• Addressing a complex resource conflict: humans, sea otters, and shellfish in Southeast Alaska

      Ibarra, Sonia Natalie; Eckert, Ginny L.; Monteith, Daniel; Pyare, Sanjay; Langdon, Stephen J.; VanBlaricom, Glenn (2021-05)
      Complex resource conflicts may benefit from the inclusion of social-ecological systems approaches that recognize the complex linkages between humans and their environment. Competition for shared shellfish resources by sea otters and humans in Southeast Alaska has caused food security concerns, cultural and economic losses, and uncertainty about the future of various fisheries, including rural subsistence-based fisheries. In rural Alaska Native communities, access to subsistence resources are critical to maintaining a way of life, with deeply rooted knowledge systems that are tied to the land, water, and natural resources. This dissertation documents Indigenous and local knowledge of Alaska Native customary and traditional food experts, sea otter hunters, and elders (hereafter harvest experts) to understand empirical observation and interpretations of restoring balance with sea otters. This work took place within the traditional territories of the Tlingit and Haida people of Southeast Alaska in four rural communities, Kake, Klawock, Craig, and Hydaburg. With Tribal leaders and harvest experts, my collaborators and I used a participatory framework that became a formal partnership to co-develop study goals, objectives, and methodology. Through a multiple evidence-based approach, I co-conducted semidirected and site visit interviews, structured questionnaires, mapping exercises, and participant observation in all four communities, and intertidal bivalve (shellfish) surveys in Hydaburg and Kake. Qualitative and quantitative approaches revealed local and Indigenous knowledge about sea otters caused changes to subsistence shellfish resources and harvesting patterns that included declines in availability and spatial extent of shellfish harvests, and shifts in shellfish harvest hotspots. Community adaptive strategies to observed shellfish declines include shifting harvest locations away from sea otter presence. Community management recommendations about restoring balance with sea otters include increasing sea otter hunting locally using spatially explicit techniques. Financial subsidies for sea otter hunters, creating local tanneries, legal changes to the Marine Mammal Protection Act, and market creation and development for sea otter handicrafts were noted as solutions to barriers of local implementation to management recommendations. Commercial and charter fisheries are other factors that have contributed to shellfish declines. Butter clam (Saxidomus gigantea) size and density declined with increased distance to community and increased sea otter activity near Hydaburg, demonstrating the influence of sea otters and human harvests on bivalve population dynamics. Application of these results about Indigenous knowledge, management, and governance systems to sea otter management in Alaska could create a more inclusive, equitable and community-driven management approach.
    • Bristol Bay dual permit operations, vessel heterogeneity, and the migration of Alaskan permit holders

      Gho, Marcus J.; Criddle, Keith; Adkison, Milo; Adkison, Milo; Twomley, Bruce; Brown, Benjamin (2020-08)
      This dissertation examines three aspects of Alaska's Limited Entry program. Chapter 1 explores the outcome of dual-permit regulations. The Alaska Board of Fisheries passed regulations allowing for dual permit operations in the Bristol Bay Pacific salmon drift gillnet fishery starting in 2004. These regulations allow two permit holders to fish from a single vessel with additional gear. Policymakers anticipated that the dual permit regulations would encourage young fishermen to enter the fishery and reduce the number of limited entry permits transferred from local fishermen to nonlocal fishermen and nonresidents. Statistical analyses reported in Chapter 1 indicate that the dual-permit program successfully offset part of the adverse influence of increases in the market value of permits on the number of new entrants and that implementation of dual-permit regulations was followed by a reduction in the median age of new entrants, particularly among nonresidents. However, the implementation of dual-permit regulation failed to staunch the outflow of limited entry permits. Chapter 2 examines the persistence of heterogeneity in the size of fishing vessels active in the Bristol Bay salmon drift gillnet fishery. When entry was limited, the commercial fishing fleet included a mix of vessels up to the long-established 32-foot maximum length. The race for fish that so often arises under license limitation favors the adoption of vessel and gear configurations that maximize catch-perday and could be anticipated to lead to increased homogeneity in fleet composition. Yet, statistical analyses indicate that even after over four decades, the composition of this fleet remains heterogeneous in vessel size and vessel value. Multivariate analysis of time series observations of vessel values indicates that vessels captained by permit holders who were given their permit are less capitalized than vessels captained by permit holders who purchased their permit. Likewise, vessels operated by local resident permit holders are less capitalized than vessels owned by nonlocal Alaskan or nonresident permit holders. In addition, vessels operated by older permit holders are less capitalized than vessels operated by younger permit holders. Chapter 3 examines the factors that influence the migration of permit holders. Since limitation, there have been concerns that ever more of the permits issued to individuals local to Alaska's fisheries would come to be held by individuals who were not local to the fisheries. The count of permit holders local to a fishery can change because of transfers, administrative cancellations, or because permit holders migrate either to or from fisheries where the permit is used. Chapter 3 considers possible factors that predict permit migration to or from different residency classes. Included in our analysis was a look at season length, fleet participation rates, permit transfers, the size of the fleet, gear type, wages of construction workers to serve as a proxy for substitute employment, and the local unemployment rate. Statistical analyses indicate that fisheries with longer seasons show slightly elevated migration from local to nonresident status of permit holders. Permit latency and permit holder migration have a negative relationship among the significant variables. Transfers serve as a substitute for permit migrations and provide the largest influence on permit migrations. For every resident type of migration, as the transfer rate increases, fewer permit holders migrate. The total number of permits within the fishery also affects the migration of permit holders, albeit only minimally. The second-largest influence on permit migration is gear type. Migrations to local setnet permit holders had a smaller magnitude of change than migrations from permit holders across most categories. Generally speaking, migration tends to move towards a nonresident status of permit holders. Wages of construction workers were only significant at the 5% level for transfers from locals to nonresidents and from nonresidents to locals, but both variables were positive. As the local unemployment rate increases, the rate of locals emigrating outside of Alaska increased.
    • Broad whitefish (Coregonus nasus) ecology and habitat use in Arctic Alaska: spawning habitat suitability, isotopic niches, life-history variations, and climate change risks to subsistence fisheries

      Leppi, Jason C.; Wipfli, Mark S.; Rinella, Daniel J.; Seitz, Andrew C.; Falke, Jeffrey A. (2021-08)
      Broad Whitefish (Coregonus nasus) is a critically important subsistence species for Alaska's Indigenous communities, yet little is known about the basic ecology of this species at the individual level. Understanding habitat use by Broad Whitefish is challenging due to their mobility and our limited ability to track fish throughout their lives as they move among a suite of habitats that are spatially dispersed, change over time, and are often temporary. The Arctic is undergoing major landscape and ecosystem transformation from climate change and oil and gas development, which may threaten Arctic ecosystems used by Broad Whitefish. This dissertation presents new information on the ecology of Broad Whitefish captured in the Colville River, Alaska. In Chapter 1, an intrinsic potential (IP) model for Broad Whitefish was used to estimate the potential of streams across the watershed to provide spawning habitat. Results were compared with movement patterns of radio-tagged prespawn Broad Whitefish. In Chapter 2, ecological niches utilized by Broad Whitefish were investigated via stable isotope analyses of muscle and liver tissue and otoliths from mature fish. In Chapter 3, strontium isotope (⁸⁷Sr/⁸⁶Sr, ⁸⁸Sr) otolith chronologies across individuals' lives were used to quantify life-history attributes and reconstruct migration patterns of fish. Finally, in Chapter 4, the current understanding of ongoing and future changes to the habitat, productivity, and behavior of Broad Whitefish were summarized to assess risks facing Arctic freshwater ecosystems and fishes more broadly. IP model results showed the majority of habitat with high IP (≥ 0.6) was located within the braided sections of the main channel, which encompassed > 1,548 km, and starting in mid-July, prespawn fish used habitats in the middle and lower watershed. Stable isotope analysis revealed a range of [delt]¹³C (-31.8- -21.9‰) and [delta]¹⁵N (6.6- 13.1‰) across tissue types and among individuals. Cluster analysis of muscle tissue δ¹³Cˈ, δ¹⁵N, δ¹⁸O, and δD indicated that Broad Whitefish occupied four different foraging niches that relied on marine-and land-based (i.e., freshwater and terrestrial) food sources to varying degrees across the summer period. Strontium isotopes revealed six main life histories, including three anadromous types (59%), one semi-anadromous type (28%), and two nonanadromous types (13%), suggesting greater complexity in life-history types than previously documented. Climate change is expected to continue to alter Arctic hydrology and, therefore, suitability, connectivity, and availability of habitats critical for Broad Whitefish population persistence. Warming and lengthening of the growing season will likely increase fish growth rates; however, the exceedance of threshold stream temperatures will likely increase physiological stress and alter life histories, which is likely to have mixed effects on Arctic subsistence fishes and fisheries. This information on Broad Whitefish spawning intrinsic potential, foraging niches, and life histories provides crucial knowledge to understand critical habitats used across time and space, which will help managers and conservation planners better understand the risks of anthropogenic impacts, such as climate change and oil and gas development, and help conserve this vital subsistence resource.
    • Current and novel tools in the health assessment of large whales

      Cates, Kelly Ann; Atkinson, Shannon; Bejder, Lars; Cunningham, Curry; Mueter, Franz; Straley, Janice (2021-08)
      Alaskan marine ecosystems are undergoing unprecedented change and species are facing increasingly variable and potentially inhospitable habitats. As top predators, marine mammals serve an important role as sentinels of ecosystem health. With their high site fidelity, abundant numbers, coastal presence and role as a top predator, humpback whales (Megaptera novaeangliae) provide a meaningful view into current ecosystem conditions and processes. In order to tap into their usefulness as bioindicators the basic physiology of humpback whales needs to be understood. Physiological indices can provide valuable information about fecundity, survival, health and population age structuring which is fundamental to cetacean research and population management. However, such information is often difficult to obtain from wild cetaceans as they surface infrequently and often live in remote or logistically challenging locations. As such, few methods currently exist for the assessment of physiological parameters of free ranging, large cetaceans. This dissertation paired existing methods of physiological examination with novel approaches in order to better understand the basic physiology and overall health of humpback whales. Specifically, six enzyme immunoassays were validated for use in humpback whales for progesterone, testosterone, cortisol, corticosterone, aldosterone and DHEA-S, an algorithm termed "Morphometer" was developed to automate the process of measuring and analyzing morphometric measurements, and hormones and body condition metrics were paired to determine whether pregnancy status can be detected from aerial photographs. This project seeks to lay the groundwork for long term monitoring of humpback whales that can provide critical information to managers. By using baseline physiological indices and tools to rapidly analyze these metrics that I developed here, managers and researchers will be able to analyze current and future samples within a longitudinal context and make management decisions based on more accurate biological information for these populations.
    • Environmental impacts on reproductive responses of Pacific walruses (Odobenus rosmarus divergens) and subsistence users of St. Lawrence Island

      Larsen Tempel, Jenell T.; Atkinson, Shannon; Kruse, Gordon H.; Fugate, Corey; Pyenson, Nick (2020-08)
      An interdisciplinary approach is used in understanding change and resiliency in St. Lawrence Island (SLI) resources and resource users throughout this dissertation. Historically SLI inhabitants have relied on the Pacific walrus (Odobenus rosmarus divergens) for their survival and this resource is still highly valued for cultural and dietary purposes. The responses of Pacific walruses and SLI subsistence users to environmental change was analyzed. In walruses, reproductive capacity was analyzed using an anatomical approach as well as reproductive plasticity which was determined using a physiological approach to characterize their estrus cycle. A suite of anatomical measurements were developed to characterize reproductive capacity of walruses by analyzing ovaries from three distinct time frames during a 35-year period. Reproductive capacity was reduced during time frames when carrying capacity (K) was reached and when large environmental changes occurred in the Bering Sea, including years of very low sea ice extent. Reproductive capacity was high in times when K was lower and harvest levels were greater. Our results explained how perturbations in K and environmental changes may have influenced reproductive capacity of the population in the past. Endocrine techniques were used in ovarian tissues to determine if progesterone and total estrogens are useful indicators of female reproductive status in walruses harvested during the spring hunt. Progesterone and total estrogen concentrations were greater in the reproductive tissues of unbred and pregnant females than postpartum females, however neither hormone could distinguish between pregnant and unbred animals. These results provide the first physiological evidence for pseudopregnancy in this species, rather than a postpartum estrus. Lastly, discussions were held with SLI community members to determine changes in key subsistence resources and community resiliency with regard to food security. Walruses ranked highest among key resources. Stakeholders reported limited access and increased effort to hunt walruses, changes in crab abundance, and increases in commercially exploitable fish stocks. Changes were attributed to loss of sea ice, "bad" weather, and climate change. In order for SLI communities to continue their subsistence-based way of life, inhabitants may need to expand their diet to include less-preferred food items in place of harvested ice-associated species. In conclusion, loss of sea ice and rapid environmental changes in the Bering Sea have the potential to greatly impact walrus reproduction and the marine subsistence way of life that is practiced by SLI stakeholders.
    • Reproduction and stress response endocrinology in blue (Balaenoptera musculus) and gray (Eschrichtius robustus) whales

      Melica, Valentina; Atkinson, Shannon; Mueter, Franz; Tamone, Sherry; Gendron, Diane; DeMaster, Doug (2020-12)
      Identification of biomarkers that reflect physiological status is fundamental for assessing population health, as well as providing more accurate estimates of life history parameters. Blue (Balaenoptera musculus) and gray (Eschrichtius robustus) whale populations feed on lower trophic levels and migrate between the eastern Tropical and the eastern North Pacific Ocean. With increasing disturbances (e.g., changing environment and human activities), understanding the stress response, resultant coping mechanisms, and the subsequent effects on reproduction, is of growing importance. While extensive knowledge is available on photo-identification and ecology of these two species, information on physiology is limited and what exists is outdated. This dissertation validated and measured a suite of steroid hormones in blubber tissue using an enzyme immunoassay technique to develop physiological biomarkers for reproduction and metabolism in these two species. Coupled with sighting history data, progesterone and testosterone were validated as biomarkers for reproductive physiology. In both species, progesterone concentrations were higher in pregnant females and mixture models were developed to estimate reproductive status for whales of unknown status. Testosterone showed greater variability in adult males and concentrations were higher in samples collected during fall, suggesting physiological preparation for mating. Additionally, progesterone concentrations in gray whales were higher in calves of both sexes, indicating maternal transfer through lactation, while in blue whales, testosterone was detectable only in males and in pregnant whales, suggesting its biosynthesis or metabolism is altered during gestation. Biomarkers for stress response were developed through analytical and biological validation of three corticosteroid hormones: cortisol, corticosterone and aldosterone. First, analytical validations (i.e., parallelism and accuracy tests) were used to determine detectability and measurement accuracy of these hormones using commercially available kits. Hormone concentrations were tested for any relationships with life history parameters (e.g., age and reproductive state) as well as with area and time of sampling within presumably "healthy" (biopsies) whales and "stressed" (stranded) whales. "Stressed" whales, especially those that perished due to trauma and/or nutritional stress, had higher concentrations of all three corticosteroid hormones than "healthy" whales, suggesting ongoing alteration of metabolic status due to a stress response. In female "healthy" whales, reproductive status appeared to be a major factor influencing corticosterone concentrations in blue whales and for cortisol in gray whales. Overall, cortisol was determined to be a valid marker for body conditions in both species. These results set a milestone for assisting to better understand the impact of a changing environment on the physiology of these species and can be used to develop more accurate reproductive and survival rates to use in population dynamics models for management of subsistence resources and for conservation of endangered species.
    • Sea otters in Southeast Alaska: subsistence harvest and ecological effects in seagrass communities

      Raymond, Wendel W.; Eckert, Ginny L.; Beaudreau, Anne H.; Galloway, Aaron W.E.; Mueter, Franz J. (2020-08)
      The recovery of sea otters (Enhydra lutris) to Southeast Alaska is a conservation success story, but their increasing population raises questions about sea otter population dynamics and the ecological role of this top-level predator. In Chapter 1, we addressed these questions by investigating patterns and population effects of subsistence sea otter harvest. Subsistence harvest reduced populations at a small scale, with potential to slow or stop population growth, but across Southeast Alaska the population continues to grow, even with an average 3% subsistence harvest rate. In Chapters 2 and 3 we investigated the ecological role of sea otters in seagrass (Zostera marina) communities. When we tested for generality in a sea otter - seagrass trophic cascade across a large spatial scale in Southeast Alaska, we found a positive relationship between sea otters and seagrass. However, we found no evidence of a relationship between crabs and epifauna, suggesting that the ecological mechanisms in Southeast Alaska may differ from other regions. Our comparison of carbon and nitrogen stable isotopes (SI) to assess the role of sea otters on trophic structure and energetic pathways of seagrass beds found little effect of sea otters in overall community trophic niche space, suggesting similar carbon sources and food chain length in seagrass meadows regardless of sea otters. Conversely, the FA profiles of diverse consumer suggest variation in dietary sources with and without sea otters. This result suggests that the trophic cascade may not be the only or primary energetic pathway in Southeast Alaska seagrass communities. In all, our studies have revealed that sea otters in Southeast Alaska are linked to both people and a common Southeast Alaska nearshore habitat, seagrass. These results describe the varied interactions of a recovering top predator and highlight a need to consider these diverse interactions in resource management, conservation, and ecological research.
    • Spatio-temporal genetic structure, effective population size, and parentage simulations from contemporary genetic samples and historic demographic data of sockeye salmon (Oncorhynchus nerka) in Auke Lake, Alaska

      Barry, Patrick D.; Gharrett, Anthony; McPhee, Megan; Anderson, Eric; Tallmon, David (2021-08)
      Pacific salmon (Oncorhynchus spp.) have great ecological, economic, and cultural importance. Accordingly, understanding the genetic diversity of Pacific salmon populations is critical for their effective management and conservation. Spatial and temporal homing fidelity, a central life-history characteristic of Pacific salmon, generates genetic structure through reproductive isolation. Within and among populations, heterogeneity in the freshwater environment should lead to selection for traits that maximize fitness resulting in local adaptation. This adaptation increases productivity of individual populations while diversity among populations can promote long-term stability. Additionally, the demographic properties (age structure, generation length, size) of a population will affect genetic structure by regulating its response to the evolutionary forces of selection, migration, and genetic drift. The scale and extent to which reproductive isolation can produce genetic structure is incompletely understood. In this dissertation, I investigated spatial and temporal trends in population genetic structure and estimated the effective population size (Ne) of Sockeye Salmon from Auke Lake in Southeast Alaska from contemporary genetic samples (2008, 2009, 2011) and historic demographic data (1980-2017). A simulation library in the R statistical environment was developed to assess the accuracy of parentage and sibship inference from genetic markers. This library proved useful in evaluating the sibship method for estimating Ne from genetic data and evaluating genetic markers for a large-scale parentage project. I detected substantial genetic differentiation between Auke Lake and other Southeast Alaska populations (average FST = 0.1137) and an isolation-by-time pattern within the Auke Lake population. A genetically distinct cluster was identified in the late portion of the 2008 return. This group may represent a spatially segregated spawning aggregation previously described in tagging studies; however, because fish were sampled as they passed through the weir, spatial structure within Auke Lake could not be evaluated. Genetic tests for demographic change within the population indicated that the Auke Lake Sockeye Salmon population underwent a historical bottleneck event but has since increased in size. Demographic estimates of Ne from a long-term dataset from the Auke Creek weir revealed that the effective population size was low in the early 1980s and has since increased. Over the six generations evaluated, the major demographic factors that determined Ne were variance in family size, variable contribution to the next generation by brood years within a generation, and fluctuations in population size. Contemporary estimates of Ne from genetic methods were smaller than those from demographic methods and indicated that Ne may be roughly the size of an individual return year. Genetic estimates of the ratio of the effective population size to the census size (Ne/Nc = 0.21) were consistent with values previously reported for other salmonids. Collectively, these chapters contribute to an improved understanding of Sockeye Salmon population genetics and provide a useful tool to assess the power of genetic markers for parentage and sibship inference.
    • Spawning migration characteristics and ecology of Eulachon (Thaleichthys pacificus)

      Spangler, Robert E.; Norcross, Brenda; Hay, Douglas; López, J. Andres; Seitz, Andrew (2020-12)
      Eulachon Thaleichthys pacificus has experienced dramatic reductions in their distribution and abundance along the west coast of North America. This prompted the listing of this species as "Threatened" under the U.S. Endangered Species Act (ESA) of 1973 for populations found in the southern portions of their range, but not in Alaska. Key gaps in knowledge of Eulachon spawning ecology exist that impede population monitoring efforts and habitat protection. Currently, many monitoring efforts ignore estuaries as possible spawning habitat leading to inaccurate estimates of population abundance and trends. Furthermore, estuaries are not designated as critical spawning habitat for Eulachon. This is important because a critical spawning habitat designation under the ESA provides for a regulatory framework on which to focus conservation and restoration efforts for some of the most imperiled aquatic habitats in North America. I hypothesized that Eulachon spawn in estuaries based on limited observations in other research and the close phylogenetic relationship between Eulachon and other smelts (Osmeridae) that can tolerate salinity. To test this hypothesis, I first studied the effects of salinity on the fertilization and hatching success of Eulachon in a laboratory setting to determine salinity tolerance. Second, I investigated estuary spawning in the Twentymile and Antler rivers, Alaska using radio telemetry and substrate surveys to confirm spawning areas. Third, I examined the relationship between adult spawning run intensity and the environmental variables of tide height, water discharge, and day or night to better inform future population monitoring efforts. My findings in the laboratory indicated that Eulachon can fertilize eggs and produce viable offspring in brackish water. These results were confirmed by egg areas observed in the estuaries of the Twentymile and Antler rivers. Furthermore, spawning run intensity increased in association with spring tides, but there were no clear relationships between spawning run strength and freshwater discharge or day and night. Based on the results of my work, I recommend changes to population monitoring study design and designation of critical spawning habitat to include estuaries. Future research should focus on determining the lower limits of Eulachon spawning habitat to further improve population monitoring and habitat protection.