanting program to recover the species. To inform outplanting efforts, I modeled broad-scale (17 km) historical (fishery-dependent) and contemporary (fishery-independent) distributions of white abalone habitat using random forest and maximum entropy (MaxEnt), respectively. I projected models to future scenarios in 2050 and 2100 to assess the quality of habitat under climate change. Using MaxEnt, I developed fine-scale (10 m) models with fishery-independent data. I also conducted interviews with former abalone fishermen who observed white abalone during the fishery.

Fishery-dependent and -independent based models revealed differing outcomes of suitable habitat and ensuing effects of climate change. These differences in suitability resulted from differences in the spatial distribution of white abalone between the two data sets. Fine-scale fishery-independent data was limited in its spatial extent, yet in places with sufficient data, I generated high resolution suitability maps. These maps comported with oral histories from fishermen regarding fine-scale habitat, and can help guide site selection within broadly suitable geographic regions. This study provides managers with potential areas to outplant that are resistant to climate change and a framework to design experimental outplanting to adaptively manage a successful recovery effort.

My dissertation is motivated by the desire to achieve balance between conservation and exploitation of marine populations (i.e., sustainable harvest). Navigating between the extremes of preservationism and extinction with any confidence requires that we assess the status of exploited populations and the ecosystems that support them. Single-species, equilibrium-based fisheries management has been somewhat divisive, with proponents giving it credit for largely ending overfishing and critics citing spectacular examples of failing to prevent fisheries collapses. One of the primary critiques of traditional fisheries management is that it ignores important ecological realities, such as variability in vital population rates stemming from: 1) environmental variability, 2) spatial population structure and movement, and 3) species interactions.

My dissertation focuses on improving management of exploited species by adapting models to species' life history, with particular emphasis on the effect of spatial structure. Chapter 1 improves stable isotope mixing models, used to estimate animal diets, by introducing a new statistical structure makes more ecologically-realistic assumptions about the relationship between predator and prey isotope signatures. We demonstrate that this new parameterization implicitly estimates predators’ consumption rate and outperforms existing models. Chapter 2 considers how fisheries bycatch species' life history traits, use of space, and catch rates affect models used to predict spatiotemporal bycatch risk. We find that machine learning approaches (e.g. random forests) outperform recently developed semiparametric spatial models for the purpose of generating fisheries bycatch predictions to be used in dynamic management tools. Chapter 3 develops assessment methodology for protected fish species that form spawning aggregations, a life history strategy particularly vulnerable to overexploitation. While no catch or effort data can be collected from the protected population, we demonstrate the efficacy of length-frequency time-series collected in situ to detect recruitment spikes and population recovery. Chapter 4 investigates the mortality and 3-dimensional dispersal of eggs and larvae from a Nassau Grouper (Epinephelus striatus) spawning aggregation, and discusses the likelihood of large self-recruitment events.

Surveying the abundance, demography and behaviors of marine fishes is a difficult task due to the challenge of collecting observations in environments that are difficult for researchers to access. Moreover, these challenges are often magnified when attempting to study fishes that are rare, threatened or endangered. In many instances, such species have become rare because they aggregate to reproduce at known times and places, and, are thus, susceptible to harvest during reproduction. Here, I focus on three species in two different environments: Steelhead (Oncorhynchus mykiss) returning to streams to spawn in Washington, and spawning aggregations of Nassau Grouper (Epinephelus striatus) and Tiger Grouper (Mycteroperca tigris) in the Cayman Islands. By taking advantage of the reproductive aggregations of these species, I can generate observations of behavior and life-history to inform effective management. For Steelhead, I developed a new hierarchical nested Bayesian patch occupancy model that estimates movement rates throughout a river network based on the observed movements of PIT (passive integrated transponder) tagged fish from a network of in-stream tag detectors. Using these movement rates and estimates of dam passage below the in-stream detectors, I was able to, for the first time, generate estimates of abundance of this threatened species throughout the river network. For Nassau Grouper, I developed an integrated population model that incorporated both video observations and tagging data to obtain a fourteen-year time series of abundance in the Cayman Islands. Based on these modeling efforts, I demonstrated that management efforts have resulted in a dramatic recovery of this endangered fish in the Cayman Islands. Finally, using eggs collected from spawning aggregations of Nassau Grouper and Tiger Grouper, I documented fertilization rates and the variable morphology of eggs between spawning events. Using laboratory studies, I demonstrated that warming water temperatures are likely to decrease larval survival for Nassau Grouper, although the impact was variable, suggesting there may be adaptive capacity within the population to respond to impending warming. Across each of these studies, I leveraged reproductive aggregation, a perceived vulnerability in the life history of fishes, to generate observations and synthesis in support of fisheries restoration and conservation.

Manta and mobula rays (collectively mobulids) are planktivorous pelagic rays that have received little scientific attention in comparison to many other marine megafauna species. Major knowledge gaps remain in the biology and ecology of mobulid rays, often hindering effective management of these species. In the past decade, substantial declines in mobulid populations have been recorded in response to targeted fisheries and bycatch of these species in both commercial and artisanal fisheries. This dissertation seeks to fill several critical knowledge gaps in the spatial ecology and foraging behavior of mobulid rays in the Indo-Pacific. Chapter 1 uses a combination of satellite archival tagging, stable isotope analysis, and high-throughput genetic sequencing to examine the horizontal movements and population structure of oceanic manta rays (Manta birostris) in the Indo-Pacific. We find that oceanic manta populations exhibit philopatry within relatively restricted home ranges, and demonstrate little connectivity between both neighboring and distant populations. These findings suggest that management and conservation action can be applied effectively at local scales in addition to the international agreements that are typically relied upon for marine megafauna species. Chapter 2 examines the diving behavior of oceanic manta rays at a remote archipelago off of Mexico’s Pacific coast using satellite archival tagging and opportunistic submersible observations. We found evidence of multiple feeding modes with different vertical distributions, seasonal changes in vertical habitat use, deep-water foraging behavior, and association with both the thermocline and the deep scattering layer. Taken together, these findings suggest a high degree of behavioral plasticity in oceanic manta rays that may explain their ability to remain resident by shifting their prey targets vertically rather than over large horizontal distances. Chapter 3 uses stable isotope analysis and Bayesian mixing models to assess the trophic overlap in five species of sympatric mobulid rays at three sites across the Indo-Pacific. We find that the degree of trophic overlap is inversely related to regional primary productivity characteristics, with greater overlap in lower-productivity regions. We posit that this is a result of prey density thresholds required by mobulids to make foraging energetically profitable. The trophic relationships we observe help explain the patterns of multispecies mobulid bycatch in regions such as Sri Lanka and the Philippines, and interspecies seasonal and spatial differences in bycatch risk of mobulid rays in Peru. This dissertation contributes substantially to our understanding of mobulid ray spatial ecology and foraging dynamics, and appropriate management and conservation approaches for these threatened species.

Fisheries are economically and culturally important features of coastal communities around the globe. Ranging from recreational fishing to commercial harvest, fisheries represent the final large-scale vestige of humans hunting for food. While terrestrial food systems shifted almost entirely toward agriculture and cultivation, aquatic and marine food systems are still remarkably reliant on wild capture for their supply. As a result, fisheries and the species they target are inextricably linked to human behavior. Ecologists wishing to better understand fisheries and how to make them more sustainable must account not only for variables in the natural environment, but also variables associated with the anthropogenic use of fisheries resources. My dissertation explores this notion by addressing applied fisheries ecology questions across species, fishery, and global scales. At the species scale, chapters one and two investigate the trophic and movement ecology of Giant Sea Bass (Stereolepis gigas), a species nearly extirpated from United States waters by fishing activities. At the fishery scale, chapter three explores the interdependencies between species harvested by a multispecies fishery and how those relationships change as a function of sea surface temperature. And finally at the global scale, chapter four looks at the nature of global seafood trade and characterizes the management intensity associated with production versus consumption of seafood across countries. Each chapter and scale of fisheries ecology investigated contributes a different type of information to the broader knowledge base of fisheries science, and combined they present a valuable contribution to the field.

Passive acoustic monitoring (PAM) is commonly used to study behavior and population dynamics of soniferous fish species in a cost-effective, minimally invasive manner. However, understanding the strengths and limitations of PAM for this purpose requires an assessment of variability in CAS of target species as a function of time, space, and proximity of spawning fishes. In this study we evaluate temporal and spatial trends in CAS by Nassau Groupers (Epinephelus striatus) using an array of six hydrophones deployed at a large Nassau Grouper FSA on Little Cayman, Cayman Islands. We collected continuous data for nine days during the winter spawning season, and subsequently employed an automatic classifier to extract the embedded Nassau Grouper CAS. Using these data, we qualitatively and quantitatively analyzed variability in temporal trends across the spatial array with a Bayesian mixed effects model. We found a clear degradation in accuracy of temporal calling patterns at the FSA as distance from the spawning site increased beyond 200 meters, and observed higher correlations among the most proximal hydrophone pairs than the most separated pairs. Our model predicted strong effects of fish proximity, spawning behavior, and crepuscular periods on detected calling rates of Nassau Grouper that corroborate with and add to the present literature. Our findings suggest a high degree of variability within relatively short distances from a sonic target, thus imploring a need for spatial resolution in acoustic analyses.

Fishery managers are tasked with preparing our fisheries for climate change, but doing so requires data to assess population status and environmental drivers, both of which are typically limited. Many small-scale fisheries, like recreational-only fisheries, have a paucity of information and resources to perform robust assessments, which results in data-limited management measures that can inadvertently increase the vulnerability of the resource to detrimental harvest and climate change impacts. Here I focus on the popular and overexploited southern California recreational saltwater bass fishery, which despite its economic and cultural significance to the state, lacks long-term species-specific data and formal population assessments. By leveraging a variety of disparate data sets, taxonomy methods, and advanced quantitative methods, I reconstruct the population dynamics of the two focal species, Barred Sand Bass (Paralabrax nebulifer) and Kelp Bass (P. clathratus), over most of the last century and across rapidly changing ocean conditions. I begin with Barred Sand Bass and build a bespoke Bayesian capture-mark-reencounter model to estimate demographic rates over three historical periods spanning 54 years. Using these rates, I generate, for the first time, estimates of abundance, and along with other data sources (juvenile recruitment, adult densities, harvest, and sea surface temperature) and historical accounts in the literature, I demonstrate how the environment and harvest have contributed to long-term fluctuations in productivity. I then develop a robust method to construct and validate a taxonomic key for distinguishing southern California Paralabrax spp. larvae and use this key to unlock a larval abundance data set with high spatial and temporal resolution. Using these larval data within a geostatistical modeling framework, I generate species-specific standardized indices of larval abundance, quantify the influence of environmental covariates on their long-term spatiotemporal patterns, and explore the predictive power of the larval time series to anticipate future catches. Based on these modeling efforts, I contribute improved fishery management tools for monitoring status and trends and demonstrate species-specific population dynamics, highlighting the species’ different susceptibilities to harvest and climate change impacts. Taken together, these studies pave the way toward an ecosystem and climate-ready approach to fisheries management for this important group of fishes.

Fisheries size limits are a fundamental harvest control rule intended to support sustainability, usually by allowing fish to reach maturity and reproduce before harvest. California relies on size limits for the management of some, but not all, recreational fisheries. For those with size limits, it is unclear whether existing control rules are sufficient to achieve sustainable levels of spawning potential. For those without size limits, the potential benefits of instituting length-based control rules for improving harvest efficiency have not been assessed. In this study, we used Length-Based Spawning Potential Ratio (LBSPR) to conduct a data-limited assessment of equilibrium stock status for a subset of high value recreational fishes and make inferences about the cumulative performance of existing management regulations. Using these model products, we then simulated stock status under alternative size limit scenarios in order to estimate the benefit of new or alternative minimum size limits on a species-by-species basis. To validate our methodology for assessing alternative size limit regulations, we leveraged data on two species of Paralabrax from before and after a recent increase in the recreational minimum size limit regulations. Our findings provide valuable insight on the status of five recreationally important yet unassessed fisheries stocks in California and identify situations where LBSPR may be successfully applied and where it may fail. Furthermore, we developed and validated a procedure for evaluating alternative minimum size limit scenarios that can easily be applied to other fisheries worldwide.

Survival through the larval phase greatly affects the population dynamics of most fishes, and both diet and maternal investment have long been hypothesized as important contributors to interannual recruitment variability. This study examines the feeding ecology of larval Sebastes spp. rockfishes with respect to ontogeny, selectivity, and the respective influences of diet and maternal investment on size and growth. Prey selection was calculated from larval gut contents, maternal investment was estimated using otolith core radii, and recent growth was derived from outer increment widths. Bayesian multilevel models were used to describe independent and interactive effects of diet and core on length and growth. Larval rockfishes were observed to primarily select for Calanoid nauplii and copepodites, modulating feeding with ontogeny and in response to prey availability. Models that accounted for maternal investment and prey specificity more effectively predicted length and growth than models that only accounted for total gut content biomass. Calanoid copepodite gut content carbon biomass was generally more correlated with length and growth than gut content carbon biomass of other taxa, but older and younger larvae experienced different growth rates in association with different prey. Positive relationships between core and both length and age suggest that maternal provisioning increases the likelihood of larval survival. These findings provide evidence of selective feeding throughout larval Sebastidae development, support the notion that maternal investment may positively influence larval survivorship across coastal Sebastes species assemblages, and emphasize the importance of taxonomical prey preference in facilitating growth and survival of larval rockfishes.