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  • Identification of spawning areas and the influence of environmental variation on freshwater migration timing and in-river movements of adult coho salmon in the Buskin River, Alaska

    Stratton, Michelle Eileen; Westley, Peter; Finkle, Heather; Falke, Jeff (2019-08)
    The timing of freshwater entry by anadromous salmonids varies markedly among species and populations within species and is frequently used as an indicator of local adaptation to sitespecific patterns of selection. Although complex stock structure is most often associated with large watersheds that have extensive habitat diversity, even small drainages can produce multiple co-occurring stocks that differ in migratory timing. In addition, migration timing can be influenced by within-year environmental conditions experienced by migrating individuals en route to spawning sites, staging near the river mouth in the ocean, or within the river itself. Each stage of migration through both freshwater and saltwater could be altered based on climatic drivers and how each individual fish reacts to these stressors. The objective of this thesis was to assess the potential for stock structure in Coho Salmon within a small coastal watershed on Kodiak Island, Alaska by 1) identifying important differences in spawning and holding locations associated with run timing, length, and stream life between main stem and tributary spawners, 2) quantifying the influence of large-, intermediate-, and local-scale climate variables on freshwater entrance timing and in-river movements. To address the first objective, fish were tracked to their spawning locations using acoustic telemetry in three spawning seasons (2015-2017). I detected no statistically or biologically meaningful differences in body size (length, mm) or migration timing into the river between main stem and tributary spawning fish. Unexpectedly, I found that a large portion of fish (80%) utilize the lake during their in-river migration suggesting the lake may represent critical staging habitat for adult Coho Salmon prior to spawning. I also identified holding habitat throughout the river that both spawning groups consistently used across years that also appears to be important to premature migrating Coho Salmon. In Chapter Two, I analyzed 33 years of freshwater entrance timing data and utilized radio tags to track in-river movement to quantify the influence of precipitation and temperature on total distance moved and probability of moving. Despite marked variation among years, I found no evidence of a temporal trend in entrance timing based on escapement counts, which contrasts with other recent examples throughout Alaska reporting changes in run timing. The strongest influence on timing of freshwater entry was ocean sea surface temperature, where cold temperatures delayed entry up to 11 days. Within-river movements were positively related to precipitation and temperature, confirming local traditional knowledge in this system, and consistent with life history patterns of Coho Salmon. The primary messages of this thesis are that i) any within-watershed stock structure is unlikely to be differentially affected by harvest or management given overlapping run timing, body size, and use of main stem holding areas; future population genetics analyses would be an obvious and illuminating next step to assess the extent to which main stem and tributary spawners are reproductively isolated groups; ii) both main stem and tributary spawners use Buskin Lake as holding habitat prior to spawning, and thus assumptions that fish that enter the upper watershed are destined to spawn in headwater tributaries are invalid, which in turn limits the utility of enumerating adult passage into the lake for escapement-based management, iii) adult freshwater entrance timing is highly variable but not changing systematically through time, though the extent to which the variation in timing reflects environmental response vs. uncertainty in the counts at the weir is unknown, and iv) low precipitation and warm temperatures suppress movement and result in protracted use of main stem and lake habitats for holding, which may put some individuals at risk to angler harvest or, in extreme events, potentially low dissolved oxygen environments. Spatial management that restricts fishing in locations of known primary holding habitats may be an option to reduce probability of mortality and stress in years of low adult abundance.
  • Whale-watching in Juneau, AK: assessing potential effects on humpback whales and understanding passenger perceptions

    Schuler, Alicia Rinaldi; Pearson, Heidi C.; Atkinson, Shannon; Mueter, Franz J. (2019-08)
    The feeding grounds of the North Pacific humpback whale (Megaptera novaeangliae) in Juneau, Alaska have rapidly developed into a popular whale watch destination during the summer (May-September). The whale watch industry has tripled in size in the last 18 years, currently numbering approximately 65 vessels. The sustainability of this industry could be jeopardized if the health and dependability of the resource, the whales, is negatively affected by increasing vessel pressure. The aim of this project is to provide a holistic understanding of whale watch tourism in Juneau by assessing 1) humpback whale responses to whale-watching vessels and 2) passenger experiences as a conduit for conservation of whales and the environment. Data were obtained during 2016 and 2017, comprising observations of 201 humpback whale groups and collection of 2331 passenger surveys. To address the first objective, shore-based measurements and observations of humpback whales were conducted to assess potential impacts of whale-watching vessels on short-term movement and behavioral patterns of whales. Linear mixed effects models indicated that the presence (vs. absence) of vessels was related to significantly higher deviation in linear movement, increased swimming speed, and shorter inter-breath intervals (IBI). For each additional vessel present, deviation increased and IBI significantly decreased. Linear regression models also indicated that as time spent in the presence of vessels increased, respiration rate (breaths per minute) increased. Markov chain analyses indicated that feeding and traveling humpback whales were likely to maintain their behavioral state regardless of vessel presence, while surface active humpback whales were likely to transition to traveling in the presence of vessels. To address the second objective, surveys were administered to passengers before, immediately after, and six months after a whale-watching tour to measure knowledge, intentions, behaviors, and attitudes over time. Following a whale-watching tour, awareness of whale-watching guidelines/regulations doubled and support for guidelines/regulations significantly increased and remained high six months later. Binomial logistic regression models determined that strong support for guidelines/regulations was more likely if participants were aware of guidelines/regulations and less likely if participants disagreed that vessels have a negative impact on whales. Lastly, linear regression models revealed that participants that acknowledged human impacts on whales and their habitat had stronger pro-environmental attitudes. As vessel presence increases in this region, adherence to whale watching guidelines/regulations is likely to become increasingly important to mitigate cumulative effects that may arise from short-term changes in whale behavior in a changing environment. It is recommended that management revisit the current measures in place to better suit the industry today, and that education during whale watching tours be included as a potential management tool to encourage operator compliance. The results presented in this thesis indicate that both management and the industry itself can help to develop a mutually beneficial industry for the whale watching operators, the whales, and the people that come to watch them.
  • Evaluation of marine and freshwater growth and survival of Auke Creek coho salmon

    Russell, Joshua R.; Tallmon, David; McPhee, Megan; Adkison, Milo; Vulstek, Scott (2019-08)
    Coho Salmon (Oncorhynchus kisutch) are a species of great social and economic importance for commercial, sport, personal-use, and traditional harvest. We explored factors influencing Auke Creek Coho Salmon smolt production, growth, and marine survival. We analyzed 35 years (1980-2014) of data collected at the Auke Creek Research Station weir in Juneau, Alaska. This extensive data series allowed for an analysis of Auke Creek Coho Salmon growth and survival that is not possible elsewhere. Creek flow best explained variation in smolt-per-adult production. Analysis of freshwater and saltwater scale growth zones failed to identify a specific growth zone with a significant influence on marine survival. Marine survival had a positive relationship with the magnitude of regional hatchery releases and the Pacific Decadal Oscillation. Changes in climate and hatchery production could have negative effects on survival of Auke Creek Coho Salmon, as evidenced by low returns in recent years associated with anomalously high temperatures in the Gulf of Alaska. The impact of climate change and increased hatchery production should be considered in future management decisions.
  • The response of juvenile coho and chinook salmon stocks to salmon spawner abundance: marine nutrients as drivers of productivity

    Joy, Philip J.; Wipfli, Mark S.; Adkison, Milo D.; McPhee, Megan V.; Stricker, Craig A.; Rinella, Danial J. (2019-08)
    Resource subsidies from spawning Pacific salmon (Oncorhynchus spp.) in the form of marine-derived nutrients (MDN) benefit juvenile salmonids while they rear in fresh water, but it remains unclear if the abundance of spawners in a watershed affects the productivity of salmon stocks that rear in those riverine systems. This dissertation aimed to provide a better understanding of these dynamics by evaluating whether the response of juvenile salmon to MDN is sufficient to enhance overall stock productivity. In Chapter 1, I examined correlative relationships in the abundance of Pink (O. gorbuscha) and Coho (O. kisutch) salmon and simulated spawner-recruit dynamics to determine if those correlations were produced by a Coho Salmon response to marine subsidies from Pink Salmon, a shared response to marine conditions, and/or autocorrelations in the returns of both species. Results demonstrated that observed correlative patterns most closely resembled simulated freshwater effects, providing evidence that marine subsidies from Pink Salmon influence Coho Salmon productivity. In Chapter 2, I examined the relationship between spawner abundance and MDN assimilation by juvenile Coho and Chinook (O. tshawytscha) salmon in the Unalakleet River watershed. Stable isotope analysis demonstrated that after salmon spawned, MDN assimilation by juvenile salmon in the fall was a function of adult Pink and Chinook salmon spawner abundance, regardless of the habitat occupied by rearing juveniles. However, by the following summer, high retention of MDN in complex habitat masked seasonality of MDN assimilation in sloughs and river sections with abundant lentic-lotic exchanges. As such, MDN assimilation in the summer (prior to arrival of spawners) bore only a faint relationship to spawner abundance and distribution from the previous year. In chapter 3 I examined the relationship between MDN assimilation (Chapter 2) and juvenile salmon growth, size, body condition, and abundance. Prior to salmon spawning, residual MDN from past years offered little advantage to juvenile salmon. However, after the arrival of spawning salmon, MDN enhanced juvenile salmon size, growth, and condition in fall and winter. The collective results from this dissertation thus provides compelling evidence that MDN from spawning Pink Salmon may enhance the productivity of Coho and Chinook salmon. Management agencies should explore modified spawner-recruit models that incorporate MDN relationships to determine if they more accurately describe population dynamics. Where they do, such models may be used to forecast salmon returns and possibly adjust escapement goals (the number of spawners desired on the spawing grounds) to improve maximum-sustained yields (MSY).
  • Commercial fishing livelihoods, permit loss, and the next generation in Bristol Bay, Alaska

    Coleman, Jesse M.; Carothers, Courtney; Donkersloot, Rachel; Adkison, Milo; Greenberg, Joshua (2019-08)
    Fishing people across the globe have experienced a fundamental restructuring of their livelihoods, communities, and economies as the result of shifts to rights-based fisheries management in the past halfcentury. The ideological underpinnings of this movement are based in neoliberalism, which is a belief system that values individualism, competition, private property, and governance by the free market. I examine some of the long-term and latent effects of this and other significant historical transitions in the fishery-dependent Bristol Bay region of Alaska. Relationships between humans and salmon in Bristol Bay evolved over thousands of years and inform the way that many fishing livelihoods are pursued today. In addition to these foundational relationships, many significant changes have occurred that have shocked and stressed the livelihood "fabric" woven many interlocking threads (i.e., the sociocultural, economic, knowledge/skill, political, natural, physical building blocks needed to construct a fishing livelihood in the region). Informed by literature review and ethnography, I describe in detail four such changes: colonization of Bristol Bay's Indigenous peoples, industrialization of the commercial fishery, implementation of a rights-based access regime (i.e., limited entry permit program), and the sockeye salmon price crash of the early 2000s. These effects linger today and raise questions for the future of the Bay and its fisheries, with respect to two particular issues: the uncertainty around the next generation of fishermen, and the severe loss of locally held permits in the Bay. To address the former, I conducted a survey of local students to measure their perceptions of the fishing industry and of community life. The results of this survey suggest that familial fishing ties, experience in the fishery, subsistence fishing activity, and household economic dependence on commercial fishing income are strong predictors of a student's desire to be engaged in commercial fishing as an adult. I examine the second issue--the loss of locally held fishing rights since the implementation of limited entry--through the combined analysis of qualitative ethnographic data and quantitative data on commercial fishery permit holdings, subsistence activity, permit holder age, and new entry trends by community and residence category. The immense loss of limited entry permits continues to challenge livelihoods because access to local fisheries is the foundation of not only the region's economy, but also of the shared identity, history, and culture of local people, family and social networks, and the mechanism by which fishing knowledge, skills, values, and ethics are transferred to the next generation. I suggest that policymakers and fishery managers dispense with neoliberal panaceas, and design fisheries policies that reflect the multiplicity of worldviews held by the policy's target populations by diversifying their own means and methods for understanding fishery systems.
  • Examination of saffron cod (Eleginus gracilis) population genetic structure

    Smé, Noël A.; Gharrett, Anthony; Mueter, Franz; Heifetz, Jonathan (2019-05)
    The Saffron Cod (Eleginus gracilis) is an abundant forage fish that inhabits the coastlines of the north Pacific and Arctic oceans. We examined Saffron Cod population genetic structure to provide a reference baseline in anticipation of human and climate-change alterations of the Arctic environment. Nine microsatellites were designed to describe the genetic compositions of and variation among 40 collections of Saffron Cod from four regions (northwestern Alaska, Gulf of Alaska, Sea of Okhotsk, and Gulf of Anadyr). The northwestern Alaska collections (Bering Sea, Norton Sound, and Chukchi Sea) exhibited little genetic divergence. The Gulf of Anadyr collection differed from other regions but was most similar to those of the northwestern Alaska region. The two collections within the Sea of Okhotsk (Sakhalin Island and Hokkaido Island) differed genetically, but not to the extent they did from other regions. The collections from the Gulf of Alaska (Kodiak Island and Prince William Sound) comprised a lineage that was distinct from all of the other collections, including the geographically adjacent northwestern Alaska collections. The absence of genetic structure among northwestern Alaska collections probably reflects their recent expansion into previously unavailable habitat that became available after the Last Glacial Maximum (~16,000 years ago). The divergence of the Gulf of Alaska lineage may have resulted from recurrent episodes of isolation from previous glaciations.
  • Linking freshwater growth to size-dependent marine survival of sockeye salmon: interactions between processes of climate, density, and natural selection

    Ree, Marta Elizabeth; Westley, Peter; Finkle, Heather; Beaudreau, Anne (2019-05)
    Due to the mediating role of body size in determining fitness, the 'bigger is better' hypothesis still pervades evolutionary ecology despite evidence that natural selection on phenotypic traits varies in time and space. For Pacific salmon (genus Oncorhynchus), the size at which juveniles migrate to sea (i.e., smolts) has been linked to survival during the early marine period, where larger smolts typically survive at a higher rate than their smaller counterparts. However, the relationship of smolt size and survival becomes more ambiguous when considering confounding factors of age, ocean entry timing, and environmental variability. Despite equivocal results, smolt size appears to be a key trait and therefore changes in freshwater conditions may have consequences for population productivity. Furthermore, due to differences in site-specific habitats, trophic dynamics, and population traits the response of specific populations to these changes is likely to be context specific. The objective of this thesis was to 1) quantify the direction and magnitude of natural selection on smolt size for three age classes of sockeye salmon in a small watershed on Kodiak Island, AK and 2) explore stock-specific effects of temperature and conspecific density on smolt size over a multi-decade time-series to understand historic and possible future trends. To address our first objective, we calculated standardized selection differentials by comparing observed size distributions of out-migrating juvenile salmon to back-calculated smolt length from the scales of surviving, returning adults. Results reveal the magnitude of selection on size was very strong and consistent among years. However, the direction of selection on size consistently varied among age classes. The absolute magnitude of selection was negatively correlated to apparent marine survival and positively correlated to late mean ocean entry timing. To address our second objective, we back-calculated smolt size from returning adult scales to reconstruct a time-series of smolt length of two stocks within a small Alaska watershed on Kodiak Island. Using a dynamic linear model framework, we detected evidence that for one stock, temperature was important in explaining smolt length, and density effects influenced both stocks utilizing the same lakes. Furthermore, forecasts of smolt length showed highly variable responses under scenarios of increasing temperature and high and low densities. Collectively, these results demonstrate that interactions between processes of climate, density, and natural selection are highly context-specific in terms of both inter- and intra- population variability.
  • Evaluating potential age structures for three Alaska crustacean species

    Rebert, April L.; Kruse, Gordon; Webb, Joel; Tamone, Sherry (2019-05)
    Banding patterns are observed in calcified structures of red king crab (Paralithodes camtschaticus), snowcrab (Chionoecetes opilio), and spot shrimp (Pandalus platyceros). Recent research supports an age determination method based on these banding patterns; however, processing methodologies for these structures have not been established. Further, species-specific evidence is needed to determine whether these patterns indicate actual age or growth. The objectives of this thesis are to: (1) describe optimal species-specific methods for producing and evaluating band counts for red king crab, snow crab, and spot shrimp; and (2) use differences in shell condition to test whether band counts indicate age for snow crab. For each species, we comprehensively thin-sectioned structures, evaluated each section for banding pattern presence (readability), and developed band count criteria. To address objective 1, we used generalized additive models to describe readability across structures to find the location that optimizes the production of readable sections. For objective 2, we used a one-way ANOVA to compare band count and endocuticle measurements among shell conditions in snow crab. Results indicated preferred structures, locations, section orientation, and thickness. Results also indicated that there is no relationship between band count and shell condition for terminally molted snow crab. These results describe optimal methods for processing crustacean structures and suggest that the potential age structures may not continue to produce bands after terminal molt in the case of snow crab. Further evaluation is needed to validate potential age relationships and the use of this technique for age estimation.
  • Multi-scale movement of demersal fishes in Alaska

    Nielsen, Julie K.; Seitz, Andrew C.; Loher, Timothy; McDermott, Susanne F.; Mueter, Franz J.; Adkison, Milo D. (2019-05)
    Information on the movement of migratory demersal fishes such as Pacific halibut, Pacific cod, and sablefish is needed for management of these valuable fisheries in Alaska, yet available methods such as conventional tagging are too coarse to provide detailed information on migration characteristics. In this dissertation, I present methods for characterizing seasonal and annual demersal fish movement at multiple scales in space and time using electronic archival and acoustic tags. In Chapter 1, acoustic telemetry and the Net Squared Displacement statistic were used to identify and characterize small-scale movement of adult female Pacific halibut during summer foraging in a Marine Protected Area (MPA). The dominant movement pattern was home range behavior at spatial scales of less than 1 km, but a more dispersive behavioral state was also observed. In Chapter 2, Pop-up Satellite Archival Tags (PSATs) and acoustic tags were deployed on adult female Pacific halibut to determine annual movement patterns relative to MPA boundaries. Based on observations of summer home range behavior, high rates of year-round MPA residency, migration timing that largely coincided with winter commercial fisheries closures, and the demonstrated ability of migratory fish to return to previously occupied summer foraging areas, the MPA is likely to be effective for protecting both resident and migrant Pacific halibut brood stock year-round. In Chapter 3, I adapted a Hidden Markov Model (HMM) originally developed for geolocation of Atlantic cod in the North Sea for use on demersal fishes in Alaska, where maximum daily depth is the most informative and reliable geolocation variable. Because depth is considerably more heterogeneous in many regions of Alaska compared to the North Sea, I used simulated trajectories to determine that the degree of bathymetry heterogeneity affected model performance for different combinations of likelihood specification methods and model grid sizes. In Chapter 4, I added a new geolocation variable, geomagnetic data, to the HMM in a small-scale case study. The results suggest that the addition of geomagnetic data could increase model performance over depth alone, but more research is needed to continue validation of the method over larger areas in Alaska. In general, the HMM is a flexible tool for characterizing movement at multiple spatial scales and its use is likely to enrich our knowledge about migratory demersal fish movement in Alaska. The methods developed in this dissertation can provide valuable insights into demersal fish spatial dynamics that will benefit fisheries management activities such as stock delineation, stock assessment, and design of space-time closures.
  • Diets, distribution and population dynamics of Arctic cod (Boreogadus saida) in Arctic shelf ecosystems

    Marsh, Jennifer M.; Mueter, Franz; Danielson, Seth; Iken, Katrin; Quinn, Terrance J. II (2019-05)
    With climate warming and longer open-water seasons in the Arctic, there is an increased interest in shipping, oil exploration and the expansion or development of commercial fisheries. Anticipated natural and anthropogenic changes are expected to alter the Arctic shelf ecosystems, including their fish communities. As a component of the Arctic Ecosystem Integrated Survey (Arctic Eis), this project presented a unique opportunity to assess the ontogenetic, spatial and temporal variability in the distribution, abundance and trophic roles (trophic level and diet sources) of key fish species in the Chukchi Sea. For my dissertation, I addressed three objectives to advance our understanding of Arctic cod (Boreogadus saida) as a key component of Arctic ecosystems. First, I characterized the current range of variability in trophic roles within the system and explored the role of advection in shaping the fish communities' diet (isotopic signatures) with a focus on Arctic cod. Second, I examined environmental and biological influences on the distribution and abundance of Arctic cod and provided an updated stock assessment for the Chukchi Sea. Finally, I broadened the geographic scope and used available time series of survey data at the southern margin of their range in the Pacific (eastern Bering Sea) and Atlantic (Newfoundland/Labrador shelves) sectors to assess the influence of temperature, predators and competitors on their distribution. Compared to age-1+ Arctic cod, age-0 Arctic cod had a less diverse diet regardless of water mass and were limited to colder temperatures. Together, this suggests that younger Arctic cod are more vulnerable to climate change. Estimates of egg production and early survival suggest that the numbers of mature Arctic cod present in the survey area during summer are unlikely to produce the observed high abundances of age-0 Arctic cod in the Chukchi Sea. Moreover, Arctic cod distributions in their southern ranges were highly influenced by temperature and to a lesser extent by competitors and predators. When temperatures were warmer, Arctic cod occupied a smaller area. These results inform the management of Arctic cod in a rapidly changing environment and provide benchmarks against which to assess future changes.
  • Genetic diversity and population genetic structure of tanner crab Chionoecetes bairdi in Alaskan waters

    Johnson, Genevieve M.; López, J. Andrés; Eckert, Ginny L.; Hardy, Sarah M. (2019-05)
    Tanner crab (Chionoecetes bairdi) is a large-bodied species of crab harvested in commercial, personal use, and subsistence fisheries across Alaska. The commercial fisheries were highly productive until the 1980s, when most stocks faced major declines and were closed to harvest. The recovery success of stocks throughout the state has been variable throughout the subsequent decades, leading managers to question whether there are aspects of the population dynamics that are not accounted for. There is limited information on the genetic population structure of C. bairdi in Alaskan waters, which has caused uncertainty about whether established management areas align well with distribution and migration patterns for this species. I applied novel high throughput sequencing methods to measure genetic diversity and investigate the genetic population structure of C. bairdi in Alaskan waters. Genomic DNA was isolated from samples collected from Southeast Alaska, Prince William Sound, and the Eastern Bering Sea, both east and west of 166°W longitude, and processed according to a Double-Digest Restriction-Associated DNA Sequencing protocol. The final genotype assembly included 89 individuals that were genotyped at 2,740 independent, neutral single-nucleotide polymorphism (SNP) sites, and contained 3.06% missing data. The average observed heterozygosity across SNP sites within regions was significantly lower than the average heterozygosity expected for populations in Hardy-Weinberg equilibrium. An analysis of molecular variance indicated that genetic variability was mostly found within individuals (90%), 10% of variability was observed between individuals within sampling regions, and no significant amount of variation was detected between sampling regions. Furthermore, pairwise FST estimates between sampling regions were low, and thus the null model of panmixia could not be rejected. Principal components analysis was also congruent with a model of no differentiation among regions. Bayesian analysis implemented in the program STRUCTURE did not support any population partitioning above K = 1 clusters, again indicating that there is not substantial genetic differentiation among the regions sampled from across the state of Alaska. These results indicate high gene flow throughout the distribution of Tanner crab across the Alaska continental shelf. Recognized stocks are genetically indistinguishable from each other. This may indicate that stocks exchange a substantial number of migrants, and may not operate independently. This new information can provide insights as management plans are evaluated and refined.
  • Spatial patterns, environmental correlates, and potential seasonal migration triangle of Arctic cod (Boreogadus saida) distribution in the Chukchi and Beaufort seas

    Forster, Caitlin; Norcross, Brenda; Mueter, Franz; Seitz, Andrew; Longerwell, Elizabeth (2019-05)
    Arctic Cod (Boreogadus saida) is a key forage fish species in the Arctic marine ecosystem and provides a critical energetic link between lower and upper trophic levels. Despite its ecological importance, spatially explicit studies synthesizing Arctic Cod distribution across a multitude of research efforts previously have not been conducted in the western portion of its range. I used spatial generalized additive models (GAM) to map the distribution of Arctic Cod by size class and relative to environmental variables. I compiled demersal trawl data from 21 research cruises conducted from 2004 to 2017 in the Chukchi and Beaufort seas, and investigated size-specific patterns in distribution to infer movement ecology of Arctic Cod as it develops from juvenile to adult life stages. High abundances of small, juvenile Arctic Cod (<70 mm total length) in the northeastern Chukchi Sea and western Beaufort Sea were separated from another region of high abundances in the eastern Beaufort Sea, near the US and Canadian border, suggesting possible population structure in the Pacific Arctic. In both the Chukchi and Beaufort seas, large, adult Arctic Cod (>130 mm total length) were found offshore and spatially segregated from small and medium (71-130 mm total length) fish, indicating an ontogenetic offshore movement of Arctic Cod as it matures. Relating environmental correlates to Arctic Cod abundance demonstrated that temperature and salinity were related to juvenile distribution patterns, while depth was the primary correlate of adult distribution. Furthermore, a comparison of spring and summer 2017 abundances of Arctic Cod in the southern Chukchi Sea, from the Bering Strait to Cape Lisburne found low abundance in the spring when compared to the summer. Differences in Arctic Cod abundance at different times of year suggest that Arctic Cod migrate seasonally, potentially following patterns of biological production in the Chukchi Sea. Arctic Cod migration may follow a classical 'migration triangle' route between nursery grounds as juveniles, feeding grounds as subadults, and spawning grounds as adults, in relation to ice cover and seasonal production in the Chukchi Sea. The analysis presented here is necessary to address federally mandated research requirements, which include improving understanding of stock structure and resolving essential fish habitat (EFH) for different life stages, as well as to gain better general understanding of the role of Arctic Cod in the Pacific Arctic.
  • Mercury concentrations and feeding ecology of fishes in Alaska

    Cyr, Andrew Philip; López, Juan Andres; O'Hara, Todd; Wooller, Matthew; Seitz, Andrew (2019-05)
    Mercury (Hg) is a ubiquitous contaminant found in nearly every fish species analyzed. Certain forms of Hg accumulate efficiently in fish tissues, sometimes reaching concentrations of concern for human and wildlife health when consumed. This has motivated considerable research and interventions surrounding fish consumption with Hg concentrations as the underlying cause of over 80% of fish consumption advisories in the United States and Canada. The ecological and physiological drivers that influence the concentrations of Hg in fishes are complex and vary among taxa spatially and temporally. Studying these drivers and their respective influences on Hg concentrations can help elucidate observed differences in Hg concentrations across space and time, which can then be used to improve management and consumption strategies. Here I present a series of studies focused on the chemical feeding ecology of Hg by measuring total Hg (THg) concentrations and ratios of nitrogen and carbon stable isotopes in multiple fish species from three regions in Alaska. In Chapter 2 I described foundational field collection efforts to characterize the fish communities from West Creek and the Taiya River in Klondike Gold Rush National Historical Park, and the Indian River in Sitka Historical National Park, Alaska. This chapter and agency report presents a survey of the fish species assemblage of the rivers and laid the framework for the regional analyses I conducted in the study presented in Chapter 3. In Chapter 3 I report inter- and intra-river comparisons of THg concentrations and associated feeding ecology of riparian Dolly Varden, separated by anadromous barriers in each system. I concluded that resident Dolly Varden that co-habit riverine locations with spawning salmon consume more salmon eggs than resident Dolly Varden from other locations of the same river that do not co-habit with spawning salmon. This is reflected in the isotopic composition of their tissues, and subsequently the THg concentrations of these fish are lower relative to Dolly Varden from parts of the same river above anadromous barriers. In Chapter 4, I describe regional patterns of THg concentrations and stable isotope values of carbon and nitrogen in nine species of fish and invertebrates from the Bering Sea and North Pacific Ocean along the Aleutian Islands, using Steller sea lion management zones as a spatial framework. I determine that most species from the Western Aleutian Islands have greater THg concentrations, and more negative δ¹³C values than those from the Central Aleutian Islands, indicating ecosystem-wide differences in THg concentrations and fish feeding ecology. I also determined that Amchitka Pass, a well-documented oceanographic and ecological divide along the Aleutian Island chain, aligns better with differences in THg concentrations than the boundary between Steller sea lion management zones. In Chapter 5, I report THg and methylmercury concentrations in fishes of Kotzebue Sound, including seven species that are important for subsistence users. I determined that fork length influences Hg concentrations within individual species, and that trophic relationships within a food web, a factor associated with biomagnification, influences Hg concentrations across the entire food web. I also observed that muscle tissues from virtually every individual fish had Hg loads below the State of Alaska's criteria for unlimited consumption. Taken together, the work conducted in this dissertation helps us better understand the ecological dynamics of Hg in aquatic food webs and has contributed to Hg monitoring of fish resources across parts of Alaska.
  • The seasonal dynamics of coastal Arctic lagoons in Northwest Alaska

    Tibbles, Marguerite; Seitz, Andrew C.; Falke, Jeffrey A.; Prakash, Anupma; Robards, Martin D. (2018-12)
    Lagoons are zones of habitat transitions between freshwater and marine ecosystems, providing safe and productive feeding habitats for whitefishes in Northwest Alaska, important to subsistence users in the region. However, many important lagoon processes are not understood. Therefore, the goal of this thesis was to gain a baseline understanding of two important seasonal processes of lagoons in Northwest Alaska. First, I attempted to identify environmental processes correlated with Arctic lagoon breaching for three indicator lagoons that represent a range of environmental characteristics using generalized linear models (GLM) in an information theoretic approach and model averaging. Second, I developed a habitat suitability (HS) model to identify the range of physical conditions that whitefishes may experience if overwintering under ice of these lagoons during the Arctic winter, for the same three lagoons. The GLM model suggested that lagoon breaching day of year was slightly negatively related to day of year of river break-up, but other unconditional confidence intervals for the covariate parameters overlapped zero indicating considerable uncertainty in these estimates. Further data collection and monitoring in the region is needed to improve and verify lagoon breaching modelling results. The HS model indicated that lagoons have reduced suitability as whitefish habitat in winter due to loss of habitat due to the presence of bottomfast ice and a reduction of liquid water quality due to cold temperatures, high salinities and low dissolved oxygen levels. Importantly, small lagoons without freshwater inputs were potential sinks for fish populations. The results from this research will help the National Park Service and the Native Village of Kotzebue in a joint effort to understand and manage these important habitats that are critical for subsistence fisheries as the Arctic faces an uncertain future with climate change, oil spill threats, and increased coastal development.
  • Growth of juvenile Chilkat Lake sockeye salmon in response to density-dependent and environmental factors

    Neil, Jodi C.; McPhee, Megan V.; Adkison, Milo D.; Agler, Beverly A.; Ruggerone, Gregory T. (2018-12)
    Chilkat Lake, in northern Southeast Alaska, is home to a Sockeye Salmon Oncorhynchus nerka population that is an important component in local commercial, sport, and subsistence fisheries, and has been monitored since the late 1960s. The population began declining in the late 1980s, prompting fishery managers to evaluate the production potential of Chilkat Lake to determine if it could be a candidate for enhancement efforts such as fry stocking or lake fertilization. Sockeye Salmon fry were stocked into Chilkat Lake intermittently from 1989 to 2004 in both small- (<50,000) and large-scale (2.6-5.3 million) events. The purpose of this study was to determine whether stocking of fry resulted in decreased freshwater growth due to density-dependent processes. Fish scales from the Alaska Department of Fish and Game's archived collection of adult Chilkat Lake Sockeye Salmon were measured and used as a proxy for fish growth. The objectives of this thesis were to 1) examine changes in juvenile Chilkat Lake Sockeye Salmon freshwater growth over time (1978-2012); 2) determine whether increased density of juvenile fry coupled with simultaneous climate events negatively affected freshwater growth of Chilkat Lake Sockeye Salmon; and 3) determine whether increased density of juvenile fry affected age at smoltification of Chilkat Lake Sockeye Salmon. We hypothesized that high fry density would slow growth and delay smoltification; however, these analyses produced variable results. We did not detect an effect of increased fry density on growth in the first year of fresh water, but found evidence for a subtle, negative relationship between fry density and second year freshwater growth of those fish that delayed migration. We also found that age at smoltification decreased with increasing fry density. Overall, the model results indicated that no factor or combination of factors related to stocking activity or climate consistently affected juvenile Sockeye Salmon scale growth, suggesting either unidentified, equally influential, or confounding mechanisms (e.g., high adult escapement and anomalous weather patterns).
  • Factors influencing chinook salmon spawning distribution in the Togiak River, Alaska

    Meggers, Stephanie L.; Seitz, Andrew; Prakash, Anupma; Lopez, Andres; Tanner, Theresa (2018-12)
    Salmonids are heavily dependent on specific habitat characteristics for survival, yet few studies in Alaska have examined the relationship between habitat and spawning distribution, using remote sensing approaches. To better understand the relationship between Chinook Salmon Oncorhynchus tshawytscha spawning distribution and environmental variables like habitat type (e.g., run, riffle, pool), temperature, and proximity to channel islands, optical and thermal imagery were collected on the Togiak and Ongivinuk rivers in southwest Alaska. Object-based image analysis was used to classify and quantify habitat types, while thermal characteristics and the proximity of spawning locations to channel islands were determined in a GIS framework. Object-based image analysis was useful for classifying habitat and may provide a better alternative to pixel-based image analysis. However, rule sets were nontransferable and inconsistent among river reaches, and caution should be taken when these methods are used on large river sections. Chinook Salmon showed a preference for spawning in river runs, 80% of fish spawned in water temperatures between 8.6° and 9.4°C, and nearly 61% of Chinook Salmon spawned within 100 m of a channel island. This study provided a baseline understanding of environmental correlates of spawning for Chinook Salmon at the northern extent of their range.
  • Exploring the potential role of late stage predation and Chinook salmon age structure

    Manishin, Kaitlyn A.; Seitz, Andrew C.; Westley, Peter A. H.; Cunningham, Curry J.; Goldman, Kenneth J. (2018-12)
    Chinook salmon (Oncorhynchus tshawytscha) populations across the North Pacific have displayed a decrease in body size-at-return resulting from declines both in age- and body size-at-maturity. These changes have precipitated the loss of the oldest age classes in some populations and have occurred throughout the range of this species, suggesting a shared - yet currently unknown - driver in the common marine environment. A hypothesis for the cause of these changes is intense and/or selective predation marine mortality after the first winter in the ocean, potentially from predators selectively removing relatively large sub-adult Chinook salmon. Here I consider the question: under what circumstances could predation on large sub-adult individuals by salmon sharks (Lamna ditropis) change the age structure of a Chinook salmon population? To address this question, I first estimated total per capita prey consumption by salmon sharks - an increasingly acknowledged predator of salmon on the high seas - using three methods: 1) daily ration requirement, 2) bioenergetic mass balance, 3) and a von Bertalanffy growth model. Second, I examined the effects of additional predation on an indicator Chinook salmon population from the Yukon River by simulating alternative predation scenarios with a stage-structured life cycle model. Scenarios described the strength and selectivity of predation, and the resulting simulated age structure was then compared to observed demography. The selectivity and intensity of removals required to produce this change in age structure were considered in the context of top predators, focusing on salmon sharks. The daily ration method yielded individual salmon shark consumption estimates of 1461 and 2202 kg·yr-1, the mass-balance method produced estimates of 1870 kg·yr-1, 2070 kg·yr-1, 1610 kg·yr-1, and 1762 kg·yr-1, depending on assumed diet, and the growth model output estimates of 16,900 kg·yr-1 or 20,800 kg·yr-1, depending on assumed assimilation efficiency. The per capita prey consumption estimates from the mass-balance method may be the most realistic because they incorporated life history data specific to salmon sharks and did not produce extreme values. Taken as a whole, these estimates suggest salmon sharks have energetic requirements similar to those of piscivourous marine mammals and corroborates conclusions of previous research suggesting that endothermic fishes exhibit metabolic rates similar to marine mammals. The simulated mortality scenarios that most closely mimicked observed shifts in age structure of the indicator Chinook salmon population focused intense and selective predation on the third year of Chinook salmon residence in the ocean. This simulated predation is corroborated by emerging results from an independent electronic tagging study in which tagged Chinook salmon experienced high predation rates, and research suggesting that killer whales (Orcinus orca) selectively prey upon Chinook salmon in their third year at sea. In summary, salmon sharks likely have high energetic requirements that could result in a large biomass of prey consumed, Chinook salmon populations are sensitive to predation during the third ocean year, and salmon sharks and other predators appear to frequently consume fish at that ocean stage. Taken together, these lines of evidence point to a potentially important mechanism for top down pressure on Chinook salmon populations that may explain observed changes in age-at-return, which in turn can affect population productivity. Future work and more robust data on predator distributions and abundances are needed to explore this finding further.
  • Impacts of a top predator (Esox lucius) on salmonids in Southcentral Alaska: genetics, connectivity, and vulnerability

    Jalbert, Chase S.; Falke, Jeffrey; Westley, Peter; López, J. Andrés; Dunker, Kristine (2018-12)
    Worldwide invasion and range expansion of northern pike (pike; Esox lucius) have been linked to the decline of native fishes and new techniques are needed to assess the effects of invasion over broad geographic scales. In Alaska, pike are native north and west of the Alaska Mountain Range but were introduced into Southcentral Alaska in the 1950s and again in the 1970s. To investigate the history of the invasion into Southcentral Alaska, I identified 7,889 single nucleotide polymorphisms (SNPs) from three native and seven introduced populations in Alaska and examined genetic diversity, structure, and affinities of native and invasive pike. Pike exhibited low genetic variability in native populations (mean heterozygosity = 0.0360 and mean π = 0.000241) and further reductions in introduced populations (mean heterozygosity = 0.0227 and mean π = 0.000131), which suggests a bottleneck following introduction. Population differentiation was high among some populations (global FST = 0.424; max FST = 0.668) when compared to other freshwater fishes. I identified five genetically distinct clusters of populations, consisting of three native groups, a single Susitna River basin invasive group, and a Kenai Peninsula group, with little evidence of admixture among groups. The extremely reduced genetic diversity observed in invasive northern pike populations does not appear to affect their invasion success as the species range Southcentral Alaska continues to expand. To assess the vulnerability of five species of Pacific salmon (Oncorhynchus spp.) to the invasion, I combined intrinsic potential habitat modeling, connectivity estimates, and Bayesian networks across 22,875km of stream reaches in the Matanuska-Susitna basin, Alaska, USA. Pink salmon were the most vulnerable species, with 15.2% (2,458 km) of their range identified as "highly" vulnerable. They were followed closely by chum salmon (14.8%) and coho salmon (14.7%). Finally, analysis of the intersection of vulnerable salmon habitats revealed 1,001 km of streams that were highly vulnerable for all five Pacific salmon. This framework is easy to implement, adaptable to any species or region, and cost effective. With increasing threats of species introductions, fishery managers need new tools like those described here to efficiently identify critical areas shared by multiple species, where management actions can have the greatest impact.
  • Assessment and application of DNA metabarcoding for characterizing Arctic shorebird chick diets

    Gerik, Danielle Elizabeth; López, J. Andrés; Lanctot, Richard; Gurney, Kirsty; Wipfli, Mark (2018-12)
    Climate change in the Arctic is affecting the emergence timing of arthropods used as food by nesting shorebirds and their young. Characterizing the diets of shorebird young is a prerequisite to evaluate the potential for asynchrony to occur between the timing of arthropod emergence and when shorebird young hatch, an example of trophic mismatch. In this study, DNA metabarcoding was used to identify arthropod remains in feces collected from wild-caught Red Phalarope (Phalaropus fulicarius), Pectoral Sandpiper (Calidris melanotos), and Dunlin (Calidris alpina), young in Utqiaġvik, Alaska between 2014 and 2016. Arthropod specimens were collected at the field site to generate DNA reference sequences from potential prey items. The newly generated sequences in combination with publicly available sequences served as a reference set for species determinations. I assessed the ability of two mitochondrial markers (CO1 and 16s) to detect arthropods in the feces of captive pre-fledged young in controlled feeding experiments. After combining information from both markers, experimental prey taxa were detected in chick feces 82-100% of the time, except for Trichoptera which was never detected. I used the same strategy to characterize the diets of wild-caught shorebird young. The technique detected nearly all prey families documented in historical gut content analyses, as well as 17 novel families. Some of the novel prey diversity may be the result of detecting the prey of prey, known as secondary consumption. We observed that the diets of shorebird young shifted over the course of a summer. Changes in diet generally reflected arthropod composition in the environment estimated from collection of arthropods in pitfall traps. Evidence of diet flexibility by shorebird young suggests that chicks can shift their diets to take advantage of intra-seasonal changes in prey availability. Here, I provide an evaluation and application of DNA metabarcoding to characterize prey resource use by shorebird young for assessing the presence and impacts of trophic mismatch.
  • Navigating the predator gauntlet: consumption of hatchery- and wild-born juvenile chum salmon (Oncorhynchus keta) by common nearshore marine fishes in Southeast Alaska

    Duncan, Douglas H.; Beaudreau, Anne H.; McPhee, Megan V.; Westley, Peter A. H. (2018-12)
    Juvenile chum salmon (Oncorhynchus keta) undergo extensive mortality at marine entry, a period which is believed to be a potential population bottleneck. Although this early mortality has been consistently observed, our understanding of the mechanisms responsible is limited. Furthermore, the implications of large-scale salmon hatchery releases for the ecology of juvenile chum salmon and their consumers is another important knowledge gap. To better understand the predation responses of abundant consumers to hatchery- and wild-born juvenile chum salmon, we examined the diets of Pacific staghorn sculpin (Leptocottus armatus) and Dolly Varden (Salvelinus malma) near Juneau, Alaska, in 2016 and 2017. Chum salmon composed 4.5% and 19.6% of the diets of staghorn sculpin and Dolly Varden by weight, respectively, and 88% of chum salmon individuals consumed were of hatchery origin. Chum salmon prey were shorter than average when compared to chum salmon concurrently collected by beach seine and hatchery releases of chum salmon. Regression analyses indicated that occurrence of juvenile chum salmon in diets varied primarily by date and site. Predation generally occurred more frequently at sites closer to hatchery release areas. The quantity of chum salmon in staghorn sculpin stomachs was related to predator length, chum salmon catch-per-unit-effort (CPUE), and the proportion of hatchery fish present; however, date was the only important predictor explaining quantity of chum salmon in Dolly Varden stomachs. To translate diet data into consumption rate, we experimentally determined gastric evacuation rate for staghorn sculpin and implemented a field-based consumption model. Average daily consumption of chum salmon was low relative to all other prey groups. Estimates of average seasonal consumption of juvenile chum salmon by staghorn sculpins suggest that predator populations would have to be implausibly large to consume even 1% of local hatchery chum salmon production. Together, these results yield new insights into the interactions between the predators of wild-born and hatchery-born salmon during the critical stage of marine entry.

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