Graduate Theses & Dissertations

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Comparative Evaluation of Effective Population Size Genetic Estimation Methods in Wild Brook Trout (Salvelinus fontinalis) Populations
Effective population size (Ne) is a key concept in population genetics, evolutionary biology and conservation biology that describes an important facet of genetic diversity and the capacity of populations to respond to future evolutionary pressures. The importance of Ne in management and conservation of wild populations encouraged the development of numerous genetic estimators which rely on a variety of methods. Despite the number and diversity of available Ne methods, however, tests of estimator performance have largely relied on simulations, with relatively few tests based on empirical data. I used well-studied wild populations of brook trout (Salvelinus fontinalis) in Algonquin Park, Ontario as a model system to assess the comparative performance of multiple Ne estimation methods and programs, comparing the resultant Ne estimates against demographic population size estimates. As a first step, the genetic diversity and ancestry of wild brook trout populations was determined using 14 microsatellite loci. Genetic structure of brook trout populations showed variable contributions from historical supplemental stocking and also identified localized gene pools within and between watersheds, reflecting variable levels of connectivity and gene flow. Once the genetic ancestry and connectivity of populations had been resolved, single sample (point) and two samples (temporal) genetic estimators were used to estimate Ne of populations with pure native ancestry. Values obtained from genetic estimators utilizing both methods were variable within as well as among populations. Single sample (point) estimators were variable within individual populations, but substantially less than was observed among the temporal methods. The ratios of Ne to the estimated demographic population size (N) in small populations were substantially higher than in larger populations. Variation among estimates obtained from the different methods reflects varying assumptions that underlay the estimation algorithms. This research further investigated the effect of sampling effort and number of microsatellite loci used on Ne values obtained using the linkage disequilibrium (LD) estimation method. Ne estimates varied substantially among values generated from subsets of loci and genotyped individuals, highlighting the necessity for proper sampling design for efforts aiming to measure Ne. Despite the variation observed among and within estimation methods, the Ne concept is a valuable for the conservation and management of both exploited and endangered species. Author Keywords: Brook Trout, Effective population size, Genetic Diversity, Genetic Structure
Shorebird Stopover Ecology and Environmental Change at James Bay, Ontario, Canada
I examined how shorebirds respond to environmental change at a key subarctic migratory bird stopover site, the southwestern coast of James Bay, Ontario, Canada. First, I investigated if the morphology of sandpipers using James Bay during southbound migration has changed compared to 40 years prior. I found shorter, more convex and maneuverable wings for sandpipers in the present-day compared to the historical monitoring period, which supports the hypothesis that wing length change is driven by increases in predation risk. Secondly, I assessed the relationship between migration distance, body condition, and shorebird stopover and migratory decisions. Species that travelled farther distances from James Bay to wintering areas migrated with more characteristics of a time-minimizing migration strategy whereas species that travelled shorter distances migrated with energy minimizing strategies. Body condition impacted length of stay, wind selectivity at departure, groundspeeds, and probability of stopover and detection in North America after departing James Bay. Thirdly, I examined annual variation in dry/wet conditions at James Bay and found that shorebirds had lower body mass in years with moderate drought. In the present-day, drought resulted in lower invertebrate abundance and refuelling rates of shorebirds during stopover, which led to shorter stopover duration for juveniles and a higher probability of stopover outside of James Bay for all groups except white-rumped sandpiper. Finally, I estimated the relative importance of intertidal salt marsh and flat habitats to the diets of small shorebirds and found that semipalmated and white-rumped sandpiper (Calidris pusilla and C. fuscicollis) and semipalmated plover (Charadrius semipalmatus) diets consist of ~ 40 – 75% prey from intertidal marsh habitats, the highest documented in the Western Hemisphere for each species. My research shows that James Bay is of high importance to white-rumped sandpipers, which are unlikely to stop in North America after departing James Bay en route to southern South America. Additionally, intertidal salt marsh habitats (and Diptera larvae) appear particularly important for small shorebirds in the region. My thesis shows that changing environmental conditions, such as droughts, can affect shorebird refuelling and stopover strategies. Author Keywords: body condition, diet, environmental change, migration, ornithology, stopover ecology
Behavioural ecology and population dynamics of freshwater turtles in a semi-urban landscape at their northern range limit
Species are faced with a variety of challenges in the environment, including natural challenges, such as variability in ambient temperature, and anthropogenic threats, such as habitat transformation associated with urbanisation. Understanding how animals respond to these kinds of challenges can advance the field of behavioural ecology and guide management decisions for wild species. Yet, we still have limited understanding of the extent of natural and human-caused impacts on animal behaviour and population dynamics, and lack robust assessment of behaviour in free-ranging animals. Using novel miniaturised biologging technologies, I characterised and validated behaviour in two freshwater turtle species: Blanding’s turtles (Emydoidea blandingii) and Painted turtles (Chrysemys picta). Further, I investigated how these two ectothermic species navigate a thermally heterogeneous landscape near their northern range limit, by comparing selected and available ambient temperatures. I showed that turtles preferred locations that were, on average, warmer and less variable in temperature than the available environment, and that this thermal sensitivity was greatest early in the year, and at fine spatial scales that likely matched the species' perception of the environment. Lastly, I assessed whether urban development was compatible with long-term viability of a Blanding’s turtle population, by monitoring habitat change and turtle survival over one decade of ongoing residential and road development. I found that Blanding’s turtle habitat quantity and connectivity declined in the area, which coincided with high road mortality and severe declines in turtle survival and population size, especially in adult females. I concluded that urban development and current road mortality rates are incompatible with the long-term viability of this at-risk turtle population. Overall, my findings demonstrate the importance of variation in the thermal environment and anthropogenic impacts on habitat in shaping the behaviour and population dynamics of this species-at-risk. Author Keywords: animal behaviour, biologging, ectotherms, habitat selection, temperature, urbanisation
Demography and habitat selection of Newfoundland caribou
The objective of this thesis is to better understand the demography and habitat selection of Newfoundland caribou. Chapter 1 provides a general introduction of elements of population ecology and behavioural ecology discussed in the thesis. In Chapter 2, I examine the causes of long-term fluctuations among caribou herds. My findings indicate that winter severity and density-dependent degradation of summer range quality offer partial explanations for the observed patterns of population change. In Chapter 3, I investigate the influence of climate, predation and density-dependence on cause-specific neonate survival. I found that when caribou populations are in a period of increase, predation from coyotes and bears is most strongly influenced by the abiotic conditions that precede calving. However, when populations begin to decline, weather conditions during calving also influenced survival. I build on this analysis in Chapter 4 by determining the influence of climate change on the interplay between predation risk and neonate survival. I found that the relative equilibrium between bears and coyotes may not persist in the future as risk from coyotes could increase due to climate change. In Chapter 5, I investigate the relationships in niche overlap between caribou and their predators and how this may influence differential predation risk by affecting encounter rates. For coyotes, seasonal changes in niche overlap mirrored variation in caribou calf risk, but had less association with the rate of encounter with calves. In contrast, changes in niche overlap during the calving season for black bears had little association with these parameters. In Chapter 6, I examine broad-level habitat selection of caribou to study trade-offs between predator avoidance and foraging during the calving season. The results suggest that caribou movements are oriented towards increased access to foraging and the reduction of encounter risk with bears, and to a lesser extent, coyotes. Finally, I synthesize the major findings from this thesis and their relevance to caribou conservation in Chapter 7, to infer that Newfoundland caribou decline is ultimately driven by extrinsic and intrinsic elements related to density-dependence. Reduction in neonate survival emerged from nutritionally-stressed caribou females producing calves with lower survival. Author Keywords: Behavioural ecology, Black bear (Ursus americanus), Coyote (Canis latrans), Population ecology, Predator-prey interactions, Woodland caribou (Rangifer tarandus)
Investigating the sources and fate of monomethylmercury and dimethylmercury in the Arctic marine boundary layer and waters
Monomethylmercury (MMHg), the most bioavailable form of mercury (Hg) and a potent neurotoxin, is present at elevated concentrations in Arctic marine mammals posing serious health threats to the local populations relying on marine food for their subsistence living. The sources of MMHg in the Arctic Ocean surface water and the role of dimethylmercury (DMHg) as a source of MMHg remain unclear. The objective of this research was to determine the sources and fate of methylated Hg species (MMHg and DMHg) in the marine ecosystem by investigating processes controlling the presence of methylated Hg species in the Arctic Ocean marine boundary layer (MBL) and surface waters. A method based on solid phase adsorption on Bond Elut ENV was developed and successfully used for unprecedented measurement of methylated Hg species in the MBL in Hudson Bay (HB) and the Canadian Arctic Archipelago (CAA). MMHg and DMHg concentrations averaged 2.9 ± 3.6 (mean ± SD) and 3.8 ± 3.1 pg m-3, respectively, and varied significantly among sampling sites. MMHg in the MBL is suspected to be the product of marine DMHg degradation in the atmosphere. MMHg summer (June to September) atmospheric wet deposition rates were estimated to be 188 ± 117.5 ng m-2 and 37 ± 21.7 ng m-2 for HB and CAA, respectively, sustaining MMHg concentrations available for bio-magnification in the pelagic food web. The production and loss of methylated Hg species in surface waters was assessed using enriched stable isotope tracers. MMHg production in surface water was observed from methylation of inorganic Hg (Hg(II)) and, for the first time, from DMHg demethylation with experimentally derived rate constants of 0.92 ± 0.82 x 10-3 d-1 and 0.04 ± 0.02 d-1 respectively. DMHg demethyation rate constant (0.98 ± 0.51 d-1) was higher than that of MMHg (0.35 ± 0.25 d-1). Furthermore, relationships with environmental parameters suggest that methylated Hg species transformations in surface water are mainly biologically driven. We propose that in addition to Hg(II) methylation, the main processes controlling MMHg production in the Arctic Ocean surface waters are DMHg demethylation and deposition of atmospheric MMHg. These results are valuable for a better understanding of the cycle of methylated Hg in the Arctic marine environment. Author Keywords: Arctic Ocean, Atmosphere, Demethylation, Dimethylmercury, Methylation, Monomethylmercury
Constraints on phenotypic plasticity in response to predation risk
Inducible defenses are plastic responses by an organism to the perception of predation risk. This dissertation focuses on three experiments designed to test the hypothesis that plastic ability is limited by energetic constraints. Chapter 1 provides a general introduction to phenotypic plasticity research and the theoretical costs and limitations affecting the expression of plastic traits. In Chapter 2, I tested the hypothesis that costs of early plasticity may be manifested by a reduced response to risk in later life stages. I found that amphibian embryos are able to detect and respond to larval predators, but that the energetic cost of those plastic responses are not equivalent among behavioural, growth, and morphological traits, and their expression differs between closely-related species. Chapter 3 explicitly examines the relationship between food resource availability and plasticity in response to perceived predation risk during larval development. Food-restricted tadpoles showed limited responses to predation risk; larvae at food saturation altered behaviour, development, and growth in response to predation risk. Responses to risk varied through time, suggesting ontogeny may affect the deployment of particular defensive traits. Chapter 4 examines the influence of maternal investment into propagule size on the magnitude of the plastic responses to predation risk in resulting offspring. I found that females in better body condition laid larger eggs and that these eggs, in turn, hatched into larvae that showed greater morphological plasticity in response to predation risk. Maternal investment can therefore affect the ability of offspring to mount morphological defenses to predation risk. Last, Chapter 5 provides a synthesis of my research findings, identifying specific factors constraining the plastic responses of prey to perceived predation risk. Overall, I found constraints on plastic responses imposed by the current environment experienced by the organism (resource availability), the prior experience of the organism (predator cues in the embryonic environment), and even the condition of the previous generation (maternal body condition and reproductive investment). Together, these findings both provide new knowledge and create novel research questions regarding constraints limiting phenotypic variation in natural populations. Author Keywords: behaviour, inducible defense, Lithobates pipiens, morphometrics, phenotypic plasticity, predation risk
Hybridization Dynamics between Wolves and Coyotes in Central Ontario
Eastern wolves (Canis lycaon) have hybridized extensively with coyotes (C. latrans) and gray wolves (C. lupus) and are listed as a `species of special concern' in Canada. Previous studies have not linked genetic analysis with field data to investigate the mechanisms underlying Canis hybridization. Accordingly, I studied genetics, morphology, mortality, and behavior of wolves, coyotes, and hybrids in and adjacent to Algonquin Provincial Park (APP), Ontario. I documented 3 genetically distinct Canis types within the APP region that also differed morphologically, corresponding to putative gray wolves, eastern wolves, and coyotes. I also documented a substantial number of hybrids (36%) that exhibited intermediate morphology relative to parental types. I found that individuals with greater wolf ancestry occupied areas of higher moose density and fewer roads. Next, I studied intrinsic and extrinsic factors influencing survival and cause-specific mortality of canids in the hybrid zone. I found that survival was poor and harvest mortality was high for eastern wolves in areas adjacent to APP compared with other sympatric Canis types outside of APP and eastern wolves within APP. Contrary to previous studies of wolves and coyotes elsewhere, I hypothesized that all Canis types exhibit a high degree of spatial segregation in the Ontario hybrid zone. My hypothesis was supported as home range overlap and shared space use between neighboring Canis packs of all ancestry classes were low. Territoriality among Canis may increase the likelihood of eastern wolves joining coyote and hybrid packs and exacerbate hybridization. Canids outside APP modified their use of roads between night and day strongly at high road densities (selecting roads more at night), whereas they responded weakly at lower road densities (generally no selection). Individuals that survived exhibited a highly significant relationship between the difference in their night and day selection of roads and availability of roads, whereas those that died showed a weaker, non-significant response. My results suggest that canids in the unprotected landscape outside APP must balance trade-offs between exploiting benefits associated with secondary roads while mitigating risk of human-caused mortality. Overall, my results suggest that the distinct eastern wolf population of APP is unlikely to expand numerically and/or geographically under current environmental conditions and management regulations. If expansion of the APP eastern wolf population (numerically and in terms of its geographic distribution) is a conservation priority for Canada and Ontario, additional harvest protection in areas outside of APP may be required. If additional harvest protection is enacted, a detailed study within the new areas of protection would be important to document specific effects on eastern wolf population growth. Author Keywords: Canis, coyotes, eastern wolves, hybridization, resource selection, survival
Effect Assessment of Binary Metal Mixtures of Ni, Cu, Zn, and Cd to Daphnia magna
Mixtures of metals occur in surface waters, toxicity of which has drawn world-wide attention due to their crucial role in both ecotoxicology and regulations. The present research was undertaken to study the acute toxicity of binary mixtures of Ni, Cu, Zn, and Cd to the freshwater organism, Daphnia magna. The experimental approach included single and binary metal toxicity tests based on the 48h acute toxicity bioassay of Environment Canada. The acute toxicity of single metals followed the order of Cd > Cu > Zn > Ni. Based on the calculated 48h EC50 value of single metals, a toxic unit (TU) approach was used to combine two metals in a binary mixture, in which 1TU was equal to the 48h EC50 value of a metal in single exposure. The toxicity of binary metal mixtures to D. magna followed the order of Cu-Cd > Cu-Zn > Zn-Cd > Cu-Ni > Zn-Ni > Cd-Ni, which demonstrated three types of toxicity (i.e., less than additive, additive, and greater additive). Predictions from additivity models (including concentration addition (CA) and independent action (IA) models), a generalized linear model (GLM), and a biotic-ligand-like model (BLM-like) were compared to the bioassay results. The CA and the RA models also predicted three types of toxicity of the binary metal mixtures (i.e., less than additive, additive, and greater than additive). However, the CA model mostly overestimated the toxicity of binary mixtures. Predictions from the GLM supported the inclusion of the interaction between two metals in a mixture to predict the toxicity of binary metal mixtures. The binary metal toxicity was also predicted using a BLM-like model based on the calculated concentrations of free ionic forms of the metals, affinity constants, and toxic potency of each metal. In this model, it was hypothesized that the toxicity of metal mixture is the result of competition of metals with Ca2+ at biotic ligands, which can lead to whole-body deficiency of Ca2+ in D. magna. The BLM-like model provided the toxic potency of single metals with the following order, Cu > Cd > Zn > Ni. Although the prediction of the BLM-like model was not in good agreement with the observed toxicity of binary metal mixtures, an overestimation of risk of mixture toxicity was obtained using this model, which could be promising for use in environmental risk assessment. Author Keywords: biotic ligand model, concentration addition, Daphnia magna, independent action, metal toxicity, modeling
cascading effects of risk in the wild
Predation risk can elicit a range of responses in prey, but to date little is known about breadth of potential responses that may arise under realistic field conditions and how such responses are linked, leaving a fragmented picture of risk-related consequences on individuals. We increased predation risk in free-ranging snowshoe hares (Lepus americanus) during two consecutive summers by simulating natural chases using a model predator (i.e., domestic dog), and monitored hare stress physiology, energy expenditure, behaviour, condition, and habitat use. We show that higher levels of risk elicited marked changes in physiological stress metrics including sustained high levels of free plasma cortisol which had cascading effects on glucose, and immunology, but not condition. Risk-augmented hares also had lowered daily energy expenditure, spent more time foraging, and decreased rest, vigilance, and travel. It is possible that these alterations allowed risk-exposed hares to increase their condition at the same rate as controls. Additionally, risk-augmented hares selected, had high fidelity to, and were more mobile in structurally dense habitat (i.e., shrubs) which provided them additional cover from predators. They also used more open habitat (i.e., conifer) differently based on locale within the home range, using familiar conifer areas within cores for rest while moving through unfamiliar conifer areas in the periphery. Overall, these findings show that prey can have a multi-faceted, highly plastic response in the face of risk and can mitigate the effects of their stress physiology given the right environmental conditions. Author Keywords: behaviour, condition, daily energy expenditure, predator-prey interactions, snowshoe hare, stress physiology
Nunavik Inuit Knowledge of Beluga
Socio-ecological systems are inherently complex and marine mammals are fundamentally challenging to study. In the Arctic, marine mammals occupy a central ecological role, as nutrient cyclers and as a source of food and culture for Indigenous peoples. Inuit have developed a rich knowledge system, which has not been fully actualized in application in most Arctic research. Considering the need for the best available information in marine mammal ecology, the research question guiding this dissertation was: How can multiple methods and approaches be used to more effectively gather, understand, and represent Inuit Knowledge for an improved understanding of marine mammal ecology? The dissertation investigates this question using a case study of beluga in Nunavik (Arctic Quebec) drawing on the expertise of hunters and Elders to better understand complex questions in marine mammal ecology. The thesis uses a transdisciplinary approach to address the dissertation objective and is comprised of a general introduction, followed by four chapters formatted as journal manuscripts, and closes with an integrated discussion and conclusion. The first manuscript examines the contributions of Traditional Ecological Knowledge (TEK) of beluga to marine mammal literature. The second manuscript uses a sub-set of data gathered through participant mapping to apply a mapping method to explore how the spatial aspects of TEK could be better documented, analyzed, and represented. The third and fourth papers are based on the knowledge shared by hunters and Elders. The third explores the questions ‘why do beluga migrate?’ and ‘what factors influence beluga movement?’. The fourth investigates aspects of beluga foraging ecology. This dissertation makes methodological contributions through the application of kernel density estimators to participant maps as a method for transforming multiple mapped narratives into a quantitative database. The understandings shared by hunters and Elders make significant ecological contributions, particularly to foraging (e.g. diet composition and seasonal energy intake), and movement ecology (e.g. potential drivers of migration). Broadly these findings contribute to our collective understanding of beluga ecology and have implications for wildlife management. Author Keywords: Arctic, Beluga biology, foraging ecology, Inuit Knowledge, migration, transdisciplinary
collaborative ecotoxicological risk assessment of in-place pollutants in Owen Sound Bay, Lake Huron within the Saugeen Ojibway Nation Territory
Owen Sound Bay, which is located within the traditional territory of the Saugeen Ojibway Nation (SON), is contaminated as a result of historical industrial and shipping activity. Gross contamination of the sediments in the inner part of the Bay (i.e., Owen Sound Harbour) includes high concentrations of polycyclic aromatic hydrocarbons (PAHs) and other organic compounds, as well as metals that may pose a risk to the SON fishery for lake whitefish (Coregonus clupeaformis). However, evaluating the environmental risks posed by contaminated sediments is a challenge, as these risks are dependent upon several factors and require multiple lines of evidence. Including Indigenous communities in environmental risk assessment and the management of those risks is vital for sustaining ecosystem integrity, as well as respecting Treaty Rights. In this study, a risk assessment framework was developed that included several risk assessment tools used in Western science and also encompassed the concerns and values of the SON, including the application of SON-ecological knowledge. Methods for risk evaluation included gathering lines of evidence though community workshops, as well as field sampling in the Bay to determine the concentrations of PAHs and other organic contaminants in sediments and in the water column. Laboratory studies of toxicity to early life stages of lake whitefish and Japanese medaka (Oryzias latipes) and sediment disturbance simulations to evaluate biological responses in juvenile lake whitefish were also completed as lines of evidence. The results indicate that leaving the harbour “as is” without a thorough analysis of remediation options fails to address the concerns of the people within the SON communities. Overall, this research demonstrated a successful process for developing a collaborative risk assessment framework that recognizes the sovereignty of Indigenous peoples and promotes Nation-to-Nation decision making. Author Keywords: biomarkers, Coregonus clupeaformis, Indigenous knowledge, polycyclic aromatic hydrocarbons, risk assessment, source tracking
Hydroclimatic and spatial controls on stream nutrient export from forested catchments
Winter nutrient export from forested catchments is extremely variable from year-to-year and across the landscape of south-central Ontario. Understanding the controls on this variability is critical, as what happens during the winter sets up the timing and nature of the spring snowmelt, the major period of export for water and nutrients from seasonally snow-covered forests. Furthermore, winter processes are especially vulnerable to changes in climate, particularly to shifts in precipitation from snow to rain as air temperatures rise. The objective of this thesis was to assess climatic and topographic controls on variability in stream nutrient export from a series of forested catchments in south-central Ontario. The impacts of climate on the timing and magnitude of winter stream nutrient export, with particular focus on the impact of winter rain-on-snow (ROS) events was investigated through a) analysis of long-term hydrological, chemical and meteorological records and b) high frequency chemical and isotopic measurements of stream and snow samples over two winters. The relationship between topography and variability in stream chemistry among catchments was investigated through a) a series of field and laboratory incubations to measure rates and discern controls on nitrogen mineralization and nitrification and b) analysis of high resolution spatial data to assess relationships between topographic metrics and seasonal stream chemistry. Warmer winters with more ROS events were shown to shift the bulk of nitrate (NO3-N) export earlier in the winter at the expense of spring export; this pattern was not observed in other nutrients [i.e. dissolved organic carbon (DOC), total phosphorus (TP), sulphate (SO4), calcium (Ca)]. Hydrograph separation revealed the majority of ROS flow came from baseflow, but the NO3-N concentrations in rainfall and melting snow were so high that the majority of NO3-N export was due to these two sources. Other nutrient concentrations did not show such a great separation between sources, and thus event export of these nutrients was not as great. Proportionally, catchments with varying topography responded similarly to ROS events, but the absolute magnitude of export varied substantially, due to differences in baseflow NO3-N concentrations. Field and laboratory incubations revealed differences in rates of net NO3-N production between wetland soils and upland soils, suggesting that topographic differences amongst catchments may be responsible for differences in baseflow NO3-N. Spatial analysis of digital elevation models revealed strong relationships between wetland coverage and DOC and dissolved organic nitrogen (DON) concentrations in all seasons, but relationships between topography and NO3-N were often improved by considering only the area within 50 or 100m of the stream channel. This suggests nutrient cycling processes occurring near the stream channel may exert a stronger control over NO3-N stream outflow chemistry. Overall, topography and climate exert strong controls over spatial and temporal variability in stream chemistry at forested catchments; it is important to consider the interaction of these two factors when predicting the effects of future changes in climate or deposition. Author Keywords: biogeochemistry, forest, nitrate, south-central Ontario, stream chemistry, winter

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