Fisheries

Permanent URI for this collectionhttps://digital.lib.washington.edu/handle/1773/4921

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Incorporating spatial and temporal dynamics into evaluations of fish populations and habitat
(2025-10-02) Indivero, Julia Lindsay; Essington, Timothy E
The ocean is rapidly changing, with impacts on both the physical environment and ecological systems. In my dissertation, I seek to understand how variations in fish populations over space and time are driven by environmental conditions in the ocean, and to improve statistical methods to accomodate this variation and thereby contribute to sustainable fisheries. In the following four chapters of my dissertation, I develop, test, and apply improved methodologies that link fish demographics to environmental conditions and address pressing management concerns. A spatio-temporal model of weight-at-age of walleye pollock improved our understanding of the dynamics of local and population-level demographic processes and can be used in future stock assessment models. I developed a statistical model that incorporated a physiological response to temperature and oxygen into distribution modeling to better capture this joint effect, in the context of predicting impacts of climate change on local fish densities. Because spatial statistical models rely on environmental data, I used statistical approaches to expand oxygen data available and test the sensitivity of ecological models to environmental data. Lastly, I applied these improved techniques in retrospective statistical models to evaluate evidence for oxygen limitation on the distribution of 32 groundfish species in the northeastern Pacific Ocean. Overall this dissertation advances statistical solutions for accomodating spatio-temporal data in estimates and predictions of fish ecological responses to environmental change.
Emerging technologies to assess human benefits from and risks to water resources
(2025-10-02) Fricke, Rachel; Olden, Julian D
Humans benefit from water resources by deriving cultural ecosystem services (CES) such as numerous types of recreation (e.g., fishing, boating, swimming), improved mental health, and artistic inspiration. However, we also pose a significant risk to waterbodies by altering water chemistry, introducing invasive species, and degrading habitat quality. Thus, understanding human activity on freshwaters is critical for preserving not only aquatic ecosystems, but also the benefits we gain from them. Traditionally, human activity on waterbodies across time and space is inferred from sparsely conducted surveys that provide data with limited spatiotemporal scope. Volunteered geographic information (VGI) – user-generated, geotagged metadata from posts on mobile device applications – is a promising data source to examine human activity over broad scales of space and time.Here, I show how technological innovations – particularly VGI – can be leveraged to support management and conservation of freshwaters. First, I offer a review of innovative technologies with applications for invasive species management related to pathway intervention, spread prevention, impact mitigation, and public engagement. I also explore challenges and opportunities for successful integration of emerging technologies into invasive species management, focusing on pipelines that enable practitioners to integrate tools into practice while recognizing logistic and financial constraints (Chapter 2). Next, I model visitation at lakes from multiple VGI sources to demonstrate that these data reflect empirical visitation. I also show that diverse VGI sources are likely to characterize the broad diversity of reasons motivating people to interact with nature (Chapter 3). My fourth chapter demonstrates the value of intentionally surveying waterbody visitors to identify their activities and desired amenities, thus informing the support of these activities across urban blue-green spaces. Improved access to close-to-home waterbodies and adjacent green spaces is fundamental to helping close the nature gap in urban environments where people of color, families with children, and low-income communities are most likely to be deprived of the benefits that nature provides (Chapter 4). Lastly, my fifth chapter visualizes and quantifies connections between waterbodies across the Western US in terms of the magnitude, direction and timing of human movements to identify potential invasion hubs. Identification of specific waterbodies at highest risk of invasive species introductions will allow state resource management partners to prioritize waterbody locations for preventative measures such as educational signage, boat inspection stations, and gear cleaning services (Chapter 5). Collectively, my research demonstrates the value of emerging technologies for informing freshwater conservation and management, as well as the integralness of quality empirical data for validating big data methods.
Dispersal of Fry and Distribution of Redds Interact to Shape Density Dependence in Winter Steelhead of the Skagit River
(2025-08-01) Chambers, Nicholas; Schindler, Daniel
The spatial scale of dispersal during early life stages when mortality rates are high is essential for understanding the relationship of the distribution of spawners to population productivity. In this study, we quantified the fine-scale distribution of age-0+ (fry) steelhead (Oncorhynchus mykiss) near redds across multiple sites in the Skagit River, WA. The estimated mean downstream displacement of fry was 145m with 95% of fry remained within 312m of their natal redd. Evidence of density-dependent dispersal was found at sites with multiple redds, where mean displacement increased to 270 m, though individual kernel tails could not be resolved. This limited dispersal resulted in strong spatial clustering of fry in areas with multiple redds. To evaluate effects of limited dispersal, we applied simulated dispersal kernels to ten years of spatially located redds to simulate fry distributions across a 31.5 km stream network, scaling each kernel to represent the same number of potential fry. The distance of stream channel accessed by fry increased linearly with increasing redd abundance, demonstrating spatial expansion and contraction of spawners in relation to abundance. Core spawning areas were consistently reused across years, with higher proportions in core areas in low abundance years. Increasing spawner abundance led to a shift in the proportion of fry from a majority in low density areas to a majority in high density areas. This provides strong evidence that density dependence was present across the range of observed spawner densities. Despite the change in average fry density, the number of fry in low density areas remained relatively constant due to spatial expansion of spawners. Expansion into heterogenous habitats would lead to habitat mediated effects on recruitment, where if habitat quality is spatially uniform then expansion would increase recruitment proportionally with spawner abundance. Our findings highlight the importance of incorporating spatial structure and fry-scale dispersal into models of habitat capacity and recruitment, particularly when evaluating restoration or harvest strategies aimed at conserving the full range of life-history diversity.
Potential Mechanisms of Population Change in Southwest Alaskan Sockeye Salmon
(2025-08-01) Henry, Naomi Grace; Schindler, Daniel E; Holtgrieve, Gordon W
Bristol Bay, Alaska, is home to the world’s largest commercial sockeye salmon (Oncorhynchus nerka) fishery. This fishery not only produces more than half of all sockeye salmon globally, but also supports cultural and economic livelihoods across North America. Over the last century, there have been substantial changes in this fishery due to shifts in climate, biological composition of the ocean, and management practices and sockeye populations fluctuated drastically in response. The freshwater and marine life stages of Pacific salmon are deeply interconnected and although historically the freshwater life stage has been much more thoroughly researched, substantial knowledge gaps exist in both of sectors. In order to thoroughly understand how the dynamics of this valuable resource have shifted through time, it is necessary to fill in the knowledge gaps in both the marine and freshwater systems impacting sockeye salmon population responses. I explore two potential mechanisms of sockeye salmon production through time; marine trophic shifts and density dependence on the spawning grounds. In chapter 1 I use a novel compound specific isotope analysis (CSIA) approach to reconstruct 60 years of trophic position and nitrogen assimilation in the North Pacific Ocean and relate observed changes to regionally relevant environmental shifts. I find that periods of high productivity are associated with truncated food chain lengths and enrichment of the nitrogen isotope baseline of the ecosystem. Although I do not directly assess how food chain length relates to salmon production in the region, I identify this as an area that requires future exploration. In chapter 2 I build a population model to explore how density dependence on the spawning ground impacts recruitment and apply this model to a case study of two small creeks in Southwest Alaska. This model suggests a relationship between environmentally optimal spawn timing in a system and stock-recruit relationships, however when applied to our empirical data, this relationship does not hold up, indicating the need for further investigation.
Marine conservation in a changing climate and for deep ecosystems
(2025-08-01) Jacquemont, Juliette; Tornabene, Luke
Human uses of the ocean are intensifying, diversifying, and spatially expanding to respond to the ever-growing food, energy, and material demand of humanity. In this context, marine protected areas (MPAs) have been increasingly promoted as a tool to mitigate impacts from extractive activities and promote sustainable uses of marine resources. However, while the ecological benefits of highly protected coastal MPAs are well-established, many controversies remain on whether these benefits will perdure under future climatic conditions, and whether MPAs are relevant tools to protect deep offshore ecosystems. This dissertation aims at addressing these uncertainties by (1) clarifying the climate benefits that MPAs can provide, (2) assessing the conservation status across depth zones of the ocean, and (3) advancing the ecological knowledge of deep-reef ecosystems to better inform their conservation. In chapter 1, I conduct a meta-analysis and demonstrate that MPAs with high levels of protection can significantly enhance multiple climate mitigation and adaptation pathways including carbon sequestration, coastal protection, species richness, and fishers’ catch and income. In chapter 2, I found that conservation efforts are unevenly distributed among depths and tend to be biased towards areas with the lowest fishing efforts. In chapter 3 and 4, I evaluate the taxonomic and functional diversity of Caribbean reef-fish communities across multiple depth zones from the surface to the deep-sea boundary (< 300 m). This dissertation highlights the importance of MPAs in supporting the resilience of socio-ecological systems to climatic pressures and sheds light on the unique diversity of deep reefs, which require dedicated conservation efforts to achieve targets of ecological representation.
Population ecology and decision analysis to inform seabird conservation
(2025-08-01) DuVall, Amelia Jade; Converse, Sarah J
Seabirds are among the most threatened vertebrate groups globally, facing a range of anthropogenic threats from invasive species and fisheries bycatch to increasingly pervasive climate-driven changes in ocean ecosystems. Despite the availability of proven conservation strategies, effective management of seabird populations is often constrained by ecological complexity, logistical challenges, and uncertainty in species-specific responses. Seabirds’ long lifespans, low fecundity, and use of vast marine habitats create additional challenges for monitoring and decision-making. At the same time, these species play critical ecological roles as nutrient vectors and ecosystem indicators. As climate change alters the structure and productivity of marine environments, there is an urgent need to better understand how seabird populations respond to environmental variability—and how that understanding can inform conservation decisions. The research I present here explores the use of population ecology and decision analysis to evaluate seabird demography and improve conservation outcomes using case studies from the California Channel Islands, USA. First, I developed a novel daily nest survival model to assess how spatial and temporal variation in oceanographic conditions affect reproductive success for the Cassin’s Auklet (Ptychoramphus aleuticus), a sentinel species of marine climate change (Chapter 2). I then extend this work by building an integrated population model to quantify how environmental drivers influence demographic rates, abundance, and population growth across two colonies and to determine the role of demographic buffering in population stability (Chapter 3). In a separate case study, I model marine and terrestrial drivers of nest survival for a rare seabird with a restricted breeding range, the Scripps’s Murrelet (Synthliboramphus scrippsi), to support targeted management and conservation efforts (Chapter 4). Finally, I apply structured decision-making tools to evaluate uncertainty in seabird management and conservation, using constructed value of information to prioritize research and monitoring priorities across six species (Chapter 5). Together, this research shows how linking ecological modeling with decision analysis can improve seabird conservation under dynamic and uncertain conditions.
Trends in juvenile sockeye salmon rearing capacity, stock specific growth performance, and estuarine habitat use in the Chignik watershed, Alaska
(2025-08-01) Gammelin, Cirque; Schindler, Daniel E
Coastal watersheds provide a network of interconnected heterogeneous habitatsaccessible to mobile species. Multiple populations can exploit alternative habitats, buffering overall abundances against perturbations in climate and ecosystem processes. In the Chignik Lakes watershed, Alaska, sockeye salmon (Oncorhynchus nerka) populations exhibit a diversity of juvenile life history strategies, exploiting diverse freshwater and estuarine rearing habitats. In 2018, Chignik sockeye salmon stocks experienced a catastrophic collapse, threatening the viability of commercial and subsistence harvest. The overall goal of this thesis was to investigate how changes in juvenile sockeye salmon rearing capacity, growth performance, and habitat use within the Chignik watershed may have contributed to the 2018 fishery disaster. We compiled and analyzed multiple decades of habitat quality data to explore long-term trends in the freshwater rearing capacity and growth performance of juvenile sockeye salmon in iii the years preceding the 2018 collapse. We identified increasing water temperatures in a shallow lake, and more stable conditions in a deeper lake. Zooplankton prey quality increased in response to both bottom-up and top-down food web dynamics. We observed strong effects of competition and density dependence in sockeye salmon populations throughout the watershed. Although we detected no evidence that freshwater habitat quality has declined, the data suggest that high early life stage mortality in brood years of the 2018 collapse likely contributed to poor adult returns. Using Single Nucleotide Polymorphisms, we successfully assigned individual juvenile sockeye salmon to two distinct populations. We reenforced previous findings that body condition reflects the productivity of an individual’s rearing habitat, regardless of stock of origin. Additionally, we observed multiple stocks exploiting estuarine habitat for juvenile rearing for the duration of the summer growing season. Together, our results suggest habitat heterogeneity and population diversity buffer sockeye salmon populations in the Chignik watershed. By exploiting alternative habitats, multiple populations are able to achieve sufficient growth despite variability in local habitat quality.
Lifetime Trophic Ecology of Fishes and Invasive Species Management in Dryland Streams
(2025-08-01) Diallo, Jessica O.; Olden, Julian
Invasive species are one of the greatest threats to freshwater fish biodiversity, with numerous documented impacts on freshwater food webs. This threat is especially acute in the American southwest, a region that is home to many endemic freshwater fishes. Invasive fish impacts have been studied most often at discrete points in time for pairs of species, but knowledge gaps remain regarding impacts across ontogeny in multi-species communities. Stable isotope analysis is commonly used to infer trophic ecology, including species interactions through competition and predation. We used a novel method of fish eye lens stable isotope analysis coupled with otolith growth measurements to construct lifetime trophic trajectories for native and nonnative fishes in Burro Creek, Arizona. Our results provide support for asymmetric competition wherein native species exhibited displaced trophic trajectories with respect to δ13C and δ15N, which may lead to reduced fish growth and fitness, with implications for population persistence.Competition for shared resources is a powerful mechanism in community ecology, contributing to the success of many invasive species. The balance between intra- and inter-specific competition is predicted to influence species coexistence, with theoretical and empirical studies historically focusing on single life stages. However, many fish species undergo ontogenetic dietary shifts, resulting in dynamic competitive interactions. Using the lifetime trophic trajectories of fishes from Burro Creek, Arizona, we measured isotopic niche distance as a proxy for competitive interaction strength and found shifts in competition through ontogeny within and between native and nonnative species pairs. Invasive species are increasingly targeted for suppression or eradication to reduce impacts on native communities. We leveraged two invasive green sunfish removal programs in intermittent streams of the Bill Williams River, Arizona, to quantify removal success and explore alternative effort allocation in time and space. Bayesian hierarchical modeling of removal data was used to estimate demographic parameters, finding that both removal programs resulted in at least a 0.39 probability of eradication. Simulated alternative management scenarios revealed that population suppression could be achieved with reduced effort, but eradication success was dependent on the high frequency of removal events, even after zero fish were captured. Given the accelerating spread of invasive species and limited resources to control invasive populations, quantitative removal models are valuable tools for improving and evaluating invasive species removal efforts. Though native to the Columbia River Basin, northern pikeminnow have been the subject of long-term population control. This began in response to their increased predation of anadromous juvenile salmonids as a result of habitat modification due to hydropower dam construction. The Northern Pikeminnow Management Program (NPMP) is a targeted harvest program with a sport reward fishery that has been operating in the Columbia and Lower Snake Rivers since 1991. Northern pikeminnow are tagged annually to model their exploitation rate, and the model used assumes closed populations separated by dams. We studied the movement of northern pikeminnow using passively collected passive integrated transponder (PIT) tag data from 2003-2022. Movement records reveal that individuals traveled at least as far as 968 km. Nearly 13% of northern pikeminnow tagged through the NPMP were detected in different river sections, separated by dams, from where they were initially tagged. Our increased understanding of northern pikeminnow movement informs the calculation of the exploitation rate, one of the key measures of NPMP success, and may contribute to future management strategies.
Participatory modeling to evaluate tribal pinniped harvest in Puget Sound as a tool for salmon recovery
(2025-08-01) Allyn, Elizabeth Marina; Essington, Tim
Pinnipeds and salmon have been actively managed by tribes in the Salish Sea since time immemorial. Tribal pinniped harvest impacted pinniped populations directly through removals, indirectly through disturbance, and spatially by excluding them from frequently utilized areas near village sites, which often included important salmon migration routes. Current management practices struggle to balance pinniped recovery success with the need to protect the threatened salmon populations they prey on. We employed a Participatory Modeling Process to collaboratively develop a modeling framework with treaty tribes in Western Washington that could explore the impacts of pinniped management scenarios on the survival of returning adult salmon in terminal areas. We developed a model that simulates the dynamics between pinnipeds and salmon using a combination of agent-based and dynamic components to represent aspects of pinniped behavior, foraging decisions, fear conditioning, individual learning, and social contagion. Using this model, we explored different management regimes for pinniped harvest and evaluated success by monitoring the number of salmon who survive predation by pinnipeds and are therefore available to fulfill other management objectives. We carried out these simulations in two case study locations: the Ballard Locks in collaboration with the Muckleshoot Indian Tribe, and the Nisqually River in collaboration with the Nisqually Indian Tribe. We found that management scenarios where pinniped management was carried out in a way that allowed pinniped predators to develop fear of management activity were more effective at improving salmon survival. We also identified specific scenarios for each case study that benefitted the specific salmon runs that use those systems and described the general characteristics of successful management strategies. The results from this study will be used by our partners in tribal resource management agencies to structure pinniped management in their Usual & Accustomed areas and identify data gaps for future monitoring efforts. Providing pathways for tribes in Washington to exercise their treaty rights to harvest pinnipeds in a way that mitigates salmon predation hotspots could be an effective management strategy that balances complex conservation objectives while operating within existing legal and political frameworks.
Confronting uncertainty in the contribution of mesopelagic fishes to the biological carbon pump
(2025-05-12) McMonagle, Helena; Essington, Timothy E; Hilborn, Ray
The framework of ecosystem services is one way of understanding and describing the beneficial processes and functions that humans receive from the natural world. Many ecosystem services come from the oceans, such as benefits we receive from marine fisheries and the role the oceans play in regulating global climate and mitigating climate change. Some of the world's most abundant fishes—mesopelagic fishes like myctophids—contribute to each of the major categories of ecosystem services including provisioning services, regulating services, cultural services, and supporting services. This dissertation focuses on further quantifying their role in regulating services, specifically carbon transport and sequestration. Findings related to key sources of uncertainty in estimating fish-mediated carbon transport can be used in prioritizing research efforts to further describe this ecosystem service, while minimum and maximum estimates of mesopelagic fish carbon transport further our understanding of this ecosystem service despite uncertainty. Quantitative findings from these chapters may be used in the future to inform decision-making processes that evaluate potential trade-offs among ecosystem services associated with mesopelagic fishes.
The Coastal cutthroat trout (Oncorhynchus clarki clarki) : genetic population structure, migration patterns, and life history traits
(1998) Wenburg, John Keim
Coastal cutthroat trout (Oncorhynchus clarki clarki) populations have undergone major range wide declines over the past two decades. This study was initiated in light of their declining status in an effort to augment the paucity of existing data, both in terms of their general ecology and genetic population structuring. Multiplexed groups of fluorescently labeled microsatellite primers were used in an analyses of allelic variation, both on a statewide and microgeographic scale. Analysis of six loci for 13 anadromous populations from throughout Washington revealed high within population variability (He = 71%; mean # alleles/locus = 24), significant differences in genotypic frequencies for single-locus pairwise comparisons between all populations, and substantial population subdivision (Fst = 0.121, Rst - 0.093). Similarly, analysis of allelic variation at 10 loci for 10 populations from within Hood Canal revealed high within population variability (He = 69%; mean # alleles/locus = 17), significant differences in genotypic frequencies between all populations across all loci, and in 304 of 450 single-locus pairwise comparisons, and significant population subdivision (Fst = 0.030, Rst = 0.029); all of which suggest that individual creeks form the basis for distinct breeding units in this subspecies. Mantel tests supported an isolation by distance model of population structure within Hood Canal using both Fst (P=0.015) and the Cavalli-Sforza and Edwards’ (1967) chord distance (P=0.001) as measures of genetic distance, and for the latter on a statewide scale (P=0.0l). Estimated levels of gene flow from direct observations, through a 3-year tag-recapture study, were similar to those estimated indirectly from allele frequency data, being on average approximately 5 to 10 effective migrants per generation between neighboring populations. Intensive ecological study of the Big Beef Creek population (Hood Canal, WA) revealed: differing migration patterns between the sexes, with males migrating into freshwater sooner and remaining longer than females; significant correlation between the upstream migration date for individuals across years (R^2 = 0.43, P=0.002); and evidence that some individuals likely overwintered at sea. Survival estimates averaged 54% for the overwintering period in freshwater, and 12-24% and 33-59% during salt water migrations for first and second-time migrants, respectively.
Examining hair growth rates and dietary patterns of wild and captive bears
(2025-01-23) Stern, Jennifer Hedi; Laidre, Kristin
The feeding ecology of wildlife has important implications for individual health, population productivity, community structure, and ecosystem functioning. For bears of the family Ursidae, food resources and feeding behavior primarily impact population dynamics via effects on cub production and survival. Much of what is known about the feeding ecology of bears is based on analyses of various tissues collected from capture-based research efforts, harvested animals, or non-invasive approaches. The use of multiple chemical tracer methods provides an informative view of the diet, as each tissue spans a unique timeline. However, inference about diet from hair has been limited by a lack of quantitative data on the timing of the molt and hair growth rates. Addressing physiological assumptions is essential to gain insights into the feeding patterns in wild bear populations in dynamic ecosystems. Climate change is shifting the phenology, availability, and selection of food resources for bears across multiple ecosystems. Because polar bears (Ursus maritimus) specialize in both food and habitat type, they are particularly vulnerable to environmental change. Detailed studies of polar bear foraging are necessary for a comparative and predictive understanding of how diets may change with a loss of sea ice habitat and increased use of coastal habitats. One such documented coastal habitat is freshwater glacier ice, which provides year-round access to prey for Baffin Bay polar bears, although the feeding habits of polar bears using glacier ice relative to those following the retreating ice and/or seasonally moving onshore are not known. This dissertation comprehensively investigates the interpretation of dietary data derived from hair samples and the drivers of diet variability in polar bears, with the overarching goal of contributing to an improved understanding of the feeding ecology of bears. First, methods were developed to document hair growth in three species of captive bears. The methods of hair dye and 13C- and 15N-labeled glycine identified periods of hair growth and detected individual and seasonal variations in hair growth rates, with their effectiveness not being dependent on the bear species. Second, the timing and rate of hair growth were quantified in captive polar bears across an annual cycle, incorporating variables of body location and season. Hair growth was detected at similar rates throughout spring, summer, and fall, while there was slower growth in winter, consistent with the anticipated patterns of an annual molt. Third, dietary patterns among wild polar bears of different sexes, ages, and movement patterns were evaluated in relation to sea ice metrics using stable isotopes and total mercury concentrations in hair. Baffin Bay polar bears showed limited variation in their feeding habits, as indicated by stable isotope values and total mercury concentrations, despite differences in inter-annual sea ice conditions and individual space-use strategies. Fourth, patterns of diet composition were evaluated among Baffin Bay polar bears with distinct coastal and offshore space-use strategies using relative abundances of fatty acid signatures in fat samples, a tissue representing a different time period (winter-fall) than hair (spring-summer). While demographic and short-term temporal variation was minimal, fatty acid signatures and diet estimates clearly differed between coastal polar bears using glacier fronts and offshore bears using pack ice habitat. Collectively, results from these chapters bridge experimental and applied settings, improve interpretations of bear hair samples, and provide insight into the factors driving diet variability in wild polar bears.
Diet and Biology of Deep-reef Lionfish (Pterois volitans) at CuraÃ§ao
(2025-01-23) Yerrace, Sarah; Tornabene, Luke
Indo-Pacific Red Lionfish (Pterois volitans) are a well-established invasive species in the western Atlantic Ocean and have been documented at depths of 0-304 m. However, our knowledge of lionfish biology and diet below 40 m is limited due to the constraints of recreational SCUBA diving depth limits. Communities below 40 m are distinct from communities above 40 m, thus it cannot be assumed that lionfish have the same impacts or consume the same species below 40 m. Studies targeting lionfish diet and biology below 40 m are necessary to determine potential impacts on understudied mesophotic communities and consequences for invasion management. Specifically, understanding where on the reef lionfish reach the largest sizes will give insights into what areas of the reef may experience the highest predation pressure. Understanding where lionfish are spawning on the reef may indicate long term effectiveness of removal efforts. The purpose of this study was to describe the diet, size, and reproductive characteristics of lionfish across depth in CuraÃ§ao, Southern Caribbean. Using a combination of SCUBA and manned submersible diving, 136 lionfish off the southern coast of CuraÃ§ao were collected along the reef slope down to 189 m. Lionfish below 40 m were longer and heavier than lionfish above 40 m but did not have better body condition (Fulton’s condition factor). Significantly more males than females were collected above 40 m. Fertile females were present along the entire depth range, however no actively spawning females, based on gross morphology of gonads, were found below 126 m. Using DNA metabarcoding of the mitochondrial COI gene of gut contents, 598 exact sequence variants from prey species were recovered representing 51 species of fishes from 18 families and an additional 13 families of invertebrates. Across all individuals, the four most commonly occurring teleost families were Pomacentridae, Apogonidae, Gobiidae, and Scorpaenidae. Gobiidae was frequently consumed above and below 40m, while Apogonidae and Serranidae were more frequently consumed below 40m. No dietary trends were detected with increasing lionfish length or mass. Eighteen teleost taxa were recorded for the first time from lionfish guts. Overall, species of fishes identified in lionfish guts closely reflect prey that is available at the depth at which the lionfish were collected, suggesting that lionfish on mesophotic and rariphotic reefs are consuming mesophotic and rariphotic prey. These deep-reef taxa may be especially vulnerable to lionfish predation given their naturally low abundances coupled with the larger sizes and lack of top-down control of lionfish on deep reefs. Given that culling has been successful in controlling local shallow populations, developing an effective means of culling lionfish below 40 m may be critical reducing the impact of lionfish predation on vulnerable deep-reef fishes.
Causes of Infection and Disease Progression of Hematodinium sp. in the Tanner crab, Chionoecetes bairdi
(2025-01-23) Coyle, Aspen Elizabeth; Roberts, Steven
In the past several decades, parasites of the genus Hematodinium have become prevalent in crustaceans around the globe. One such host is the Tanner crab (Chionoecetes bairdi), which supports a number of commercially and culturally valuable fisheries in the North Pacific. This thesis explores the host-parasite relationship between C. bairdi and Hematodinium sp. through two avenues. The first was an analysis of gene expression, in which individual crabs were captured, their infection status was checked, and they were exposed to one of three temperatures - elevated, decreased, and control. Throughout the 17-day experiment, hemolymph was drawn and sequenced for gene expression. Differences in gene expression for both host and parasite were then analyzed, and a number of genes in both host and parasite were identified as linked to temperature response. Numerous parasite expression pathways changed over the course of the experiment, including changes in RNA processing and microtubule development. The second avenue of analysis utilized generalized linear mixed models to investigate a long-term survey dataset from southeast Alaskan crab surveys, with the goal of determining the association between infection status and a variety of biological and environmental factors. A number of factors were found to be correlated to infection status. Among them: females were more likely to be infected than males, immature crab were more likely to be infected than mature individuals, recently-molted crabs were more likely to be infected, and larger crabs were more likely to be infected. Together, these findings improve our understanding of the relationship between C. bairdi and Hematodinium. They provide a window into the internal host-parasite dynamics and how temperature and time alter gene expression. They also demonstrate that infection rates vary substantially within subsets of the host population, and indicate those subset-specific impacts should be considered when analyzing the ramifications of outbreaks.
Spatiotemporal controls on nutrient source and transport in Puget Sound rivers
(2025-01-23) Elmstrom, Elizabeth; Holtgrieve, Gordon
Understanding the factors controlling nitrogen (N) and phosphorus (P) in rivers is critical to preserve ecosystem functioning from land to the coast yet challenging given the complexity of climate and landscape interactions. These interactions operate across multiple spatial and temporal scales, often manifesting differently across rivers depending on watershed-scale controls, underscoring the need to study river N and P dynamics across diverse systems. My dissertation research investigates river N and P sources and transport in a human-influenced, mountainous region in western Washington state, aiming to disentangle the roles of climate and landscape variation in driving nutrient entry and delivery in coastal rivers. Using two large regional datasets at different temporal scales (i.e., seasonal, multi-decadal), I demonstrate the strong influence of regional and macro-scale climate patterns in driving seasonal river nutrient transport regimes, while highlighting the distinct role of watershed topography modifying river nutrient responses to hydroclimatic change. Further, by using stable isotopes to trace N sources in rivers, I show the origins of N entering these human-influenced, coastal rivers are closely linked to upland soils in the forested landscape, the flushing of which is dependent on seasonal climate. To mitigate the effects of climate and landscape alterations on riverine ecosystems, there is a pressing need to understand how the interaction of ecological controls will play out across river systems. Findings from my dissertation research elucidate these interactions, demonstrating the strength of climate and the physical environment in driving river nutrient delivery to the coastal environment, and enhancing the predictability of river nutrient transport in mountainous regions facing increasing impacts from climate change and human activity.
Lakeshore development and lake food web structure in the Puget Sound lowlands
(2024-10-16) Jameson, Emily; Olden, Julian D
Anthropogenic modification of lake shorelines can eliminate or sharply reduce the elements of shorelines that provide structural diversity in littoral habitats, such as macrophyte and woody debris densities. These changes have been linked to alterations in species abundances, diet patterns, and nearshore food web structure at altered and unaltered shoreline locations within a lake. Few studies, however, have quantitatively examined the association between lakeshore development and food web network structure across lakes with varying levels of lakeshore development. Considering the lake-specific food web networks across multiple lakes could reveal differences in interactions and structural patterns not captured in within-lake studies. In this study, I quantified community structure and species’ positions in food webs across lakes with varying degrees of lakeshore residential development to identify associations between the two. I selected 12 lakes in the Puget Sound lowlands, and for each conducted standardized habitat surveys by measuring littoral and riparian habitat complexity, and recording dock density along the lakeshore, pelagic chlorophyll-a concentration, and lake area. To estimate feeding habits of fish, I employed both stable isotope analysis and stomach content analysis. Additionally, I used stable isotope analyses to examine diet patterns in aquatic macroinvertebrates. I integrated data from both techniques with preexisting information from the literature within a relatively new analytical framework, EcoDiet, to estimate the proportion of each prey type in the diets of fish and predacious macroinvertebrates within the food web. To quantify species’ roles within the food web I calculated diet breadth, diet evenness, and betweenness centrality (relative importance in connecting disparate parts of the food web, hereafter centrality) for each predatory species. I then quantified food web metrics from the estimated lake-specific food webs using network analyses to calculate the connnectance, mean link strength, and mean degree within each food web. Finally, I assessed the correlations among these network metrics and the measured environmental variables using redundancy analysis (RDA), principal component analysis (PCA), and bivariate regressions. My results suggest that while pelagic chlorophyll-a concentration and the presence of largemouth bass were associated with changes in diet patterns within the food web, lakeshore development had little effect on overall food web connectance. Yellow perch and pumpkinseed exhibited a positive correlation between centrality and both pelagic chlorophyll-a concentrations and the presence of largemouth bass. Thus, both yellow perch and pumpkinseed were more important in connecting basal resources to upper trophic levels when primary production was high and largemouth bass were present in the lakes. Fish species exhibited different associations with lakeshore development and diet breadth and diet evenness. For instance, yellow perch (Perca flavescens) diet breadth and diet evenness were positively correlated with lakeshore residential development, whereas largemouth bass (Micropterus salmoides) diet breadth was negatively correlated, and pumpkinseed (Lepomis gibbosus) displayed little change in diet breadth or diet evenness. The net effect of these species-specific responses was a weak and positive association between food web connectance and both dock density and lake area. Because none of the lakes in this study were undisturbed (the least developed lake having residential development on 25% of its lakeshore), it is possible that changes to food web connectance occur at lower levels of lakeshore residential development than was measured in this study. High network connectance can stabilize food webs, therefore, the weak correlation between connectance and lakeshore residential development suggests that food web stability may be similar among the disturbance levels measured in this study. Future research could directly examine the relationship between lakeshore development, food web network structure, and stability across a wider range of lakeshore development.
Using Integrated Models to Improve Management of Imperiled Salmon and Steelhead
(2024-10-16) Buehrens, Thomas Ward; Schindler, Daniel E
Exploited wild animals include some of the most charismatic and celebrated species globally. They feed civilizations, are foundational to economies, are the subject of socially and culturally important recreational and ceremonial harvests and provide ecosystem services beyond human use. Yet, despite their importance to humanity, the history of management of these species is checkered, demonstrating both successes involving stable populations and long-term sustained harvests, and failures including overexploited species where population collapses and even extinction have occurred. Sustainable exploitation depends entirely on the fundamental principle of compensatory recruitment, wherein population growth rates approach zero when populations are close to their carrying capacities, but as abundance declines due to harvesting, per capita growth rates increase in response to decreasing competition, thereby enabling populations to recover toward their carrying capacities. However, to ensure harvest is implemented sustainably, answers to a few fundamental questions are required: 1) how many animals does a population contain? How many are being harvested? and, 3) What is the relationship between adult abundance and recruitment? Although natural resource managers have attempted to answer these questions for decades, the need for improved answers is greater than ever for species like Pacific Salmon (Oncorhynchus spp.) in the continental United States, where most populations are listed under the Endangered Species Act and face elevated risk of extinction yet remain subject to exploitation. This dissertation uses modern statistical modeling to address each of the fundamental questions necessary for the sustainable management of exploited but imperiled Pacific Salmon in Washington State. Chapter 1 estimates the relationship between spawner abundance and recruitment to the smolt life stage for coastal steelhead (O. mykiss) populations in Washington State. By re-parameterizing the Beverton-Holt and hockey-stick stock-recruitment functions, the study incorporated habitat characteristics to explain variation in biological reference points among populations. The findings indicated strong effects of habitat quantity and quality on smolt carrying capacity, with estimates of capacity and the spawner abundance producing the maximum sustained yield (SMSY) aligning with previous studies but demonstrating previously underappreciated sensitivity to smolt and kelt survival. The study highlighted the importance of geomorphic features in informing estimates of smolt capacity in stream-rearing salmonids and identified a minimum smolt-to-adult return rate required for population viability at around two percent based on maximum per-capita smolt productivities around 50 in the least productive populations. Chapter 2 focuses on estimating the abundance of coho salmon (O. kisutch) for Washington State’s populations in the Lower Columbia Evolutionarily Significant Unit (ESU). The study used data from an ESU-wide monitoring program initiated in 2010, which included spawning ground surveys, mark-recapture experiments, and trap-and-haul counts of migrating coho at dams, complemented by fishery catch estimation programs. The multivariate state-space integrated population model that was developed provided estimates of coho salmon population parameters, revealing that coho salmon abundance ranged between 12-86,000 wild spawners (median = 28,310) from 2010-2022. Several populations periodically exceeded their ESA recovery goals but remained below densities seen in healthy populations elsewhere. Chapter 3 develops a Bayesian multivariate state-space model to improve estimates of catch in sport fisheries using creel survey and effort count data. This model, applied to data from the 2021 Skagit River wild winter steelhead catch-and-release sport fishery, robustly quantified uncertainty and was developed to flexibly accommodate multiple study designs. The model estimates of catch were used within a probabilistic management framework, helping fishery managers balance the risks of overfishing and unnecessarily restricting fishing opportunities. This approach demonstrated how robust quantification of uncertainty could optimize study designs for desired precision and cost efficiency.
Cryptobenthic Coral Reef Fishes: Resolving Critical Gaps in Species Delimitation, Sampling Techniques, and Phylogenetic relationships
(2024-10-16) Gomez-Buckley, Marta; Tornabene, Luke
Cryptobenthic reef fishes (CRF) are the smallest vertebrates on coral reefs but represent about 40% of the fish species and about 50% of fish abundance in coral reef ecosystems. Their diversity can be explained by their extremely limited dispersal abilities and short generation times (promoting allopatric speciation) coupled with their ability to partition microhabitats at a very fine scale. One of their main contributions to coral reef ecosystems is as food for larger piscivorous fishes and invertebrates. Despite their importance, CRF are often overlooked, as their cryptic nature and very small size make them difficult to assess using visual methods. The prevailing method for quantifying communities of CRF is to use enclosures and anesthetics to collect fishes from within the reef. Environmental DNA (eDNA) sampling of water around reefs may be an alternative or supplemental way to quantify CRF communities. In Chapter 1, I compared the ability to characterize CRF communities using eDNA sequences from water samples collected from within the interstices of the reef, with corresponding anesthetic stations from the same microhabitat. A total of 676 CRF from 33 species were collected from anesthetic stations, whereas only four species of CRF were detected from the eDNA samples taken at the same locations. Main factors contributing to these results may have been: (1) low standing biomass of CRF, thus low abundance of detectable DNA in the eDNA water samples; (2) large number of non-targeted metazoan reads that “drowned” the detections of specific CRF sequences; and (3) lack of sequences available in public databases that represent the high level of endemism present in CRF and a need for more complete taxonomic inventory. For some groups of CRF, their small size, cryptic nature, and conserved morphology have resulted in many undetected cryptic species, which may require a genome-wide species delimitation approach to discern how many species are present. One of the most species-rich groups of CRF, the genus Eviota, has 132 species described to date, is widely distributed from the Red Sea to Hawaii and French Polynesia, and is known to comprise numerous cryptic species. In Chapter 2, I focused on the Eviota sigillata complex which is represented by two nominal species described by morphological characters, yet preliminary genetic data suggest the presence of multiple cryptic lineages. I use molecular data from mitochondrial DNA and genome-wide SNP data generated via double digest restriction site associated sequencing (ddRADseq), in combination with morphological data to infer the number of species in the E. sigillata complex. Specifically, I constructed phylogenetic trees and conducted several types of single-locus and multilocus species delimitation analyses and compared these to groupings based on morphology, as well as their geographic distribution. Overall, I found evidence for the presence of 9-13 lineages within the E. sigillata species complex, with genetic lineages corresponding well with the biogeography of the group. I further confirmed that the original morphological diagnostic characters used for the separation of the two nominal species were not useful for distinguishing each of the nine clades in the complex but may be helpful in diagnosing groups of species. Overall, Chapter 2 shed light onto the patterns of speciation within CRF and provided a glimpse of the tremendous hidden diversity that remains in coral reef fishes. The goby genera Eviota and Sueviota (family Gobiidae) are commonly known as dwarfgobies, and collectively, the two genera are among the most abundant and diverse groups of fishes on coral reefs. Despite the diversity, abundance, and ecological importance of this group, and the large and growing number of species described to date (132 Eviota, 9 Sueviota), there is a lack of understanding of the phylogenetic relationships among the major clades of Eviota, poor knowledge of the relationships between dwarfgobies and other Gobiidae species, and no information on the placement of Sueviota. In addition, as is the case with most small reef fishes, a clear understanding of taxonomically informative phenotypic characters is also lacking. In Chapter 3, to resolve the evolutionary history of dwarfgobies, I inferred a time-calibrated phylogeny of the group using genome-wide data from 440 ddRADseq loci captured across 98 Eviota and Sueviota specimens, plus 66 specimens of other related gobies. I also assessed the distribution of 14 external and osteological morphological characters across the tree to assess which may be useful for diagnosing clades. Results from my Chapter 3 robustly established the non-monophyly of the genus Eviota, which was resolved into two separate clades, both of which were resolved within a lineage of other coral associated genera (Gobiodon, Paragobiodon, Pleurosicya, Minisicya and Bryaninops). One of the two clades is herein elevated to its own genus, Eviotops, a name which was previously considered synonymous with Eviota. Additionally, I established that the genus Sueviota is deeply nested within one of the Eviota clades and is herein synonymized with Eviota. Furthermore, I found strong phylogenetic signals for 12 out of the 14 phenotypic traits examined, providing strong complementary support for the two recovered clades and establishing the validity of phenotypic traits that strongly correspond with genetic groupings that should aid in future taxonomic studies for this group.
Probabilistic statistical and agent-based encounter-impact models for fish and tidal turbine interactions
(2024-10-16) Peraza, Jezella Ileana; Horne, John K
Marine Renewable Energy has potential to become a valuable and predictable energy source in regions with strong tidal and ocean currents. Tidal energy is a prominent sector within the industry but concerns regarding its potential impact on marine life hinder its development and deployment. Concerns include animal-turbine encounters, collisions with turbine structures, blade strikes, and risk of injury or mortality. Statistical and simulation models are employed to assess encounter and interaction risks between aquatic animals and tidal turbines, yet there is a need for a comprehensive model incorporating animal trajectories and behaviors. This study aims to develop an encounter-impact probability model, using acoustic and hydrodynamic data from Admiralty Inlet, Washington, USA, and insights from published literature. Our encounter-impact model calculates conditional probabilities of fish-turbine interactions in sequential steps by incorporating empirical data and considering factors such as avoidance behavior and turbine dimensions. The model evaluates collision and blade strike risks, employing published values and empirical measurements, to assess overall impact probabilities. The statistical, encounter-impact model assesses probabilities of fish-turbine interactions influenced by turbine type, time of day, and avoidance behavior. As an agent-based simulation, the probability model assesses fish-turbine interactions considering factors of animal behaviors and tidal flow. Fish locomotion and aggregation behaviors are simulated, incorporating active and passive avoidance of turbines. Interactions between fish and turbines (i.e., collision and/or blade strike) are simulated. Experimental factors like fish abundance, aggregation, and tidal speeds are explored to understand their effect on fish avoidance and potential interactions. Lastly, results from the statistical and agent-based model are compared. For the statistical model, probabilities of fish presence vary between turbine type and avoidance scenarios, with collision, blade strike, and combined impact probabilities spanning several orders of magnitude. Light cycles slightly influence probabilities, with higher estimates observed at night. Turbine size also influences interaction probabilities, with larger turbines posing higher risks. Results from the agent-based model found that probabilities depend on aggregation behavior and tidal speed for both axial and cross-flow turbines. As expected, zone of influence and entrainment probabilities decrease with increasing tidal flow, while asocial fish are unaffected by changes in current speed. Overall impact probabilities increase with tidal speed for both turbine types and are primarily observed when fish are within social groups. Comparison between the simulation and statistical model reveals differences in mean probabilities for each model component. While both models rely on empirical data and literature values, there remain knowledge gaps in estimating potential impacts and turbine avoidance. Future research should focus on validating encounter-impact models with real-world data to enhance mitigation efforts and conservation strategies.
Interactions of Pigeon Guillemots and Rhinoceros Auklets with the marine environment
(2024-10-16) Pendleton, Liam C; Converse, Sarah J
Pigeon Guillemots (Cepphus columba) and Rhinoceros Auklets (Cerorhinca monocerata) are seabirds with a widespread year-round distribution throughout the Salish Sea, where they have a long history of study. They have been identified as indicators, i.e., Puget Sound Vital Signs, by the Puget Sound Partnership. The purpose of a Vital Sign is to act as a benchmark measure of the ecological health of Puget Sound and to guide recovery goals. Despite their status as indicators, major gaps exist in our knowledge of their relationship to the marine environment, including the relationship between marine conditions and their demography, and characteristics of their foraging habitat. These knowledge gaps limit their utility as indicators. In this thesis, I address some of these gaps using data from Protection Island in the Salish Sea. In Chapter 1, I developed hierarchical models in a Bayesian framework to understand the relationships between Pigeon Guillemot reproductive outcomes and oceanographic conditions. I considered the influence of multiple indicators of oceanographic conditions across different temporal scales relative to the breeding season to learn how the temporal occurrence of these conditions influences Pigeon Guillemot breeding outcomes. Pigeon Guillemot reproductive success, defined as the probability of a nest fledging at least one chick, was positively correlated with the North Pacific Gyre Oscillation (NPGO) index. Higher NGPO values are indicators of increased upwelling in the northeast Pacific and higher marine productivity. Guillemot reproductive success did not appear to be influenced by local marine conditions including sea surface temperature or chlorophyll-a concentration, or by the broader conditions described by the Pacific Decadal Oscillation. The lack of influence of any other covariate considered may be explained by the Pigeon Guillemots’ generalist nature, in particular their ability to prey switch depending on the abundance or quality of prey species available to them, which may buffer them against variability in marine conditions. My results provide a better understanding of how the Pigeon Guillemot population at Protection Island responds to marine conditions and informs their use as a Puget Sound indicator species. In Chapter 2, I conducted preliminary analyses of the behavior-specific movements of Pigeon Guillemots and Rhinoceros Auklets nesting at Protection Island. I tracked individuals during the breeding seasons of 2022 and 2023 and used these location data to fit discrete-time hidden Markov models to characterize behavioral states of both species, which have very different foraging and provisioning strategies during the breeding season. I used step length and turn angle to model movements of tracked birds across resting, transiting, and foraging states. Fitted models largely conflated movements associated with resting and foraging states, and predicted that foraging behavior occurred on or near Protection Island. These findings suggest the importance of fixing the resting state in these models, given that we know when and where resting, or stationary, behavior is primarily occurring, such that the models are only distinguishing transit and foraging states. I discuss future directions for this analysis. The utility of Pigeon Guillemots and Rhinoceros Auklets as indicators of environmental conditions in the Salish Sea is contingent on our understanding of how they respond to and use their habitat. Together, these chapters explore aspects of their breeding ecology and behavior and suggest processes through which we can productively view their relationship with the environment in the Salish Sea.

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