Graduate Theses & Dissertations

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Nutrigenomics of Daphnia
Organismal nutrition lies at the interface between biotic and abiotic factors in an ecosystem, dictating the transfer of energy and nutrients across trophic levels. Our ability to detect nutritional limitation in consumers is reliant on a priori knowledge of dietary history due to our inability to differentiate nutrient stress based on body-wide responses. Molecular physiological responses are increasingly being used to measure physiological stress with high levels of specificity due to the specific modes of action ecological stressors have on organismal molecular physiology. Because animal consumers respond to varying nutrient supplies by up- and down-regulating nutrient-specific metabolic pathways, we can quantify nutritional status by quantifying the expression of those pathways. Here I present an investigation into the use of transcriptomics to detect nutritional stress in the keystone aquatic herbivore, Daphnia pulex, I use RNAseq and quantitative PCR (qPCR) identify nutritional indicator genes. I found that nutritional status could be determined with 100% accuracy with just ten genes. Additionally, the functional annotation of those genes uncovered previously unidentified responses to dietary stress. Further testing and validation of the selected indicator genes is required however these findings have the potential to revolutionize our ability to measure and monitor consumer nutritional stress. Author Keywords: Biomarkers, Daphnia, Gene expression, Nutrigenomics, Nutritional ecology, RNAseq
Assessing Molecular and Ecological Differentiation in Wild Carnivores
Wild populations are notoriously difficult to study due to confounding stochastic variables. This thesis tackles two components of investigating wild populations. The first examines the use of niche modeling to quantify macro-scale predator-prey relationships in canid populations across eastern North America, while the second examines range-wide molecular structure in Canada lynx. The goal of the first chapter is to quantify niche characteristics in a Canis hybrid zone of C. lupus, C. lycaon, and C. latrans to better understand the ecological differentiation of these species, and to assess the impacts of incorporating biotic interactions into species distribution models. The goal of the second chapter is to determine if DNA methylation, an epigenetic marker that modifies the structure of DNA, can be used to differentiate populations, and might be a signature of local adaptation. Our results indicated that canids across the hybrid zone in eastern North America exhibit low levels of genetic and ecological differentiation, and that the importance of biotic interactions are largely lost at large spatial scales. We also identified cryptic structure in methylation patterns in Canada lynx populations, which suggest signatures of local adaptation, and indicate the utility of DNA methylation as a marker for investigating adaptive divergence. Author Keywords: Ecological Epigenetics, Ecological Genetics, SDM
ASSESSING THE IMPACT OF ATMOSPHERIC DEPOSITION AND HARVEST INTENSITY ON SOIL ACIDITY AND NUTRIENT POOLS IN PLANTATION FORESTS
The objective of this thesis was to assess the influence of anthropogenic sulphur (S) and nitrogen (N) deposition, and harvesting on soil acidity and calcium (Ca2+), magnesium (Mg2+), potassium (K+) and N soil pools in plantation forest soils in Ireland. The response to reductions in anthropogenic S deposition was assessed using temporal trends in soil solution chemistry at two long-term monitoring plots--one on a blanket peat, the other on a peaty podzol. At the peat site, there was little evidence of a response to reductions in throughfall non marine sulphate (nmSO42-) and acidity; soil water acidity was determined by organic acids. In addition, temporal variation in soil water did not respond to that in throughfall. In the podzol, reductions in anthropogenic S and H+ deposition led to a significant improvement in soil water chemistry at 75 cm; pH increased and total aluminum (Altot) concentrations declined. The impact of harvest scenarios on exchangeable Ca2+, Mg2+ and K+ pools was assessed using input-output budgets at 40 sites (30 spruce, 10 pine). Harvest scenarios were stem-only harvest (SOH), stem plus branch harvest (SBH) and stem, branch and needle harvest (whole-tree harvesting; WTH). Average K+ and Mg2+ budgets were positive under these scenarios. However, exchangeable K+ pools were small and due to uncertainty in K+ budgets, could be depleted within one rotation. Average Ca2+ budgets for spruce were balanced under SOH, but negative under SBH and WTH. Nitrogen deposition was high, between 5 and 19 kg N ha-1 yr-1, but was balanced by N removal in SOH. However, N budgets were under SBH and WTH, indicating that these harvesting methods would lead to depletion of soil N over the long-term. Finally, monitoring of N cycling at a spruce plot indicated that N deposition was contributing to large NO3- leaching, and as such the site was N saturated. However, N cycling did not fit the criteria of the N saturation hypothesis; instead leaching was directly related to N deposition and supported the model of kinetic N saturation. Author Keywords: acidic deposition, base cations, input-output budgets, Ireland, nitrogen, whole-tree harvesting
Monitoring and fate of selected tire-derived organic contaminants
Road runoff is a vector for the transport of potentially toxic chemicals into receiving waters. In this study, selected tire-derived chemicals were monitored in surface waters of rivers adjacent to two high traffic highways in the Greater Toronto Area in Ontario, Canada. Composite samples were collected from the Don River and Highland Creek in the GTA during 5 hydrological events that occurred in the period between early October 2019 and late March 2020, as well as an event in August 2020. Grab samples were collected from these rivers during a period of low flow in August 2020, as well as during a storm event in July of 2020. Analysis was performed using ultra-high pressure liquid chromatography with high resolution mass spectrometric detection (UHPLC-HRMS). Hexamethoxymethylmelamine (HMMM), a cross-linker of tire material, was detected at elevated concentrations (> 1 µg/L) during rain events in the fall and winter of 2019-20 and during a period of rapid snow melt in early March of 2020. These samples were also analyzed for the tire additive, 6PPD, and its oxidation by-product, 6PPD-quinone, as well as 1,3-diphenylguanidine (DPG). In many samples collected from the Don River and Highland Creek during storm events, the estimated concentrations of 6PPD-quinone exceeded the reported LC50 of 0.8 µg/L for Coho salmon exposed to this compound. Temporal samples collected at 3-hour intervals throughout rain event the October 2020 showed that there was a delay of several hours after the start of the event before these compounds reached their peak concentrations. In addition, 26 candidate transformation products and precursor compounds of HMMM were monitored; 15 of these compounds were detected in surface waters in the GTA. The maximum total concentration of this class of methoxymethylmelamine compounds in surface water samples was estimated to be 18 µg/L. There is limited knowledge about the properties of HMMM, its precursor contaminants, and its transformation compounds, as well as their fate in the environment. COSMO-RS solvation theory was used to estimate the physico-chemical properties of HMMM and its derivatives. Using the estimated values for these properties (e.g., solubility, vapour pressure, log Kow) as inputs to the Equilibrium Criterion (EQC) fugacity-based multimedia model, the compounds were predicted to readily partition into aqueous media, with mobility in water increasing with the extent of loss of methoxymethyl groups from HMMM. Overall, this study contributes to the growing literature indicating that potentially toxic tire-wear compounds are transported via road runoff into urban surface waters. In addition, this study provides insight into the environmental behaviour of HMMM and its transformation products. Author Keywords: 6PPD-quinone, COSMOtherm, Fugacity, Hexamethoxymethylmelamine, Road runoff, Tire wear
Impact of Invasive Earthworms on Soil Respiration and Soil Carbon within Temperate Hardwood Forests
Improving current understanding of the factors that control soil carbon (C) dynamics in forest ecosystems remains an important topic of research as it plays an integral role in the fertility of forest soils and the global carbon cycle. Invasive earthworms have the potential to alter soil C dynamics, though mechanisms and effects remain poorly understood. To investigate potential effects of invasive earthworms on forest C the forest floor, mineral soil, fine root biomass, litterfall and litter decomposition rates and total soil respiration (TSR) over a full year were measured at two invaded and one uninvaded deciduous forest sites in southern Ontario. The uninvaded site was approximately 300m from one of the invaded sites and a distinct invasion front between the sites was present. Along the invasion front, the biomass of the forest floor was negatively correlated with earthworm abundance and biomass. There was no significant difference between litterfall, litter decomposition and TSR between the invaded and uninvaded sites, but fine root biomass was approximately 30% lower at the invaded site. There was no significant difference in soil C pools between the invaded and uninvaded sites. Despite profound impacts on forest floor soil C pools, earthworm invasion does not significantly increase TSR, most likely because increased heterotrophic respiration associated with earthworms is largely offset by a decrease in autotrophic respiration caused by lower fine root biomass. Author Keywords: Biological Invasions, Carbon, Earthworms, Forest Ecosystems, Forest Floor, Soil Respiration
Islands, ungulates, and ice
Central to wildlife conservation and management is the need for refined, spatially explicit knowledge on the diversity and distribution of species and the factors that drive those patterns. This is especially vital as anthropogenic disturbance threatens rapid large-scale change, even in the most remote areas of the planet. My dissertation examines theinfluence of land- and sea-scape heterogeneity on patterns of genetic differentiation, diversity, and broad-scale distributions of island-dwelling ungulates in the Arctic Archipelago. First, I investigated genetic differentiation among island populations of Peary caribou (Rangifer tarandus pearyi) in contrast to continental migratory caribou (Rangifer tarandus) and evaluated whether genetic exchange among Peary caribou island populations was limited by the availability of sea ice – both now and in the future. Differentiation among both groups was best explained by geodesic distance, revealing sea ice as an effective platform for Peary caribou movement and gene flow. With future climate warming, substantial reductions in sea ice extent were forecast which significantly increased resistance to caribou movement, particularly in summer and fall. Second, I assessed genetic population structure and diversity of northern caribou and deciphered how Island Biogeography Theory (IBT) and Central Marginal Hypothesis (CMH) could act in an archipelago where isolation is highly variable due to the dynamics of sea ice. Genetic differentiation among continental and island populations was low to moderate. In keeping with IBT and CMH, island-dwelling caribou displayed lower genetic diversity compared to mainland and mainland migratory herds; the size of islands (or population range) positively influenced genetic diversity, while distance-to-mainland and fall ice-free coastlines negatively influenced genetic diversity. Hierarchical structure analysis revealed multiple units of caribou diversity below the species level. Third, I shifted my focus to the terrestrial landscape and explored the elements governing species-environment relationships. Using species distribution models, I tested the response of caribou and muskoxen to abiotic versus abiotic + biotic predictors, and included distance to heterospecifics as a proxy for competitive interactions. Models that included biotic predictors outperformed models with abiotic predictors alone, and biotic predictors were most important when identifying habitat suitability for both ungulates. Further, areas of high habitat suitability for caribou and muskoxen were largely disjunct, limited in extent, and mainly outside protected areas. Finally, I modelled functional connectivity for two genetically and spatially disjunct groups of island-dwelling caribou. For High Arctic caribou, natural and anthropogenic features impeded gene flow (isolation-by-resistance); for Baffin Island caribou we found panmixia with absence of isolation-by-distance. Overall, my dissertation demonstrates the varying influences of contemporary land- and sea-scape heterogeneity on the distribution, diversity and differentiation of Arctic ungulates and it highlights the vulnerability of island-dwelling caribou to a rapidly changing Arctic environment. Author Keywords: Circuitscape, connectivity, Island Biogeography, landscape genetics, population structure, species distribution models
Combining Line Transect Sampling and Photographic-Identification Surveys to Investigate the Abundance and Distribution of Cetaceans
Line transect sampling and photographic-identification (photo-ID) are common survey techniques for estimating the abundance and distribution of cetaceans. Combining these approaches in the field (‘combined LTPI’ surveys) and using data from both components has the potential for generating comprehensive ecological knowledge that can be far more valuable than when these techniques and their data are used independently. In this thesis, I evaluated the results and conclusions from these two methods, used singly and in tandem, by investigating the population dynamics of two humpback dolphin (Sousa chinensis spp.) populations: the large and widely distributed Chinese white dolphin (S. c. chinensis) of the Pearl River estuary (PRE), and the small and geographically isolated subspecies of Taiwanese white dolphin (S. c. taiwanensis) in the eastern Taiwan Strait. Data from combined LTPI surveys in Hong Kong waters, at the eastern edge of the PRE, revealed a shift in space use with individuals spending less time in these waters than at the start of surveys. Data from combined LTPI surveys in Taiwan provided further support for a subspecies restricted to the central western waters, and identified a commonly used area at the northern part of their limited range. These two case studies demonstrated an overall efficacy of combined LTPI surveys in ecological studies of cetaceans. However, a multi-criteria analysis revealed that combined LTPI surveys with a line transect focus (e.g., Hong Kong) performed better than a LTPI survey with a photo-ID focus (e.g., Taiwan) when considering ecological aspects of the study populations, labour and data requirements, and ecological output. Even so, the photo-ID focus of Taiwan’s monitoring program led to better assessments of individual space use patterns, likely helped by the Taiwanese white dolphin population’s smaller size and intensive photographic effort. In both cases, the ecological output of combined LTPI surveys could be improved by expanding the study area or extending the field season or frequency of surveys. Overall, I showed that by following a set of general guidelines, different iterations of the combined LTPI approach (i.e., photo-ID focus or LT focus) can serve as powerful tools for uncovering multi-dimensional ecological information on cetaceans. Author Keywords: abundance, cetacean, distribution, line transect sampling, multi-criteria analysis, Photo-ID
Assessing the Potential of Permaculture as an Adaptation Strategy Towards Climate Change in Central Ontario
This thesis uses three approaches to assess the potential of permaculture in Central Ontario. This was done using a vegetable field trial and modelling programs to determine the effectiveness of permaculture to decrease negative impacts of climate change based on projected climate values derived from regional circulation models. The first approach showed no statistical difference (P<0.05) of applying varied volumes and combinations of organic amendments on crop yields. The second approach indicated permaculture may be a sustainable production system with respect to soil erosion when compared to traditional agricultural practices. The third approach was inconclusive due to the lack of quantitative literature on permaculture management impacts on biomass yields, soil carbon or nutrient retention, which were missing from basic and scientific literature searches. The models used within this thesis include USLE, RUSLE2, AgriSuite, RothC and Holos. Author Keywords: Agriculture, Climate Change, Computer Modelling, Permaculture, Soil Erosion and Assessment
effects of in-stream woody debris from selective timber harvest on nutrient pools and dynamics within Precambrian Shield streams
Timber harvest can influence the rate of transfer of organic matter from the terrestrial catchment to streams, which may have both direct and indirect effects on in-stream nutrient pools and dynamics. In the interest of developing sustainable forestry practices, the continued study of the effects of forestry on nutrient dynamics in aquatic systems is paramount, particularly in sensitive nutrient-poor oligotrophic systems. The goal of this study was to investigate the impacts of harvest-related woody debris on stream nutrient status in streams located in the Canadian Shield region of south-central Ontario. Surveys showed greater large (> 10 cm) and small (< 10 cm) woody debris dry masses and associated nutrient pools in streams located in recently (2013) selectively harvested catchments, when compared with catchments not harvested for at least 20 years. Experimental releases of flagging tape underlined the importance of woody debris as a mechanism of coarse particulate organic matter (CPOM) retention. Sediment surveys showed a significant exponential decline in both OM content and nutrients associated with coarse sediment with distance upstream from debris dams. Laboratory leaching experiments suggest that fresh woody debris may be an important short-term source of water-soluble nutrients, particularly phosphorus and potassium. This study suggests that woody debris from timber harvest is both a direct and indirect source of nutrients, as trapped wood and leaves that accumulate behind debris dams can augment stream nutrient export over long time periods. Author Keywords: nutrient leaching, nutrient pools, organic matter retention, selection harvest, southern Ontario, woody debris
Shorebird Habitat Use and Foraging Ecology on Bulls Island, South Carolina During the Non-Breeding Season
Recent declines in North American shorebird populations could be linked to habitat loss on the non-breeding grounds. Sea-level rise and increased frequency of coastal storms are causing significant erosion of barrier islands, thereby threatening shorebirds who rely on shoreline habitats for foraging. I conducted shorebird surveys on Bulls Island, South Carolina in the winters of 2018 and 2019 and examined habitat selection and foraging behaviour in Dunlin (Calidris alpina), Sanderling (Calidris alba), Semipalmated Plovers (Charadrius semipalmatus), and Piping Plovers (Charadrius melodus). Area, tidal stage, and invertebrate prey availability were important determinants of shorebird abundance, behaviour, and distribution. My study highlights the importance of Bulls Island’s habitat heterogeneity to supporting a diverse community of non-breeding shorebirds. Considering both the high rate of erosion and the increased frequency of disturbance along the shoreline of the island, intertidal habitats should be monitored to predict negative effects of changes in habitat composition and area on non-breeding shorebirds. Author Keywords: foraging behaviour, habitat loss, habitat selection, invertebrate prey, non-breeding, shorebirds
Composition and Transformation of Dissolved Organic Matter in Hudson Bay, Canada
The Hudson Bay region is a sensitive environment, where anthropogenic (e.g., dams, diversions, and/or reservoirs) impacts have increased in recent decades, potentially influencing the functioning of the ecosystem. Dissolved organic matter (DOM) entering Hudson Bay comes from both terrestrial (allochthonous) and aquatic (autochthonous) sources. The chemical composition of DOM is important, as it controls carbon biogeochemistry, nutrient cycling, and heat exchange. In rivers, estuaries, and oceans, photochemical processes and microbial degradation play a significant role in the chemical composition of DOM. Yet, our knowledge is scarce into how photochemical and microbial processes effect DOM composition specifically in Arctic aquatic systems making it difficult to predict how the carbon cycle will respond to a changing environment. This Ph.D. thesis addresses: (1) the composition of photochemically altered autochthonous and allochthonous DOM; (2) the photochemical transformations of DOM in surface waters of Hudson Bay; and (3) the microbial transformations of DOM in Hudson Bay surface waters. Using multiple analytical techniques, this work demonstrated that photochemical and microbial effects were different for light absorbing DOM compounds and ionisable DOM analyzed by Fourier transform-ion cyclotron-resonance-mass spectrometry (FT-ICR-MS). Based on FT-ICR-MS analysis, microbial processes had a greater impact on the molecular composition of allochthonous DOM originating from riverine sources and estuary whereas photochemical processes were the dominant mechanism for degradation of autochthonous DOM in Hudson Bay. Photochemical processes significantly decreased colored dissolved organic matter (CDOM) and fluorescence dissolved organic matter (FDOM) loss whereas microbial degradation was minimal in Hudson Bay river, estuary, and coastal waters. The results of this thesis highlight the importance of photochemical and microbial alteration of DOM in Arctic regions, two processes that are expected to be enhanced under climate change conditions. Author Keywords: Carbon cycle, Field flow fractionation, Microbial transformation, Optical properties, Photochemical degradation
Discriminating grey wolf (Canis lupus) predation events in a multi-prey system in central Saskatchewan
I investigated if spatio-temporal behaviour of grey wolves (Canis lupus) determined via GPS collar locations could be used to discriminate predation events generally, and among prey species, in Prince Albert National Park during winter, 2013-2017. I used characteristics of spatio-temporal GPS clusters to develop a predictive mixed-effect logistic regression model of which spatial clusters of locations were wolf kill sites. The model suffered a 60 % omission error when tested with reserved data due to the prevalence of deer kills with correspondingly low handling time. Next, I found a multivariate difference in the percentage of habitat classes used by wolves in the 2 hours preceding predation events of different prey species, suggesting that wolf habitat use reflects prey selection at a fine-scale. My results highlight the difficulty and future potential for remoting discriminating wolf predation events via GPS collar locations in multi-prey ecosystems. Author Keywords: Canis lupus, GPS clusters, GPS collars, grey wolf, habitat use, predation

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