Graduate Theses & Dissertations

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Population Dynamics of Eastern Coyotes in Southeastern Ontario
The ability of animal populations to compensate for harvest mortality provides the basis for sustainable harvesting. Coyote populations are resilient to exploitation, but the underlying mechanisms of compensation and how they inter-relate are not fully understood. Moreover, deficiencies in the quality and quantity of information about eastern coyotes preclude effective management. I combined field work, laboratory work, and genetic profiling to investigate the population dynamics of eastern coyotes in southeastern Ontario. Specifically, I conducted research on coyotes during 2010–2013 in Prince Edward County where coyote hunting and trapping seasons were open all year. First, I investigated their social status dynamics and space-use patterns. Transients exhibited extensive space-use relative to residents, potentially encountering vacant territories and/or breeding positions, and some transients became residents, potentially filling vacant territories and/or breeding positions. Accordingly, the study population demonstrated the potential to compensate for harvest mortality via source-sink dynamics and/or buffering reproductive capacity. Second, I investigated their survival and cause-specific mortality. Residents exhibited greater survival than transients, probably partly because of the benefits of holding a territory, and transients seemingly exhibited greater vulnerability to harvest than residents, probably partly because their movements exposed them to greater cumulative mortality risks over time. Accordingly, harvest mortality disproportionately impacted the non-reproductive segment of the study population and thus may have failed to substantially limit reproduction, and thus recruitment. Third, I investigated their reproduction and breeding histories. Females in the study population exhibited age-specific reproductive rates and litter sizes generally typical of those in exploited coyote populations. Accordingly, increased reproductive rates and increased litter sizes may have offset losses due to harvest mortality. There was at least some breeder turnover in the study population due to harvest mortality, but many breeders survived to reproduce for multiple years and those that died were quickly replaced. My findings have important management implications for eastern coyotes and contribute significantly to better understanding of their resilience to harvest. Indiscriminate killing of coyotes through liberal harvest is unlikely to be effective in reducing their abundance. Management strategies should consider non-lethal alternatives and/or targeted lethal control for dealing with problem coyotes. Author Keywords: Canis latrans var., eastern coyotes, population dynamics, Prince Edward County, southeastern Ontario
White-Tailed Fear
The primary method used to maintain white-tailed deer (Odocoileus virginianus) populations at densities that are ecologically, economically, socially, and culturally sustainable is hunter harvest. This method considers only the removal of animals from the population (the direct effect) and does not conventionally consider the costs imposed on deer as they adopt hunter avoidance strategies (the risk effect). The impact of risk effects on prey can exceed that of direct effects and there is interest in applying this concept to wildlife management. Deer are potential candidates as they have demonstrated behavioural responses to hunters. I explored the potential of such a management practice by quantifying how human decisions around hunting create a landscape of fear for deer and how deer alter their space use and behaviour in response. I used a social survey to explore the attitudes of rural landowners in southern and eastern Ontario towards deer and deer hunting to understand why landowners limited hunting on their property. I used GPS tracking devices to quantify habitat selection by hunters and hunting dogs (Canis familiaris) to better understand the distribution of hunting effort across the landscape. I used GPS collars to quantify the habitat selection of deer as they responded to this hunting pressure. I used trail cameras to quantify a fine-scale behavioural response, vigilance, by deer in areas with and without hunting. Human actions created a highly heterogeneous landscape of fear for deer. Landowner decisions excluded hunters from over half of the rural and exurban landscape in southern and eastern Ontario, a pattern predicted by landowner hunting participation and not landcover composition. Hunter decisions on whether to hunt with or without dogs resulted in dramatically different distributions of hunting effort across the landscape. Deer showed a high degree of behavioural plasticity and, rather than adopting uniform hunter avoidance strategies, tailored their response to the local conditions. The incorporation of risk effects into white-tailed deer management is feasible and could be done by capitalizing on a better understanding of deer behaviour to improve current management practices or by designing targeted hunting practices to elicit a landscape of fear with specific management objectives. Author Keywords: Brownian bridge movement models, hunting, landscape of fear, resource utilization functions, risk effects, white-tailed deer
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
Contemporary adaptive shifts in the physiology and life history of Pumpkinseed (Lepomis gibbosus) introduced into a warm climate
Contemporary evolution has the potential to help limit the biological impact of rapidly changing climates, however it remains unclear whether wild populations can respond quickly enough for such adaptations to be effective. In this thesis, I used the introduction of native North American Pumpkinseed (Lepomis gibbosus) into the milder climate of Europe over 140 years ago, as a 'natural' experiment to test for contemporary evolution to a change in climate in wild populations. In 2008, four outdoor pond colonies were established in central Ontario using adult Pumpkinseed from two native Canadian populations, and two non-native populations from northeastern Spain. By raising native and non-native Pumpkinseed within a common environment, this design minimized the impact of phenotypic plasticity on differential trait expression, and allowed me to interpret differences in the phenotype among pond-reared Pumpkinseed as evidence of genetic differences among populations. I demonstrated that Canadian and Spanish Pumpkinseed have similar thermal physiology except when acclimated to seasonally warm temperatures; trait differences are consistent with Spanish Pumpkinseed being better adapted to a warmer climate. Populations also had similar overwintering ecology, however some differences, such as higher survival under starvation conditions and greater energetic benefits associated with winter feeding, indicated that Canadian populations are better adapted to harsh winter conditions typical of the native range. Finally, I determined that the relatively fast life history expressed in wild European Pumpkinseed is largely driven by plastic responses to the local environment; however, the higher reproductive investment by European populations has a genetic basis. Most climate change research considers taxa that are expected to be negatively impacted by warming: my research demonstrates that even warm-tolerant taxa that are unlikely to experience strong climatic selective forces can respond to a warming environment through evolutionary changes. The potential for adaptive contemporary evolution in warm-tolerant taxa should be taken into account when predicting future ecosystem effects of climate change, and when planning management strategies for species introduced into novel climates. Author Keywords: climate change, contemporary evolution, fish, non-native species, thermal biology, winter ecology
Characterization of a Zn(II)2Cys6 transcription factor in Ustilago maydis and its role in pathogenesis
Ustilago maydis (D.C.) Corda is a biotrophic pathogen that secretes effectors to establish and maintain a relationship with its host, Zea mays. In this pathosystem, the molecular function of effectors is well-studied, but the regulation of effector gene expression remains largely unknown. This study characterized Zfp1, a putative U. maydis Zn(II)2Cys6 transcription factor, as a modulator of effector gene expression. The amino acid sequence of Zfp1 indicated the presence of a GAL4-like zinc binuclear cluster as well as a fungal specific transcription factor domain. Nuclear localization was confirmed by tagging Zfp1 with enhanced green fluorescent protein. Deletion of zfp1 resulted in attenuated hyphal growth, reduced infection frequency, an arrest in pathogenic development, and decreased anthocyanin production. This phenotype can be attributed to the altered transcript levels of genes encoding predicted and confirmed U. maydis effectors in the zfp1 deletion strain during pathogenic growth. Complementation of zfp1 deletion strain with tin2, an effector involved in anthocyanin induction, suggested this effector is downstream of Zfp1 and its expression is influenced by this transcription factor during in planta growth. When wild-type zfp1 was ectopically inserted in the zfp1 deletion strain, pathogenesis and virulence were partially restored. This, coupled with zfp1 over-expression strains having a similar phenotype as the deletion strains, suggested Zfp1 may interact with other proteins for full function. These findings show that Zfp1, in conjunction with one or more binding partners, contributes to U. maydis pathogenesis, virulence, and anthocyanin production through the regulation of effector gene expression. Author Keywords: effector, pathogenesis, transcription factor, Ustilago maydis, Zea mays, zinc finger
Hybridization dynamics in cattails (Typha spp.,) in northeastern North America
Interspecific hybridization is an important evolutionary process which can contribute to the invasiveness of species complexes. In this dissertation I used the hybridizing species complex of cattails (Typha spp., Typhaceae) to explore some of the processes that could contribute to hybridization rates. Cattails in northeastern North America comprise the native T. latifolia, the non-native T. angustifolia, and their fertile hybrid, T. × glauca. First, I examined whether these taxa segregate by water depth as habitat segregation may be associated with lower incidence of hybridization. I found that these taxa occupy similar water depths and therefore that habitat segregation by water depth does not promote mating isolation among these taxa. I then compared pollen dispersal patterns between progenitor species as pollen dispersal can also influence rates of hybrid formation. Each progenitor exhibits localized pollen dispersal, and the maternal parent of first generation hybrids captures more conspecific than heterospecific pollen; both of which should lead to reduced hybrid formation. I then conducted controlled crosses using all three Typha taxa to quantify hybrid fertility and to parameterize a fertility model to predict how mating compatibilities should affect the composition of cattail stands. I found that highly asymmetric formation of hybrids and backcrosses and reduced hybrid fertility should favour the maintenance of T. latifolia under certain conditions. Finally, I used a population genetics approach to characterize genetic diversity and structure of Typha in northeastern North America to determine the extent to which broad-scale processes such as gene flow influence site-level processes. I concluded that hybrids are most often created within sites or introduced in small numbers rather than exhibiting broad-scale dispersal. This suggests that local processes are more important drivers of hybrid success than landscape-scale processes which would be expected to limit the spread of the hybrid. Though my findings indicate some barriers to hybridization in these Typha taxa, hybrid cattail dominates much of northeastern North America. My results therefore show that incomplete barriers to hybridization may not be sufficient to prevent the continued dominance of hybrids and that active management of invasive hybrids may be required to limit their spread. Author Keywords: fertility model, genetic structure, Hybridization, invasive species, niche segregation, pollen dispersal
Fate and Effects of Silver Nanoparticle Addition in a Lake Ecosystem
The potential release of nanoparticles into aquatic environments is raising global concerns. As antimicrobials, silver nanoparticles (AgNPs) are among the most prominent form in use. Despite this, their fate, long-term toxicity, and ecological relevance have yet to be investigated largely under natural settings with seasonality and environmental complexity. To better understand the environmental significance, we released AgNPs into Lake 222 at the Experimental Lakes Area over two years. AgNPs remained suspended in the water column and were detected throughout the lake and in the lower food web. Total Ag concentrations ranged from below 0.07 to 18.9 μg L-1 in lake water, and were highly dynamic seasonally both in the epilimnion and hypolimnion depending on the physical, chemical and biological conditions of the lake. Approximately 60% of the measured Ag mass in October was present in the sediment in 2014 and 50% in 2015 demonstrating relatively high sedimentation and removal from the water column. During winter months, Ag was largely absent in the water column under the ice. After ice melt and before summer stratification, Ag concentrations increased in the lake suggesting AgNPs may not be tightly bound to the sediment and are able re-enter the water column during spring mixing events. Despite temporal variation, total Ag was highly synchronous across spatial locations for both years, indicating rapid dispersal upon lake entry. When investigating AgNP sizes using spICPMS, size distributions were similar across spatial locations, with the 40-60 nm size class constituting approximately 60% of all particles identified. Large aggregates (>100 nm) and dissolved Ag were infrequently detected within the lake. Ag accumulated in the lower food web ranging from 0.27-16.82 μg Ag mg C-1 in the bacterioplankton and 0.17-6.45 μg Ag mg C-1 in algae (particulate fraction). Partial least squares models revealed the highest predictors of Ag accumulation were dissolved nutrients including DOC, TDN, TDP in bacterioplankton. Major predictors for particulate Ag included temperature, dissolved oxygen, and sampling date. The diversity of predictors among biological compartments emphasizes the importance of understanding the role of environmental complexity within the lower food web. Despite Ag accumulation we did not detect strong negative effects on the lake food web. An increase in particulate and bacterioplankton chlorophyll-a occurred after addition in contrast to reference lakes, which may indicate a hormetic response to low dose AgNP concentrations. Our findings provide the first whole-lake perspective regarding Ag fate and toxicity, suggesting small scale experiments may overestimate environmental responses. Author Keywords: Ecotoxicity, Fate, Lower food web, Silver Nanoparticles, Whole-lake addition
successful invader in expansion
Researchers have shown increasing interest in biological invasions for the associated ecological and economic impacts as well as for the opportunities they offer to study the mechanisms that induce range expansion in novel environments. I investigated the strategies exhibited by invasive species that facilitate range expansion. Invasive populations exhibit shifts in life-history strategy that may enable appropriate responses to novel biotic and abiotic factors encountered during range expansion. The spatio-temporal scales at which these shifts occur are largely unexplored. Furthermore, it is not known whether the observed dynamic shifts represent a consistent biological response of a given species to range shifts, or whether the shifts are affected by the abiotic characteristics of the new systems. I examined the life-history responses of female round gobies Neogobius melanastomus across fine and coarser spatial scales behind the expansion front and investigated whether invasive populations encountering different environmental conditions (Ontario vs France) exhibited similar life-history shifts. In both study systems, I found an increase in reproductive investment at invasion fronts compared to longer established areas at coarse and fine scales. The results suggest a similar response to range shifts, or a common invasion strategy independent of environmental conditions experienced, and highlight the dynamic nature of an invasive population’s life history behind the invasion front. The second part of my research focused on the development of an appropriate eDNA method for detecting invasive species at early stages of invasion to enable early detection and rapid management response. I developed a simple, inexpensive device for collecting water samples at selected depths for eDNA analysis, including near the substrate where eDNA concentration of benthic species is likely elevated. I also developed a protocol to optimise DNA extraction from water samples that contain elevated concentration of inhibiters, in particular near-bottom samples. Paired testing of eDNA and conventional surveys was used to monitor round goby expansion along its invasion pathway. Round gobies were detected in more sites with eDNA, permitting earlier, more accurate, upstream detection of the expansion front. My study demonstrated the accuracy and the power of using eDNA survey method to locate invasion fronts. Author Keywords: Age-specific reproductive investment, DNA extraction, Energy allocation, Fecundity, Invasion front, Range expansion
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
Comparative phylogeography in conservation biology
Phylogeographic histories of taxa around the Great Lakes region in North America are relevant to a range of ongoing issues including conservation management and biological invasions. In this thesis I investigated the comparative phylogeographic histories of plant species with disjunct distributions and plant species with continuous distributions around the Great Lakes region; this is a very dynamic geographic area with relatively recent colonisation histories that have been influenced by a range of factors including postglacial landscape modifications, and more recently, human-mediated dispersion. I first characterized four species that have disjunct populations in the Great Lakes region: (Bartonia paniculata subsp. paniculata, Empetrum nigrum, Sporobolus heterolepis, and Carex richardsonii). Through comparisons of core and disjunct populations, I found that a range of historical processes have resulted in two broad scenarios: in the first scenario, genetically distinct disjunct and core populations diverged prior to the last glacial cycle, and in the second scenario more recent vicariant events have resulted in genetically similar core and disjunct populations. The former scenario has important implications for conservation management. I then characterized the Typha species complex (T. latifolia, T. angustifolia, T. x glauca), which collectively represent species with continuous distributions. Recent microevolutionary processes, including hybridization, introgression, and intercontinental dispersal, obscure the phylogeographic patterns and complicate the evolutionary history of Typha spp. around the Great Lakes region, and have resulted in the growing dominance of non-native lineages. A broader geographical comparison of Typha spp. lineages from around the world identified repeated cryptic dispersal and long-distant movement as important phylogeographic influences. This research has demonstrated that comparisons of regional and global evolutionary histories can provide insight into historical and contemporary processes useful for management decisions in conservation biology and invasive species. Author Keywords: chloroplast DNA, conservation genetics, disjunct populations, invasive species, phylogeography, postglacial recolonisation
Elemental Variation in Daphnia
Environmental variation can affect consumer trait expression and alter ecological and evolutionary dynamics in natural populations. However, although dietary nutrient content can vary by an order of magnitude in natural ecosystems, intra-specific differences in consumer responses to food quality have not been thoroughly investigated. Therefore, the purpose of my dissertation was to examine the influence of dietary nutrition and other environmental factors on consumer phenotypic variation using the freshwater cladoceran Daphnia. I conducted a series of complementary laboratory and field studies where I examined the effects of dietary phosphorus (P) content and additional biological/environmental variables (multi-elemental limitation, genetic variation, and temperature) on daphnid life-history, biochemistry, body elemental composition, and population growth. In general, phenotypic expression within a species varied significantly in response to all experimental variables, but the relative influence of each was highly context dependent. In my first chapter, I found that dietary P content and environmental calcium (Ca) concentrations both altered Daphnia body Ca:P ratios and growth rates of individuals and affected intrinsic rates of increase at the population level. However, food quality appeared to have a much larger effect on trait expression, and body Ca:P ratios were highly sensitive to other forms of dietary nutrient limitation. Next, I documented significant quantitative genetic variation and phenotypic plasticity in daphnid P content, growth, and P use efficiency of field collected animals grown across dietary P gradients. Trait expression was also influenced by genotype X diet interactions suggesting that consumer responses to dietary nutrient limitation can be heritable and may be adaptive in different nutrient environments. Finally, I found that temperature appeared to override food quality effects and decouple P metabolism in natural Daphnia populations, but total biomass production was affected by both dietary P content and temperature, depending on the nutrient content of the lake. Overall, my dissertation shows that consumer responses to nutrient limitation can vary significantly within a species and that changes in trait expression may be modified by other environmental variables. These results should be incorporated into existing stoichiometric models and used to investigate the eco-evolutionary consequences of consumer phenotypic variation in response to nutritional stress. Author Keywords: ecological stoichiometry, evolution, life-history, nutrient limitation, nutrient metabolism, zooplankton
Ecological and morphological traits that affect the fitness and dispersal potential of Iberian pumpkinseed (Lepomis gibbosus)
The Pumpkinseed (Lepomis gibbosus) is a sunfish that is endemic to eastern portions of Canada and the United States. During the late 19th century, the species was introduced into Europe, and it is now present in over 28 countries. Previous attempts to determine the characteristics that can predict the spread of non-indigenous species have been largely unsuccessful, but new evidence suggests that phenotypic plasticity may help to explain the dispersal and range expansion of some organisms. Experimental comparisons on lower-order taxa have revealed that populations from areas outside of their native range are capable of exhibiting stronger levels of phenotypic plasticity than counterparts from their source of origin. Using Pumpkinseed, I conducted the first native/non- native comparison of phenotypic plasticity in a vertebrate. Progeny from adult Pumpkinseed collected in Ontario, Canada and the Iberian Peninsula (Spain) were reared under variable water velocities, habitat type and competitive pressures, three ecological factors that may affect the dispersal potential of fishes introduced into novel aquatic systems. Differences in phenotypic plasticity, assessed from a morphological perspective, were compared among populations using a traditional distance-based approach. All populations exhibited divergent morphological traits that appeared to be inherited over successive generations. In each experiment, all populations responded to environmental change by developing internal and external morphological forms that, in related taxa, enhance and facilitate foraging and navigation; however, non-native populations always exhibited an overall lower level of phenotypic plasticity. Pumpkinseed from non-native areas may have exhibited a reduction in phenotypic plasticity because of population-based differences. Nevertheless, all Pumpkinseed populations studied were capable of exhibiting phenotypic plasticity to novel environmental conditions, and develop morphological characteristics that may enhance fitness and dispersal in perturbed areas. Author Keywords: Invasive species, Morphology, Phenotypic plasticity, Pumpkinseed sunfish, Reaction norm

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