Graduate Theses & Dissertations

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Comparison of the Optical Properties of Stratiotes aloids and the Local Plant Community
As part of a mandate to control the spread of Stratiotes aloides (WS; water soldier) in the Trent Severn Waterway, the Ministry of Natural Resources (MNR) created a management plan to eradicate WS. However, one of the biggest challenges in eradicating WS or any invasive aquatic plant is the ability to estimate the extent of its spread and detect new populations. While current detection methods can provide acceptable detection, these methods often require extensive time and effort. The purpose of this thesis was to assess the use optical properties of WS and WS exudates for detection, in order to improve on current detection methods. The optical properties of WS were sampled at three different sites during three different seasons (spring, summer, and fall) by a) randomly sampling tissue from WS and the local plant community at each site, and recording the reflectance properties in a laboratory setting b) collecting dissolved organic matter (DOM) samples from plant incubations and river water in the field. Significant differences in the reflectance properties of WS were observed among samples from different sites and different sampling times; however, changes in fluorescence properties were only seasonal. Despite spatial differences in WS reflectance; WS was detectable using both hyperspectral and multispectral reflectance. When hyperspectral reflectance was used, significant differences between WS and the local plant community were found in June using two bands (i.e. bands 525 and 535, R 2 = 0.46 and 0.48, respectively). Whereas multispectral reflectance was significant different in October using the coastal and blue band. While WS produced a unique signal using both reflectance types, multispectral reflectance had a greater potential for detection. Its greater potential for detection was due to the reduced noise produced by background optical properties in October in comparison to June. DOM derived from WS was also characterized and compared with whole-river DOM samples in order to find unique markers for WS exudates in river samples. While similarities in DOM concentrations of WS exudates to Trent River water limited the ability to detect WS using compositional data, the ratio of C4/C5 components were compared in order to find components that were proportionally similar. Based on the results of this study multispectral and fluorescence techniques are better suited for the detection of a unique WS signature. The results derived from this work are intended to have practical applications in plant management and monitoring, DOM tracing, as well as remote sensing. Author Keywords: Dissolved organic matter, Hyperspectral reflectance, Invasive species management, Multispectral reflectance, PARAFAC, Stratiotes aloides
Proximal Soil Nutrient Sensing in Croplands through Multispectral Imaging from Unmanned Aerial Vehicles (UAV) for Precision Agriculture Applications
Currently, UAVs are deployed to measure crop health in a timely manner by mapping vegetation indices. A study using two different fields was conducted in order to search for a relationship that may exist between crop health and soil fertility. A UAV equipped with sensor technology was used for mapping of vegetation indices which were then statistically compared to soil nutrient data collected via soil sampling. Elevation data was also collected which was then statistically compared to soil nutrients as well as crop health. Results of this study were unfortunately impacted by variables outside of the researcher’s control. Moisture became the greatest limiting factor in 2016 followed by an excess of rain in 2017. Results did not show any promising correlations as moisture uncontrollably became the defining variable. Further research in a more controlled setting will need to be conducted in order to explore this potential relationship. Author Keywords: Agriculture, Multispectral Imagery, Precision Agriculture, Proximal Soil Sensing, Remote Sensing, Unmanned Aerial Vehicle
Scarring, sex assignment, and sex-specific sociality of Indo-Pacific humpback dolphins (Sousa chinensis) in the Pearl River Estuary and eastern Taiwan Strait
The Pearl River Estuary (PRE) and eastern Taiwan Strait (ETS) populations of Indo-Pacific humpback dolphins (Sousa chinensis) contain ~600 and 100 catalogued individuals, respectively. Population demography is important for conservation actions but few animals have been sexed by conventional methods. Longitudinal analysis of tooth-rake scars on dorsal fins showed scars disappear within 7 months; sexing adults by scarring is likely not impacted by juvenile scarring. Using dorsal fin photographs, sex assigned for 87% of catalogued PRE adults (n=300) and for 93% of ETS adults (n=60), using scars hypothesized from male-male competition, was in concordance with sex assigned by DNA, calf association, and ventral photographs. Scarring was higher in presumed males than females and in PRE females than ETS females. Female:male sex ratios were 3:2 (PRE) and 2:1 (ETS), though this likely results from biases in photo-identification methods. Social analysis with presumed sexes showed strong female-female associations in both populations but stronger female-male and male-male associations in PRE. These results support sex differentiation by scarring, which was a non-invasive approach, and sex assignment for many PRE and ETS individuals. Author Keywords: Indo-Pacific humpback dolphins, photo-identification, scarring, sex differentiation, sexes, social structure
Population Genetics and Gut Microbiome Composition Reveal Subdivisions and Space Use in a Generalist and Specialist Ungulate
Natural populations are often difficult and costly to study, due to the plethora of confounding processes and variables present. This is of particular importance when dealing with managed species. Ungulates, for example, act as both consumers and prey sources; they also provide economic benefit through harvest, and as such, are of high ecological and economic value. I addressed conservation and management concerns by quantifying subdivision in wild populations and combined movement with non-invasive sampling to provide novel insight on the physiological drivers of space use in multiple species. This thesis explored biological patterns in ungulates using two distinct approaches: the first used molecular genetics to quantify gene flow, while the second examined the relationship between movement and the gut microbiome using high-throughput sequencing and GPS tracking. The goal of the first chapter was to quantify gene flow and assess the population structure of mountain goats (Oreamnos americanus) in northern British Columbia (BC) to inform management. I used microsatellites to generate genotype data and used a landscape genetics framework to evaluate the possible drivers behind genetic differentiation. The same analyses were performed at both a broad and fine scale, assessing genetic differentiation between populations in all of northern BC and in a case management study area northeast of Smithers BC. The results indicated panmixia among mountain goats regardless of scale, suggesting distance and landscape resistance were minimally inhibiting gene flow. Therefore, management at local scales can continue with little need for genetically informed boundaries, but regulations should be tailored to specific regions incorporating data on local access and harvest pressure. My second chapter aimed to determine the extent to which the gut microbiome drives space-use patterns in a specialist (mountain goat) and generalist (white-tailed deer, Odocoileus virginianus) ungulate. Using fecal samples, we generated genomic data using 16S rRNA high-throughput sequencing to evaluate gut diversity and gut microbiome characteristics. Additionally, individuals were fitted with GPS collars so that we could gain insight into movement patterns. Gut microbiome metrics were stronger predictors of space use and movement patterns with respect to home range size, whereas they were weaker predictors of habitat use. Notably, factors of both the gut microbiome and age of a given species were correlated with changes in space use and habitat use. Ultimately, this research linked high-throughput sequencing and GPS data to better understand ecological processes in wild ungulates. Author Keywords: gene flow, genomics, gut microbiome, home range, population genetic structure, ungulates
Bioremoval of copper and nickel on living and non-living Eugelna gracilis
This study assesses the ability of a unicellular protist, Euglena gracilis, to remove Cu and Ni from solution in mono- and bi-metallic systems. Living Euglena cells and non-living Euglena biomass were examined for their capacity to sorb metal ions. Adsorption isotherms were used in batch systems to describe the kinetic and equilibrium characteristics of metal removal. In living systems results indicate that the sorption reaction occurs quickly (<30 min) in both Cu (II) and Ni (II) mono-metallic systems and adsorption follows a pseudo-second order kinetics model for both metals. Sorption capacity and intensity was greater for Cu than Ni (p < 0.05) and were described by the Freundlich model. In bi-metallic systems sorption of both metals appears equivalent. In non-living systems sorption occurred quickly (10-30 min) and both Cu and Ni equilibrium uptake increased with a concurrent increase of initial metal concentrations. The pseudo-first-order model was applied to the kinetic data and the Langmuir and Freundlich models effectively described single-metal systems. The biosorption capacity of Cu (II) and) was 3x times greater than that of Ni (II). Sorption of one metal in the presence of relatively high concentrations of the other metal was supressed. Generally, it was found that living Euglena remove Cu and Ni more efficiently than non-living Euglena biomass in both mono- and bi-metallic systems. It is anticipated that this work should contribute to the identification of baseline uptake parameters and capacities for Cu and Ni by Euglena as well as to the increasing amount of research investigating sustainable bioremediation. Author Keywords: accumulation, biosorption, Cu, Euglena gracilis, kinetics, Ni
Exploring the Scalability of Deep Learning on GPU Clusters
In recent years, we have observed an unprecedented rise in popularity of AI-powered systems. They have become ubiquitous in modern life, being used by countless people every day. Many of these AI systems are powered, entirely or partially, by deep learning models. From language translation to image recognition, deep learning models are being used to build systems with unprecedented accuracy. The primary downside, is the significant time required to train the models. Fortunately, the time needed for training the models is reduced through the use of GPUs rather than CPUs. However, with model complexity ever increasing, training times even with GPUs are on the rise. One possible solution to ever-increasing training times is to use parallelization to enable the distributed training of models on GPU clusters. This thesis investigates how to utilise clusters of GPU-accelerated nodes to achieve the best scalability possible, thus minimising model training times. Author Keywords: Compute Canada, Deep Learning, Distributed Computing, Horovod, Parallel Computing, TensorFlow
Risk of Mortality for the Semipalmated Plover (Charadrius semipalmatus) Throughout Its Life Cycle
Three long-term mark and recapture/resight data sets of individually marked Semipalmated Plovers (Charadrius semipalmatus) were analyzed using Cormack-Jolly- Seber models. Data came from two breeding populations (Churchill, Manitoba, Canada, n=982, and Egg Island, Alaska, USA, n=84) and one overwintering population (Cumberland Island, Georgia, USA, n=62). For Alaska and Georgia, time-invariant models were best-supported, giving annual survival estimates of 0.67 (95%C.I.: 0.58- 0.76) and 0.59 (95%C.I.: 0.49-0.67) respectively. Data from Manitoba supported a timedependent model: survival estimates varied from 1.00 to 0.36, with lowest estimates from recent years, supporting observations of local population decline. Seasonal survival analysis of the Georgia population indicated lower mortality during winter (monthly Φoverwinter: 0.959, 95%CI: 0.871-0.988; for 6 month period Φoverwinter: 0.780 (0.440-0.929)) than during combined breeding and migratory periods (monthly ΦBreeding+Migration: 0.879 (0.825-0.918); for 8 month ΦBreeding+Migration: 0356 (0.215-0.504)). I recommend, based on high resight rates, continued monitoring of survival of wintering populations, to determine potential range-wide population declines. Keywords: survival, longevity, mortality, shorebird, overwinter, breeding, migration, life cycle Author Keywords: life cycle, longevity, mortality, non-breeding, shorebird, survival
Interpretation of forest harvest recovery using field-based and spectral metrics in a Landsat time series in Northwestern Ontario
The forestry sector has a well-developed history of using remote sensing to identify structural characteristics of forests and to detect and attribute changes that occur in forested landscapes. Monitoring the recovery of disturbed forests is an important factor in long term forest management. However, forest that is recovered spectrally may not be recovered when considered in terms of a Free to Grow assessment. A Free to Grow assessment is used in Ontario to determine whether a disturbed site will likely achieve a desired future state, i.e., is recovered according to a forestry perspective. The objective of this research was to determine the relationship between a pixel-based Landsat Time Series of spectral recovery and the results of Free to Grow assessments. Spectral trajectories were generated from representative pixels within known harvested forest areas. Results indicate that while Free to Grow sites often achieve spectral recovery (>90%), many non-Free to Grow sites were classified as spectrally recovered, suggesting that improved methods of spectral recovery monitoring are needed. Author Keywords: forest recovery, Free to Grow, Landsat Time Series, LandTrendr, Pixel-based, spectral recovery
Effect of Listing a Stock on the S&P 500 Index on the Stock’s Volatility
This paper investigates the effect of listing a stock on the S&P 500 Index on the stock’s volatility, using various econometrics models: GARCH and EGARCH. The study mainly addresses three issues; firstly, it analyzes stock volatility in two sub-periods, secondly, it determines whether the announcement can account for the fluctuations in the price of the stock, and finally, it investigates the change in the stock’s variance. After isolating the effects of external and industry shock by using the returns on the S&P 500 Index as a proxy, the author finds evidence of structural change in the volatility of stocks after that stock is added to the index. Additionally, the existence of a dominant symmetric effect, which captures the response of volatility to news, indicate that following the onset of including the stock on the index, information flowing into the market increased. However, the rate at which old news is captured in price falls. The empirical evidence also suggests that on average a stocks variance falls and that the announcement to list a stock on the index has little effect on the stock’s price. Author Keywords: EGARCH, GARCH, S&P 500 Index, Symmetric Effect, Volatility
Influence of nitrogen deposition on the vegetation community of Irish oak woodlands
In this study, the influence of N deposition on the vegetation community of semi-natural oak woodlands in Ireland was assessed through national and regional scale analysis of forest plot data. At both scales, Canonical Correspondence Analysis suggested that N deposition was a predictor of community composition, although site-specific soil characteristics were the strongest predictors of the species dataset. Threshold Indicator Taxon Analysis suggested that the vegetation community demonstrated the most change at 13.2 kg N ha-1 yr-1. While this change point falls within the current recommended critical load range for nutrient nitrogen for acidophilous oak dominated woodlands (10 to 15 kg N ha-1 yr-1), it is notable that 23% of species recorded had individual change points below this range, and could potentially be lost from this habitat if deposition increases. The results from this study suggest that, for acidophilous oak woodlands, habitat conservation policies should be unified with N emission reduction policies. Author Keywords: community composition, critical load, nitrogen depositioin, oak woodland, species richness, Taxon Indicator Threshold Analysis
Comparative efficacy of eDNA and conventional methods for monitoring wetland anuran communities
Identifying population declines and mitigating biodiversity loss require reliable monitoring techniques, but complex life histories and cryptic characteristics of anuran species render conventional monitoring challenging and ineffective. Environmental DNA (eDNA) detection is a highly sensitive and minimally invasive alternative to conventional anuran monitoring. In this study, I conducted a field experiment in 30 natural wetlands to compare efficacy of eDNA detection via qPCR to three conventional methods (visual encounter, breeding call, and larval dipnet surveys) for nine anuran species. eDNA and visual encounter surveys detected the greatest species richness, with eDNA methods requiring the fewest sampling events. However, community composition results differed among methods, indicating that even top performing methods missed species detections. Overall, the most effective detection method varied by species, with some species requiring two to three methods to make all possible detections. Further, eDNA detection rates varied by sampling season for two species (A. americanus and H. versicolor), suggesting that species-specific ecology such as breeding and larval periods play an important role in eDNA presence. These findings suggest that optimized monitoring of complex anuran communities may require two or more monitoring methods selected based on the physiology and biology of all target species. Author Keywords: amphibian, anuran, conventional monitoring, eDNA, environmental DNA, species richness
Social Anxiety, Theory of Mind, and Executive Function in Late Adolescence and Early Adulthood
Studies that have investigated the relation between social anxiety and theory of mind or executive function have shown that individuals with deficits in these cognitive processes have high levels of social anxiety. However, methodological problems make past findings questionable and difficult to interpret. The current study investigated whether deficits in theory of mind and executive function predicted symptoms of social anxiety in 99 older adolescents and young adults (18-29). On average, participants had moderate levels of social anxiety. Performance on measures of theory of mind and executive function did not predict symptoms of social anxiety. This lack of associations could be due to characteristics of the current sample, methodological differences in the current study compared to past studies, or the type of social anxiety and theory of mind measure used. Implications and directions for future research are discussed. Author Keywords: Early Adulthood, Executive Function, Late Adolescence, Social Anxiety, Theory of Mind

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Format: 2023/02/05