Graduate Theses & Dissertations

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Modelling Monthly Water Balance
Water balance models calculate water storage and movement within drainage basins, a primary concern for many hydrologists. A Thornthwaite water balance model (H2OBAAS) has shown poor accuracy in predicting low flows in the Petawawa River basin in Ontario, so lake storage and winter snow processes were investigated to improve the accuracy of the model. Lake storage coefficients, represented by the slopes of lake stage vs. lake runoff relationships, were estimated for 19 lakes in the Petawawa River basin and compared on a seasonal and inter-lake basis to determine the factors controlling lake runoff behaviour. Storage coefficients varied between seasons, with spring having the highest coefficients, summer and fall having equal magnitude, and winter having the lowest coefficients. Storage coefficients showed positive correlation with lake watershed area, and negative correlation with lake surface area during summer, fall, and winter. Lake storage was integrated into the H2OBAAS and improved model accuracy, especially in late summer, with large increases in LogNSE, a statistical measure sensitive to low flows. However, varying storage coefficients with respect to seasonal lake storage, watershed area, and surface area did not improve runoff predictions in the model. Modified precipitation partitioning and snowmelt methods using monthly minimum and maximum temperatures were incorporated into the H2OBAAS and compared to the original methods, which used only average temperatures. Methods using temperature extremes greatly improved simulations of winter runoff and snow water equivalent, with the precipitation partitioning threshold being the most important model parameter. This study provides methods for improving low flow accuracy in a monthly water balance model through the incorporation of simple snow processes and lake storages. Author Keywords: Lake Storage, Model Calibration, Monthly Water Balance, Petawawa River, Precipitation Partitioning, Snow Melt
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
Exploring the Role of Natural Antisense Transcripts in the Stress Response of Ustilago maydis
Fungal pathogens adapt to environmental changes faster than their hosts, due in part to their adaptive mechanisms exhibited in response to stress. Ustilago maydis was used to investigate potential natural antisense transcript (NAT) RNA-mediated mechanisms that enhance fungal adaptation to stress. Of the 349 NATs conserved amongst U. maydis and two related smut fungi, five NATs were identified as having altered transcript levels in response to multiple stress conditions. Subsequently, antisense transcript expression vectors were created for select NATs and transformed into U. maydis haploid cells. When exposed to stress conditions, two antisense expressing mutant strains exhibited alterations in growth. RT-qPCR analysis of mRNA complementary to expressed NATs revealed no significant change in mRNA levels, which suggests NAT expression may influence stress response through dsRNA formation or other RNA mediated mechanisms. These results establish a basis for further investigations into the connection between NATs and the stress response of fungi. Author Keywords: natural antisense transcripts, non-coding RNAs, stress response, Ustilago maydis
Enhancing forensic entomology applications
The purpose of this thesis is to enhance forensic entomology applications through identifications and ecological research with samples collected in collaboration with the OPP and RCMP across Canada. For this, we focus on blow flies (Diptera: Calliphoridae) and present data collected from 2011-2013 from different terrestrial habitats to analyze morphology and species composition. Specifically, these data were used to: 1) enhance and simplify morphological identifications of two commonly caught forensically relevant species; Phormia regina and Protophormia terraenovae, using their frons-width to head-width ratio as an additional identifying feature where we found distinct measurements between species, and 2) to assess habitat specificity for urban and rural landscapes, and the scale of influence on species composition when comparing urban and rural habitats across all locations surveyed where we found an effect of urban habitat on blow fly species composition. These data help refine current forensic entomology applications by adding to the growing knowledge of distinguishing morphological features, and our understanding of habitat use by Canada’s blow fly species which may be used by other researchers or forensic practitioners. Author Keywords: Calliphoridae, Ecology, Forensic Entomology, Forensic Science, Morphology, Urban
Selection on functional genes across a flying squirrel (genus Glaucomys) hybrid zone
While hybridization between distinct taxa can have undesirable implications, it can also result in increased genetic variability and potentially, the exchange of adaptive genes or traits. Adaptive variation acquired through introgressive hybridization may be particularly advantageous for species facing rapid environmental change. I investigated a novel, climate change-induced hybrid zone between two flying squirrel species: the southern (Glaucomys volans) and northern (G. sabrinus) flying squirrel. I was interested in the occurrence of hybridization and introgression, the type of selective pressures maintaining the hybrid zone and the potential for adaptive introgression. I found relatively low hybridization and introgression frequencies (1.7% and 2.9% of the population, respectively) and no evidence of selection on hybrids or backcrosses in particular environments. I conclude that the data are more consistent with a hybrid zone maintained by endogenous (environment-independent) selection. I tested for adaptive introgression using two functional genes: IGF-1 and CLOCK. I documented intermediate functional allele frequencies in backcrosses compared to parental populations, suggesting the alleles do not confer fitness advantages in backcrosses. Despite lack of evidence for current adaptive introgression, genetic admixture between G. volans and G. sabrinus may provide adaptive potential should these species face more rapid or drastic environmental change in the future. Author Keywords: adaptive introgression, flying squirrel, Glaucomys sabrinus, Glaucomys volans, hybridization, introgression
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
Effects of Recycled Media on Culture Growth and Hormone Profiles in Heterotrophic Euglena gracilis
The rapid expansion of the worldwide population has caused an urgent need for the development of new, more environment-conscious, food sources. In this context, algae, such as Euglena, are of interest thanks to their capacity to naturally produce essential nutrients such as proteins and oils commonly found in animals and plant sources. While these processes are currently being investigated, underlying measures affecting growth of Euglena gracilis like hormonal influences and growth stress like nutrient deprivation are poorly understood. From this vantage point, this thesis seeks to understand the role of phytohormones cytokinin (CKs) and abscisic acid (ABA) in complex mechanisms underlying heterotrophic growth of Euglena gracilis under recycled, organic media conditions with no supplementation. Hormone profiles were quantified by HPLC-ESI-MS/MS and compared to culture growth dynamics of pH, weight accumulation, glucose content, cell count and morphology. It was expected that ABA acted as an inhibitory hormone and this was confirmed by its higher levels when CKs where low and vice versa. Contrastingly, it was expected that CKs stimulated growth, in which this was shown not to be the case. Interestingly, it was revealed that both hormone groups increase with increasing recycling. Other key findings include: E. gracilis synthesizes CKs via the tRNA-degradation pathway and is cZ and iP dominated, recycling E. gracilis medium is viable for growth, however, the percentage (25% or less) is crucial to cell viability and markedly no ABA was detected in E. gracilis pellet fractions from recycled media. Therefore, this data revealed that recycled media has a striking influence on physiological aspects of growth and illustrated unique changes in hormone profiles of which could be manipulated to help the food industry. Author Keywords: cytokinin, endogenous hormones, Euglena gracilis, heterotrophic, large scale microalgae cultivation, recycled medium
Gene flow directionality and functional genetic variation among Ontario, Canada Ursus americanus populations.
Rapidly changing landscapes introduce challenges for wildlife management, particularly for large mammal populations with long generation times and extensive spatial requirements. Understanding how these populations interact with heterogeneous landscapes aids in predicting responses to further environmental change. In this thesis, I profile American black bears using microsatellite loci and pooled whole-genome sequencing. These data characterize gene flow directionality and functional genetic variation to understand patterns of dispersal and local adaptation; processes key to understanding vulnerability to environmental change. I show dispersal is positively density-dependent, male biased, and influenced by food productivity gradients suggestive of source-sink dynamics. Genomic comparison of bears inhabiting different climate and forest zones identified variation in genes related to the cellular response to starvation and cold. My thesis demonstrates source-sink dynamics and local adaption in black bears. Population management must balance dispersal to sustain declining populations against the risk of maladaptation under future scenarios of environmental change. Author Keywords: American black bear, Dispersal, Functional Genetic Variation, Gene Flow Directionality, Genomics, Local Adaptation
Sexual Dimporphism and Population Dynamics of Sub-Arctic Breding Dunlin (Calidris alpina hudsonia) near Churchill, Manitoba, Canada
Around the world, many populations of migratory shorebirds appear to be declining. Conservation strategies to reverse declining trends rely on, among other information, a firm understanding of breeding ground population dynamics. From 2010 to 2014, I studied a breeding population of Dunlin (Calidris alpina hudsonia) near Churchill, Manitoba using mark-recapture methods. I found that females were significantly larger than males. I subsequently developed an equation based on morphological features that successfully classified 87.1% of females and 92.6% of males, sexed using molecular techniques. Using program MARK, I quantified the annual apparent survival of adults (± SE) within the breeding population (0.82 ± 0.063 for males, 0.73 ± 0.12 for females). Transient adults made up a significant percentage of the female population (32%, P = 0.011), but non-significant in the male population (12%, P > 0.05). Re-sight rate was high for both sexes, and ranged from 0.86-0.90 per year. Sex, year, and nest initiation date were the factors that had the greatest influence on annual returns. There was no significant difference in mean inter-annual nest site distance between sexes (male: 82.01 ± 13.42 m, female: 208.38 ± 55.88 m, P > 0.05). The high survival estimates obtained in this study suggest that the breeding population is stable and may not be contributing to suspected population declines within the subspecies. Author Keywords: demography, discriminant function analysis, mark-recapture, sexual size dimorphism, survival
Evaluating the effects of landscape structure on genetic differentiation and diversity
The structure and composition of the landscape can facilitate or impede gene flow, which can have important consequences because genetically isolated groups of individuals may be prone to inbreeding depression and possible extinction. My dissertation examines how landscape structure influences spatial patterns of genetic differentiation and diversity of American marten (Martes americana) and Canada lynx (Lynx canadensis) in Ontario, Canada, and provides methodological advances useful for landscape geneticists. First, I identified the effects of map boundaries on estimates of landscape resistance, and proposed a solution to the bias: a buffer around the map boundary. Second, I assessed the sensitivity of a network-based estimate of genetic distance, conditional genetic distance, to incomplete sampling. I then used these landscape genetic tools in a pairwise, distance-based analysis of 653 martens genotyped at 12 microsatellite loci. I evaluated whether forest management in Ontario has influenced the genetic structure of martens. Although forest management practices had some impact, isolation by distance best described marten gene flow. Our results suggest that managed forests in Ontario are well connected for marten and do not impede marten gene flow. Finally, I used a site-based analysis of 702 lynx genotyped at 14 microsatellite loci to investigate spatial patterns of genetic diversity and differentiation at the trailing (contracting) edge of the lynx distribution in Ontario. I analyzed harvest records and found that the southern edge of lynx range has contracted by >175 km since the 1970s. I also found that neutral genetic diversity decreased towards the trailing edge, whereas genetic differentiation increased. Furthermore, I found strong correlations between gradients of lynx genetic structure and gradients of climate and land cover in Ontario. My findings suggest that increases in winter air temperature, decreases in snow depth, and loss of suitable habitat will result in further loss of genetic diversity in peripheral populations of lynx. Consequently, the adaptive potential of lynx populations on the southern range periphery could decline. In conclusion, my dissertation demonstrates the varying influences that contemporary landscape structure and climate gradients can have on genetic diversity and differentiation of different species. Author Keywords: Circuitscape, genetic network, landscape genetics, Lynx canadensis, Martes americana, range shift
Linking Inuit and Scientific Knowledge and Observations to Better Understand Arctic Char (Salvelinus alpinus (L.)) Community Monitoring
Arctic Char (Salvelinus alpinus (L.)) have been, and remain, an important subsistence resource for the Inuvialuit, the Inuit of the western Canadian Arctic. The effects of climate variability and change (CVC) in this region have been noticeably increasing over the past three decades. There are concerns as to how CVC will affect Arctic Char and the Inuvialuit who rely on this resource as they will have to adapt to changes in the fishery. Community-based monitoring, is an important tool for managing Arctic Char. Therefore, my dissertation focused on the central question of: Which community-based monitoring factors and parameters would provide the information needed by local resources users and decision-makers to make informed choices for managing Arctic Char populations in light of CVC? This question is investigated through an exploratory research approach and a mixed method research design, using both scientific and social science methods, and quantitative (scientific ecological knowledge and observation) and qualitative (Inuvialuit knowledge and observation) information. It is formatted as three journal manuscripts, an introduction, and an integrative discussion. The first manuscript examines potential habitat parameters for monitoring landlocked Arctic Char condition in three lakes on Banks Island in the Inuvialuit Settlement Region. The second manuscript examines potential local environmental parameters for monitoring landlocked Arctic Char growth in the same three lakes. The third manuscript investigates aspects of Arctic Char community-based monitoring programs (CBMP) in the Canadian North that have led to the sustained collection of useful data for management of the resource. This dissertation makes contributions to the field of research by demonstrating the utility of a mixed methods approach. The results demonstrate similarities and differences in char growth and condition within and among Capron, Kuptan and Middle lakes on Banks Island. This supports both lake-specific and regional climate-driven changes, meaning both lake habitat and local environmental monitoring parameters should be used in char CBMP. The investigation of char CBMP across northern Canada demonstrates that an adaptive monitoring approach is important for subsistence fisheries, as changing lifestyles and environmental changes impacting a fishery can have direct effects on the successful operation of char CBMP. Author Keywords: Arctic Char, community-based monitoring, environment, Inuit Knowledge, mixed methods, Traditional Knowledge
Assessment of the impacts of noise and vessel traffic on the distribution, abundance and density of Chinese humpback dolphins (Sousa chinensis chinensis) in the waters of Hong Kong
Marine mammals with near-shore distributions are susceptible to human-related recreational and commercial disturbances, particularly near densely populated and industrialized coastal areas. A population of over 2,500 Chinese humpback dolphins (Sousa chinensis chinensis) occupies the Pearl River Estuary in southern China. A part of this population uses Hong Kong’s waters off of Lantau Island, where they are subjected to a number of anthropogenic threats, including vessel disturbance, fisheries interactions, and boat-based tourism. Previous research has shown that the abundance of this subspecies in Hong Kong’s waters has declined about 60% since 2003. Using a combination of acoustic recordings, dolphin distribution and abundance data, and vessel traffic information I found that: 1) Four types of vessels common to the waters on Hong Kong generate noise that is audible to Sousa chinensis chinensis; 2) The spatial distribution of underwater noise in Hong Kong’s waters does not significantly vary among the six sites sampled; 3) High-speed ferry traffic and passenger volume has increased dramatically during the study period; 4) There has been a significant decline in dolphin density in areas within and near vessel traffic; and 5) Dolphins are most at risk of vessel collisions and being exposed to vessel noise near Fan Lau and within the Urmston Road waterway just northeast of the Sha Chau and Lung Kwu Chau Marine Park . These results can inform future acoustic studies on this species and guide conservation and management efforts in Hong Kong. Author Keywords: Human impacts, Humpback dolphin, Management, Noise, Sousa chinensis chinensis, Vessel traffic

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