Graduate Theses & Dissertations


Legume species, nitrogen rate and arbuscular mycorrhizal fungi inoculation effects on crop biomass and nitrogen requirement in a corn-legume system
Interseeding legume cover crops in grain corn may improve the environmental sustainability of corn production system in Southern Ontario. This study aimed to assess the effects of legume species, nitrogen (N) fertilizer rate and arbuscular mycorrhizal fungi (AMF) inoculation on biomass and N requirement in a corn-legume system. Corn was grown with red clover (RCl), microclover (MCl), hairy vetch (HV), or beans at 10 and 80 kg N ha-1 rates with and without AMF inoculation in a greenhouse for 7 weeks. Corn dry matter (DM) and N uptake were reduced by beans and HV (average 35%) compared with control; however, the DM for beans and HV was 7 and 3 times higher than RCl and MCl, respectively. The N2 fixation ability was similar among legume species and no significant N transfer from legume was detected. Overall, species collection was critical to the success of incorporating legumes into grain corn production. Author Keywords: Arbuscular mycorrhizal fungi, corn, legume cover crop, nitrogen
Ligand Binding Properties of Giardia Flavohemoglobin
The parasitic protist Giardia intestinalis possesses flavohemoglobin (gFlHb), an enzyme that detoxifies nitric oxide to the less harmful nitrate, and is a potential target for antigiardial drugs that act as ligands to the iron of its heme cofactor. In this work, the binding constants KD of gFlHb, three active-site variants (Q54L, L58A, Y30F) and the E. coli flavohemoglobin (Hmp) towards cyanide, azide and several substituted imidazoles were measured by optical titration. Certain cases such as gFlHb and Hmp were studied further by isothermal titration calorimetry. Binding constants for cyanide and the imidazoles ranged from 2 to 100 M, with the highest affinities observed with for miconazole, a bulky substituted imidazole. Azide was a poor ligand, with binding constants between 0.48 and 26 mM. Among gFlHb and its mutants, L58A tended to have the highest ligand affinities, as mutation of the distal leucine to a less bulky distal alanine residue facilitates the access of the exogenous ligand to the heme iron. In contrast, the Q54L and Y30F variants had binding affinities that in most cases were similar to wild type, which suggests that the inability of their side chains to form hydrogen bonds to these ligands is not a significant factor in binding of imidazole ligands to the enzyme. Comparative results for Hmp and gFlHb ligand binding affinities revealed slight differences which might be explained by the presence of different residues in their active sites apart from their conserved residues. Author Keywords: Flavohemoglobin, Giardia intestinalis, Imidazole binding, Ligand binding, Nitrosative stress
Linking large scale monitoring and spatially explicit capture–recapture models to identify factors shaping large carnivore densities
Understanding the spatial ecology of large carnivores in increasingly complex, multi-use landscapes is critical for effective conservation and management. Complementary to this need are robust monitoring and statistical techniques to understand the effect of bottom-up and top-down processes on wildlife population densities. However, for wide-ranging species, such knowledge is often hindered by difficulties in conducting studies over large spatial extents to fully capture the range of processes influencing populations. This thesis addresses research gaps in the above themes in the context of the American black bear (Ursus americanus) in the multi-use landscape of Ontario, Canada. First, I assess the performance of a widely adopted statistical modelling technique – spatially explicit capture-recapture (SECR) – for estimating densities of large carnivores (Chapter 2). Using simulations, I demonstrate that while SECR models are generally robust to unmodeled spatial and sex-based variation in populations, ignoring high levels of this variation can lead to bias with consequences for management and conservation. In Chapter 3, I investigate fine-scale drivers of black bear population density within study areas and forest regions by applying SECR models to a large-scale, multi-year black bear spatial capture-recapture dataset. To identify more generalizable patterns, in Chapter 4 I then assess patterns of black bear density across the province and within forest regions as a function of coarse landscape-level factors using the same datasets and assess the trade-offs between three different modeling techniques. Environmental variables were important drivers of black bear density across the province, while anthropogenic variables were more important in structuring finer-scale space use within study areas. Within forest regions these variables acted as both bottom-up and top-down processes that were consistent with ecological influences on black bear foods and intensity of human influences on the species’ avoidance of developed habitats. Collectively, this thesis highlights the opportunities and challenges of working across multiple scales and over expansive landscapes within a SECR framework. Specifically, the multi-scale approach of this thesis allows for robust inference of the mechanisms structuring fine and broad scale patterns in black bear densities and offers insight to the relative influence of top-down and bottom-up forces in driving these patterns. Taken together, this thesis provides an approach for monitoring large carnivore population dynamics that can be leveraged for the species conservation and management in increasingly human-modified landscapes. Author Keywords: animal abundance, black bear, capture-recapture, density estimation, statistical ecology, wildlife management
Long-Term Population Dynamics of an Unexploited Lacustrine Brook Trout (Salvelinus fontinalis) Population
Long-term studies of demographic processes such as survival and abundance conducted in unexploited systems provide unique insight into the natural population ecology of fish, but are rarely available. I used historical tagging records of a sanctuary population of brook trout (Salvelinus fontinalis) in Algonquin Park, Ontario to investigate long-term population dynamics in an unexploited population. Adult brook trout in Mykiss Lake (23.5ha) were surveyed and tagged biannually (May and October) between 1990 and 2004. Open-population capture-mark-recapture models were used to test the importance of time, size, sex and season on estimates of apparent survival and abundance. Seasonal population growth and recruitment were estimated and compared with large-scale climate indices. Time-dependent survival and abundance estimates fluctuated, with distinct periods of increase. Population growth and recruitment were positively correlated with summer NAO and ENSO values, whereas survival was negatively correlated. Seasonally, larger individuals experienced higher apparent survival during winter and decreased survival during summer. These findings provide valuable insights into the natural demography of unexploited brook trout populations, and should help inform sustainable management of inland fisheries. Author Keywords: capture-mark-recapture, long-term, population dynamics, Salvelinus fontinalis, seasonal variation, survival
Long-term Financial Sustainability of China's Urban Basic Pension System
Population aging has become a worldwide concern since the nineteenth century. The decrease in birth rate and the increase in life expectancy will make China’s population age rapidly. If the growth rate of the number of workers is less than that of the number of retirees, in the long run, there will be fewer workers per retiree. This will apply great pressure to China’s public pension system in the next several decades. This is a global problem known as the “pension crisis”. In this thesis, a long-term vision for China’s urban pension system is presented. Based on the mathematical models and the projections for demographic variables, economic variables and pension scheme variables, we test how the changes in key variables affect the balances of the pension fund in the next 27 years. This thesis applies methods of deterministic and stochastic modeling as well as sensitivity analysis to the problem. Using sensitivity analysis, we find that the pension fund balance is highly sensitive to the changes in retirement age compared with other key variables. Monte Carlo simulations are also used to find the possible distributions of the pension fund balance by the end of the projection period. Finally, according to my analysis, several changes in retirement age are recommended in order to maintain the sustainability of China’s urban basic pension scheme. Author Keywords: China, demographic changes, Monte Carlo simulation, pension fund, sensitivity tests, sustainability
Longitudinal trends of benthic invertebrates in regulated rivers
The Serial Discontinuity Concept describes the downstream recovery of key biophysical variables below an impoundment. With the proliferation of hydropower dams to meet increasing societal demands, further refinement and understanding of the Serial Discontinuity Concept is needed to accurately predict downstream impacts and ensure the proper management of rivers. In this study, I examine SDC predictions on physical, chemical and biological recovery in regulated rivers providing evidence from 1) a comprehensive literature review and 2) a formal test using two regulated rivers in Northern Ontario. I specifically address how these changes are reflected in benthic invertebrate abundance, diversity, and community composition. The literature review and case studies support the predicted recovery of temperature, periphyton, substrate, and drift. In addition, the study suggests that two recovery gradients exist in regulated rivers: 1) a longer, thermal gradient taking up to hundreds of kilometres downstream; and 2) a shorter, resource subsidy gradient recovering within 1-4 km downstream of an impoundment. Total benthic invertebrate abundance varies considerably and depends on the degree of flow alteration and resource subsidies from the upstream reservoir. In contrast, benthic diversity is reduced below dams irrespective of dam location and operation with little recovery observed downstream. Contrary to SDC predictions, the longitudinal gradient in regulated rivers is not a compaction of functional changes seen over several stream orders in natural rivers but a response to dam design and reservoir conditions. Stoneflies and dragonflies are particularly sensitive to regulation while filter feeding invertebrates are enhanced. Ward and Stanford's (1983) Serial Discontinuity Concept is still a useful framework for testing hypotheses. Future studies should further expand the SDC through empirical estimation within the context of the landscape to gain a better scientific understanding of regulated river ecology. Author Keywords: benthic invertebrates, dams, longitudinal, recovery, River Continuum Concept, Serial Discontinuity Concept
Changes to the Arctic and sub-Arctic climate are becoming increasingly evident as it warms faster than other areas of the globe, supporting evidence that predictions of future warming will be amplified due to positive feedback mechanisms. The Southern Hudson Bay polar bear (Ursus maritimus) subpopulation is one of the most southerly subpopulations in the world, putting it at increased risk due to effects of climate change. Whereas many other subpopulations have been the subject of intense research and monitoring, little research has been completed detailing the movement behaviour and space use of bears within Southern Hudson Bay. I used detailed movement data collected on female polar bears to establish a baseline of movement information for this subpopulation to which future work can be compared and effects of climate change can be assessed I evaluated the use of core areas during critical periods of the year (breeding and ice breakup) and evaluated common space use as a means of assessing site fidelity during the breeding season. Movement rates and home range sizes were comparable to those of the neighbouring Western Hudson Bay subpopulation. I also found evidence of increased occurrences of long distance, late fall movements along the coast to the northwest, presumably to gain earlier access to first ice. Though space use analysis did not reveal evidence of site fidelity to specific breeding areas in Hudson Bay, I found that core use areas are at risk of substantially shortened ice duration (x¯ =76 days shorter) using projected ice data based on the high emissions A2 climate change scenario. Author Keywords: climate change, Hudson Bay, movement, polar bear, sea ice, utilization distribution
Machine Learning Using Topology Signatures For Associative Memory
This thesis presents a technique to produce signatures from topologies generated by the Growing Neural Gas algorithm. The generated signatures have the following characteristics: The signature's memory footprint is smaller than the "real object" and it represents a point in the n x m multidimensional space. Signatures can be compared based on Euclidean distance and distances between signatures provide measurements of differences between models. Signatures can be associated with a concept and then be used as a learning step for a classification algorithm. The signatures are normalized and vectorized to be used in a multidimensional space clustering. Although the technique is generic in essence, it was tested by classifying alphabet and numerical handwritten characters and 2D figures obtaining a good accuracy and precision. It can be used for many other purposes related to shapes and abstract typologies classification and associative memory. Future work could incorporate other classifiers. Author Keywords: Associative memory, Character recognition, Machine learning, Neural gas, Topological signatures, Unsupervised learning
Machine Learning for Aviation Data
This thesis is part of an industry project which collaborates with an aviation technology company on pilot performance assessment. In this project, we propose utilizing the pilots' training data to develop a model that can recognize the pilots' activity patterns for evaluation. The data will present as a time series, representing a pilot's actions during maneuvers. In this thesis, the main contribution is focusing on a multivariate time series dataset, including preprocessing and transformation. The main difficulties in time series classification is the data sequence of the time dimension. In this thesis, I developed an algorithm which formats time series data into equal length data. Three classification and two transformation methods were used. In total, there are six models for comparison. The initial accuracy was 40%. By optimization through resampling, we increased the accuracy to 60%. Author Keywords: Data Mining, K-NN, Machine Learning, Multivariate Time Series Classification, Time Series Forest
Making eDNA count
Environmental DNA (eDNA) is rapidly becoming an established method for the detection of species in aquatic systems and has been suggested as a promising tool to estimate species abundance. However, the strength of the relationship between eDNA concentrations and taxon abundance (density/biomass) can vary widely between species. I investigated the relationship between eDNA concentration and species abundance using two common and closely-related amphibians in eastern North America, the wood frog (Rana sylvatica) and northern leopard frog (Rana pipiens). I manipulated tadpole density in 80 L mesocosms and documented the relationship between tadpole density, biomass, and eDNA concentration. Species were comparable in biomass but differed in the amount of detectible genetic material produced; density and biomass were the superior abundance metric correlated with eDNA concentration for wood frogs and leopard frogs, respectively. However, increases in eDNA concentration reflected increasing tadpole biomass, therefore biomass is likely a better metric of abundance than density. Overall my findings support that eDNA concentration can be used as an index of species abundance, but that species-specific calibration may be needed before eDNA concentration can be effectively translated to an abundance metric. Future research should refine our understanding of how biotic and abiotic factors influence eDNA production, degradation, and recovery across species, before the method can receive widespread use as a monitoring tool in natural settings. Author Keywords: abundance estimates, environmental DNA, mesocosm, Rana pipiens, Rana sylvatica
Marital Satisfaction Throughout the Journey of Weight-Loss Surgery
A mixed-methods’ approach was designed to explore the marital impacts following weight-loss surgery (WLS). In Phase 1, ten individual interviews with spouses of five couples were conducted; two of the couples had the wives preparing for WLS, two of the couples consisted of wives who had WLS, and one couple had both received the surgery. Interviews were transcribed and analyzed using a combination of interpretive phenomenological and grounded theory techniques. Findings demonstrated that WLS does have impacts on marriage regardless of where couples are in their journey. All couples discussed food as a possible source of conflict in their relationship. Interviews also reveled that self-esteem is a major factor contributing to their relationship and support is necessary throughout. In Phase 2 an online survey was developed to quantitatively explore the important constructs deemed important from the participants in Phase 1. Relationships between relationship satisfaction, sexual conflict, self-esteem, depression and body image were examined in 54 participants. Results demonstrate that higher levels of support and self-esteem and lower sexual conflict relate to a more satisfactory relationship in individuals post- WLS. Author Keywords: marital satsifaction, mixed-methods, qualitative, relationship satisfaction, weight-loss, Weight-loss surgery
Mercury and Persistent Organic Pollutants in Remote Acid Sensitive Irish Lake Catchments
A catchment-based study was carried out at three remote acid sensitive Irish lakes to determine concentrations of Hg and POPs and to investigate the factors governing the partitioning of these pollutants in various environmental matrices. Both Hg and POPs are an environmental concern due to their ability to travel long distances via atmospheric transport and their tendency to accumulate in biota and in various environmental compartments. Concentrations of POPs and Hg measured in this study were relatively low and consistent with concentrations measured at background levels around the world. Mercury concentrations appeared to be influenced by various site characteristics, specifically organic matter. Many of the POPs examined in this study appeared to be present as a result of long-range transport and more specifically; the physico-chemical properties of POPs appeared to dictate their distribution within soils, moss and sediment at each of the study catchments. Author Keywords:


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