RSS 1.0Biological Sciences
For Marine Biology, see the Marine Sciences collection.
Recent Submissions
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Environmental and demographic drivers of a rapidly expanding sub-arctic moose populationAnthropogenic forces are dramatically altering the dynamics of many populations and ranges. A thorough understanding of drivers and mechanisms underlying population dynamics is needed to better understand reasons for range shifts and broaden our understanding of how environmental and demographic drivers affect population trajectories. In this thesis, I present two chapters that investigate the population dynamics of a rapidly colonizing moose (Alces alces) population in southwest Alaska. In the first chapter, I correlated environmental variables with demographic rates estimated using a multistate model and found that annual patterns of vegetation productivity and winter severity affected calf survival most strongly, followed by twinning rate. In the second chapter, I applied transient life table response experiments (tLTREs) to demographic rates and components of population structure estimated using an integrated population model (IPM). I found that, although calf survival did not have the highest sensitivity out of all other parameters, variation in calf survival contributed the most to variation in population growth rate. Together, these chapters suggest that variation in environmental conditions drove variation in population growth rate via effects on calf survival. Results uphold and add nuance to the demographic buffering hypothesis (DBH), which states that species evolve to buffer highest sensitivity demographic rates against variation that could otherwise decrease individual fitness and population sustainability. My research indicates that an outcome of the DBH is that lower sensitivity vital rates ultimately have a higher actual impact on population growth rate. Additionally, I found that the environmental drivers that currently limit population growth exhibit long-term trends consistent with climate change in ways that are amenable to moose, which suggests climate change facilitated moose colonization of the region. The lack of shortterm trends, lower adult survival in the most heavily hunted part of the study area, and the abrupt colonization that aligned with the irruption of a local caribou (Rangifer tarandus) herd indicate that human hunting pressure also played an important role in allowing moose to establish themselves at high density. These findings pertaining to drivers and mechanisms of population dynamics are relevant for conservation and management of large herbivores across the world that might similarly expand into new areas.
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Kit-rearing in the far North: movement behavior and activity patterns of female Canada lynx (Lynx canadensis) during the denning seasonReproductive ecology research is vital for determining the timing of important life history events and improving our understanding of the space use and behavior of individuals that are rearing offspring. This is particularly relevant for wildlife populations at the northern limit of the boreal forest, where climate change is rapidly affecting the ecosystem at two to four times the rate of mid-latitude regions. In this study, I used fine-scale GPS location data (1 - 4hr fix-rates) collected near Wiseman, Alaska over the summers of 2018 and 2019 to analyze the movements of 10 female Canada lynx during their offspring-rearing periods. I identified differences in behavior across four periods of kit development: pre-denning, nursing, prey-provisioning, and post-denning. In this high-latitude study site (~67°N), parturition occurred approximately three weeks later in the season compared to lynx in the southern portion of their range (~47°N). Home range areas of females were greatly reduced following parturition, while daily travel distances were mostly unchanged. Additionally, individual females appeared to diverge from each other in the strategies they employed to meet the energetic needs of themselves and their kits. These results indicate that latitudinal differences play a role in affecting the timing of mating, gestation, and birth in Canada lynx. In addition, these observed changes in maternal movement behavior across the periods of kit development suggest that female lynx face the unique challenge of restricting their space use to a small radius around the den site while kits are young (i.e., < 2 months old). I found evidence that females likely optimize their hunting strategies in a variety of ways to address this challenge and find sufficient prey for themselves and their offspring. However, these strategies rely on access to abundant prey populations in close proximity to denning habitat, which may be negatively impacted by climate change and the development of human infrastructure in this region.
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Seasonal changes in the movement rates and activity patterns of Canada lynxAn animal's temporal niche, or when it is active during the 24-hour day, is a fundamental aspect of its overall niche and ecology. Animals are confined to a temporal niche to maximize energetic gains while avoiding agonistic encounters with predators or intraguild competitors. An animal's temporal niche can be influenced by a variety of biotic and abiotic factors, and the temporal niche of predators is often established through a careful balance of prey behavior and the predator's physiological adaptations. This study examined the seasonal change of patterns of activity in Canada lynx (Lynx canadensis) in Northern Alaska using both GPS transmitters and triaxial accelerometers. The distance between consecutive GPS locations, or step length, is a common metric used to assess how movement rates vary across space and time and is often used to examine activity patterns of free ranging terrestrial animals. However, activity can only be examined at a high resolution for a short period of time, as fix rate inversely affects battery life of the GPS transmitter. Further, animal activity includes a range of behaviors that are not always discernable by spatial displacement alone (e.g., grooming, eating, some hunting behaviors), thus GPS transmitters can sometimes lead to underestimation of activity. Triaxial accelerometers can be used in addition to GPS transmitters to record activity in the presence or absence of spatial displacement, therefore theoretically providing a more accurate index of activity of free ranging animals. Both GPS and accelerometers separately indicated that lynx were most active near twilight and maintained a bimodal crepuscular-like activity pattern in spring and fall, but they switched to a unimodal pattern of activity during mid-day in winter. Hourly GPS data alone was insufficient in detecting diel activity patterns in 6 of 12 instances. We also found that step length and vectorial dynamic body acceleration (VeDBA), an index of body acceleration, were correlated in a positive curvilinear fashion in all individuals. However, there were times when step length was disproportionately lower than acceleration. These intervals of high activity, but short spatial displacements, could be indicative of hunting in a patch of habitat. Consistent with this interpretation, animals that exhibited this dichotomy had an increased likelihood of rest in the next hour. We also found that mean VeDBA and mean step length were not correlated at a seasonal scale, and mean step length and other GPS derived metrics were much more variable between individuals than VeDBA. We conclude that there are multiple ways accelerometers can provide additional information that can supplement GPS location data to provide a more complete picture of animal activity and behavior, including using the relationship of acceleration and spatial displacement data to shed light on space use patterns that may not be apparent using GPS data alone.
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Effects of young-growth management on Sitka black-tailed deer in southeast AlaskaCommercial logging was the dominant industry in southeast Alaska during the second half of the twentieth century. Logging practices have left a landscape legacy of regenerative forest types such as clearcuts and second growth. Second-growth forest occurs about 20-30 years after a clearcut and is relatively unproductive compared to other forest types. To enhance productivity, second-growth is often thinned to a lower density of standing timber, this process is referred to as pre-commercial thinning (hereafter, thinning). Sitka black-tailed deer (Odocoileus hemionus sitkensis) are an important cultural and subsistence resource across southeast Alaska. How thinned forests affect deer is not well known. To better understand how forest management is affecting local populations of deer in southeast Alaska we examined how thinning treatments impact deer browse intensity and snow accumulation on the forest floor. In this thesis, we presented two studies that examine the effects of thinning on deer habitat quality and deer access to forage. In the first study of this thesis, we quantified browse intensity in recently thinned (≤4 years post thinning) and adjacent old-growth forests. We also explored the immediate effects of thinning and slash (felled trees left on the forest floor) on forage availability. We performed a pairwise comparison of browse intensity between thinned and adjacent old-growth forests and modeled the effects of thinned forest characteristics on browse intensity. In the second study of this thesis, we quantified maximum snow depth in thinned, unthinned second-growth, old-growth and unforested (control) habitat types. Forest structure and composition affected how snow accumulates on the ground. Snow can impede the movement of ungulates species, such as deer, and reduce available forage. We evaluated how different forest types accumulated snow in southeast Alaska to better understand the implications on winter habitat quality for Sitka black-tailed deer. To quantify browse intensity in thinned and adjacent old-growth forests, we conducted browse surveys in recently thinned stands (2017 to 2021) and adjacent middle to high volume old-growth forests. We established 50m transects and surveyed plots every five meters to quantify browse of Vaccinium sp. (blueberry and huckleberry), a preferred deer forage species. In the second study, we measured snow depths throughout thinned, unthinned, old-growth and unforested sites to identify if these forest types accumulate snow differently. We also measured forest structure variables to use as predictors when modeling maximum snow depth. Transects were 70 meters long, and snow depth and forest structure data were collected every five meters. Snow depths were measured four to six times throughout the winter. The maximum depth of each transect point was recorded and paired with the forest structure variables. For both studies, we used nonparametric tests and generalized linear mixed models to understand the interactions between forest types and their maximum snow depths or percent of a Vaccinium sp. plant browsed. From the first study, we concluded that browse intensity was significantly different in thinned and oldgrowth forests (P<0.01). We learned that thinned stands with more slash reduce browse intensity. Slash (vertical obstruction) volume and time since thinning (metrics of slash decay) best explained percent of a plant browsed. From or second study, we found that thinned forests accumulated the same amount of snow on the forest floor as unforested sites. Moreover, old-growth and unthinned sites accumulated snow on the forest floor comparably during a relatively normal snow load year. Our findings regarding browse intensity showed that thinned forests have a delayed benefit to deer because of slash abundance. Our observations regarding snow accumulation showed that thinned forests have little value to deer in a winter with deep snow accumulation. Managers can use this information to better understand the extent of forage available to deer in recently thinned forest habitat. Our findings also demonstrated that the implementation of thinning treatments that minimize slash volume and accelerate decomposition will enhance benefits for deer.
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The role of cystathionine y-lyase and hydrogen sulfide in glucose transporter Glut1 expression in macrophagesHydrogen sulfide (H₂S) is an endogenous gasotransmitter that regulates immune function and energy metabolism in macrophages. While it is known to impair mitochondrial respiration at high levels, recent studies have shown that it promotes aerobic glycolysis, highlighting its potential role in regulating macrophage inflammatory response. The investigation of the link between H₂S and glucose metabolism in macrophages is of particular significance due to the role of glycolysis in driving macrophage innate immune functions. Inflammation stimulates macrophages to increase glycolysis by upregulating the expression of Glut1, the primary glucose transporter in these cells. Nuclear factor (NF)-κB is a transcription factor that elicits inflammation by regulating the expression of pro-inflammatory cytokines and chemokines in response to stimuli such as lipopolysaccharide (LPS), a bacterial toxin. However, NF-κB controls Glut1 expression in macrophages during immune responses. The phosphoinositide 3-kinase (PI3k)/ protein kinase B (Akt) signaling also plays a role in regulating NF-κB activity and glucose metabolism. The precise impact of H₂S on the PI3k/Akt and NF-κB signaling pathways, as well as Glut1 expression in macrophages, remains poorly understood. The goal of my thesis research is to test for a link between endogenously produced H₂S and Glut1 expression during the pro-nflammatory response in macrophages. Small interfering (si)RNAs were used to knockout cystathionine g-lyase (CSE) gene expression and block endogenous H₂S production in LPS-stimulated macrophages and the effect on LPS-induced Glut1 protein and mRNA expression was measured. Silencing CSE in LPS-stimulated macrophages reduced Glut1 mRNA levels suggesting that H₂S regulates Glut1 levels in inflammatory macrophages. Pre-treatment of macrophages with drug inhibitors targeting NF-κB or PI3k/Akt prevented LPS-induced Glut1 expression, implicating the signaling activity of these proteins as regulators of inflammation induced Glut1 expression. Silencing CSE decreased NF-κB activation in LPS-stimulated macrophages, suggesting that endogenous H₂S acts via NF-κB to supports Glut1 expression. To determine whether H₂S supports the LPS/NF-κB/Glut1 response, we treated LPS induced macrophages with GYY4137, a slow releasing H₂S-donor molecule. Low levels of exogenous H₂S did not change Glut1 expression in LPS treated cells. However, high levels of H₂S inhibited NF-κB activation and Glut1 expression and increased Akt activation, suggesting an antiinflammatory role of elevated H₂S levels. The anti-inflammatory effect of elevated levels of H₂S on LPS-induced NF-κB activation and Glut1 expression shows a marked difference from the pro-inflammatory impact of enzymatically produced levels, emphasizing the importance of distinguishing between the source and concentration of H₂S. These findings suggest that H₂S plays a role in inflammatory Glut1 expression through modulating NF-κB and Akt activity in macrophages.
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Storm hydro-biogeochemistry, of boreal catchments disturbed by fire and permafrost thawHigh-latitude ecosystems are vulnerable to a rapidly warming climate, which has led to thawing permafrost and increased frequency and intensity of wildfire. Such disturbances change pools and fluxes of carbon and nutrients within boreal catchments generating biogeochemical signals apparent in streams. However, a warming climate also results in more variable precipitation and larger storms, potentially obscuring biogeochemical signals of disturbance. I used a space-for-time approach to assess how disturbances influence biogeochemistry of high-latitude catchments by monitoring catchments occupying orthogonal contrasts in permafrost extent and fire history. We analyzed concentration-discharge (C-Q) dynamics (fDOM, NO₃-, specific conductance, and turbidity) during storms, when catchments are most hydrologically connected to streams. Sourcelimited C-Q dynamics and dilution of nitrate and specific conductivity in all catchments suggested storm runoff comprises overland flow and shallow subsurface flowpaths that bypass mineral-rich soils regardless of catchment context. A positive correlation between burn extent and the variability of C-Q dynamics for inorganic solutes suggested wildfire contributes to the patchiness in hydrologic connectivity within catchments. Greater source limitation of nitrate in catchments with greater burn extent suggest smaller pools of nitrate that are accessible to shallow flowpaths. Mobilization of fDOM during storms varied among catchments, with dilution of nearstream sources of fDOM in low relief catchments and flushing following delayed mobilization in steeper catchments. A positive correlation between deciduous cover and the variability of flushing dynamics for fDOM suggest more heterogenous flowpaths in permafrost-free catchments compared to catchments underlain with permafrost. Antecedent moisture conditions and seasonality had weak effects on storm C-Q dynamics and the strong imprint of catchment attributes on hydrology and biogeochemistry during storms persisted despite storm- to seasonal-scale variation in moisture conditions. Results of this study show 1) stream biogeochemistry measurements can be used as a proxy for upstream soil, thermal, and post fire processes and 2) long-term monitoring of catchment biogeochemistry during storms could therefore provide indicators of change in the state of terrestrial ecosystems resulting from permafrost thaw or changing fire regime.
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Thermokarst-pond plant community characteristics and effects on icewedge degradation in the Prudhoe Bay region, AlaskaIce-wedge thermokarst ponds are forming in many areas of the Arctic as a result of climate warming and infrastructure development. Previous research suggests that development of aquatic vegetation within these ponds may create negative feedbacks to the process of ice-wedge degradation by reducing pond-bottom temperatures and thaw depths. The objectives of this research were to characterize thermokarst-pond plant communities and to evaluate the effects of vegetation on within-pond sediment temperatures and thaw depths. Aquatic vegetation was sampled in 39 plots within 29 thermokarst ponds in the Prudhoe Bay region of Alaska. Five floristically distinct plant communities were identified: Calliergon richardsonii comm., Scorpidium scorpioides comm., Pseudocalliergon turgescens comm., Hippuris vulgaris comm., and Ranunculus gmelinii comm. These communities had low species diversity (mean species richness 3.2 ± 1.5 SD) and were best differentiated by the single dominant species included in plant-community names. Ordination of species composition data revealed a temperature gradient, along which high biomass was associated with low sediment temperature and shallow thaw depth. The C. richardsonii and P. turgescens moss-dominated communities had very high biomass values (3079 g/m² ± 1895 SD and 3135 g/m² ± 585 SD, respectively). Examinations of temperature and thaw differences between communities were limited by sample size, as several communities were described based on only two plots each. To evaluate the potential insulative role of pond vegetation on pond-bottom temperature and thaw depth, differences between broad vegetation types (i.e., moss, forb, sparse) rather than communities were examined. Vegetation cover, total biomass, biomass of plant functional types, and soil organic horizon thickness were sampled, along with mean thaw depth and sediment temperature. Linear mixed-effects models were used to identify vegetation-related parameters with the highest predictive power of thaw and temperature. Mean sediment temperatures measured during 19 July - 23 August 2021 were warmest in the sparse plots (8.9 °C ± 0.2 SE) compared to the forb plots (8.2 °C ± 0.3 SE) and the moss plots (6.7 °C ± 0.4 SE). Moss plots also had shallower late-August thaw depths (42.5 cm ± 1.3 SE) compared to forb (52.7 cm ± 1.7 SE) and sparse (52.7 cm ± 1.4 SE) plots. Vegetation cover was negatively correlated with sediment temperature, whereas vegetation cover, moss thickness, and organic layer thickness were all negatively correlated with thaw depth. The stronger relationships observed between vegetation-related factors and thaw depth compared to sediment temperature were probably affected by the short period of temperature observations within this study. Although stochastic factors likely play a role in community establishment within thermokarst ponds, additional sampling is needed across all pond ages, ice-wedge degradation/stabilization stages, and a broader range of habitats within ponds to discern if there is a clear successional trajectory for thermokarst-pond plant communities. This study provided descriptions of relatively understudied aquatic plant communities that play an important role in Arctic landscape change. Notably, very high biomass values were found in young ponds (one with an age of only 8 years) dominated by moss communities. Results indicate that aquatic plant communities with high moss biomass have high capacity for insulation that potentially reduces permafrost thaw and ice-wedge degradation, leading to ice-wedge stabilization.
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Exploring the evolution of fishes at high latitudesFish species found in high latitude waters are especially vulnerable to climatic changes due to their inability to regulate body temperature and long evolution in cold, oxygen-rich aquatic environments. Antarctic notothenioid fishes have evolved to thrive in an extremely stable, cold, oxygen-rich environment. Likewise, lake trout live in a cold, oxygen-rich environment, but commonly experience a wider range of temperatures than notothenioids. Millions of years of evolution in the cold have shaped the genetics of these fishes, but the effects on their biology remain largely unexplored. This dissertation seeks to learn from the past evolution of these two evolutionarily distant types of high latitude fishes to enhance predictions for how these animals can cope with future environmental changes. Specifically, this dissertation examines the genetics of fishes with limited thermal tolerance from the population level down to a single gene. These studies relied on DNA sequence evidence produced with two different technologies and analyzed under functional, phylogenetic, and population genetic frameworks. In the first study, mitochondrial DNA (mtDNA) variation is examined to determine ancestral affinities and geographic distribution of mtDNA variants in lake trout across Alaska. Lake trout in Alaska descend from two distinct mtDNA lineages. One mtDNA lineage is restricted to Arctic Alaska, north of the Brooks Range, while the other lineage is found across Alaska. Lake trout likely dispersed from glacial refugia in western Canada to recolonize Alaska and the movement patterns from recolonization assist in determining how lake trout are likely to move across the landscape in the future. In the second study, genome wide genetic diversity of lake trout in seven Alaskan lakes is explored to determine ancestral affinities and colonization pathways. Despite past movement, the lake trout population currently found in each of the sampled lakes is genetically distinct from all other sampled populations and no migration currently seems to be occurring, even between lakes less than 20 km from each other. This research shows lake trout in Alaska are genetically diverse, but with little gene flow, genetic rescue and transfer of genetic variation between populations is unlikely to occur. In the third component of this dissertation, the evolution of the critical hypoxia transcription factor is examined in Antarctic notothenioids. The hypoxia-inducible factor-1alpha (HIF-1alpha) of Antarctic notothenioids contains a polyglutamine/glutamic acid insert that may impact the function of this key transcription factor. Thus, Antarctic notothenioids may have difficulties in responding to climate change induced hypoxia. Overall, the adaptive consequences of evolution in high latitude aquatic environments may be detrimental to fishes as they face climate changes. Other high latitude freshwater fishes like lake trout may have limited gene flow among populations, reducing potential for adaptation and genetic rescue in response to climate change. More research into the evolution and functional implications of different natural genetic variants is needed to protect these unique high latitude species.
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Cryptic population structure and differentiation in three species of Alaska ClaytoniaBeringia is an extensive geographic region noted for high levels of taxonomic complexity among closely related species. Three such species distributed across Beringia (Claytonia arctica, C. scammaniana, and C. sarmentosa,) exhibit low morphological differentiation between the species, while C. scammaniana includes two additional described morphologies of questionable taxonomic standing, C. "noatakensis" and C. "porsildii". Taxonomic boundaries within this group have been historically disagreed upon and are susceptible to confounding factors such as isolation-by-distance (IBD), discontinuous sampling of continuous variation, and low sequence divergence and morphological differentiation. To assist in species delimitation, multiple approaches combining phylogenomics and spatially explicit population genetics analyses should be used. Genetic material was collected from herbarium specimens at the University of Alaska Museum Herbarium (ALA). Sequence data were extracted and sequenced using the GoFlag target probe set. Phylogenomic analysis and consensus tree reconstruction were performed in ASTRAL. Principal Component Analysis (PCA), Discriminate Analysis of Principal Components (DAPC), and spatial Principal Component Analysis (sPCA) were performed in R ("adegenet" package), and ancestral clustering was calculated in ADMIXTURE. We found clear genetic differentiation between all three species with a close genetic relationship between C. arctica and C. sarmentosa. Neither of the morphotypes "noatakensis" or "porsildii" were genetically differentiable from C. scammaniana, but a strong genetic signal divided the species into northern and southern populations. We conclude that species delineations between C. arctica, C. sarmentosa and C. scammaniana are genetically defensible despite low morphological differentiation. The genetic relationship between C. sarmentosa and C. arctica appears to be closer than previously thought, and further research including the western C. joanneana is needed. The current circumscription of C. scammaniana is correctly inclusive of "noatakensis" and "porsildii", but further research is needed to investigate the genetic divide between northern and southern populations.
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Human-polar bear interactions on the northern coast of AlaskaPolar bears (Ursus maritimus) are sea ice-dependent marine mammals that, due to reductions in sea ice extent in the southern Beaufort Sea, are increasing their time spent on shore. Simultaneously, the anthropogenic footprint on the northern coast of Alaska is growing. As a result, human-polar bear interactions in this region are increasing. These interactions have the potential to be dangerous for humans, harmful to polar bears, and, therefore, require deliberate management. In this thesis, I examined two study systems that lacked the depth of knowledge necessary to craft defensible management plans. My research generated information regarding human-polar bear interactions that could be used to shape policy in the Arctic. In Chapter 1, I explored a dataset that documented human-polar bear interactions at a popular polar bear viewing area in Kaktovik, Alaska. My objectives were to determine what factors influence 1) polar bear displacement (temporary or permanent) from the viewing area and 2) human response (assertive or neutral) to an approaching bear. Using logistic regression, I determined that permanent polar bear displacement was more likely later in the observation season and when the bear's initial reaction to a human approach occurred as a greater distance. I also found that humans were more likely to act assertively towards a bear when food resources (i.e., whale bone pile) in the area were depleted. These behavioral patterns indicate that human and bear tolerance change over time and in relation to resource availability. In Chapter 2, I conducted the first systematic evaluation of polar bear behavioral response to overhead aircraft traffic. I conducted field sampling in a fixed-wing aircraft and observed polar bear response at varying altitudes. My goal was to intentionally elicit a behavioral response that, under the guidelines in the Marine Mammal Protection Act, would be considered biologically significant. My objectives were then to 1) predict when a polar bear would exhibit a biologically significant behavioral response and 2) estimate the probability of an aircraft eliciting a biologically significant response at different altitudes above the animal. Using linear regression and a hierarchical Bayesian approach, I found that bears were most likely to exhibit a biologically significant response when they were active prior to sampling, located on the mainland coast, and the aircraft approach altitude was less than 457m (1500ft). Furthermore, I found that the probability of eliciting a biologically significant behavioral response at a flight altitude of 30m (100ft) was 21.31% for an inactive bear on a barrier island and 61.46% for an active bear on the mainland coast. Together, these research efforts address pressing knowledge gaps related to polar bear behavior on the northern coast of Alaska. Information generated from this project can be used to inform management and reduce disturbance for polar bears in a changing Arctic.
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Soundscapes on the Arctic Coastal Plain: assessing sound disturbance and the auditory sensitivity of caribou (Rangifer tarandus)The Arctic Coastal Plain of Alaska is a region on traditional Inupiat land that supports millions of migratory birds and over half a million caribou (Rangifer tarandus) at the most critical time in their life-histories. They are an important part of seasonal subsistence activities for the surrounding rural Indigenous communities. Therefore, conservation efforts that support this ecosystem also bolster food security in the region. Monitoring this system has increasingly become a necessary and prudent task as the landscape evolves under the pressures of resource extraction and climate change. To date, limited research has been conducted on the sounds present in this environment (i.e., 'soundscape'). Monitoring sounds may help reveal the impact of these stressors and ecosystem-wide changes. There is also a need for researchers to evaluate what portion of the soundscape wildlife can actually hear, so we can better understand how soundscape change might affect them. I conducted two studies that apply soundscape monitoring and acoustic perception to the landscape and wildlife of the Arctic Coastal Plain. First, I evaluated the hearing thresholds of domestic Rangifer tarandus (reindeer) at the Large Animal Research Station at the University of Alaska Fairbanks in 2019 in order to help infer what anthropogenic sounds wild caribou may be sensitive to. Using Brainstem Auditory Evoked Response methods, I found that a caribou's auditory system can detect all forms of anthropogenic sounds that they might encounter on the Arctic Coastal Plain, including low frequency sounds associated with oil and gas exploration. Specifically, I found they can detect sounds as low as 30 Hz with great sensitivity, expanding the known lower limit of their auditory capabilities. This means that caribou may detect sounds of seismic exploration, gravel mine blasting and other anthropogenic sounds associated with resource extraction at a great distance, and may be more affected by these sounds than previously thought. From May through August of 2019, I used acoustic recording units stationed in a random grid across the Arctic Coastal Plain to passively monitor the soundscape study region-wide sound characteristics and their impact on vocal wildlife. Anthropogenic sound (i.e., anthrophony) is a pervasive and often overlooked consequence of land-use change, and something that has been relatively understudied in northern Alaska. For my soundscape research, I modeled the spatial and temporal distribution of anthrophony and bird vocalizations (i.e., biophony) across developed (Oilfields surrounding Prudhoe Bay), and undeveloped (Arctic National Wildlife Refuge) areas of the Arctic Coastal Plain. Hourly detections of anthrophony were not associated strongly with infrastructure but tended to increase as the season went on. Birds were more likely to vocalize in hours when anthrophony was present, and this effect was the strongest in the early season, during migratory bird arrival and breeding. Anthrophony's effect on the soundscape may alter biological cues that vocal and non-vocal migrants use to assess habitat patches, and fitness consequences will vary by species. Further research is needed to assess how bird communities and caribou movement respond to anthrophony.
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Timing of flowering affects pollination and fruit set in Viburnum edule in boreal forests of AlaskaSpring flowering in Alaskan boreal forests is happening earlier on average; how this relates to the pollination of plants and their pollinator community is unknown. Highbush cranberry (Viburnum edule) is one of the first herbaceous understory plants to flower every year, and in years when it flowers early there are fewer other species in bloom compared to years when it flowers at a more average time. Highbush cranberry is also important as a subsistence food and many boreal animals consume these fruits as a regular part of their diet. The potential for change may lead to differences in the response of pollinators and plants under early season conditions which could alter resources for pollinators and impact fruit production. This research looks at the impact of flowering timing on pollen deposition on Viburnum edule, and the composition of the pollinator community visiting the available flowers. Using an experiment with flowers placed in boreal forest sites either at an early time or at a peak flowering time across two years, we found that early flowering highbush cranberry received fewer pollen grains than peak flowering highbush cranberry and were visited less. V. edule was primarily visited by syrphid flies, native bees, and muscoid flies. We also observed a lower total number of visitors, and a lower proportion of visitors that were bees during an early flowering time than at peak flowering time. Floral visitors were more abundant during the advanced flowering year than during an average flowering year. We do not currently think that pollen limitation is causing a reduction in fruit set of early flowering V. edule because at all flowering times observed, we found over 50% of flowers to have been presumed visited while less than half of flowers in an inflorescence form fruits on average. More information on boreal pollinators triggers for diapause break and floral visitation is necessary to make more reliable predictions of the future impacts of phenology shifts in flowering plants and insect pollinators.
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Applying third-generation sequencing to pathogen surveillance and mixed infection detectionOne Health is the concept of interconnected health between plants, animals, humans, microorganisms and the environments they live in. One Health issues surround many important viral pathogens, including influenza, SARS-CoV-2, and Ebola, that have likely come from zoonotic spillovers. Genomic epidemiology combines pathogen genomes with metadata to forecast, track, and prepare for future pathogens and pathogen variants that may cause epidemics. Genomic epidemiology has been used to detect and track viral variants that have the potential to escape vaccines for viruses like porcine circovirus type 2 (PCV2). PCV2 causes porcine circovirus associated diseases (PCVAD), which results in weight loss and death in pigs around the world. The correlation between PCVAD and mixed infections shows that disease severity is linked to the microbial community in a host. Metagenomics allows researchers to sequence samples and sort out the individual community member genomes by bioinformatic analyses, allowing the study of the host microbiome. In this thesis, I tested if long read nanopore sequencing can uncover PCV2 diversity and reliably detect co-infections. I also assessed the accuracy and efficiency of long read metagenomic assemblers as a potential method for detecting mixed infections. In my first chapter, I found that nanopore sequencing can be used to understand PCV2 diversity and detect co-infections. This evidence shows that nanopore sequencing is a viable alternative to Sanger sequencing for PCV2 surveillance. In my second chapter, I found Flye built the most complete and accurate genomes for bacterial community members and their plasmids. Throughout my thesis I have shown that nanopore sequencing is a viable solution for modern surveillance. The lower cost of nanopore sequencing may allow more specific pathogen and metagenomic surveillance in regions with high risk of zoonotic spillovers, which may allow early detection of epidemic causing pathogens.
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Seeing the forest through the trees: how site conditions mediate white and black spruce responses to climate in Interior AlaskaThe boreal forest provides essential ecosystem services and helps regulate global climate. With climate change occurring at a faster rate at high latitudes, including in the boreal forest biome, it is critical to understand how boreal forests are responding to these unprecedented changes. Despite much effort, uncertainty remains as to how boreal forest productivity has and will change with ongoing climate changes. Some of the uncertainty reflects the complex mosaic of regional climatic patterns, direct and indirect species-specific responses to regional climate, and heterogenous local site conditions that affect boreal forest productivity. I focused on the latter uncertainty: the potential role of topographic, edaphic, and biotic conditions in mediating the climate-growth responses of boreal tree species. My overarching goal was to quantify the radial growth response of black spruce (Picea mariana) and white spruce (Picea glauca), the two most common tree species in interior Alaska, to climate variability across a suite of site conditions to better understand the observed and predicted variation in climate driven productivity across a variable landscape. I employed a systematic sampling design to quantify the landscape-scale patterns in both environmental conditions and incremental annual growth of trees distributed across a 1.28 million-ha study area in Denali National Park and Preserve (and beyond in Chapter 4). I also used targeted sampling of carbon isotopes in tree rings to investigate potential drought stress. I found that near-surface permafrost, slope angle, and elevation strongly modified the magnitude, shape, and, in some cases, the direction of radial growth response of both species. For white spruce, the negative growth response to warm and dry summer conditions intensified in high competition stands and in areas receiving high potential solar radiation. During years with high cone and seed production, white spruce shifted its current year's carbon resources from radial growth to reproduction and showed signs of drought stress. I also observed differences between black and white spruce climate-growth responses, with near-surface permafrost driving their contrasting responses to June-July temperatures and with black spruce growth showing an overall more positive response to summer precipitation. These results demonstrate that local site and stand variables can force contrasting growth responses to similar climate conditions and help predict how future black and white spruce growth may play out with climate changes across a heterogeneous landscape. My results underscore the pivotal role of near surface permafrost in both the climate-growth responses and competitive dynamics of black and white spruce. Consequently, my results emphasize the importance of ongoing and predicted changes in the distribution and prevalence of permafrost for the future of the boreal forest.
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Snow as structural habitat for wolverines in a changing ArcticArctic snowpack provides critical wintertime habitat for animals to facilitate thermoregulation and avoid predators. Wolverines (Gulo gulo) are iconic among such animals, relying on snow burrows for resting sites and reproductive dens. Most of the knowledge regarding this mesocarnivore's association with snow, however, has so far originated in more southerly latitudes. In this dissertation, I investigated Arctic wolverines' behaviors associated with snow, focusing on how specific snow properties influence resting, habitat selection, and avoiding predators. Motivated by the paucity of published descriptions of wolverine resting burrows and reproductive dens on tundra, I first described terrain features and architecture of such sites. I found that resting burrows typically consist of a single tunnel leading to a resting chamber, sometimes associated with non-snow structure such as stream cutbanks and river shelf ice. By contrast, reproductive dens typically consist of longer tunnels associated with snowdrift-forming terrain. Second, I used GPS collar data from 21 adult wolverines, coupled with snowpack information at 10 meter pixel resolution, to evaluate wolverine habitat selection and movement response to snow depth, density, and melt status. I found that wolverines select deeper, denser snow, except when snow is melting, likely reflecting resting site use. Third, I developed a machine learning model to classify wolverine behaviors using tri-axial accelerometers based on direct observations of three captive wolverines, and applied this model to free-living wolverines in Arctic Alaska. I found that the model performs better when allowed to predict behaviors as "unknown," and that it accurately predicts resting, food handling, running, and scanning surroundings. Finally, based in part on this classification model, I evaluated the extent to which wolverines' use of snow burrows and surface beds for resting sites is influenced by thermoregulatory needs versus predation avoidance. I found evidence in support of both demands driving resting behavior; wolverines trade thermoregulation off against predation avoidance by resting on the snow surface on warm, sunny days, but use snow burrows on cold, dark days to meet both demands simultaneously. Collectively, this dissertation demonstrates the importance of Arctic snowpack to wolverines, a topic of increasing importance as the snow season shortens with climate change, and serves as a model for investigating behavioral processes associated with snow among other species.
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Drivers and mechanisms of migration in an Arctic caribou herdMigration is one of the world's great natural wonders and the scale of some migratory journeys is astounding. Yet migration is globally imperiled and effective conservation of the remaining migrations will require a thorough understanding of the drivers and mechanisms underlying how migrants complete such journeys. In this dissertation, I present three chapters that sought to better understand spring and autumn migration for the Western Arctic Herd, a population of barren-ground caribou (Rangifer tarandus) that complete some of the longest terrestrial migrations on the planet. In the first chapter, I applied and validated an analytical method to infer parturition events from GPS data with robust statistical confidence. In the second chapter, I examined the parturition events detected with these methods to better understand the drivers and mechanisms of spring migration because the calving grounds are the destination for pregnant females in spring. I quantified annual spatial patterns of calving and assessed what environmental factors influenced calving site selection by caribou through time. I found evidence of both memory and perception influencing spring migration, such that caribou use memory to return to an area of generally high-quality forage at the time of calving, and consequently adjust calving sites each year based on experienced conditions. In the third chapter, I sought to understand the environmental cues caribou respond to in deciding when to migrate in autumn. I found that decreasing temperatures and the timing of first snowfall events of the season had the greatest influence on migratory movements, but notably, caribou re-assessed decisions throughout the migration period as the conditions they experience changed. I also found that the cues caribou used are similar across individuals despite the herd being broadly dispersed in late summer, and the variability in migration timing observed each year is likely due to variability in environmental conditions experienced across the range. These findings pertaining to the drivers and mechanisms of migratory behavior, and broader aspects of movements by caribou, are highly relevant for conservation and management of the species across the circumpolar North. Moreover, the observation that caribou movement exhibits strong responses to particular climate phenomena, such as temperature and precipitation, have important implications for how caribou might respond as the climate of the Arctic continues to change.
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Rooted in environmental justice: phytogeography and ethnoecology of SerianthesSerianthes Benth. (Fabaceae) is one of the most endangered plant genera in the world, with 12 of the 18 species listed on the IUCN Red List of Threatened Species. Serianthes trees are culturally important to island communities of the Indo-Pacific region for canoes, boats, traditional houses, and medicine. Habitat loss and ecosystem degradation increased pressure on these trees, also threatening its Indigenous cosmology and traditional practices. This interdisciplinary study integrated genomic, biogeographic and ethnoecological approaches to develop appropriate policies that protect the Indigenous biocultural diversity of Serianthes. Phylogenomics of 401 nuclear exons and non-coding flanking regions using both a multi-species coalescent model and a partition gene tree analysis confirmed the monophyly of the genus and inferred the biogeography and phylogenetic relationships within Serianthes. The Guåhan (Guam) and Luta (Rota) endemic Serianthes nelsonii (known locally as Håyun lågu and Tronkon guåfi respectively) are closely related to South Pacific species. Serianthes kanehirae from Belau (Palau) and Wa'ab (Yap) are closely related to Malesian and Papuasian species. Phylogeographical patterns of Serianthes in Micronesia are discussed to inform conservation management. The ethnoecological study revealed interspecies relationships between people, animals, and plants remain strong. The traditional use of Ukall and Gumor (Serianthes kanehirae) on Belau and Wa'ab respectively remain part of Belau and Wa'ab's culture and are intertwined with rituals respecting the spiritual world. On Luta, Tronkon guåfi is an established flagship for endangered species conservation, while the last adult Håyun lågu tree on Guåhan became a rallying point for spiritual resistance when its habitat became threatened by military plans to construct a firing range. Despite its listing as critically endangered by the Endangered Species Act, its habitat is still at risk of being lost. The social movement guided by Prutehi Litekyan brought the community together to protect the Håyun lågu tree based on Indigenous belief systems. The social movement and policy research used a qualitative mixed-method approach to evaluate the dimensions of the Endangered Species Act in relation to environmental justice and biocultural rights. I concluded that a bottom-up co-management approach with polycentric networks best fits the social-cultural system of Guåhan. I propose Indigenous participation and the creation of an advisory council, comprising traditional and scientific knowledge holders, to advise on biocultural diversity preservation in the Mariana Islands.
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Naturally occurring etiologic factors affecting the health of breeding seabirds in the Bering SeaSeabird populations across the globe have experienced both significant instability and consistent overall declines in recent history. Seabirds in the Bering Sea of Alaska, USA appear to be severely affected by environmental changes, exhibiting large-scale shifts in behavior and distribution and increases in unusual mortality events (UMEs) in recent years. I analyze a selection of the naturally occurring pathogenic and toxicological factors affecting breeding seabirds in the Bering Sea region using an approach focusing on zoonoses and bioaccumulating toxins. Specimens were collected at three breeding colonies in the Bering Sea in 2018 and 2019, and were evaluated for the presence of several pathogens and toxins. First, I examined the frequency of Influenza A Virus (IAV) in several understudied clades of seabird host species (n=146 individuals) across the Bering Sea. Second, I used a novel set of genetic amplification and sequencing techniques for metagenomic analysis both to determine the respiratory microbiome and to detect the presence of potentially pathogenic microorganisms in northern fulmars (Fulmarus glacialis) on St. Matthew and Hall islands (n = 15). Finally, I sought to evaluate the levels of paralytic shellfish toxins (PSTs) in the digestive tracts of northern fulmars from St. Matthew and Hall islands (n = 14). Together, these studies detected several viral and bacterial pathogens, many with zoonotic potential. These included Coxiella, Plasmodium, Toxoplasma, and IAV. PSTs were also detected in birds sampled from 2019, indicating the presence of harmful algae in the Beringian food web. The detection of these etiologic factors along with the incidence of major morbidity and mortality events suggest these birds might serve as sentinel species, indicating variations in environmental change that can pose a significant risk to both ecological stability and human health in the region.
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Interpretations of climate change on grazing systems: the comparison of Arctic and Subarctic carexStresses imposed by climate change are altering arctic and subarctic ecosystem structure and function. On the Yukon-Kuskokwim River Delta (YKD) in subarctic western Alaska, Pacific Black Brant geese (Branta bernicla nigricans) are losing their available grazing lawns of shortstatured Carex subspathacea due to its conversion into a taller, less nutritious growth form. However, C. subspathacea on Alaska's Arctic Coastal Plain (ACP) grows in extensive lawns that remain short even when ungrazed. Our goal was to compare the growth responses between arctic C. subspathacea and subarctic C. subspathacea when grown in arctic and subarctic conditions. We used reciprocal common gardens to study the variation in height, tiller density, aboveground biomass, and green leaf nitrogen percentage between these reputed taxa. We explored the growth responses that occur in C. subspathacea when grown in the arctic and subarctic using linear mixed effect models. We found that environmental differences between these regions influence the morphology of these taxa. Subarctic C. subspathacea is phenotypically plastic, and was able to grow tall in subarctic conditions, while remaining short in the Arctic. However, arctic C. subspathacea was short in both gardens, suggesting arctic C. subspathacea will not grow tall under warming conditions. Understanding the functional causes of the difference between these two grazing systems is important for predicting the effects of future climate change on both regions. This study provides insight to how changing climate will impact these different growth forms and affect future grazing dynamics along arctic and subarctic coasts.
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Fasting status of Steller sea lion pupsFollowing population declines in species of concern, wildlife managers often seek to identify underlying causes to understand and predict population dynamics for better future management. Often, physiological and/or behavioral metrics are measurable markers of decline, and these are often detectable well before declines are measurable through population surveys. During the 1970's, 80's, and 90's Steller sea lion (SSL; Eumetopias jubatus) populations in the western portion of their breeding range declined by ~85%. Though declines in most regions have since stabilized or exhibited modest recovery, some subpopulations breeding in the Aleutian Islands continue to decline. In contrast, SSL subpopulations in eastern regions of their range have steadily grown since the 1970s. Prior studies on the maternal attendance behaviors of SSL have noted differences in the timing of parturition, the duration of the perinatal period, foraging trip duration of nursing females, and the duration of periods dams spend ashore tending their pups. Variability in these metrics has been associated with year, location, the dam's age and parity, environmental oscillations (i.e. El Niño Southern Oscillation), and pup age over the lactation period. This study utilized prior findings of predictable changes in metabolite concentrations while pups fasted during their mother's foraging trips as a new approach for assessing maternal attendance patterns. The distributions of fasting phase categories, assigned based on the relative concentrations of plasma betahydroxybutyrate and blood urea nitrogen, were compared across 12 subpopulations extending from eastern Russia along the coastal northern Pacific into southeastern Alaska from blood samples of 1528 SSL pups. Fasting phase categories were merged into Short and Long fasting durations to compare pups sparing critical proteins (relying on lipid reserves) to those with plasma profiles indicative of metabolic protein reliance (muscle & organ breakdown), respectively. Notably the subpopulations with the maximal (western Aleutian Islands) and minimal (eastern Aleutian Islands) observed proportions of Long fasting pups were in the same broad Aleutian Island region. Three metapopulations had significantly greater proportions of Long fasting pups: the western and central Aleutian Islands and the southern portion of southeastern Alaska. Due to contrasting population trends among these metapopulations, we suggest that both density-dependent and density-independent factors contributed to extended fasting durations in SSL pups.
