RSS 1.0Fisheries
Recent Submissions
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Spawning stocks and juvenile summer habitat of rainbow trout and steelhead, Gulkana River, AlaskaThe Gulkana River supports the northernmost population of steelhead and rainbow trout Oncorhynchus mykiss in North America. The summer habitat of Gulkana River juvenile trout (i.e., steelhead and rainbow trout) was identified and described. Analysis of geomorphological features of stream reaches (stream entrenchment, bankfull width-to-depth ratio, sinuosity, channel material, and slope) in relation to differential use of habitat by juvenile trout indicated a strong preference for type C reaches (predominately riffle/run habitat) over type E reaches (predominately slow run habitat). A comparison of micro-habitats (riffle, run, pool, slow run) within those same reaches and distribution of juvenile trout indicated a preference for riffle and run habitat. Most type C reaches in the Mainstem were sparsely populated by juveniles throughout summer. The Middle Fork was devoid of juveniles in early summer. In mid- and late summer, coinciding with the arrival of spawning chinook O. tshawytscha and sockeye salmon O. nerka, most riffle/run reaches in the Middle Fork were occupied by juvenile trout. The steelhead spawning population has declined from an estimated 200-1,000 fish two decades ago to 20-50 fish during this study (1993-1995). Rainbow trout stocks are also apparently low. Monitoring of Copper River fisheries and Gulkana spawning populations and an investigation into other steelhead spawning populations in the Copper River basin are recommended
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Lake productivity indices as estimators of carrying capacity for burbot and northern pike in Interior AlaskaTwo Alaska sport fish species, burbot and northern pike, were used to test the ability to estimate carrying capacity of fishes based on biotic and abiotic indices of lake productivity. Understanding the quantitative relationships between the potential fish productivity of freshwater lakes and physical, biological, or chemical characteristics could provide models sufficient for calculating a timely prediction of carrying capacity to evaluate the population status. This would provide a technique for allocating limited resources for fishery stock assessment as an aide in resource management of sport fisheries. The lakes covered in the study lie in an area spanning West 151°--142°/North 64°30ʹ--61°52ʹ. They are Fielding Lake, George Lake, Glacier Lake, Harding Lake, Hudson Lake, Jatahmund Lake, Lake Louise, Landlocked Tangle Lake, Moose Lake, Paxson Lake, Sevenmile Lake, T Lake, Tolsona Lake, Volkmar Lake, and West Twin Lake.
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Estimation of aging accuracy and precision, growth, and sustained yield of coastal cutthroat trout in Southeast AlaskaThis study was designed to validate and estimate accuracy and precision of ages determined from scales sampled from coastal Cutthroat trout Oncorhynchus clarki clarki in Southeast Alaska; to model growth of these fish; and to evaluate the sensitivity of sustained yield estimates to aging error. Cutthroat trout scales sampled in Southeast Alaska did not always form an annulus during the first year, although the number of circuli up to the first apparent annulus was a good indicator that one was missing. Reader error generally resulted in significant underaging of older fish from scales. However, aging error models developed in this study significantly improved the accuracy of ages estimated from scales. Growth of cutthroat trout was best described by a Gompertz growth curve and was significantly different between the populations studied. Underaging of cutthroat trout resulted in underestimates of optimum levels of fishing mortality and yield.
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Combining Alaska forage fish data from research surveys and predator diets to assess forage fish response to climatic regime shiftsForage fish play a crucial role in the marine ecosystems of Alaska through the transfer of energy from lower trophic levels to marine predators. Understanding and quantifying Alaskan forage fish responses to rapid climatic shifts is needed to inform adaptive management strategies under a warmer and more variable future in Alaska. However, data on the occurrence and abundance of forage fish in Alaska are limited due to the diversity of life history strategies and patchy distribution that make their capture in fisheries-independent surveys difficult. In this thesis, I address current gaps in the data available on forage fish through the publication of an Alaska Forage Fish Database (AFFD) comprised of data from trawls, beach seines, and the diets of predator consuming forage fish, collected by a variety of contributing agencies and organizations. This data compilation effort resulted in a database containing forage fish abundance data from 461,449 sampling events spanning the years 1953 - 2023. Using the compiled dataset, I then assess large-scale spatial and temporal patterns in the occurrence of Pacific capelin (Mallotus catervarius), Pacific herring (Clupea pallasii), and sand lance (Ammodytes spp.) in the Bering Sea and Gulf of Alaska. Interannual trends in the encounter probability for each species, based on models fit to data from fisheries surveys, groundfish diets, and seabird diets, exhibit coherence in large-scale changes among observation types in the Gulf of Alaska (1972 - 2023) and Bering Sea (1980 - 2023). I compare the distribution of species’ encounter probability across decadal climate stanzas and demonstrate the differences in distribution of species during the 2014 - 2019 heatwaves compared to prior stanzas, as well as reoccurring distribution patterns in response to similar climatic characteristics among stanzas. Findings from this thesis facilitate an expanded understanding of forage fish population dynamics and spatial distribution in response to rapid climatic shifts.
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Centering community and joy through co-production: tracking the seasonal changes of Utqiaġvik’s spring whalingUsing mixed methods and multimedia approaches, I investigated the multigenerational perspectives and seasonal changes in Utqiaġvik’s spring whaling. As an Iñupiaq living in my home community of Utqiaġvik, it was important to me to center my community’s knowledge and Iñupiaq-led entities. I used various tools and resources such as conducting semi-directed interviews, hiring a local Iñupiaq videographer to take photos and videos of spring whaling preparations, and using observational data from the Alaska Arctic Observatory and Knowledge Hub. The interviews, conversations with local Iñupiat-led entities and whalers, and the observational data guided my research goals and objectives and, more importantly, determined what key whaling events to research and analyze. Here, I am combining these techniques and resources to address the seasonal changes of our spring whaling key events (e.g., breaking trail) in the context of coastal Iñupiaq communities of northern Alaska and how we can use observations from our Indigenous Knowledge holders to inform scientists and managers of what is happening during spring whaling. In my research, science communication and community engagement occurred concurrently. Therefore, my thesis presents two chapters and a video project, all using excerpts from the interviews and footage and photos from museum archives and the videographer. The two main objectives of this research were communicating the observations of seasonal changes of Utqiaġvik’s spring whaling and centering Inupiat voices and resources. This research embodies significant Indigenous Knowledge and centers hunter and whaler experiences. As an Iñupiaq resident of Utqiaġvik, I hope the research will uplift Indigenous Knowledge and center it in decision-making. Indigenous Knowledge is critical for understanding change in the Arctic.
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Salmon, stewardship, and indigenous livelihoods: bridging knowledge systems and reshaping research relationality in the Kuskokwim Region of southwestern AlaskaThis dissertation research is situated in southwestern Alaska, in the communities of Kongiganak, Quinhagak, Bethel, Aniak, and McGrath, spanning the Kuskokwim Bay and Kuskokwim River, and with Alaska Native Peoples (primarily Yup'ik and Athabascan fishing families) who have been salmon peoples and stewards of their ancestral homelands since time immemorial. This Indigenous-led project documented historical and current ways in which Yup'ik and Athabascan Peoples have served as salmon stewards, and the values and governance mechanisms pertaining to salmon stewardship. We utilized a participatory approach by involving Tribal governments, communities, and Indigenous local youth in all aspects of our research. We carried out multiple methods including: participant observation, circle dialogues, and individual and multigenerational fishing family interviews with Kuskokwim fishers in the coastal, lower, middle, and headwater communities of the Kuskokwim Region. We used a grounded theory approach to qualitative data analysis that generated five key themes that form the first chapter of this dissertation including: traditional Indigenous ways of life, Indigenous stewardship, self-determination, food and livelihood sovereignty, and ecosystem changes. This chapter identified equitable and sustainable paths forward for salmon and people in Alaska. Chapter two of this dissertation bridged perspectives and experiences around the state of salmon management and research, with a focus on Alaska Native inclusion in these processes and organizations, equity, equality, and relationships. Lastly, the third chapter of this dissertation research highlights the methodologies utilized in this research process, with an emphasis on circle dialogues as a core methodology for building initial relationships and partnerships between Tribes and universities, and as a mechanism to shape the research in a way that is aligned with Tribal priorities and respecting Tribal sovereignty. This chapter highlights the importance of including local Alaska Native youth in research, spending time in community and building relationships, because it is these relationships that serve as a core foundation for carrying out research in a 'good way'.
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Addressing non-stationary fishery dynamics and demographic complexity in integrated stock assessment modelsIntegrated stock assessment models are complex non-linear statistical models that fit a variety of fishery-dependent and independent data sources to estimate the status and trends of fish populations, providing recommendations for sustainable harvest levels. Given their complexity, simplifying assumptions are necessary in stock assessment models to balance model parsimony versus complexity, while also considering data limitations. In this dissertation, I investigated considerations for addressing non-stationary fishery dynamics and evaluated the consequences of oversimplified assumptions of fishery dynamics and sex-specific demography in stock assessment models. Using Alaska sablefish (Anoplopoma fimbria) as a case-study, I developed a generalized framework to standardize fishery-dependent abundance indices, while incorporating various data sources and catch records from multiple gear types to address rapid shifts in fishery fleet structure (Chapter 2). Building on this foundation, I then explored the implications of accounting for, or ignoring, complex temporal changes in fishery fleet structure in stock assessment models by comparing multi-fleet and single-fleet models (Chapter 3). Here, I found that the treatment of fleet structure generally had minimal impacts on quantities of management interest, but selectivity assumptions had large impacts on recommended harvest levels. I then employed a generalized simulation-estimation framework to evaluate the performance of different stock assessment approaches for addressing changes in fleet structure (Chapter 4), which suggested that single-fleet models with time-varying selectivity are adequate for accounting for changes in fleet structure. To understand the consequences of oversimplified assumptions of sex-specific demography in stock assessment models, I developed a simulation estimation framework (Chapter 5), which revealed that such simplifications led to suboptimal management advice. Collectively, this dissertation underscores the various approaches available for addressing non-stationary fishery dynamics, the importance of biologically motivated models that adequately reflect a population's demographic characteristics, and the necessity of expert judgment in stock assessment models given the constraints of data limitations.
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Stable isotope analyses of eye lenses and stomach-content analysis reveal ontogenetic variation in arctic whitefish trophic dynamicsDetermining the ontogenetic trophic ecology of sympatric, morphologically similar fishes is critical for increasing our understanding of life history. We combined bulk and amino acid compound-specific stable isotope analysis of eye lenses with stomach-content analysis to examine ontogenetic trophic dynamics of four amphidromous whitefishes (Arctic Cisco Coregonus autumnalis, Least Cisco C. sardinella, Broad Whitefish C. nasus, Humpback Whitefish C. pidschian) from the central Beaufort Sea, Alaska. Compound-specific stable nitrogen isotope results showed slight increases in trophic position across ontogeny for each species and indicated the feasibility of this method for comparing the trophic ontogenetic development of closely related, mobile predator species. Bulk δ15N and δ13C ontogenetic timelines were reflective of an amphidromous geographic life-history strategy, where foraging occurs primarily in freshwater habitats early in life and nearshore marine habitats at larger sizes. Stomach-content analysis revealed that diet was dominated by a single prey item (amphipods) in all four species, but that short-term diets differed for five of six pairwise species interactions (only Arctic and Least Cisco had diet compositions that overlapped). This was the first study to compare trophic ontogenies of multiple fish species through eye lens compound-specific stable nitrogen isotope analysis. Trophic dynamics were similar among whitefishes from the central Beaufort Sea, highlighting the vulnerability of this ecologically and culturally important clade.
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Unlocking over a decade of insights: large bull shark (Carcharhinus leucas) movement behaviors in the Western North Atlantic OceanMarine predators, particularly elasmobranch species like bull sharks (Carcharhinus leucas), play crucial roles in maintaining marine ecosystems but face threats due to anthropogenic impacts and global climate change. Management and conservation of these species incorporate an understanding of their movement behaviors and spatial distribution, which is currently understudied for large bull sharks in the Western North Atlantic (WNA). Therefore, this thesis focuses on understanding bull shark movement patterns in the WNA, including pregnant females. We first examine the movement behaviors of bull sharks from 2009 to 2023 using extensive passive acoustic telemetry data from the Bimini Biological Field Station (BBFS) and its collaborators. Network analysis of acoustic detections revealed partial migration, based on the presence of mobile and resident clusters of bull sharks in the WNA, which are theorized to represent behavioral contingents. The presence of contingents is thought to influence the resilience of populations by spreading risk from external threats, but on the other hand may also increase the risk of localized depletion from fishery pressure. Additionally, this research qualitatively examined the movements of pregnant bull sharks. By determining the locations of pregnant individuals during the theorized pupping window, we were able to infer pupping locations and identify differences in the regional dispersal of individuals that gave birth in either the Gulf of Mexico or the Atlantic Ocean. Furthermore, three female bull sharks exhibited site fidelity behavior to waters near Bimini, The Bahamas, as they returned annually following a seasonal migration during both pregnant and non-pregnant periods, suggesting Bimini is a seasonally important area for mature female bull sharks of all reproductive stages. Overall, the findings of this research provide valuable insights into the movement dynamics of bull sharks, which may contribute to conservation and management strategies.
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Development of a Bayesian framework for Canadian-origin Yukon River Chinook salmon inseason abundance projection and the exploration of run timing information on run size projection accuracyThe Yukon River is the longest river in Alaska, stretching 3,700 km from British Columbia, Canada to the Bering Sea. Chinook salmon (Oncorhynchus tshawytscha) harvest in the U.S. portion of the river is managed by the Alaska Department of Fish & Game (ADF&G), which requires robust inseason abundance predictions for returning Canadian-origin Chinook salmon to regulate fisheries and comply with the Yukon River Salmon Agreement. Chinook salmon returning to the Yukon River are an important resource for residents of the region; however, in recent years little-to-no harvest opportunity has been available due to low run sizes which are complicated by a high degree of uncertainty in annual run size predictions. Currently, the ADF&G treats the preseason run size forecast separately from inseason run size projections based on information collected at the Pilot Station Sonar (PSS) and Eagle Sonar projects. As a result, the ADF&G inseason projection methods may not fully account for uncertainty in the data or the increase in precision and accuracy of inseason information relative to preseason forecasts as the season progresses. To address lack of integration between preseason and inseason projections, I implemented a Bayesian updating approach where preseason forecasts for Canadian-origin Chinook salmon are updated with inseason sonar passage information to project the total end of season abundance. I explored differences in inseason projection accuracy among multiple methods for relating PSS and Eagle Sonar daily passage to the season total Canadian-origin Chinook salmon abundance, as well as genetic stock identification data collected at PSS. Next, I developed a run timing model based on environmental covariates, to address uncertainty in abundance projections associated with interannual variation in run timing. I found that treating the preseason forecast as a prior and updating it daily with inseason passage observations resulted in more accurate projections of the season total Canadian-origin Chinook salmon run size and that run timing information did not improve run size projection accuracy.
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Early life biology and ecology of king and tanner crabs in the Bering and Chukchi seasPelagic larvae and early benthic juveniles are believed to be the most vulnerable life stages for crabs. Where and when young crab occur and their response to environmental conditions is poorly understood. I present two case studies that demonstrate the importance of monitoring crab early life stages of economically and ecologically important species in the Bering and Chukchi Seas. First, collapsed fisheries and poor juvenile recruitment are recurring issues for many Alaska king crab stocks. Among the most notable examples, Pribilof Islands blue king crab is a federally overfished stock that has failed to rebuild after decades of conservation. Comparison of field assessments from modern and historical periods suggests a current bottleneck in larval supply, severely limiting blue king crab recruitment. Supplementary assessments showed available nursery habitats and fish predation pressure do not appear to be limiting for juvenile king crabs. Blue king crab are unlikely to recover by natural means, therefore juvenile enhancement may be an appropriate tool for possible restoration. Second, larval crab dispersal during the pelagic life phase is relatively unknown across the Pacific Arctic. A multiyear study of larval crab abundance and distribution during late summer months, and their association with environmental covariates, was completed for the north Bering and Chukchi Seas. Larval community structure varied strongly across regions from south to north and many species and stages had specific associations with coastal or offshore water masses. Snow crab larvae were relatively abundant and ubiquitous across the study region and appear to originate from both Pacific and Arctic spawning stocks. Blue king crab larvae were relatively rare in the Chukchi Sea and likely dispersed away from north Bering Sea natal areas. Larvae likely experience increased growth rates and northward dispersal in warm years, which could impact delivery to and survival of settling crabs in nursery habitats. Across analyses, these results improve our understanding of early life dispersal, settlement processes, and possible recruitment bottlenecks for Arctic crab stocks.
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Synergistic effects of climate and invasions: a case study of juvenile Pacific salmon and their introduced freshwater predator (Esox lucius) in a changing Alaska riverClimate change and invasive species are major individual drivers of declines in freshwater productivity and diversity, yet the potential for these factors to interact is poorly understood. I explored the synergistic effects of climate change and invasion to better understand observed changes in a freshwater community comprised of socially valuable salmonid fishes. I modeled daily predation and annual consumption of juvenile salmon by an introduced apex predator, Northern Pike (Esox lucius), as a function of time, streamflow, water temperature, and Northern Pike demography in a rapidly warming system in Southcentral Alaska. I hypothesized that Northern Pike predation would shift from juvenile salmon to alternative prey as a function of progressed invasion and that salmon predation would peak during species-specific out migrations. I also hypothesized that predation on juvenile salmon would be positively correlated with streamflow because high water would cause juvenile salmon to seek refuge in off-channel habitats instigating interaction with Northern Pike. Daily predation and annual consumption of Northern Pike in this system have shifted away from salmon-dominated to dominated by resident fishes over the past decade (2011 to 2022). Streamflow was positively correlated with daily predation on juvenile Chinook Salmon and total Oncorhynchus species in diets. Between 2011-2012 and 2021-2022 the population of Northern Pike shifted to younger individuals with increased growth. Estimates revealed that annual consumption of Chinook Salmon and Coho Salmon by Northern Pike decreased between time periods. Bioenergetic simulations revealed increases of 6 to 12.5% in total per capita consumption of prey by Northern Pike under end of century scenarios. These findings collectively suggest that Northern Pike have switched to alternative fish prey as salmon declined. Seasonal high streamflows and increased water temperature consistent with observed and predicted climate change in Southcentral Alaska appear to increase predation rates on juvenile Chinook Salmon by Northern Pike, while patterns in predation for juvenile Coho Salmon are more uncertain. Predicted future temperatures may increase total consumption of Northern Pike enough to appreciably increase mortality of salmon exacerbating changes in species composition and community structure and further jeopardizing struggling salmon runs. These findings suggest that invasive predators may also become more impactful in other systems undergoing rapid climate change.
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Improving species identification, age, and life history information for shortraker rockfish (Sebastes borealis) in Prince William Sound, Alaska, using sagittal otolith analysesShortraker rockfish (Sebastes borealis) are a long-lived species found in the North Pacific Ocean. Limited life history information compels fishery managers to apply conservative estimates of allowable bycatch for this species. To improve the available life history information, we analyzed sagittal otoliths, targeting fish from Prince William Sound, to assess (1) age estimation errors, (2) species misidentification, and (3) relationships between environmental factors and annual growth. To assess errors in age data, otoliths were analyzed for core Δ¹⁴C activity. Those values were compared with bomb radiocarbon reference curves for other North Pacific species (i.e., known age Pacific halibut, Hippoglossus stenolepis, and yelloweye rockfish, S. ruberrimus). Shortraker rockfish Δ¹⁴C activity followed reference curves, partially validating current age estimation techniques. To identify species, otolith shape analyses were performed on putative shortraker and rougheye rockfish (S. aleutianus). Clusters of shortraker, rougheye, and blackspotted rockfish (S. melanostictus) data were identified using random forest algorithms and otolith wavelet estimates. Misidentification rates were examined using out-of-sample error estimates and otoliths from fish whose species was validated using single nucleotide polymorphisms. Model classification errors suggest that historically assigned species were accurate and shortraker rockfish can be identified with 94% success. To investigate potential drivers of fish growth, a chronology of shortraker rockfish otolith increment widths was developed and related to environmental variables using dendrochronology methods. Model comparisons showed significant correlations between annual increment widths (i.e., an indicator of fish somatic growth) and environmental variables, specifically negative correlations with winter temperature at depth, spring surface salinity, and the North Pacific Gyre Oscillation, and positive correlations with spring and winter upwelling and the Pacific Decadal Oscillation 2-years earlier. These three analyses validate and improve data and life history information and support incorporating age and growth data into stock assessment models used to calculate allowable bycatch levels for shortraker rockfish.
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Summer ecology and behavior of the grayling of McManus Creek, AlaskaA study of the summer ecology and behavior of the Arctic Grayling was undertaken on the summer population of McManus Creek, Alaska. An effort to determine the distribution and the patterns of the fish’s movements in the stream was made. The grayling spent the summer months in pools where they established feeding territories. Within each feeding territory a feeding range, where all feeding activities took place, was found. In each pool a hierarchial ordering based on a dominant subordinate relationship existed. This hierarchy was established and maintained by a series of displays. The grayling of McManus Creek were found to feed solely on the surface and at mid-depth. The food items consisted both of flying insects and aquatic insects, the latter making up the largest portion of their diet. It appeared that the fish relied primarily upon benthic drift for nutrition. Being visual feeders, the fish were unable to utilize the large numbers of organisms known to drift during periods of high and muddy water.
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Relative abundance and movement ecology of tiger sharks Galeocerdo cuvier in the waters surrounding Bimini, the BahamasShark populations are under increased anthropogenic pressures around the world. Large-bodied shark species are upper trophic level predators, and therefore there is concern that declining numbers of sharks may have significant implications for ecosystems. In response to these conservation concerns there has been increased focus on the implementation of regulations, fishery management plans, national plans of action, and marine management zones in some nations. However, large sharks are often highly mobile and can move readily across jurisdictional boundaries. Therefore, there is a need to monitor long-term relative abundances within regions and simultaneously examine the duration to which species remain in these areas. The Bahamas was established as a 'Shark Sanctuary' in 2011, but long-term abundance and movement data are lacking for many species. The goal of this study is to determine the relative abundance and movement ecology for tiger sharks Galeocerdo cuvier in the waters around Bimini, The Bahamas. Fishery independent ongline surveys from 1984 to 2019 suggest that the local relative abundance remained stable during this time. Gear selectively prevented direct comparisons of catch rates to other surveys, but for context abundance trend were analyzed from the directed shark fishery in the nearby southeastern USA, which interacts with the same population of tiger sharks. This analysis showed an increasing abundance trend in USA waters during the late 1990s and early 2000s, after which abundances stabilized. Conventional tagging and passive acoustic and satellite telemetry were used to determine residency, regional movements, and long-term philopatry of young-of-the-year to mature tiger sharks. Overall data for juveniles were sparse, likely due to constraints of energetic condition and high natural mortality. Large juvenile and mature tiger sharks displayed seasonal local residency that was negatively correlated with water temperature, but also dispersed widely throughout the region, and spent significant time outside of Bahamas territorial waters. Taken together, these results highlight that localized conservation measures offer some level of protection for tiger sharks, however they do spend time in multiple jurisdictions and regional cooperation on management plans is important.
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Estimating relative indices of groundfish abundance from multiple fishery-independent data sources: a comparison of intercalibrating model-based abundance estimatorsStock assessments are critical tools for sustainable fisheries management, and abundance indices estimated from fishery-independent data represent a crucial data source for these assessments. However, financial constraints on these surveys limit the number of samples taken per year, and/or the frequency with which regions are sampled. Additionally, it remains challenging for any individual survey to sample the entire domain of a stock due to contact-selectivity of the sampling gear and the accessibility of specific habitats to specific gear types. Further, the cost of operating fishery-independent surveys can result in surveys conducted on biennial or triennial schedules, resulting in temporal gaps in survey timeseries that may limit their ability to adequately index short lived species. One method by which these challenges might be addressed is through the use of model-based estimators, which estimate relative and/or absolute indices of abundance by intercalibrating data collected by multiple surveys with different spatial, temporal, or habitat footprints. While recent research has explored a number of potential applications of these methods, little to no prior research has assessed the relative performance of these methods in terms of the accuracy or uncertainty of their estimates. In the first chapter of this thesis, I fit Random Walk Timeseries (RWTS) models, Generalized Additive Models (GAM), and Vector Autoregressive Spatiotemporal Models to data collected by three fishery-independent surveys across four species/region case studies, and compare the model-estimated indices to design-based indices estimated by the Alaska Fisheries Science Center (AFSC) Bottom Trawl Survey (BTS) as a reference abundance timeseries. In the second chapter, I then simulate an age-structured and spatially heterogenous population dynamics for the Pacific Cod (Gadus macrocephalus)) stock in the Gulf of Alaska, to explore the reliability of intercalibrated indices of abundance. To do so I generate artificial survey catch data for three fishery-independent surveys, fit GAM and VAST survey intercalibration models, and then assess the accuracy and precision of the model-based indices. Results from the real species-region case studies in Chapter 1 suggest that RWTS, GAM, and VAST models all exhibit comparable performance, but the model structures used in this analysis struggled to estimate indices of abundance consistent with established abundance estimates in the presence of conflicting survey catch-rate signals. Results from the simulation experiment in Chapter 2 also suggest that the accuracy of the model-estimated indices is strongly influenced by the level of contrast in the size-selectivity profiles of the constituent surveys, and the rate at which the size-composition of the surveyed stock changes. I recommend that future work explores forms of these model-based estimators which estimate size-specific changes in abundance, and whether or not the inclusion of those elements improved the accuracy and precision of the estimated indices of abundance.
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When beavers get burned, do fish get fried? The role of beavers to mediate wildfire effects on arctic grayling in boreal AlaskaWildfire is a dominant natural disturbance process throughout boreal North America and fires are increasing in size, frequency, and severity. However, little is known about how wildfire affects boreal fish populations and aquatic habitat despite the substantial impacts of fire on ecosystem processes, and even less is known about how fire effects are mediated by species interactions. For example, North American Beavers (Castor canadensis) are affected by and can influence wildfire dynamics, and their engineering has complex effects on aquatic habitats. North American Beavers therefore have the potential to mediate wildfire effects on aquatic ecosystems and fish populations. Here I investigated relationships between wildfire and the distribution of beavers and a common fish species across a fire-dominated riverscape in Interior Alaska. First, I used satellite imagery to locate and enumerate beaver ponds throughout five large watersheds (total area: 20,711 km²) and modeled the relationship of beaver pond density (ponds per km²) as a function of wildfire history, stream geomorphology, hydrology, and vegetation composition. I then used a simulation to conceptualize the impacts of wildfire and beaver dams on Arctic Grayling (Thymallus arcticus) habitat availability under variable hydrologic conditions. Next, I sampled 62 streams for Arctic Grayling environmental DNA (eDNA) and sampled 10 of those streams for Arctic Grayling abundance. I used a generalized linear model (GLM) and N-mixture model to understand the relationship between eDNA concentration and Arctic Grayling abundance and distribution throughout the study area. I found that wildfire metrics explained most variation in beaver pond density (pseudo R² = 0.75) across the landscape and were positively associated with beaver pond density, although geomorphological and hydrological parameters were also important. My simulations indicated that beaver dams can create substantial barriers to fish dispersal during low water conditions (up to 20% reduced habitat availability in some river basins) and can severely reduce (up to 65%) habitat availability in some tributary streams. I found that eDNA concentration was moderately correlated with Arctic Grayling abundance (GLM: pseudo R² = 0.45) and unexplained variation was likely due to the spatial mismatch between fish sampling and scale of eDNA representation. However, I estimated eDNA residence time of about 6.7 hours in one stream, and eDNA appeared to accumulate longitudinally throughout the tributary, indicating that an eDNA sample near the downstream end was likely a good relative representation of Arctic Grayling abundance in a tributary. Results from the N-mixture model indicated that stream geomorphology and hydrology were the most important predictors for Arctic Grayling abundance (eDNA concentration), wildfires had a negative effect, and beaver dam density had a mixed effect on Arctic Grayling abundance. Overall, this study illustrated that beaver densities can increase after wildfires in Interior Alaska stream networks, which could result in negative impacts on Arctic Grayling habitat availability if beavers impair fish passage; however, these effects are dependent on the environmental context and suggest beaver-fish interactions may be best managed on a case-by-case basis.
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Model-based estimation of juvenile salmon spatial ecology in the eastern Bering Sea, AlaskaQuantitative descriptions of juvenile salmon spatial ecology during the marine phase of their lifecycle are needed to help direct conservation efforts and uncover latent relationships between juvenile salmon and their environment. The NOAA Fisheries Essential Fish Habitat (EFH) program contributes to the conservation of species in the marine waters off of the coast of Alaska by identifying areas of particular importance to reproduction and growth. Salmon EFH definitions have not yet been updated using the species distribution modeling approach taken most recently in defining Alaska groundfish and crab EFH. Current EFH definitions for Alaskan salmon are geographically broad, do not quantitatively describe relationships between marine conditions and salmon, and lack estimates of uncertainty. This research estimated static (time-averaged) and dynamic (time-varying) juvenile salmon distributions in the eastern Bering Sea (EBS) by fitting species distribution models (SDMs) to fishery-independent survey data and environmental indices spanning the years 2002-2019. Following model selection, species distribution maps were generated using predictions based upon the best-performing static and dynamic models to inform EFH definitions for the juvenile life stage. In Chapter 1, roughly parallel nested model structures were fit within two SDM frameworks: generalized additive models (GAMs) and Vector Autoregressive Spatio-temporal (VAST) models. Results from Chapter 1 indicate that while there was evidence for spatial variation in juvenile salmon distributions through time, this variation was encompassed by the EFH boundaries predicted by static models. In terms of performance, GAM and VAST frameworks were largely comparable, although VAST models appeared to be more robust to issues associated with spatial imbalance in survey data. In Chapter 2, nested GAM model structures tested the influence of environmental covariates on variability in the abundance and/or distribution of five species of juvenile Pacific salmon in the EBS. Model selection results and mapping indicated that in-situ environmental covariates significantly influenced abundance of juvenile salmon, while annual covariates significantly influenced the distributions of juvenile salmon. Center of gravity estimates found some evidence for species distribution shifts inshore/offshore and to the north/south in response to specific hindcast environmental conditions. This work might be leveraged to update current salmon EFH definitions and inform future model-based conservation efforts.
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Uncovering patterns and mechanisms of paralytic shellfish toxicity in Alaska's geoduck clam fisheryThis dissertation explores the patterns and mechanisms of paralytic shellfish toxicity in commercially harvested geoduck clams caused by the toxin-producing dinoflagellate Alexandrium catenella in Southeast Alaska. Alaska's commercial fishery for geoduck clams (Panopea generosa) is a small but lucrative fishery, with annual ex-vessel values averaging US $3.9 million (2010-2022). In recent years, the presence of paralytic shellfish toxins (PSTs) in clam tissue resulted in declines in fishery openings and harvest. PSTs can bioaccumulate in the tissues of filter feeders when A. catenella blooms in the spring and summer seasons. However, high levels of toxicity in geoduck clams occur sporadically during the fishery in the fall and winter months long after toxic blooms have subsided. Levels of PSTs in geoduck clams vary substantially from week-to-week, and elevated PSTs are increasingly causing economic loss to the fishery through sampling costs from repeated testing and by delaying or closing harvests. In the past decade (2011-2021), about 60% of geoduck clams tested for PST failed regulatory screenings, up from a 36% failure rate in the decade prior (2001-2010). Knowledge about patterns and distributions of this harmful algal species and its toxins will help improve management of geoduck dive fisheries and provide information to reduce impacts of PSTs on this fishery. In Chapter 1, Patterns in geoduck clam paralytic shellfish toxicity from two decades of shellfish testing in southeast Alaska, we show that geoduck clams are increasingly failing biotoxin screening tests in some areas and these patterns are most closely correlated with regional air temperatures. In Chapter 2, Alexandrium catenella benthic cyst distribution, sediment characteristics, and geoduck clam (Panopea generosa) toxicity in Southeast Alaska, we provide the first A. catenella cyst distribution map for this region and found that cyst counts declined over the three-year study, but patterns were not related to geoduck PST levels or sediment characteristics. Lastly in Chapter 3, Geoduck clam (Panopea generosa) toxicity dynamics across harvest areas, time, age, and cyst gut content in Alaska's commercial fishery, we confirmed the ability for geoduck clams to ingest dormant A. catenella cysts but revealed that neither this process, nor the age of a clam, is directly related to patterns of paralytic shellfish toxicity in this clam species. All together, these findings lead to a better understanding of the variability of PSTs in geoduck clams and are informative to future fishery management and the protection of human health.
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The role of apex predators, habitat, and seascape complexity on nearshore fish assemblages in Southeast, AlaskaNearshore marine ecosystems contain dynamic and complex submerged vegetated habitats that offer shelter and prey for juvenile, migratory, and residential species, including many commercial, subsistence, and recreationally important species. The efficacy of the nursery role, shelter, and source of prey of the nearshore is influenced by various abiotic and biotic forces and in this dissertation, we examine the influence of submerged vegetation type, presence of apex predators, and the seascape context on patterns of nearshore fish assemblages in southern Southeast Alaska. We found species-specific responses by juvenile salmon in the nearshore, with seasonality overwhelmingly driving juvenile salmon abundance in eelgrass meadows and Chum Salmon present in greater abundance in understory kelp beds compared to eelgrass meadows, whereas Pink Salmon exhibited no difference. As a known apex predator, the reintroduction of sea otters likewise altered the nearshore fish assemblage with increased richness in eelgrass meadows and assemblage-wide shifts in understory kelps. Finally, in addition to habitat type and apex predators, spatial patterning and presence of adjacent vegetation can affect the nursery role of nearshore habitats. We observed differences in the fish assemblage in eelgrass meadows sampled in homogeneous seascapes with continuous eelgrass meadows and heterogeneous seascapes that included adjacent habitats, including more abundant commercial and forage species in heterogeneous seascapes. This research reinforces the importance of nearshore ecosystems in supporting robust fisheries and highlights the structuring role that submerged vegetation, apex predators, and complex seascapes have in sustaining diverse fish populations. Considering the greater ecological dynamics in the nearshore is vital for decision making in habitat conservation and management and for evaluating its role for fisheries, particularly in the context of increased threats to nearshore ecosystems.
