Graduate Theses & Dissertations


Environmental structure, morphology and spatial ecology of the five-lined skink (Plestiodon fasciatus) at high latitude range limits
Detecting relevant and meaningful patterns from the complex, interconnected network of relationships between organisms and their environment is a primary objective of ecology. Ecological patterns occur across multiple scales of space and time. In this dissertation, I examine aspects of environmental structure that influence a species’ distribution and are expressed in that species’ population dynamics. I compare the morphology of the five-lined skink (Plestiodon fasciatus) near its high latitude range limits with a lower latitude population and evaluate the economics of their behaviour in the context of its reproductive strategy. I tested the conformity of this species to biogeographical rules postulated by MacArthur, Bergmann, and Rensch. Spatial ecology was investigated in the context of the environmental potential for polygamy proposed by Emlen and Oring (1977) The five-lined skink, Plestiodon fasciatus, conformed to these biogeographic rules. Specifically, abiotic factors were the primary limiting factors affecting distribution at the high latitude range limits of the species; body size was larger in high latitude populations; and the degree of sexual size dimorphism was greater at high latitude than at low latitude. Spatial ecology at the individual scale was influenced by sites with suitable thermal conditions which facilitate the polygynandrous mating system documented in P. fasciatus in high latitude populations. My results confirm the importance of microsites with suitable thermal profiles as key habitat for ectothermic vertebrates at high latitudes. The influence of temperature as a limiting abiotic factor is expressed in population density, body size, spatial ecology, and reproductive strategy of P. fasciatus. Conservation and restoration of high latitude populations of ectothermic vertebrates should focus on ensuring thermal requirements of the species of concern are met before other factors are addressed, as temperature is likely the single most important limiting factor at high latitude range limits. Author Keywords: biogeography, lizard, Plestiodon fasciatus, range limits, sexual size dimorphism, spatial ecology
Involvement of Endogenous Plant Hormones in The Regulatory Network of Fatty Acid Biosynthesis in Soybean Seed
The activities of phytohormones during the reproductive phase have been partially clarified in seed physiology while the biological role of plant hormones in oil accumulation during seed development has been investigated in part only. In this research, fatty acid (FA) contents and hormone profiles, including abscisic acid (ABA) and cytokinins (CKs) of seed samples in four different stages and comparing six soybean varieties have been investigated in order to examine the hypothesis that the endogenous plant hormones play important roles in FA production in soybean seeds. The FA contents increased significantly during this period while the hormone concentrations gradually declined towards the seed physical maturation. However, the interactions between FA contents and hormone profiles were complex and went beyond linear correlations. Hormone metabolism in the earlier stages of seed maturation period demonstrated numerous robust relationships with FA accumulations, as derived from several simple and multiple regression models in the determination of different FA contents. Evaluation of the effects of exogenous ABA and trans-Zeatin (tZ) on FA biosynthesis has revealed that ABA appears to be involved in the accumulations of unsaturated FAs while tZ participated in the synthesis of saturated and unsaturated FAs. Notably, the alterations of FA synthesis differ according to what exogenous hormone concentrations could be used. Author Keywords: Abscisic acid, Cytokinin, Fatty acid, Seed development, Soybean
Elemental Variation in Daphnia
Environmental variation can affect consumer trait expression and alter ecological and evolutionary dynamics in natural populations. However, although dietary nutrient content can vary by an order of magnitude in natural ecosystems, intra-specific differences in consumer responses to food quality have not been thoroughly investigated. Therefore, the purpose of my dissertation was to examine the influence of dietary nutrition and other environmental factors on consumer phenotypic variation using the freshwater cladoceran Daphnia. I conducted a series of complementary laboratory and field studies where I examined the effects of dietary phosphorus (P) content and additional biological/environmental variables (multi-elemental limitation, genetic variation, and temperature) on daphnid life-history, biochemistry, body elemental composition, and population growth. In general, phenotypic expression within a species varied significantly in response to all experimental variables, but the relative influence of each was highly context dependent. In my first chapter, I found that dietary P content and environmental calcium (Ca) concentrations both altered Daphnia body Ca:P ratios and growth rates of individuals and affected intrinsic rates of increase at the population level. However, food quality appeared to have a much larger effect on trait expression, and body Ca:P ratios were highly sensitive to other forms of dietary nutrient limitation. Next, I documented significant quantitative genetic variation and phenotypic plasticity in daphnid P content, growth, and P use efficiency of field collected animals grown across dietary P gradients. Trait expression was also influenced by genotype X diet interactions suggesting that consumer responses to dietary nutrient limitation can be heritable and may be adaptive in different nutrient environments. Finally, I found that temperature appeared to override food quality effects and decouple P metabolism in natural Daphnia populations, but total biomass production was affected by both dietary P content and temperature, depending on the nutrient content of the lake. Overall, my dissertation shows that consumer responses to nutrient limitation can vary significantly within a species and that changes in trait expression may be modified by other environmental variables. These results should be incorporated into existing stoichiometric models and used to investigate the eco-evolutionary consequences of consumer phenotypic variation in response to nutritional stress. Author Keywords: ecological stoichiometry, evolution, life-history, nutrient limitation, nutrient metabolism, zooplankton
Carbon Exchange along a Natural Gradient of Deciduous Shrub Coverage in the Low-Arctic
Arctic terrestrial ecosystems have experienced substantial structural and compositional changes in response to warming climate in recent decades, especially the expansion of shrub species in Arctic tundra. Climatic and vegetation changes could feedback to the global climate by changing the carbon balance of Arctic tundra. The objective of this thesis was to investigate the influence of increased shrub coverage on carbon exchange processes between atmosphere and the Arctic tundra ecosystem. In this study a space-for-time substitution was used, referred to as a shrub expansion “chronosequence”, with three sites along a natural gradient of deciduous shrub coverage in the Canadian low Arctic. Leaf-level photosynthetic capacity (Amax) of dominating birch shrub Betula glandulosa (Michx.) was significantly higher (P<0.05) at the site where shrubs were more abundant and taller than at the other sites. For all sites, mean Amax in 2014 was significantly lower than in 2013, in part potentially due to differences in precipitation distribution. Bulk soil respiration (RS) rate was significantly higher (P<0.05) at the site with more shrubs compared with the other sites. The differences in RS across sites appeared to be driven by differences in soil physiochemical properties, such as soil nitrogen and soil bulk density rather than soil microclimate factors (e.g. soil temperature, moisture). The three sites were either annual CO2 sources (NEP<0) to the atmosphere or CO2 neutral, with strongest annual CO2 sources (-44.1±7.0 g C m-2) at the site with most shrubs. Overall this study suggests that shrubs tundra carbon balance will change with shrub expansion and that shrub ecosystems in the Arctic currently act as annual carbon sources or neutral to the atmospheric CO2 and further shrub expansion might strengthen the CO2 emissions, causing a positive feedback to the warming climate. Author Keywords: arctic tundra, carbon exchange, climate change, photosynthetic capacity, shrub expansion, soil respiration
Identification and Quantification of Organic Selenium Species Produced by Microbiological Activity in Freshwater Environments
Despite being an essential nutrient at trace levels, selenium can be devastating to aquatic environments when present in excess. There is no apparent correlation between total aqueous selenium concentrations and observed toxic effects because bioaccumulation varies over several orders of magnitude depending on the chemical species of selenium and the biological species present in the lowest trophic level of the aquatic food chain. Despite being used in toxicity models due to its high bioavailability, free selenomethionine had not been found previously in the environment outside of a biological entity. Here, it is confirmed that selenomethionine is produced during the biological treatment of selenium-contaminated wastewater, and released in the effluent along with other discrete organic selenium species, including selenomethionine oxide. This identification followed the development of a rigorous preconcentration and cleanup procedure, allowing for the analysis of these organic selenium species in high-ionic strength matrices. A newly optimized anion-exchange chromatographic separation was coupled to inductively-coupled plasma mass spectrometry for the simultaneous quantification of these organic selenium species along with the more ubiquitous selenium oxyanions, selenite and selenate. This separation method was also coupled to electrospray tandem mass spectrometry for structural confirmation of selenomethionine and selenomethionine oxide. High resolution orbitrap mass spectrometry was used to identify another oxidation product of selenomethionine – a cyclic species which was tentatively identified, by coelution, in a selenium-contaminated river water sample. The production and release of selenomethionine, selenomethionine oxide, Se-(methyl) selenocysteine, and methyl selenic acid were observed for various laboratory algal cultures. Once the presence of free selenomethionine in a water system was confirmed, factors affecting its uptake into algal cultures were examined. The uptake of selenomethionine into Scenedesmus obliquus was noted to be significantly higher under low nitrate conditions, where it was incorporated into selenium-containing proteins more readily than at higher nitrate conditions where other metabolites were produced. With the increasing popularity of biological treatment systems for the remediation of selenium-contaminated waters, these observations, combined with existing knowledge, could be used to make predictions regarding the potential toxicity of selenium in various environmental scenarios. Author Keywords: bioremediation, electrospray mass spectrometry, inductively-coupled plasma mass spectrometry, selenium, selenoamino acids, selenomethionine
Size and fluorescence properties of allochthonous dissolved organic matter
Dissolved organic matter (DOM) is a mixture of molecules with dynamic structure and composition that are ubiquitous in aquatic systems. DOM has several important functions in both natural and engineered systems, such as supporting microorganisms, governing the toxicity of metals and other pollutants, and controlling the fate of dissolved carbon. The structure and composition of DOM determine its reactivity, and hence its effectiveness in these ecosystem functions. While the structure, composition, and reactivity of riverine and marine DOM have been previously investigated, those of allochthonous DOM collected prior to exposure to microbes and sunlight have received scant attention. The following dissertation constitutes the first in-depth study of the structure, composition, and reactivity of allochthonous DOM at its point of origin (i.e. leaf leachates, LLDOM), as detected by measuring its size and optical properties. Concomitantly, novel chemometric methods were developed to interpret size-resolved data obtained using asymmetrical flow field-flow fractionation, including spectral deconvolution and the application of machine learning algorithms such as self-organizing maps to fluorescence data using a dataset of more than 1000 fluorescence excitation-emission matrices. The size and fluorescence properties of LLDOM are highly distinct. Indeed, LLDOM was correctly classified as one of 13 species/sources with 92.5% accuracy based on its fluorescence composition, and LLDOM was distinguished from riverine DOM sampled from eight different rivers with 98.3% accuracy. Additionally, both fluorescence and size properties were effective conservative tracers of DOC contribution in pH-controlled mixtures of leaf leachates and riverine DOM over two weeks. However, the structure of LLDOM responded differently to pH changes for leaves/needles from different tree species, and for older needles. Structural changes were non-reversible. Copper-binding strength (log K) differed for the different fluorescent components of DOM in a single allochthonous source by more than an order of magnitude (4.73 compared to 6.11). Biotransformation preferentially removed protein/polyphenol-like fluorescence and altered copper-binding parameters: log K increased from 4.7 to 5.5 for one fluorescent component measured by fluorescence quenching, but decreased from 7.2 to 5.8 for the overall DOM, as measured using voltammetry. The complexing capacity of DOM increased in response to biotransformation for both fluorescent and total DOM. The relationship between fluorescence and size properties was consistent for fresh allochthonous DOM, but differed in aged material. Since the size and fluorescence properties of LLDOM are strikingly different from those of riverine DOM, deeper investigation into transformative pathways and mixing processes is required to elucidate the contribution of riparian plant species to DOM signatures in rivers. Author Keywords: Analytical chemistry, Chemometrics, Dissolved organic matter (DOM), Field-flow fractionation, Fluorescence spectroscopy, Parallel factor analysis (PARAFAC)
Nutrient Metabolism of an Aquatic Invertebrate and its Importance to Ecology
Aquatic consumers frequently face nutritional limitation, caused in part, by imbalances between the nutrients supplied by primary producers and the metabolic demands of the consumers. These nutritional imbalances alter many ecological processes including consumer life-history traits, population dynamics, and food web properties. Given the important ecological role of organismal nutrition, there is a need to have precise and specific indicators of nutritional stress in animals. Despite this need, current methods used to study nutrition are unable to distinguish between different types of nutritional limitation. Here I studied nutritional metabolism in the freshwater zooplankter, Daphnia. A greater understanding of nutritional metabolism would allow for the development of dietary bio-indicators that could improve the study of the nutritional ecology of animal consumers. Specifically, I addressed the question: What affects the biochemical composition of a generalist aquatic consumer? My overall hypothesis was that the quantity and quality of the diet affects the biochemical composition in a nutrient specific manner. To test this hypothesis, I examined various response variables involved in nutrient metabolism such as alkaline phosphatase activity, whole metabolome, and free amino acid composition. For each response variable, I grew Daphnia under various nutritional stressors and determined if responses are nutrient specific or are a general stress response. I found the current method of measuring alkaline phosphatase was not a phosphorus specific indicator, as activity increased in all nutrient stressed treatments. Analyzing the whole metabolome resulted in nutritional stressors being separated in multivariate space, with many identified metabolites being significantly different from nutrient rich Daphnia. Upon further examination the daphnids free amino acids profiles are caused by differences between the supply of amino acids from the algae and the demand within the Daphnia. These differences in supply and demand resulted in the ability to classify the nutritional status of Daphnia with the use of discriminant analysis, a classification multivariate model. In addition to a deeper understanding and advanced knowledge of the physiological changes caused by nutrient limitation, this research has provided strong evidence for the application of nutritional biomarkers/profiles to identified the nutritional status of Daphnia. Author Keywords: Bio-indictor, Ecological stoichiometry, Metabolism, Nutritional limitation, Nutritional status
Assessing the Potential for Contamination of Lakes from Upwelling of Arsenic-Laden Groundwater Through Sediments
A bedrock fracture hosting arsenic (As) contaminated groundwater was suspected to be transported to Ramsey Lake, a drinking water resource for more than 50,000 residents of Sudbury, Ontario. A high resolution, spatial, water quality mapping technique using an underwater towed vehicle (UTV) was used to identify sources of upwelling groundwater into lake water and localize the upwelling As contaminated groundwater vent site. The top 7 cm of lake sediments (in-situ) at this vent site were observed to adsorb 93 % of the dissolved As, thus inhibiting lake water quality degradation from this contaminant source. Sediment samples from this location were used in laboratory experiments to assess the potential for this system to become a source of As contamination to Ramsey Lake water quality and elucidate As(III) fractionation, transformation and redistribution rates and processes during aging. Arsenic speciation is important because As(III) has been shown to be more toxic than As(V). To accomplish this a sequential extraction procedure (SEP) that maintains As(III) and As(V) speciation in (sub)oxic sediments and soils was validated for the operationally defined fractions: easily exchangeable, strongly sorbed, amorphous Fe oxide bound, crystalline Fe oxide bound, and the residual fraction for total As because the characteristics of the reagents required to extract the final fraction do not maintain As species. Batch reaction experiments using sediment spiked with As(III) or As(V) and aged for up to 32 d were sequentially extracted and analysed for As(III) and As(V). Consecutive reaction models illustrate As(III) is first adsorbed to the sediment then oxidized to As(V). Fractionation analyses show As(III) most rapidly adsorbs to the easily exchangeable fraction where it is oxidized and redistributes to the strongly sorbed and amorphous Fe oxide bound fractions. Oxidation of As(III) adsorbed to the amorphous and crystalline Fe oxide bound fractions is less efficient and possibly inhibited. Select samples amended with goethite provide evidence supporting Mn(II) oxidation is catalyzed by the goethite surface, thus increasing As(III) oxidation by Mn(III/IV) complexed with the strongly sorbed fraction. Although As immobilization through groundwater sediment interactions may be inhibited by increased ion activity, particularly phosphate or lake eutrophication, this threat in Ramsey Lake is likely low. Author Keywords: arsenic, fractionation, modelling, redistribution, speciation, water quality mapping
Characterization of frog virus 3 and its binding partner LITAF
Iridoviruses are large (120-200nm) double stranded DNA viruses that contain an icosahedral capsid. The iridoviridae family is composed of five genera that infect a wide range of poikilothermic vertebrates (Lymphocystivirus, Ranavirus and Megalocyivirus) and invertebrate hosts (Iridovirus, Chloriridovirus). Frog virus 3 (FV3) is a member of the Ranavirus genus, and is commonly used as a model system to study iridoviruses. I was interested in understanding virus-host interaction in FV3. I studied two viral genes, FV3 97R and FV3 75L. Here I demonstrate that 97R localizes to the endoplasmic reticulum (ER) at 24 hours post-transfection. However, at 35 hours post-transfection 97R localizes to the ER but also begins to form concentrated pockets, continuous with the nuclear membrane This study found that 97R possess a unique phenotype and that its localization to the ER is mediated through its C-terminus transmembrane domain. FV3 75L encodes an 84 amino acids protein. I showed that FV3 75L localizes to the early endosomes, while its cellular binding partner, LITAF, localizes to late endosome/lysosome. Interestingly, when FV3 75L and LITAF are co-transfected into cells, LITAF can alter the subcellular localization of FV3 75L to late endosome/lysosomes. A physical interaction between LITAF and FV3 75L was demonstrated through a pull-down assay and that a highly conserved domain found in both proteins may mediate the interaction. LITAF has been proposed to function in protein degradation, but there is still uncertainty on LITAF's specific role. I was interested in further characterizing LITAF and its implications in protein degradation and a neurodegenerative disorder. At least 9 mutations of LITAF are associated with Charcot-Marie-Tooth disease type 1C (CMT1C), which belongs to the group of most common heritable neuromuscular disorders, affecting approximately one in 2500 people. We show that LITAF mutants G112S and W116G mislocalize from the late endosome/lysosome to the mitochondria while the T49M and P135T mutants show partial mislocalization with a portion of the protein present in the late endosome/lysosome and a portion of the protein localized to the mitochondria. Since LITAF is believed to play a role in protein degradation, it is possible that the specific characteristics of CMT1C may occur though impaired degradation of Schwann cell membrane proteins, such as PMP22. I was able to show that when WT LITAF is present, there is a decrease in the PMP22 intracellular levels, which suggest that LITAF plays an important role in protein degradation, and also in other types of CMT. Insight into how mutations in LITAF cause CMT1C may not only help better understand cellular pathways, but also further elucidate the role LITAF's viral homolog FV3 75L during viral infection. Author Keywords: 75L, Charcot-Marie-Tooth, CMTC1, ER, FV3, LITAF
Beyond Habitat
My objective was to understand how individual variation, in conjunction with variation in habitat, can affect individual and population-level variation in animal space use. I used coyotes (Canis latrans) as a model species to investigate the roles of hybridization, an inherited intrinsic factor, and spatial memory, a learned intrinsic factor, on space use. I used a diversity of methods and approaches, including meta-regression, multiple imputation, simulations, resource selection functions, step selection functions, net-squared displacement analysis, and survival analysis. A major contribution was my investigation of the performance of multiple imputation in a meta-regression framework in Chapter 2. My simulations indicated that multiple imputation performs well in estimating missing data within a meta-regression framework in most situations. In Chapter 3, I used published studies of coyote home range size in a meta-regression analysis with multiple imputation to examine the relative roles of hybridization and environmental variables on coyote home range size across North America. I found that hybridization with Canis species was a leading factor driving variation in coyote space use at a continental scale. In Chapter 4, I used telemetry data for 62 coyotes in Newfoundland, Canada, to investigate the influence of cognitive maps on resource use. I found that resident coyotes used spatial memory of the landscape to select or avoid resources at spatial scales beyond their immediate sensory perception relative to transient coyotes, presumably increasing their fitness. Taken together, my dissertation demonstrates that intrinsic factors, such as genetic ancestry and spatial memory, can have substantial influences on how animals use space at both individual and population levels, and at both a local and a continental scales. Author Keywords: canis latrans, hybridization, meta-regression, multiple imputation, Newfoundland, spatial memory
Conservation Genetics of Woodland Caribou in the Central Boreal Forest of Canada
Maintaining functional connectivity among wildlife populations is important to ensure genetic diversity and evolutionary potential of declining populations, particularly when managing species at risk. The Boreal Designatable Unit (DU) of woodland caribou (Rangifer tarandus caribou) in Ontario, Manitoba, and Saskatchewan has declined in southern portions of the range because of increased human activities and has been identified as 'threatened' by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). In this dissertation, I used ten microsatellite DNA markers primarily from winter-collected fecal samples to delineate genetic structure of boreal caribou in declining portions of the range and increase understanding of the potential influence of the non-threatened Eastern Migratory DU of woodland caribou on genetic differentiation. Eastern migratory caribou are characterized by large home ranges compared to boreal caribou and migrate seasonally into portions of the Boreal DU range. A regional- and local-scale analysis using the spatial Bayesian clustering algorithm in program TESS delineated four regional clusters and 11 local clusters, with the majority of local clusters occurring along the southern periphery of the range. One of those clusters in Ontario corresponded spatially with the seasonal overlap of boreal and eastern migratory caribou and was characterized by substantial admixture, suggesting that the two DUs could be interbreeding. Next, I decoupled the impacts of historical and contemporary processes on genetic structure and found that historical processes were an important factor contributing to genetic differentiation, which may be a result of historical patterns of isolation by distance or different ancestry. Moreover, I found evidence of introgression from a currently unsampled population in northern Ontario, presumably barren-ground caribou (R. t. groenlandicus). Finally, because our analysis suggested recent processes were also responsible for genetic structure, I used a landscape genetics analysis to identify factors affecting contemporary genetic structure. Water bodies, anthropogenic disturbance, and mobility differences between the two DUs were important factors describing caribou genetic differentiation. This study provides insights on where conservation and management of caribou herds should be prioritized in threatened portions of the boreal caribou range and may have implications for future delineation of evolutionarily significant units. Author Keywords: boreal forest, genetic structure, landscape genetics, microsatellite DNA, Rangifer tarandus, woodland caribou
effects of Dissolved Organic Matter (DOM) sources on Pb2+, Zn2+ and Cd2+ binding
Metal binding to dissolved organic matter (DOM) determines metal speciation and strongly influences potential toxicity. The understanding of this process, however, is challenged by DOM source variation, which is not always considered by most existing metal speciation models. Source determines the molecular structure of DOM, including metal binding functional groups. This study has experimentally showed that the allochthonous-dominant DOM (i.e. more aromatic and humic) consistently has higher level of Pb binding than the autochthonous-dominant DOM (i.e. more aliphatic and proteinaceous) by more than two orders of magnitude. This source-discrimination, however, is less noticeable for Zn and Cd, although variation still exceeds a factor of four for both metals. The results indicate that metal binding is source-dependent, but the dependency is metal-specific. Accordingly, metal speciation models, such as the Windermere Humic Aqueous Model (WHAM), needs to consider DOM source variations. The WHAM input of active fraction of DOM participating in metal binding (f) is sensitive to DOM source. The commonly-used f = 0.65 substantially overestimated the Pb and Zn binding to autochthonous-dominant DOM, indicating f needs to be adjusted specifically. The optimal f value (fopt) linearly correlates with optical indexes, showing a potential to estimate fopt using simple absorbance and/or fluorescence measurements. Other DOM properties not optically-characterized may be also important to determine fopt, such as thiol, which shows strong affinity to most toxic metals and whose concentrations are appreciably high in natural waters (< 0.1 to 400 nmol L-1). Other analytical techniques rather than Cathodic Stripping Voltammetry (CSV) are required to accurately quantify thiol concentration for DOM with concentration > 1 mg L-1. To better explain the DOM-source effects, the conditional affinity spectrum (CAS) was calculated using a Fully Optimized ContinUous Spectrum (FOCUS) method. This method not only provides satisfactory goodness-of-fit, but also unique CAS solution. The allochthonous-dominant DOM consistently shows higher Pb affinity than autochthonous-dominant DOM. This source-discrimination is not clearly observed for Zn and Cd. Neither the variability of affinity nor capacity can be fully explained by the variability of individual DOM properties, indicating multiple properties may involve simultaneously. Together, the results help improve WHAM prediction of metal speciation, and consequently, benefit geochemical modelling of metal speciation, such as Biotic Ligand Model for predicting metal toxicity. Author Keywords: Dissolved organic matter, Metal binding, Source, Windermere Humic Aqueous Model


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