• Assessing a macroalgal foundation species: community variation with shifting algal assemblages

      Metzger, Jacob Ryan; Konar, Brenda; Edwards, Matthew; Beaudreau, Anne (2018-08)
      Foundation species provide critical food and habitat to their associated communities. Consequently, they are disproportionately important in shaping community structure, promoting greater biodiversity and increased species abundance. In the Aleutian archipelago, once extensive kelp forests are now relatively rare and highly fragmented. This is due to unregulated urchin grazing shifting the majority of nearshore rocky-reefs from kelp forests to either urchin barrens or "transition forests" - kelp forests devoid of understory algae. The algal communities within kelp forests, transition forests, and urchin barrens represent a stepwise loss in fleshy algal guilds, a regression from a full algal community, to having only canopy kelp, to areas largely denuded of all fleshy algae. This stepwise loss of algal guilds was used to test the designation of the resident canopy-forming kelp, Eualaria fistulosa, as a foundation species--a species that has strong, positive effects on communities where it occurs. Therefore, I assessed the impact that E. fistulosa's occurrence had on faunal community structure (in terms of species diversity, abundance and biomass, and percent bottom cover)and invertebrate size-structure. This study found that the presence of E. fistulosa does not correspond to strong differences in invertebrate size-structure or faunal community structure. However, in kelp forests where E. fistulosa exists in tandem with a variety of subcanopy macroalgae, faunal communities are more species rich, have significantly different community structures with notably higher abundance, biomass, and percent cover of filter feeding taxa, and support sea urchin populations containing significantly higher proportions of larger individuals. Consequently, this study stresses the context dependent role of foundation species and suggests their strong, positive effects on associated communities may change with perturbations to ecosystems. To that end, this study suggests that we may need to reconsider the designation of E. fistulosa as a foundation species following the extensive fragmentation and range restriction that has occurred throughout much of the Aleutian Archipelago.
    • 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.
    • Biochemical and microbiological assessments of dried Alaska pink salmon, red salmon and Pacific cod heads

      Biceroglu, Huseyin; Smiley, Scott; Crapo, Charles; Bechtel, Peter J. (2012-05)
      Fish heads are generally considered as unsuitable byproducts for human consumption in the United States. The initial objective was to compare the moisture content and water activity levels on dried pink salmon (Oncorhynchus gorbuscha) and dried red salmon (O. nerka) using different temperature and time integration. The secondary objective was to compare shelf life characteristics, rancidity and mold growth, between dried pink dried salmon and dried Pacific cod (Gadus macrocephalus) heads stored for up to 180 days at the ambient temperature (21°C) for East African seafood markets. The third objective was to assess the antioxidant effects for frozen and dried pink salmon heads stored for up to 60 days. In a preliminary experiment, dried red salmon heads were found unsuitable due to the water activity levels above 0.6. The critical moisture contents were detected around 10% for pink salmon heads and were around 15% for Pacific cod heads to reduce water activity levels below 0.6 in these products. The applicable drying temperatures of 50°C lasting over 50 hours for pink salmon heads and 50°C for over 24 hours followed by 30°C for over 24 hours for Pacific cod heads were found optimal. Dried Pacific cod heads showed shelf stability as a potential dried seafood product. Frozen pink salmon heads had 60 days shelf life, while heads with antioxidant glazing retarded oxidation levels (p <0.05). The antioxidant treatment in dried pink salmon heads kept oxidation levels lower than the acceptable limit up to 60 days. This study provided essential information to improve the utilization of these Alaskan seafood byproducts.
    • Characterizing the diet and population structure of lampreys Lethenteron spp. using molecular techniques

      Shink, Katie G.; López, Andrés; Murphy, James M. (2017-08)
      Lampreys contribute to the health of aquatic ecosystems and are targeted in both subsistence and commercial fisheries. Despite their ecological and commercial importance, the management and conservation of native lampreys have been largely overlooked. The goal of this study was to close current knowledge gaps of lamprey biology through the examination of Lethenteron spp. in Alaska. This study applied two molecular techniques, DNA metabarcoding and microsatellite genotyping, to (1) characterize the diet of marine-phase Arctic lamprey Lethenteron camtschaticum (N = 250) in the eastern Bering Sea and (2) investigate the population structure of larval lampreys Lethenteron spp. (N = 120) within and among three Yukon River tributaries. A combination of visual observations and DNA metabarcoding revealed the presence of diagnostic structures/tissues (i.e., eggs, fin[s], internal organs, otoliths, and vertebrae) and detected DNA sequences of ten ray-finned fishes in the diets of L. camtschaticum. The most frequent prey taxa were Pacific sand lance Ammodytes hexapterus, Pacific herring Clupea pallasii, gadids, and capelin Mallotus villosus. Five of the ten taxa identified in this study were reported for the first time as prey for L. camtschaticum. To investigate the genetic diversity of larval lampreys, a recognized knowledge gap for populations in Alaska, a total of 81 larval lampreys were successfully genotyped at all loci. Global FST of larvae was 0.074 (95% CI: 0.042 - 0.110), while pairwise FST values among the three localities examined ranged from 0.066 - 0.081. Hierarchical model-based Bayesian clustering analyses detected three genetic clusters (K = 3) among all larval lampreys and two genetic clusters (K = 2) among Chena River larvae; no further genetic clustering was identified within the remaining two tributaries. Estimates of contemporary gene flow indicated reciprocal migration among sites. The diet analyses indicated anadromous L. camtschaticum function as flesh-feeding predators that prey upon pelagic fishes in the eastern Bering Sea, while genetic analyses suggested that larval lamprey aggregations within three Yukon River tributaries exhibited higher levels of genetic diversity than are typically found among broad-ranging populations of anadromous lamprey species. Ultimately, this study highlighted the value of molecular techniques to improve our understanding of the biology of a poorly studied fish species in Alaska.
    • Characterizing the fish community in turbid Alaskan rivers to assess potential interactions with hydrokinetic devices

      Bradley, Parker T.; Seitz, Andrew; Sutton, Trent; McPhee, Megan; Burr, John (2012-12)
      The Yukon and Tanana rivers are two large, glacially turbid rivers in Alaska, where hydrokinetic projects are being explored for feasibility of electricity production. Downstream migration behavior of fishes in these rivers is poorly understood; as a result, the potential impacts of hydrokinetic devices, which will be placed in the deepest and fastest part of the river, on fishes are unknown. Downstream migrating fishes were sampled during the ice-free season along the river margins of the Yukon River in 2010 and the river margins and mid-channel of the Tanana River in 2011. Results suggest that the river margins in the Yukon and Tanana rivers are primarily utilized by resident freshwater species, the mid-channel is utilized by Pacific salmon (Oncorhynchus spp.) smolts, and only chum salmon (Oncorhynchus keta) smolts utilize both of these areas. Some species exhibited distinct peaks and trends in downstream migration timing including longnose suckers (Catostomus catostomus), whitefishes (Coregonine), Arctic grayling (Thymallus arcticus), lake chub (Couesius plumbeus), Chinook salmon (O. tshawytscha), coho salmon (O. kisutch), and chum salmon. As a result of these fishes' downstream migration behavior, hydrokinetic devices installed in surface waters of the middle of the river channel will have the most potential interactions with Pacific salmon smolts during their downstream migration to the ocean from May through July.
    • 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.
    • Defining genetic population structure and historical connectivity of snow crab (Chionoecetes opilio)

      Albrecht, Gregory T.; Hardy, Sarah M.; Lopez, J. Andres; Hundertmark, Kris J. (2011-08)
      The snow crab (Chionoecetes opilio) is a valuable commercial resource within the Bering Sea, as well as other areas in the North Pacific and Atlantic Oceans. Large populations are known to exist within the Chukchi and Beaufort Seas, including recently discovered commercial sized individuals (Beaufort). However, genetic connectivity throughout these regions has not been examined until now. Based on seven polymorphic microsatellite loci, relatively low population genetic structuring occurs throughout the Alaskan region (Gst = 0.001). This homogeneity is likely due to long-distance larval dispersal, adult migrations, and a possible recent population expansion following the last glacial maximum. Furthermore, meta-population analysis was conducted for Alaskan and Northwest Atlantic stocks. Although significant genetic divergence characterizes the West Greenland stock in relation to all other populations, low divergence (Gst = 0.005) was found between Atlantic Canada crabs and those from the Alaska region. Larval dispersal between regions is highly unlikely due to the transit distance. Therefore, low divergence is likely the result of a recent population expansion into the Northwest Atlantic <5000 years ago.
    • Diet composition and fate of contaminants in subsistence harvested northern sea otters (Enhydra lutris kenyoni) from Icy Strait, Alaska

      Brown, Kristin Lynn; Atkinson, Shannon; Andrews, Russel; Pearson, Heidi (2020-05)
      Northern sea otters (Enhydra lutris kenyoni) in Southeast Alaska have experienced a significant population increase since their successful reintroduction to the area after previous near extirpation owing to historic fur trading. The purpose of this study was to examine sea otter diet and metals contamination in an area of Southeast Alaska with the most robust increases in sea otter numbers, Glacier Bay/Icy Strait, with the intent of gathering baseline data for a healthy population of sea otters and as a reflection of the local coastal environmental health of the area. This research was a collaborative effort with Alaska Native subsistence hunters and the Alaska Department of Environmental Conservation. In Chapter 1, sea otter stomachs (n=25) were obtained in April 2015 and April 2016 from Alaska Native subsistence hunters in Icy Strait, Alaska. There were no differences in sea otter diet between years. Bivalves dominated the sea otter diet. Northern horsemussels (Modiolus modiolus) made up the greatest proportion of the diet (0.46 ± 0.48). Fat gaper clams (Tresus capax) and northern horsemussels were found in the highest proportion of stomachs (0.64 and 0.60, respectively). There was not an apparent trend between sea otter age and the minimum number of total prey items, stomach contents mass, or mean frequency of occurrence of the top four prey species. Sea otters from this study are likely to be dietary generalists throughout their lives. In Chapter 2, brain, gonad, kidney, and liver tissues, as well as stomach contents were analyzed for arsenic, cadmium, copper, lead, total mercury, and selenium for the 2015-harvested sea otters that were also referenced in Chapter 1 (n=14). In general, arsenic and lead had the highest concentrations in stomach contents, cadmium and selenium were highest in the kidneys, and copper and total mercury were highest in the livers. While brains and gonads had the lowest metals concentrations of any tissue, the metal with the greatest concentration within the brain was copper, and within the gonads was selenium. Concentrations of arsenic, cadmium, total mercury, and lead demonstrated a relationship with sea otter length. In general, all the mean metals concentrations for these sea otters were below published effects threshold values for marine mammals. Only total mercury demonstrated biomagnification from the stomach contents (i.e., the prey) to all higher-level tissues. Selenium health benefit values were positive in all sea otter tissue types analyzed in the present study, indicating that concentrations of selenium had an overall health benefit in protecting those tissues against mercury toxicity. Evaluating how contaminants concentrate and get distributed in tissues of top trophic levels provides an indication for potential exposure to humans and demonstrates how these keystone species act as indicators of local coastal ecosystem health. The results of studies on dietary exposure and metals contamination in top trophic level consumers such as sea otters can be used in monitoring the health of sea otter populations and the local environment that they inhabit.
    • Dietary effects on protein turnover in three pinniped species, Eumetopias jubatus, Phoca vitulina, and Leptonychotes weddellii

      Inglis, Susan D.; Castellini, Michael; Atkinson, Shannon; Barboza, Perry; Carpenter, James; Rea, Lorrie (2019-05)
      The role of dietary protein in pinniped (seal and sea lion) nutrition is poorly understood. Although these marine mammals derive the majority of their daily energetic needs from lipid, lipids cannot supply essential amino acids which have to come from protein fractions of the diet. Protein regulation is vital for cellular maintenance, molt, fasting metabolism, exercise and development. Proteins are composed of linked amino acids (AA), and net protein turnover is the balance between protein synthesis from component AA, and degradation back to AA. Protein regulation is influenced by dietary intake and quality, as well as physiological and metabolic requirements. In this work, pinniped diet quality was assessed through comparisons of amino acid profiles between maternal milk, blood serum, and seasonal prey of wild juvenile Steller sea lions (Eumetopias jubatus) in Southcentral Alaska. Both Pacific herring (Clupei pallasi) and walleye pollock (Gadus chalcogramma) showed similar patterns to milk in essential and branched chain amino acid content. Serum amino acid profiles suggest the juvenile sea lions were not in protein deficit at the time of capture. Protein metabolism in the blood and urine was assessed through turnover studies using amino acid tracers. The turnover kinetics of ¹⁵N-labelled glycine in the blood amino acid and protein pool, red blood cells, and urine urea were measured in wild adult female Weddell seals (Leptonychotes weddellii) in the Antarctic. Labelled glycine moved quickly into serum protein and red blood cells (1-2 hours) and urinary urea (2-4 hours). The turnover rates in the blood amino acid and urine urea pools demonstrated a reduced turnover rate associated with molting. Lastly, whole body protein turnover experiments using a single bolus ¹⁵N-labelled glycine tracer method with endproduct collection of blood, feces and urine were conducted on 2 Cohort groups of captive Alaskan harbor seals over 2 years. Season was found to have the greatest effect on whole body protein turnover, which increased during the winter and decreased in the summer molt. Conversely, protein intake decreased during the winter and increased in the summer molt. This pattern corresponded with an increase in mass and protein synthesis in the winter, while mass decreased and protein degradation rates increased in molting seals. Weaning also influenced the patterns with reduced protein turnover in newly weaned animals that had recently transitioned from milk to a fish diet. This project presents results on whole body protein turnover rates in nonfasting pinnipeds and reveals that protein turnover is strongly regulated by developmental and seasonal physiological and metabolic demands.
    • Early marine growth patterns of Situk River steelhead, Oncorhynchus mykiss

      Catterson, Matthew R.; McPhee, Megan; Love, David; Sutton, Trent (2017-08)
      Steelhead Oncorhynchus mykiss exhibit complex life-history patterns described by variable freshwater and marine residency periods, maturation patterns, and reproductive characteristics. Over 300 small populations of Steelhead are present in Southeast Alaska, and similar trends in abundance among these populations suggest the influence of population-regulating forces operating on a regional scale. The Situk River, near Yakutat, Alaska, supports the largest known population of Steelhead in Alaska. Stock assessment studies on this river have collected the longest set of biological data and scale samples for Steelhead in the state. For this study, retrospective scale pattern analysis of samples from Situk River Steelhead was synthesized with regional abundance information to investigate patterns in early marine growth among different life-history and demographic groups, as well as to explore linkages between growth, abundance, and marine environmental variables. Positive correlations were identified between freshwater growth, first ocean-year growth, and adult length, while first ocean-year growth was negatively correlated with second ocean-year growth. Early maturing Steelhead were found to have increased first ocean-year growth and reduced adult length relative to later maturing Steelhead, confirming connections between growth and maturation. Correlations in abundance among Southeast Alaska Steelhead populations suggest that marine and climatic drivers may impact these populations in a regionally coherent manner. Correlations among patterns in abundance also varied along a distance gradient: populations located closer to the Situk River were more correlated with the Situk River than more distant populations. Positive relationships between Gulf of Alaska sea surface temperature, North Pacific Gyre Oscillation, and Situk River Steelhead abundance further supported the importance of climate-driven marine conditions to Steelhead productivity. While conservation concerns for Steelhead in Southeast Alaska are currently minimal, proactive investigations into life-history diversity and population linkages may become more relevant with increased marine ecosystem variability related to climate change.
    • Ecological interactions among important groundfishes in the Gulf of Alaska

      Barnes, Cheryl L.; Beaudrea, Anne H.; Dorn, Martin W.; Holsman, Kirstin K.; Hunsicker, Mary E.; Mueter, Franz J. (2019-12)
      Complex ecological interactions such as predation and competition play an important role in shaping the structure and function of marine communities. In fact, these processes can have greater impacts than those related to fishing. We assessed ecological interactions among economically important fishes in the Gulf of Alaska - a large marine ecosystem that has recently undergone considerable shifts in community composition. Specifically, we developed an index of predation for Walleye Pollock (Gadus chalcogrammus) to examine spatiotemporal changes in consumption, quantify portfolio effects, and better understand diversity-stability relationships within the demersal food web. We also evaluated the potential for competition between two important pollock predators, Arrowtooth Flounder (Atheresthes stomias) and Pacific Halibut (Hippoglossus stenolepis). We found highly variable predation intensity on Gulf of Alaska pollock. The combination of a single dominant predator and synchronous consumption dynamics indicated strong top-down control in the region. Spatial heterogeneity, however, may offset trophic instability at the basin scale. Assessments of resource partitioning provided little indication for competition between Arrowtooth Flounder and Pacific Halibut of similar lengths. Morphological differences between the two flatfish predators prompted an exploration into whether our conclusions about resource partitioning were dependent upon the size metric used. From this study, we found a relatively early onset of piscivory for Arrowtooth Flounder. Relationships between predator size and prey size also suggested gape limitation among Pacific Halibut sampled. Trophic niche separation was more pronounced for fishes with larger gapes, indicating greater potential for competition among smaller Arrowtooth Flounder and Pacific Halibut in Southeast Alaska. Reexamining basin-scale relationships between spatial and dietary overlap according to gape size would further elucidate the effects an increasing Arrowtooth Flounder population has had on changes in Pacific Halibut size-at-age. Results from this dissertation improve our understanding about the impacts of complex ecological interactions on population and community dynamics, and how those interactions may change in time, space, and under different environmental conditions.
    • Effects of elevated sediment levels from placer mining on survival and behavior of immature arctic grayling

      Scannell, Patrick O. (1988-12)
      The effect of placer mining effluents on Arctic grayling (Thymallus arcticus) fingerling and egg survival was tested in mined and unmined streams in interior Alaska. Also the influence of turbidity on Arctic grayling reactive distance and avoidance behavior was tested in a laboratory choice chamber. Arctic grayling fingerlings suffered less than 1% mortality during a 96-hr toxicity test in both clear (mean NTU = 1.4) and mined (mean NTU = 445) streams. Arctic grayling eggs did not show significantly (p > 0.1) higher mortality in mined streams than in unmined streams. In a laboratory choice chamber test, Arctic grayling avoided water with a turbidity above 20 NTU (nephelometric turbidity units). Arctic grayling reactive distance diminished proportional to the natural logarithm of turbidity.
    • Effects of jet boats on salmonid reproduction in Alaskan streams

      Horton, Gregg E.; Reynolds, James; Kane, Douglas; Barry, Ronald; Kavanagh, Ross (1994-09)
      Freshwater angling has increased dramatically in recent years in southwestern Alaska, and jet boat operators serve some of these anglers. Resources agencies are under pressure to regulate use of jet boats in waters that support spawning populations of salmonids, but they need more information regarding these potential effects. This thesis describes the methods and results of experiments to determine the effects of water turbulence from passing boats on embryo mortality and behavior of spawning adults. Field experiments on sockeye salmon were conducted in American Creek (in the Naknek drainage in Katmai National Park and Preserve) in 1992 and 1993. Laboratory experiments on rainbow trout were conducted at Fort Richardson Hatchery. These two species were viewed as surrogates for all species of genus Onorhynchus.
    • Estimating sizes of fish consumed by ice seals using otolith length-fish length relationships

      Walker, Kelly; Norcross, Brenda L.; Brown, Randy; Lopez, Andres; Quakenbush, Lori (2017-12)
      Arctic fishes and ice seals are key components of the Alaskan Arctic ecosystem. Bearded (Erignathus barbatus), spotted (Phoca largha) and ringed (Pusa hispida) seals are consumers of Arctic marine fishes. Little is known about the sizes of fish that ice seals consume because prey items are digested quickly once exposed to stomach acids. Otoliths, fish ear bones, are often the only parts of a fish that remain in a seal stomach. Otolith length relates directly to fish length, making size estimations of consumed fish possible for piscivore diet studies. Otoliths were measured from fishes collected from cruises in the Beaufort and Chukchi seas during 2009 - 2014. Otolith length - fish length and fish length - fish weight relationships were developed for 11 Arctic marine fish species that are commonly consumed by ice seals in Alaska. Otoliths from seal stomachs provided by subsistence hunters to the Alaska Department of Fish and Game were identified to species level and measured for total length. A mixed effects model was used to determine how the variables of seal species, harvest location, seal age class and sex influenced the sizes of fish consumed. Harvest location and seal age class were the primary factors that affected fish size in ice seal stomachs. Estimating length and weights of fishes consumed by ice seals will help further diet and energetics studies that have not previously been possible in the Alaskan Arctic.
    • 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.
    • 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.
    • Evaluation of prey composition and nutritional value of diets of free-ranging harbor seals (Phoca vitulina) from Tugidak Island

      Geiger, Gretchen L.; Atkinson, Shannon; Carpenter, James; Horstmann-Dehn, Larissa; Wynne, Kate (2012-12)
      Changes in climate can cause shifts in ecosystem structure that can affect quantity or quality of prey available to predator populations. Due to sex or age-specific behaviors of predators, certain classes within a population may be more severely impacted by changes in their diet. This study evaluated prey composition and nutritional value of summer diets of harbor seals (Phoca vitulina richardii) from Tugidak Island, Alaska from 2001-2009. The MIXIT-WIN program was used to estimate the nutritional value of average harbor seal diets. Changes in relative abundance of certain prey species were correlated to sea surface temperature anomalies. Despite changes in prey composition, the nutritional value of the average harbor seal diet did not change. Fecal corticosteroid metabolite profiles were analyzed to identify age and sex of individual harbor seals from scats. Profiles obtained from a known adult male harbor seal could be differentiated from those of known adult female and juvenile male seals. Similar profiles were observed in unknown age and sex samples. Even though diet diversity differed between these groups, the nutritional quality of consumed diets was not significantly different. Tugidak Island harbor seals have flexible diets allowing them to capitalize on available prey to maintain their nutritional intake.
    • 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.
    • 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.
    • Fifty years of Cook Inlet beluga whale ecology recorded as isotopes in bone and teeth

      Nelson, Mark A.; Wooller, Matthew J.; Iken, Katrin; Quakenbush, Lori T. (2017-12)
      Beluga whales (Delphinapterus leucas) are found across the Arctic and Subarctic in seasonally ice covered waters. Five stocks of beluga whales are associated with the waters near Alaska for at least part of the year and four of those five stocks are abundant and commonly hunted by Alaskan Natives. The belugas resident in Cook Inlet are also an important cultural and subsistence resource to Alaskan Natives in the area, but a ~50% decline in abundance in the 1990's led to the stock being designated as depleted under the Marine Mammal Protection Act in 2000 and listed as endangered under the Endangered Species Act in 2008. Numerous studies of beluga whales in relation to stranding events, predation (killer whales), parasitism, disease, contaminants, and other potential population threats have not identified the reason for their inability to recover. Changes in diet have been considered, but are difficult to study because observations of feeding in muddy water and beluga stomachs are difficult to obtain. To investigate the past feeding ecology of beluga whales from Cook Inlet I sampled bone and teeth for isotopic analyses. I sampled bone from 20 individuals that died between 1964 and 2007 for stable carbon and nitrogen isotope analysis (values expressed as δ¹³C and δ¹⁵N values). I also micro-sampled annual growth layer groups in the teeth of 26 individuals representing the years from 1962 to 2007. Bone and tooth data showed a general decrease in δ¹³C and δ¹⁵N values over time. The δ¹³C values from analyses of growth layer groups declined from -13.4‰ to -16.2‰ and δ¹⁵N values declined from 17.2‰ to 15.4‰. Although these values are consistent with a change in feeding ecology over time, the magnitude of the decrease in δ¹⁵N values (~2‰) is insufficient for a full trophic level shift (~3‰).The relatively large decrease in the δ¹³C values over the same time period (~3‰), however, is much greater than a full trophic level shift (~1‰) and suggests an increase in prey associated with freshwater, which typically have lower δ¹³C values than prey associated with marine water. To test this hypothesis I analyzed the strontium isotope composition (⁸⁷Sr/⁸⁶Sr ratios) of growth layer groups in teeth from a sub-set of individuals. The resulting ⁸⁷Sr/⁸⁶Sr ratios trended away from the global marine signature (0.70918) over time and toward the more freshwater signatures measured in rivers flowing into the upper reaches of Cook Inlet. These results indicate that the diet of Cook Inlet beluga whales has changed over time. This could be from feeding on different, more freshwater derived prey species, or from feeding on the same species, but on individuals from locations with a more freshwater influence. Both of these interpretations are consistent with population survey data indicating a retraction in beluga range into the upper reaches of Cook Inlet. This study presents the first evidence of a long term (~50 years) change in Cook Inlet beluga whale feeding ecology. The consequences of this change toward more freshwater-influenced prey, and how this change relates to Cook Inlet beluga whales' decline or recovery remains unknown. However, to better examine this change in feeding ecology a follow-up study will; 1) develop a strontium isoscape for the Cook Inlet watershed; 2) analyze more teeth to better analyze changes in feeding ecology by demographic group (sex, age); and 3) analyze growth layer groups from Bristol Bay beluga teeth for a comparison with Cook Inlet belugas to determine if the changes represent an ecosystem change within Cook Inlet or a broader scale change affecting another region. This study builds towards a better understanding of the changes in Cook Inlet beluga feeding ecology and will help to determine if changes in diet could be a factor in their recovery.