• Ocean and stream ecology of adult hatchery and wild pink salmon

      McMahon, Julia; Westley, Peter; Gorman, Kristen; McPhee, Megan; Rand, Peter (2021-08)
      In this thesis I investigate potential interactions of hatchery and wild pink salmon (Oncorhynchus gorbuscha) at sea and on the spawning grounds, in the context of the ecological and economic importance of modern Alaskan hatcheries. Although hatchery and wild salmon are known to interact, the nature and outcome of those interactions remain unclear. Here, I identify potential mechanisms of competition and hatchery salmon fitness with two datasets from Prince William Sound, Alaska, home to the largest pink salmon hatchery program in the world. First, I compared fitness-related traits such as body length, return timing, instream lifespan, and egg retention between straying hatchery and homing wild pink salmon to identify potential barriers or bridges to gene flow with over 120,000 individuals sampled over six years (2013-2018). Predicted lengths of hatchery and wild fish depended on the even or odd year lineage, return timing, and sex. Odd year pink salmon were smaller on average than even year pink salmon, odd year hatchery fish were smaller than wild fish, odd year length decreased over the season, and odd year males tended to be larger than females. In even years, hatchery pink salmon were larger on average than wild pink salmon, length increased over the season, and hatchery females were larger on average than any other group. I found no statistically significant differences in instream lifespan (2017: t-test (₂₀.₅₄), P = 0.41; 2018: t-test(₆.₂₆), P = 0.556) or egg retention (x²₍₂₎= 4.5, p = 0.11; 2017 and 2018 combined) between hatchery and wild fish. In contrast, I detected significant differences in stream life of the wild fish between two different sized streams in a manner consistent with observed black bear (Ursus americanus) predation; specifically stream life was shorter in the smaller stream with markedly higher predation. Second, I used stable carbon and nitrogen isotope analysis to test the hypothesis that hatchery and wild pink salmon have distinct foraging niches during their last months at sea, which could underpin observed differences in length between hatchery and wild pink salmon. Using data from 2015, I fit linear models and detected no difference in broad-scale foraging locations (delta¹³C values) of hatchery and wild pink salmon. However, trophic positions (delta¹⁵N values) for hatchery and wild pink salmon were inversely related to size where large wild salmon and small hatchery salmon tended to have the highest delta¹⁵N values. Because delta¹³C values and delta¹⁵N values of wild fish were positively associated with body size, it is likely that hatchery and wild pink salmon have size-dependent, yet still overlapping foraging niches. Overall, these results are consistent with the potential for hatchery and wild pink salmon to compete for resources on the spawning grounds and at sea to the extent that resources are limiting.
    • On estimating rotor noise generated by small unmanned multirotors

      Holst, Brian; Peterson, Rorik; Chen, Cheng-fu; Hatfield, Michael (2021-08)
      Unmanned aerial vehicles are utilized for missions ranging from wildlife surveillance to delivery of commercial goods. Previous research at the Alaska Center for Unmanned Aircraft Systems Integration (ACUASI) at the University of Alaska Fairbanks has focused on the monitoring of different species of wildlife, and some of this research was conducted utilizing multirotors. This work presents an introductory investigation and analysis of the acoustic noise generated by a single 15-inch rotor and applies this noise model to multiple rotors on a multirotor. The rotor is analyzed utilizing semi-empirical calculations and this work presents the process to continue acoustic analysis through simulation and analytical computation. Although this work studies, specifically, the 1555MR propeller designed by Advanced Precision Composites Propellers, the semi-empirical equations can be applied to other rotor designs. By investigating the analytical process, this work also presents a potential route through theory to identify the sound produced by these multirotors. The flow solution requires computational fluid dynamics software to output the flow on and around the rotors; this output can then be used for the analysis of noise. The total noise generated in stable hover is considered with certain assumptions about the blade geometry and aircraft motion. This work is organized into four chapters that detail the background, motivation, theory, setup, methods, results and conclusion. By utilizing this work and the works cited, readers and the researchers at ACUASI should understand the theory and be able to reproduce the results herein. With the estimation of noise of these multirotors, ACUASI will be able to refine their wildlife monitoring missions to ensure the observed animals are less affected by the noise generated by these vehicles.
    • Paleocene depositional history of the Cretaceous-Paleogene impact basin, Yucatan Peninsula, Mexico

      O'Malley, Katherine E.; Whalen, Michael; Fowell, Sarah; McCarthy, Paul (2020-12)
      In the spring of 2016, the International Ocean Discovery Program set out on Expedition 364 to recover core from the peak ring of Chicxulub Impact Crater at Site M0077. In total, 829 m of core was collected spanning granite to Paleogene sedimentary rocks. From this core, we have a well-preserved record of the Paleocene, which represents ~10 million years post impact in just under 10 m of sedimentary rock record. This has presented an incredible research opportunity, as we have gained invaluable information on how the environment responded and recovered from the global catastrophe that was the Chicxulub Impact. The Paleocene at M0077 is highly condensed and comprised of predominantly pelagic carbonate rocks. High resolution core logging and thin section analysis were used to identify facies in the Paleocene. Facies include marlstone, argillaceous wackestone, foraminiferal wackestone, and rare coarser grained lithologies such as packstone and grainstone. Overall, the Paleocene exhibits a succession of rhythmically bedded cycles composed of marlstones grading to argillaceous wackestones and capped by foraminiferal wackestones. Coarser grained lithologies only exist in the lower and uppermost portion of the core. In total, 72 cycles that ranged from 5-30 cm thick are identified and grouped into six larger packages based on pattern similarities in color, lithology, ichnofabric indices, and geochemical data. These cycles are interpreted as parasequences, and show predictable stacking patterns that allow us to make sequence stratigraphic analyses. Each package represents one to two systems tracts, and some can be correlated to eustatic sea level change. Recorded in this core is the progression of an initial sea level lowstand immediately post impact, and the fluctuation between highstands, lowstands, and transgressive systems tracts that follow. Major and trace elements were analyzed throughout the core, as well as delta¹³Corg and delta¹⁵Nbulk values. Three sets of geochemical proxies (paleoredox, detrital input, productivity) were used to provide insight into paleoecological conditions. Initial conditions in the crater show a period of high productivity, which tapers off within a million years post impact. Redox conditions vary, and show one major anoxic event, with other enrichments likely representing periods of pore water euxinia or increases in stratification leading to a more robust redox gradient.
    • Photosensitized degradation of chlorothalonil and chlorpyrifos in the presence of Arctic derived dissolved organic matter

      Quesada, Ginna; Guerard, Jennifer; Rasley, Brian; Green, Thomas (2021-05)
      Pesticides used at mid latitudes can accumulate in Arctic environments. Two commonly detected pesticides in Arctic lakes are chlorothalonil and chlorpyrifos. In surface waters, photolysis can play an important role in the attenuation of contaminants. The chemical characteristics of dissolved organic matter (DOM) can further alter the extent of photolytic degradation of pollutants. To determine the relative effect of natural Arctic lake water and its DOM on the photolysis of chlorpyrifos, experiments were conducted under natural Arctic irradiation and under artificial irradiation. Similarly, the effect of Arctic DOM was investigated for chlorothalonil under artificial irradiation. The fulvic acid (FA) fraction of DOM was isolated from Fog 1 and from Toolik Lake in May and July. Lake waters significantly enhanced the photodegradation of chlorpyrifos under natural light by up to an order of magnitude. FA's significantly increased the degradation of chlorpyrifos (>2x) and chlorothalonil (>100x) under artificial irradiation relative to 18 MΩ-cm Water. Toolik Lake FA isolated in May, significantly enhanced the photolysis of both contaminants relative to the isolate collected in July. In the presence of iron, a lower ratio of carbohydrates and peptides to aromatics in the FA's was associated with faster degradation for chlorothalonil.
    • Plasma transport and magnetic flux circulation in Saturn's magnetosphere

      Neupane, Bishwa Raj; Delamere, Peter; Ng, Chung-Sang; Newman, David; Wackerbauer, Renate (2021-08)
      The magnetospheres of outer planets are very different than the terrestrial magnetosphere. The magnetosphere of Saturn is rapidly rotating, and has its own plasma source. Enceladus located around 4Rs is the main source of plasma. The strong magnetic field of Saturn's magnetosphere picks up the plasma which experiences a strong centrifugal force in the non-inertial reference frame. The plasma produced in the inner magnetosphere has to be transported radially outward and lost to the solar wind. The transport of plasma in Saturn's magnetosphere is not fully understood. It is believed that transport is centrifugally-driven, occurring via flux tube interchange motions in the inner magnetosphere and via plasmoid expulsion in the magnetotail due to reconnection. It has been found that these mechanisms are not sufficient to explain the transport. We tried to determine different possible transport mechanisms that could exist in the outer planetary magnetosphere. Ma et al. (2019a) showed the low-specific entropy plasma with a narrow distribution in Saturn's inner magnetosphere and suggests a significant nonadiabatic cooling process during the inward motion while high specific entropy suggests the nonadiabatic heating during the outward transport. We have estimated the outward plasma transport rate about 55 kg s⁻¹. The calculation of magnetic flux transport and analysis of magnetic field data indicates that plasma transport in the Saturn magnetosphere could be dominated by small scale magnetic reconnection.
    • The politics of penguin pleasure: why animal sexualities matter to humans

      Emanuel, Nicole; Schell, Jennifer; Heyne, Eric (2021-08)
      This thesis is about what it means to think with penguins. It explores the ways in which we form ideas about these animals, and how those ideas can impact our beliefs about our own lives, penguins' lives, and the kinds of relationships that exist among humans and non-humans. It includes a survey of penguin representations across media and culture, particularly focusing on children's television and movies, nature documentaries, and non-fiction accounts of polar travel. While these penguin-centric texts can vary strikingly in tone, the penguins themselves appear again and again in an appealing light. Across a wide range of time and media, penguins are frequently portrayed as spunky, determined, and battling incredible odds to survive. That popular image of the plucky penguin has lent itself surprisingly well to debates about the naturalness of same-sex parenting in human society. The film The March of the Penguins (which was embraced by conservative Christians for its depiction of "traditional family values") and the picture book And Tango Makes Three (about two male chinstrap penguins who managed to successfully hatch an egg together at the Central Park Zoo) illustrate two sides of these public conversations. As the close reading and theoretical analysis performed in this thesis indicate, both views fail to truly understand penguins as living, courting, mating, reproducing beings. The behaviors of these actual animals are far too complex and varied to reduce to an alignment with either side of this fight over human concepts and morals.
    • Presentation of immunodominant peptides is strongly dependent on cathepsin resistance and preliminary cleavage of antigens

      Becker, Tynan; Ferrante, Andrea; Kuhn, Thomas B.; Chen, Jack; Leigh, Mary Beth (2021-08)
      An understanding of the basis for immunogenicity (the ability of a foreign substance to induce an adaptive immune response) is critical for advancing our knowledge of infectious or autoimmune diseases, as well as contributing to the design of vaccines and biologics. A key step in the initiation of an adaptive immune response is the presentation of pathogen-derived peptides by major histocompatibility class II (MHCII) molecules on the surface of antigen-presenting cells (APC) such as a dendritic cell (DC) to CD4⁺ T cells. Peptides that are superior at eliciting strong T-cell responses are termed immunodominant. The generation and selection of peptides occurs within a system of endosomal compartments that form when a DC takes up the antigen. These compartments become increasingly more acidic and reducing as proteolytic enzymes, MHCII and a peptide binding modulator human leukocyte antigen DM (HLA-DM, DM) are trafficked through to facilitate the degradation of proteins and the loading of peptides onto the MHCII. Although the general aspects of the antigen processing and presentation mechanisms are understood, important details of the endosomal machinery have yet to be determined. These studies focus on the elucidation of the pathways of antigen processing, the contribution of proteolytic cleavage to immunodominance, and the activity of four proteases in the cysteine family of cathepsins. Our findings strongly implied the existence of multiple, parallel pathways within antigen processing. These include the ability of MHCII to capture the native form of hemagglutinin (HA) from influenza A/New Caledonia 20/99 (H1N1), our model antigen, and the production of unique peptidomes through cleavage alone or through cleavage and capture by MHCII, in the presence or absence of DM, at varying pH. I demonstrate that one determinant for immunodominance is peptide resistance to cleavage by cathepsins, although it does not hold true for every immunodominant peptide. I establish that the cleavage of a protein and the generation of peptides available for binding to MHCII is strongly influenced by the pH and reducing potential of the cleavage environment as well as the flexibility of microdomains of the protein itself. Collectively, these results show that the cleavage events of antigen processing are pivotal to the generation of a broad and diverse peptidome available for binding to MHCII, and presentation to T-cells, that may lead to a more robust adaptive immune response.
    • Reevaluating recent temporal trends in animal body size: the role of demography

      Theriot, Miranda K.; Olson, Link; Doak, Patricia; Millien, Virginie (2021-05)
      Climate change over recent decades is associated with varied responses in animals, including both increases and decreases in body size. These opposing trends are often attributed to two primary hypotheses. In warm-blooded vertebrates, Bergmann's rule predicts decreases in average size with increasing temperature, based on the relationship between body size and thermoregulation. Alternatively, increased average body size is linked with changes in resource availability as summer growing seasons lengthen and winters becomes milder. We propose a third explanation, that shifts in demography underlie some of these observed trends, as many species change in size or shape throughout life. The influence of thermoregulatory demands, resources, and demography on body size trends are not mutually exclusive; disentangling these effects and identifying overarching patterns requires detailed analyses across multiple locations and taxa, which in turn necessitates repeatable and expandable studies. To that end, here we propose three best practices in body size research: defining and justifying measures of size, citing museum specimens, and accounting for demography. We employed these guidelines in a study on masked shrews (Sorex cinereus) in Alaska. We found evidence of age-based differences in total body length, tail length, skull length, and skull width; however, correcting for age did not have a strong effect on the apparent trends in size over time. Based on linear mixed models, mean total length and tail length increased from 1951-1991, consistent with previous findings. Additionally, our results revealed slight increases in mean skull length and toothrow length over the 40-year study period. There was some indication of differing trends between age classes in both of these measurements. These results were not statistically significant, but our sample size of overwintered adults was relatively small, so further study is needed to fully investigate age-specific size trends in masked shrews. In summary, this thesis highlights the importance of repeatability in body-size research and emphasizes the importance of demography in the study of these trends.
    • 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.
    • The reproductive biology of yelloweye rockfish (Sebastes ruberrimus) in Prince William Sound and the Northern Gulf of Alaska

      Arthur, Donald E.; Falke, Jeffrey; Beaudreau, Anne; Sutton, Trent; Blain-Roth, Brittany (2020-12)
      Over the last half century, Yelloweye Rockfish Sebastes ruberrimus have experienced dramatic declines along the West Coast of the United States and British Columbia. Efforts have been made throughout the species' range to rebuild and sustainably manage stocks, including the introduction of a Statewide Rockfish Initiative by the State of Alaska, which intends to develop management strategies for Yelloweye Rockfish in the Gulf of Alaska. To support this effort and address information gaps in Yelloweye Rockfish reproductive biology throughout their range, I estimated important reproductive parameters and life history information for Yelloweye Rockfish in Prince William Sound and the Northern Gulf of Alaska, Alaska, that included maturity, parturition timing, skip spawning, and fecundity relationships. I identified that ages-at-50% maturity (A50) for males and females were similar (A50 = 15 years and A50 = 16, respectively), but males reached full maturity (A95) earlier than females (male A95 = 19 years and female A95 = 31 years). Female Yelloweye Rockfish fork length-at-50% and 95% maturity (L50 and L95) was greater in the Northern Gulf of Alaska (L50 = 46.7 cm and L95 = 55.8 cm) than in Prince William Sound (L50 = 41.1 cm and L95 = 50.2 cm). Similarly, male L50 and L95 was greater in the Northern Gulf of Alaska (L50 = 44.0 cm and L95 = 49.2 cm) relative to Prince William Sound (L50 = 40.8 cm and L95 = 46.0 cm), and males matured at a smaller size than females. Female L50 was consistent with data from southern populations, but A50 was younger than predicted based on a latitudinal trend, indicating that Yelloweye Rockfish in this region may experience greater than expected growth rates. Yelloweye Rockfish underwent parturition between May and August and peaked in June and July, and parturition timing was earlier for larger and older females. I documented that female Yelloweye Rockfish skip-spawned at a rate of 9.8%. Skip spawning rate was associated with fork length and peaked at sizes between 40.2 cm and 52.3 cm; the peak in stock reproductive potential is shifted toward larger females in response to skip spawning. I conducted egg and larvae counting in an image-analysis software, which was more than four times faster than manual counting and was equally accurate and precise. Yelloweye Rockfish fecundity scaled hyperallometrically with FL and relative fecundity increased with length, indicating that spawning stock biomass may not be proportional to total egg production. Combining these results, I found that ignoring the hyperallometric fecundity relationship and skip spawning could overestimate reproductive potential by as much as 66% and 45% for Prince William Sound and the Northern Gulf of Alaska, respectively. The results of this study will improve the estimates of stock-recruitment dynamics and can be readily integrated into a stock assessment that will guide the sustainable management of Yelloweye Rockfish in Prince William Sound and the Northern Gulf of Alaska.
    • The rocky shores of Prince of Wales, Alaska: intertidal ecology, abalone, and community sustainability

      Bolwerk, Ashley; Eckert, Ginny L.; Carothers, Courtney; Dethier, Megan (2021-05)
      Rocky, nearshore ecosystems are diverse and dynamic environments that function as the link between land and sea and provide important resources for people. In this two-part thesis, I first examined rocky intertidal ecological communities to better understand biotic and abiotic drivers in this system, and then I investigated the abundance of pinto abalone (Haliotis kamtschatkana), a key subsistence resource that local community members identified as the most important because of limited harvest and drastic declines. Pinto abalone are tied to Haida subsistence, culture, and spiritual identity and have been a traditional harvest species for the Haida people for millennia. Pinto abalone were harvested by non-Native fishermen through heavy commercial (1970-1996) and personal use harvest, causing a crash of the population. In the rocky intertidal I surveyed the upper and lower extents of major biobands, frequency of occurrence of sessile organisms, and abundance of mobile invertebrates across a vertical gradient at 18 sites near the west coast of Prince of Wales Island. A multivariate approach was used to identify the major drivers of rocky intertidal community composition and structure. Sea otter (Enhydra lutris) occupation time, average fetch, beach aspect, rugosity, and rock texture were all identified as influential forces for at least one tidal zone and/or biological metrics. Sea otters were not found to restructure the ecosystem, as they do in deeper kelp forest habitats. To assess the current viability of pinto abalone harvest, concerns about sustainability, and their ecological relationships, I partnered with local harvesters within the community of Hydaburg on Prince of Wales Island to combine Indigenous Knowledge about pinto abalone harvest with SCUBA surveys at historically productive traditional harvest sites. Only four (out of 17) of our shallow transects (2 x 20 m), which are within the depth range for traditional harvest methods, had legal-sized pinto abalone (max = 1 abalone). The traditional pinto abalone harvest fishery failed three out of four fishery recovery criteria that were examined. Fourteen out of eighteen sites did not have large (≥ 100 mm) pinto abalone, and pinto large abalone densities were below 0.1 abalone/m2 at all sites. All intermediate size classes of pinto abalone were represented within the fishery, but only 20% of large size classes were observed. Low pinto abalone abundance leads to concerns about traditional harvest viability and spawning failure and thus recruitment failure, for this density-dependent spawning species. In our generalized linear models, pinto abalone presence, density, and biomass were affected by sea urchin biomass. This baseline study of the current state of pinto abalone at traditional harvest sites bestows critical information to a community that depends on pinto abalone as a resource. The Hydaburg Cooperative Association, as a federally recognized Tribe, can use this information to make local management decisions, which include adjustments to harvest guidelines, implementation of sea otter management zones, and/or the establishment of pinto abalone restoration projects. Working with the Tribe and community members throughout the research process led to better science, applicable data, and took a step toward equity and reciprocity in the research processes.
    • Safety analysis of off-highway vehicles use within public rights-of-way in Alaska

      Sayre, Tristan; Belz, Nathan; Barnes, David; Falchetto, Augusto (2020-08)
      Many Alaskans own and operate off-highway vehicles (OHVs) for recreational purposes or for use as primary and secondary modes of transportation. However, the reported crash rate shows that 80 on-road crashes, resulting in five fatalities, occur each year statewide. As a result, the use of OHVs has been identified as a safety concern in the Alaska State Highway Safety Improvement Plan. Minimal research dedicated to understanding OHV use in Alaska exists which limits the potential for improvements that address safety concerns in an equitable fashion. The research presented here contributes to better understanding of on-road OHV use through observational and retrospective analysis. Field-based observations were conducted within highway rights-of-way in 14 strategic locations across Alaska to quantify OHV use and the risk-taking behaviors of riding without helmets, passengers riding without a designated seat, and riding unlawfully on the road. Additional risk factors from the field observations and Alaska Department of Motor Vehicles (DMV) crash data for the period from 2000 through 2016 were identified using the Chi-Square test for independence. Spatial analysis of the Alaska DMV crash data for the period from 2009 through 2016 tested for complete spatial randomness of crashes and identified clusters of crashes by frequency and severity using neighborhood point density statistics. Frequent OHV use was observed with daily traffic volumes exceeding 40 vehicles per day in three field study locations. Several risk-tolerant behaviors were observed including users riding without helmets and vehicles carrying passengers without a designated seat an average of 70 and 20 percent of the time, respectively. Additionally, over half the OHV users were observed to be riding unlawfully using the road. Risk-tolerant behaviors were most frequently observed in communities where on-road use is legal and happened to be coincident with the highest on-road use rates. Overrepresented risk factors for high crash severity incidents included riding at night, in summer, on unpaved roads, on local roads or collectors, in rural areas, for single-vehicle crashes with the occupant not using safety equipment and riding under the influence of alcohol. Crashes were observed to be clustered around towns with the highest frequencies occurring near town centers. The prevalence of risk-tolerant riding behaviors and unlawful on-road riding indicates the need for improvements to existing laws and the education and enforcement thereof. Changes must address the unique needs of users while also considering local jurisdiction such that safety can be improved while also maintain transport equity for residents of rural and isolated communities in Alaska.
    • Salmonid distribution models to support restoration planning across the fragmented Chehalis River basin, WA

      Walther, Eric J.; Westley, Peter; Zimmerman, Mara; Falke, Jeffrey; Seitz, Andrew (2021-05)
      Understanding the factors that influence the distribution of species through time and across space is a fundamental goal of ecology and crucial information needed to effectively manage and recover populations. Anthropogenic fragmentation of habitat disrupts ecological processes and is an on-going threat to species persistence across taxa. River ecosystems are particularly vulnerable to disruptions in connectivity and are the focus of extensive restoration efforts and financial investment. For example, over $300 million/year is invested towards restoration in the Columbia River basin. However, restoration is often impeded by knowledge gaps in distribution that can result in omitting locations that would benefit from restoration. For mobile species within dendritic freshwater networks, the boundary that demarcates the total quantity of available habitat can be defined by the upper limit of occurrence (ULO) and is a useful metric for assessing the extent of habitat to consider for restoration. The first goal of this work was to identify the ULO boundary for three socially and ecologically important anadromous fishes (Oncorhynchus spp.) in a subset of representative streams across a complex river network in southwestern Washington State, USA, and quantify the relationship of the ULO with landscape attributes for these species. Extensive field surveys covering 669 river km across two years documented the ULO in 115 terminal streams (i.e., uppermost independent stream segment within a stream network) for coho salmon (O. kisutch), 97 terminal streams for steelhead trout (O. mykiss), and 57 terminal streams for chum salmon (O. keta). The landscape attributes associated with these ULO locations varied among species. For example, precipitation was an important predictor only for coho salmon, whereas slope was an important predictor only for steelhead trout. In contrast, drainage area, elevation, and geology were important predictors for all species; while the direction was the same for drainage area and elevation, the magnitude of the effect of each landscape attribute varied among species. I demonstrated that large-scale landscape attributes can accurately and consistently detect species-specific distribution boundaries across broad and diverse habitat (percent correct classification:78%-89%; area under the receiver operating characteristic curve: 0.87-0.96). The ability to quantify landscape attributes related to distribution boundaries illuminates how the biology and life history of a species is captured across the landscape. The second goal of this work was to predict the range of occurrence as a function of landscape attributes for coho salmon, steelhead trout, and chum salmon across a range of probability decision thresholds, that reflect different risk-tolerance scenarios and determine whether stream reaches are within or outside the range of occurrence. Generalized linear mixed models were used to compare the quantity of currently described distribution used in restoration planning in the basin and quantify the amount of habitat inaccessible due to anthropogenic barriers. The change in amount of habitat within the predicted range of occurrence across probability decision thresholds ranged from 60%-74% among species. Differences between the model predictions and the currently described distribution for each species ranged from -14% to 171%, which on a whole indicates that the amount of habitat being considered for restoration is currently underestimated. As predicted, species with a greater range of occurrence (e.g., coho salmon) had a greater percentage of predicted suitable habitat inaccessible due to anthropogenic barriers (coho salmon:17.4%-28.8%, 0.75-0.25 PDT; steelhead trout:10.2%-17.5%; chum salmon: 3.9%-12.3%), and the locations of these barriers varied among species. Modelling species distributions at multiple levels of risk-tolerance allows practitioners to weigh the ecological benefits and financial investment when considering locations for restoration. Ultimately, the effective consideration of restoration actions requires tools such that managers can weigh the trade-offs of their decisions given that not all actions equitably benefit all species.
    • Sea otter diet composition with respect to recolonization, life history, and season in southern Southeast Alaska

      LaRoche, Nicole; Pearson, Heidi C.; Eckert, Ginny L.; Miller, Todd (2020-12)
      Until translocation efforts in the 1960s, sea otters (Enhydra lutris) were absent from Southeast Alaska due to extirpation by the fur trade in the 18th and 19th centuries. About 400 sea otters were reintroduced to six Southeast Alaska locations, including two sites near Prince of Wales Island in southern Southeast Alaska. The most recent US Fish and Wildlife Service population count, completed in 2012, estimated that about 25,000 sea otters inhabited Southeast Alaska. Sea otters will reduce invertebrate prey biomass when recolonizing an area. By quantifying sea otter diets and caloric intake according to recolonization patterns, we can better understand the ecosystem impacts of sea otter population increase and range expansion. The goal of this study was to quantify changes in seasonal diet composition and assess the energetic quality of sea otter prey in southern Southeast Alaska. I made visual foraging observations of 3,385 sea otter dives around Prince of Wales Island (POW) to determine diet composition during the spring and summer months. I then collected vibrissae from 45 sea otters obtained from subsistence hunters to assess year-round sea otter diets using stable isotopes. I collected sea otter prey items throughout POW in three seasons (May 2018, August 2018, and February 2019) to measure energy, lipid and protein content, and delta¹³C (carbon) and delta¹⁵N (nitrogen) values. Sea otter diets mainly consisted of clams, as quantified both from visual observations and stable isotope analysis. However, there was more variation in the diet estimates from stable isotope analysis. Stable isotope analysis revealed variation among individual diets of sea otters and individuality in diet within the POW region of sea otters. Sea otters seasonally increased consumption of some prey when the prey was highest in lipid and overall caloric content. Sea otters switched prey types when the prey was more energetically valuable. The results of this study will aid in future management of shellfisheries, subsistence hunting, and implementing co-management of a protected species by providing quantitative diet composition data for stakeholders. This work is a part of a large-scale project examining how the recovery of sea otters structures nearshore marine ecosystems, provides ecosystem services, and affects community sustainability.
    • 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.
    • Sea urchin ecology: effects of food-web modification, climate change, and community structure

      Weitzman, Benjamin P.; Esler, Daniel; Konar, Brenda H.; Hardy, Sarah M.; Johnson, Mark A.; Tinker, Martin T. (2020-08)
      Ecosystem structure and function of temperate rocky reef habitats are subject to change as a result of food-web modification, climate change, and changes in biological community interactions. Sea urchins are a global driver of change in nearshore marine habitats though their ability to heavily graze marine vegetation and force rocky reef ecosystems from kelp forest to sea urchin barren ground states. The Aleutian Archipelago in southwest Alaska provided an ideal natural laboratory to study sea urchin (Strongylocentrotus spp.) ecology following the functional loss of the keystone predator, the sea otter (Enhydra lutris) during the 1990s. The objectives of this dissertation were to 1) determine the important drivers of sea urchin demographics following the functional loss of their keystone predator; 2) determine how projected ocean warming and acidification may affect sea urchin physical condition; and 3) identify biological drivers of sea urchin recruitment in both kelp forest and barren ground habitats. To determine demographic drivers, I used a time series of benthic habitat, sea urchin demographic, and environmental data, dating back almost forty years. In the absence of sea otters, environmental conditions, specifically ocean temperatures, became more important to sea urchin demographics, but recruitment was the primary process affecting the resultant abundance and size class structure over time. To understand how predicted ocean warming and acidification could impact S. polyacanthus survival, growth, calcification, gonad development, and energy content, a 108-day laboratory experiment was conducted. This experiment determined that temperature caused a greater reduction in survival than acidification, and that projected changes in temperature and acidification will result in investment trade-offs between reproduction and maintenance or growth of somatic and calcified tissues. To determine how recruitment varied between kelp forest and sea urchin habitats, fine-scale surveys of benthic community structure found that specific taxa, and not overall community structure, correlated with sea urchin recruitment. Results from this dissertation will allow managers to make predictions about how sea urchin demography will change as a result of keystone predator loss and climate change and how that will affect nearshore community structure and function. Overall, my dissertation establishes likely pathways by which coastal habitats may change over time, in a system no longer under strong top-down control.
    • Searching the soil: characterizing the effects of disturbance on soil microbial communities and plant productivity

      Seitz, Taylor J.; Drown, Devin M.; Mulder, Christa; Briggs, Brandon (2021-08)
      The effects of global climate change are accelerated and more pronounced in northern regions, and Alaska is at the forefront of that change. Permafrost, which underlies much of the Alaskan landscape, is rapidly thawing and degrading leading to shifts in hydrology, soil chemistry, and nutrient availability. As permafrost thaws, soil microbial communities have the potential to be influenced taxonomically and functionally. However, it is unclear how active layer microbial communities, which play a role in plant-microbe interactions, are affected by increasing soil disturbance, and how soil microbiomes can influence above ground plant communities. In this study, I aimed to understand how soil microbial communities from Interior Alaska are affected by increasing disturbance, and how they in turn drive the productivity of several plants found in boreal regions. Here I used a growth experiment and found that plant productivity was affected by the disturbance level of the microbial inoculant. Plants grown in soils inoculated with microbes associated with disturbed soils demonstrated significantly decreased productivity compared to plants inoculated with microbes from undisturbed soils. Through metagenomic sequencing, I observed broad scale shifts in community membership across the gradient of soil disturbance. I then continued to characterize the microbial communities used as inoculants in the greenhouse growth experiment through 16S rRNA amplicon sequencing. Microbial communities from disturbed soils were significantly more diverse than those from undisturbed soils, and the beta diversity of communities varied significantly based on the disturbance level. We found that within disturbance level community variation can be used to predict plant growth of bog blueberry, low-bush cranberry, and Labrador tea once the disturbance passes a threshold. These results suggest that as active layer microbial communities are affected by climate-driven soil disturbance, above ground plant communities may demonstrate decreased productivity, and consequently, decreased ecosystem health as the Arctic continues to warm.
    • Seasonal variation in nutritional biomarkers and fecal cortisol concentrations in a northern population of snowshoe hares

      Montgomerie, Claire Kornet; Kielland, Knut; Breed, Greg; Lian, Marianne (2020-08)
      Blood biomarkers indicative of nutritional status, fecal cortisol metabolite concentrations and an established body condition index (BCI), were collectively examined from snowshoe hares(Lepus americanus) inhabiting northern Alaska in 2018, during five ecologically significant times of year. As a novel approach to increase our understanding of the effects of diet and predation pressure on hare physiology, I addressed how these markers were associated with seasonal timing of energetic demands and adult survival rates. Mean decreases in concentrations of total protein (TP), blood urea nitrogen (BUN), hematocrit (HCT) and glucose during spring and autumn, suggest that snowshoe hare nutritional status decreased during these two seasons in 2018. The shoulder seasons of spring and autumn coincide with energetic challenges, including molt, changes in diet and breeding. Because available forage during these seasons largely consists of winter-dormant twigs, the energy expenditure of growing a new winter coat (autumn) and breeding behavior (spring) may compromise the energy balance of hares during these periods. Male hares, whose activity levels increase during breeding, exhibited lower BCI scores and were slower to molt from white to brown than female hares in May. Furthermore, adult survival rates were lowest during spring months. Snowshoe hare mean fecal cortisol metabolite concentrations did not show associations with seasons of apparent low nutritional status. Adult hare survival rates peaked during summer and early autumn, during which mean values of TP, BUN, Hct, Cl (chloride), Na (sodium) and glucose also increased. By contrast, this period coincided with a 2-fold increase in mean fecal cortisol metabolite concentrations, suggesting that the apparent stressor was not related to nutrition. Interestingly, after having decreased in autumn, BUN, Hct, TP, and glucose mean concentrations increased in midwinter. Free calcium (iCa) and potassium (K) mean concentrations were also highest in December. Hares may have reduced activity during winter months, and metabolic rates may have increased to cope with thermoregulation demands. BCI scores decreased by December, suggesting use of endogenous reserves. Lowest seasonal mean cortisol metabolite concentrations were also observed in mid-winter. This study demonstrates the value of examining both physiological and morphological metrics of snowshoe hare condition to better our understanding of how seasonal trends in food and fear may unfold into cyclic patterns.
    • A sled dog model for positive health effects of weight management and exercise

      Falkenstein, Laura Kay; Dunlap, Kriya; Coker, Robert; Jerome, Scott (2021-08)
      Hypertrophic white adipose tissue found in obesity leads to chronic inflammation and reduced insulin sensitivity, bringing rise to a myriad of diseases and is a significant risk factor for premature death. Obesity can be combatted with physical activity, dietary restrictions, or a combination of the two. However, exercise training regardless of changes in body weight has been shown to improve metabolic health. Expanding on a previous study of changes in metabolic biomarkers upon weight gain and after a period of athletic conditioning, in this project we used a sled dog model to examine biomarker shifts over a course of sedentary weight gain, exercise training without weight loss, and exercise training accompanied by weight loss. In order to examine the benefits of exercise training both with and without weight loss, a cohort of healthy sled dogs each served as their own controls as we observed changes in metabolic indices in conjunction with moderate body weight gain, exercise training while sustaining the higher body weight, and exercise training with weight loss.We focused on indices specifically linked to type II diabetes - an obesity-linked disease affecting more than 10% of American adults. Biomarkers measured include plasma glucose, glucose transporter 4, insulin, and hemoglobin A1c. We also measured inflammatory cytokines tumor necrosis factor alpha and interleukin 6, as well as hormones leptin, adiponectin, and resistin. Many biomarkers measured produced not significant change or fell outside of our standard concentrations, but plasma glucose, glucose transporter 4, and tumor necrosis factor alpha produced intriguing results. Weight gain increased plasma glucose while exercise training increased glucose transporter 4 present on peripheral blood mononuclear cells. The changes we observed to plasma glucose, glucose transporter 4 and tumor necrosis factor alpha may be indicative of reduced insulin sensitivity with exercise and weight loss. We believe this may be the result of the high energy demand of exercise training coupled with low caloric availability.
    • Sled dogs as a model for studying dietary vitamin D

      Striker, Kali; Dunlap, Kriya; Jerome, Scott; Drew, Kelly (2021-05)
      Vitamin D deficiency (VDD) has become a pandemic and has shown to be correlated with several poor health outcomes. Many factors that lead to VDD are environmental and lifestyle. Vitamin D has physiological implications involved in all areas of human health and is also important for animal health. Canines have shown adverse health outcomes similar to humans that correlate with vitamin D deficiency such as chronic kidney disease (CKD) and irritable bowel disease (IBD). Canine vitamin D requirements are largely unknown due to the lack of research and the wide ranges of supplementation throughout dog food manufacturers. Pre-active plasma vitamin D metabolites are used as the biomarker of vitamin D status in humans and dogs but may not be representative of overall vitamin D status. Therefore, other biomarkers representing vitamin D status are often used in conjunction to determine physiological relevance. To address this gap in knowledge, this study used parathyroid hormone concentrations as well as vitamin D binding protein concentrations to establish more of an overall status of vitamin D. In canines, clinical supplementation following VDD is usually administered orally with vitamin D olive oil tablets; however, supplementation is usually unsuccessful. Vitamin D and its metabolites are lipid soluble and stored in adipose tissue. Although few foods provide appreciable levels of vitamin D, wild salmon contain some of the highest dietary vitamin D levels. People living in Alaska are at an increased risk of VDD due to reduced zenith sun angles for much of the year. Consequentially sufficient vitamin D levels need to be acquired through diet or supplementation. Historically, Alaska Natives obtained sufficient amounts of vitamin D from traditional subsistence foods, but with the progressive shift away from these foods VDD has increased in Alaskan populations. The limited research available suggests that Alaskan sled dogs in particular are a group found to be generally VDD. Sled dogs are an important part of the traditional Alaska subsistence lifestyle and have evolved alongside humans in the circumpolar north. Sled dogs, therefore, provide a valuable model for studying health outcomes associated with VDD in both people and dogs in the far north. This study provides significant evidence showing wild Alaskan salmon as a dietary source of supplementation to raise 25(OH)Vitamin D serum in dogs after only 4 weeks. We also show significance in variation by confounding factors, age and sex.