Graduate Theses & Dissertations


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
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
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
CO2 dynamics of tundra ponds in the low-Arctic Northwest Territories, Canada
Extensive research has gone into measuring changes to the carbon storage capacity of Arctic terrestrial environments as well as large water bodies in order to determine a carbon budget for many regions across the Arctic. Inland Arctic waters such as small lakes and ponds are often excluded from these carbon budgets, however a handful of studies have demonstrated that they can often be significant sources of carbon to the atmosphere. This study investigated the CO2 cycling of tundra ponds in the Daring Lake area, Northwest Territories, Canada (64°52'N, 111°35'W), to determine the role ponds have in the local carbon cycle. Floating chambers, nondispersive infrared (NDIR) sensors and headspace samples were used to estimate carbon fluxes from four selected local ponds. Multiple environmental, chemical and meteorological parameters were also monitored for the duration of the study, which took place during the snow free season of 2013. Average CO2 emissions for the two-month growing season ranged from approximately -0.0035 g CO2-C m-2 d-1 to 0.12 g CO2-C m-2 d-1. The losses of CO2 from the water bodies in the Daring Lake area were approximately 2-7% of the CO2 uptake over vegetated terrestrial tundra during the same two-month period. Results from this study indicated that the production of CO2 in tundra ponds was positively influenced by both increases in air temperature, and the delivery of carbon from their catchments. The relationship found between temperature and carbon emissions suggests that warming Arctic temperatures have the potential to increase carbon emissions from ponds in the future. The findings in this study did not include ebullition gas emissions nor plant mediated transport, therefore these findings are likely underestimates of the total carbon emissions from water bodies in the Daring Lake area. This study emphasizes the need for more research on inland waters in order to improve our understanding of the total impact these waters may have on the Arctic's atmospheric CO2 concentrations now and in the future. Author Keywords: Arctic, Arctic Ponds, Carbon dioxide, Carbon Fluxes, Climate Change, NDIR sensor
Effect of Water Surface Simulated Rain Drop Impacts on Water to Air Chemical Transfers of Perfluorinated Carboxylic Acids (PFCAs)
Perfluorinated carboxylic acids (PFCAs) are anthropogenic environmentally ubiquitous surfactants that tend to concentrate on water surfaces. This investigation looked at the effect of simulated rain on the atmospheric concentration of a suite of PFCAs (C2 - C12) above the bulk water system. Increased air concentrations of all PFCAs were detected during simulated rain events. Long chain PFCAs (>C8) were found to be much more concentrated in the air above the bulk water system than their short chain counter parts (
Effects of Silver Nanoparticles on Lower Trophic Levels in Aquatic Ecosystems
Due to their effective antibacterial and antifungal properties, silver nanoparticles (AgNPs) have quickly become the most commonly used nanomaterial, with applications in industry, medicine and consumer products. This increased use of AgNPs over the past decade will inevitably result in an elevated release of nanoparticles into the environment, highlighting the importance of assessing the environmental impacts of these nanomaterials on aquatic ecosystems. Although numerous laboratory studies have already reported on the negative effects of AgNPs to freshwater organisms, only a handful of studies have investigated the impacts of environmentally relevant levels of AgNPs on whole communities under natural conditions. This thesis examines the effects of chronic AgNP exposure on natural freshwater littoral microcrustacean, benthic macroinvertebrate and pelagic zooplankton communities. To assess the responses of these communities to AgNPs, I focused on a solely field-based approach, combining a six-week mesocosm study with a three-year whole lake experiment at the IISD – Experimental Lakes Area (Ontario, Canada). Our mesocosm study tested the effects of AgNP concentration (low, medium and high dose), surface coating (citrate- and polyvinylpyrrolidone [PVP]-coated AgNPs), and type of exposure (chronic and pulsed addition) on benthic macroinvertebrates in fine and stony sediments. Relative abundances of metal-tolerant Chironomidae in fine sediments were highest in high dose PVP-AgNP treatments; however, no negative effects of AgNP exposure were seen on biodiversity metrics or overall community structure throughout the study. I observed similar results within the whole lake study that incorporated a long-term addition of low levels of AgNPs to an experimental lake. Mixed-effects models and multivariate methods revealed a decline in all species of the littoral microcrustacean family Chydoridae in the final year of the study within our experimental lake, suggesting that this taxon may be sensitive to AgNP exposure; however, these effects were fairly subtle and were not reflected in the overall composition of littoral communities. No other negative effects of AgNPs were observed on the pelagic zooplankton or benthic macroinvertebrate communities. My results demonstrate that environmentally relevant levels of AgNPs have little impact on natural freshwater microcrustacean and benthic macroinvertebrate communities. Instead, biodiversity metrics and community structure are primarily influenced by seasonal dynamics and nutrient concentrations across both lakes. This thesis highlights the importance of incorporating environmental conditions and the natural variability of communities when examining the potential risks posed by the release of AgNPs into the environment, as simplistic laboratory bioassays may not provide an adequate assessment of the long-term impacts of AgNPs on freshwater systems. Author Keywords: Benthic macroinvertebrates, IISD - Experimental Lakes Area, Littoral microcrustaceans, Silver nanoparticles, Whole lake experiment, Zooplankton
Seasonal habitat use and movement of native brook trout (Salvelinus fontinalis) in urban headwater streams
Coldwater streams are becoming increasingly impacted due to urbanization. Using environmental surveys, mark-recapture and telemetry, I assessed factors influencing seasonal brook trout (Salvelinus fontinalis) habitat use and movement in urban headwater streams in central Ontario between 2017-18. Generalized additive models were used to assess which habitat variables best explained seasonal yearling and older brook trout abundance, while generalized least squares models were used to assess overall trends in radio-tagged brook trout movement. My research demonstrated dynamic patterns in habitat use and movement by urban stream-dwelling brook trout. Yearlings were primarily influenced by water quality (stream temperature, conductivity), while older brook trout were most strongly influenced by stream morphology (depth, undercut bank). Movement occurred disproportionately around the spawning season and was more limited in the smaller, more altered stream. These findings may be used to inform fisheries managers on crucial timing and location of brook trout habitat refugia within urbanized environments. Author Keywords: Brook trout, coldwater stream, groundwater, habitat use, radiotelemetry, urbanization
Complex niche determinants in terrestrial salamanders
I assessed how organisms having multiple biotic attributes may have conflicting niche determinants, and whether the realized niche reflects single or multiple attributes. All-female salamanders engage in two biotic states: hybridism and reproductive parasitism. Hybrids should occupy areas transitional to those used by parental species, whereas parasites that engage in competition with hosts should occupy habitats moderately suitable for hosts. Using niche models, I predicted realized niches for unisexual Ambystoma via a hybrid model (environmental predictors) and a parasite model (host suitability predictors). The hybrid model predicted that the unisexual niche would indeed be transitional between parental Ambystoma spp. The parasite model demonstrated unisexual salamanders occupied habitats moderately suitable for hosts, though model validation did not fully corroborate its predictive power. The hybrid model was more descriptive of unisexual occurrence than the parasite model. When species have competing ecological roles a primary biotic attribute may largely derive the realized niche. Author Keywords: Ambystoma, hybrid, niche, parasite, range, unisexual
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
Detecting anti-estrogens and anti-androgens in surface waters impacted by municipal wastewater discharges and agricultural runoff
This study focused on detecting 22 target anti-estrogenic and anti-androgenic compounds in surface waters influenced by both discharges of municipal wastewater and agricultural runoff in Canada and Argentina. Polar organic chemical integrative samplers (POCIS) were used to monitor the target compounds in surface waters. The removals of the target compounds in a municipal wastewater treatment plant (WWTP) in Canada were also evaluated. In both Canada and Argentina pesticides with potential anti-estrogenic and anti-androgenic activities were detected in the surface waters. The highest concentrations were found in Argentina (up to 1010 ng L-1) in areas impacted by heavy agricultural practices. Cyproterone acetate and bicalutamide were the only two anti-cancer drugs detected only at the Canadian study site, the Speed River, ON. In the Guelph WWTP, that discharges into the Speed River, these target compounds were not all efficiently removed (>70%) during treatment. Overall, this study provides insight to possible anti-estrogenic and anti-androgenic compounds that may be contributing to endocrine disrupting activities in surface waters. Author Keywords: Anti-androgens, Anti-estrogens, Cancer Therapy Drugs, Current use pesticides, Pharmaceuticals and Personal Care Products, Polar Organic Chemical Integrative Samplers
Calcium in the Muskoka River Watershed- Patterns, trends, the potential impact of forest harvesting and steps toward an ecosystem approach to mitigation
Decreasing lake calcium (Ca) concentration, in lakes located in base poor catchments of the Muskoka River Watershed (MRW) in south-central Ontario, is a well- established acid-rain driven legacy effect threatening the health and integrity of aquatic ecosystems that can be compounded by additional Ca removals through forest harvesting. The objectives of this thesis were to assess patterns and temporal trends in key water chemistry parameters for a set of lakes in forested catchments in the MRW in south- central Ontario, to predict the pre-industrial steady state lake Ca concentration and the potential impact of harvesting on lake Ca levels in lakes located in managed MRW Crown forests, and to assess potential effects of various mitigation strategies in Ca depleted managed forests. Mean lake Ca (mg L-1) in 104 lakes across the MRW have decreased by 30% since the 1980's with the rate of decrease slowing over time. Mean Lake SO4 (mg L-1), and Mg (mg L-1) concentration also decreased significantly with time (37% and 29%, respectively) again with a declining rate of decrease, while mean lake pH and DOC increased significantly between the 1980's and the 1990's (16% and 12%, respectively) but exhibited no significant pattern after that. Principal components and GIS spatial analyses of 75 lakes with data from 2011 or 2012 water seasons suggested that smaller lakes, at higher elevation in smaller catchments with higher runoff and minimally impacted by the influence of roads and agriculture are associated with lower Ca concentrations and thus are the lakes at risk of amplified Ca depletion from forest harvesting. Spatial analyses of harvested catchments indicated that, under the proposed 10 year land forest management cut volumes, 38% of 364 lakes in the MRW will fall below the critical 1 mg L-1 Ca threshold compared with 8% in the absence of future harvesting. With respect to potential mitigation measures, soil pH and foliar Ca were indicated by meta-analysis to be more responsive to lime addition studies while soil base saturation and tree growth appeared more responsive to wood-ash addition. Future research should address the spatial extent of lakes at risk and identify when critical levels will be reached under harvesting regimes. Further investigation into the use of Ca-addition as a tool for managing the cumulative effects of past, present and future stressors is recommended. Author Keywords: calcium, harvesting, lakes, lime, Muskoka River Watershed, wood-ash
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


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