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
Factors Controlling Peat Chemistry and Vegetation Composition in Sudbury Peatlands after 30 Years of Emission Reductions
Peatlands are prevalent in the Sudbury, Ontario region. Compared with the well documented devastation to the terrestrial and aquatic ecosystems in this region, relatively little work has been conducted on the peatlands. The objective of this research was to assess factors controlling peat and plant chemistry, and vegetation composition in 18 peatlands in Sudbury after over 30 years of emission reductions. Peatland chemistry and the degree of humification varies considerably, but sites closer to the main smelter had more humified peat and the surface horizons were enriched in copper (Cu) and nickel (Ni). Copper and Ni concentrations in peat were significantly correlated with Cu and Ni in the plant tissue of leatherleaf, although the increased foliar metal content did not obviously impact secondary chemistry stress indicators. The pH and mineral content of peat were the strongest determining factors for species richness, diversity and community composition. The bryophyte communities appear to be acid and metal tolerant, although Sphagnum mosses are showing limited recovery. Author Keywords: anthropogenic emissions, bryophytes, community comspoition, heavy metals, peatlands, wetland vegetation
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)
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
Dynamics and Mechanisms of Community Assembly in a Mined Carolinian Peatland
Theoretical work on community recovery, development, stability, and resistance to species invasions has outpaced experimental field research. There is also a need for better integration between ecological theory and the practice of ecological restoration. This thesis investigates the dynamics of community assembly following peat mining and subsequent restoration efforts at Canada's most southerly raised bog. It examines mechanisms underlying plant community changes and tests predictions arising from the Dynamic Environmental Filter Model (DEFM) and the Fluctuating Resource Hypothesis (FRH). Abiotic, biotic and dispersal filters were modified to test a conceptual model of assembly for Wainfleet Bog. Hydrology was manipulated at the plot scale across multiple nutrient gradients, and at the whole bog scale using peat dams. Trends in time series of hydrological variables were related to restoration actions and uncontrolled variables including precipitation, evapotranspiration and arrival of beaver. Impacts of a changing hydrology on the developing plant community were compared with those from cutting the invasive Betula pendula. Transplanting experiments were used to examine species interactions within primary and secondary successional communities. Seedlings of B. pendula and the native Betula papyrifera were planted together across a peat volumetric water content (VWC) gradient. Impacts of beaver dams were greater than those of peat dams and their relative importance was greatest during periods of drought. Cutting of B.pendula had little effect on the secondary successional plant community developing parallel to blocked drains. Phosphorus was the main limiting nutrient with optimum levels varying substantially between species. Primary colonisers formed a highly stable, novel plant community. Stability was due to direct and indirect facilitative interactions between all species. Reduction in frost heaving was the major mechanism behind this facilitation. Interactions within the secondary successional community were mostly competitive, driven by light and space availability. However, restricted dispersal rather than competition limited further species recruitment. Predictions based on the DEFM were partially correct. A splitting of this model's biotic filter into competition and facilitation components is proposed. There was little support for the FRH based on nutrient levels and VWC. B. pendula had higher germination and growth rates, tolerance to a wider range of peat VWCs and a greater resistance to deer browsing than native birch. Peat mining, combined with restoration actions and the arrival of beaver has moved much of the bog back to an earlier successional stage circa 350+ years BP. Evidence points to B. pendula being a "back-seat driver" in the ecosystem recovery process. Indirect facilitation of a native by an exotic congener, mediated through herbivory, has not been described previously. Shifts in relative contributions of facilitation, competition and dispersal limitations to community assembly may be useful process-oriented measures for gauging progress in restoration. Author Keywords: Betula pendula, community assembly, competition, facilitation, peatland, restoration
regional comparison of the structure and function of benthic macroinvertebrate communities within Precambrian Shield and St. Lawrence lowland lakes in south-central Ontario
Benthic macroinvertebrtes (BMI) are functionally important in aquatic ecosystems; as such, knowledge of their community structure and function is critical for understanding these systems. BMI were sampled from ten lakes in each of two regions of south-central Ontario to investigate which chemical and physical variables could be shaping their community structure and function. Ten Precambrian Shield lakes in the Muskoka-Haliburton region, and ten St Lawrence lowland lakes in the Kawartha lakes region were sampled. These lakes are geologically and chemically distinct, creating natural chemical and physical gradients within and between both regions. Community function was assessed using stable isotope analysis to elucidate carbon transfer dynamics (δ13C) and food web interactions (δ15N). It was predicted that the BMI from Shield lakes would have a δ13C signature indicative of allochthonous carbon subsidies, whereas the lowland lake BMI signatures would reflect autochthonous production. Additionally, it was predicted that the food web length (measured in δ15N units) would be different in Shield and lowland lakes. Both of these predictions were supported; however, the data indicate that δ13C signatures are more likely influenced by catchment geology (represented by bicarbonate concentration) than the extent of allochthony. The best predictor of food web length was found to be region. To assess BMI community structure, taxonomic richness, %EPT (% Ephemeroptera, Plecoptera, Trichoptera; a water quality index), and distribution of functional feeding groups were examined. Based on chemistry it was expected that the Shield lakes would be more speciose, and of greater water quality (relatively lower nutrient levels). These predictions were rejected; since there were no significant regional differences in taxonomic richness or biologically inferred water quality (%EPT). However, sediment size was found to best explain the variability in both metrics, with greater richness and %EPT found at sites with medium and small substrates than those with large substrates. Significant regional differences were found in the distribution of functional feeding groups. Most notably, there were significantly greater proportions of scrapers and shredders in the lowland and Shield lakes, respectively. Based on the feeding mechanisms of these invertebrates it can be inferred that allochthonous subsidies are likely of greater importance to Shield lake BMI communities than those of the lowland lakes; supporting the carbon transfer prediction. These findings provide insight about the structure and function of BMI communities from two dominant lake types in Ontario, and could be useful when determining how future chemical and physical changes will impact these communities. Author Keywords: benthic macroinvertebrates, community function, community structure, Precambrian Shield, stable isotopes, St. Lawrence lowlands
EVALUATION OF HAYFIELD MANAGEMENT STRATEGIES AND BOBOLINK TERRITORIAL HABITAT IN SOUTHERN ONTARIO
I implemented three hayfield management regimens in southern Ontario (a typical schedule at the farmer`s discretion, a delayed first harvest after July 14, and an early first harvest before June 1 with 65 days before second harvest), and evaluated the costs/benefits to farmers regarding hay quality and feasibility, and to Bobolinks (Dolichonyx oryzivorus) regarding reproductive activity and phenology. Typical management resulted in little to no Bobolink reproductive success, and early harvested sites were not (re)colonized. On delayed harvest sites Bobolinks experienced high reproductive success, but hay quality fell below ideal protein levels for most cattle before harvest. I also examined the habitat features Bobolinks use as the basis for establishing territories and associations between Bobolink territory size and habitat quality. I compared vegetation structure, patch size, and prey abundance between small and large territories. Small territories typically occurred on smaller fields with more preferred vegetation characteristics and greater prey abundance. Author Keywords: agro-ecosystem, Bobolink, Dolichonyx oryzivorus, grassland birds, hayfield management
Widespread changes in growth, diet and depth distribution of lake whitefish (Coregonus clupeaformis) in the Great Lakes are linked to invasive dreissenid mussels
Recent declines in growth and condition of Great Lakes' lake whitefish (Coregonus clupeaformis) have been linked to ecosystem-wide changes stemming from the invasion of dreissenid mussels. To test the influence of invasive mussels on this commercially important coregonid species, we collected archived scale samples from ten Great Lake locations and analyzed long-term changes in growth rates, delta 13C and delta 15N stable isotope ratios before and after mussel establishment. There was a decrease in pre-maturation growth after establishment in all four locations where we examined back-calculated growths. In six of the seven locations with dreissenid populations, a significant increase in delta 13C and a significant decrease in delta 15N was found. In dreissenid-absent locations of Lake Superior, we did not see changes in growth or isotope ratios indicative of a major regime shift. Observed shifts in isotopic signatures provide evidence for an increased reliance on nearshore food sources and shallower depth distribution as a result of dreissenids, which likely contributed to lowered growth of lake whitefish. Author Keywords: Diporeia, Dreissenids, food web, Great Lakes, invasive species, lake whitefish
Evaluating the Effects of Habitat Loss and Fragmentation on Canada Lynx
Current major issues in conservation biology include habitat loss, fragmentation and population over-exploitation. Animals can respond to landscape change through behavioural flexibility, allowing individuals to persist in disturbed landscapes. Individual behaviour has only recently been explicitly included in population models. Carnivores may be sensitive to changing landscapes due to their wide-ranging behaviour, low densities and reproductive rates. Canada lynx (Lynx canadensis) is a primary predator of snowshoe hares (Lepus americanus). Both species range throughout the boreal forests of North America, however lynx are declining in the southern range periphery. In this dissertation, I developed new insights into the effects of habitat loss and fragmentation on lynx. In Chapter 2, I created a habitat suitability model for lynx in Ontario and examined occurrence patterns across 2 regions to determine if habitat selection is flexible when different amounts of habitat are available. Although lynx avoided areas with <30% suitable habitat where suitable land cover is abundant, I found that they have flexible habitat selection patterns where suitable land cover is rare and occurred in low habitat areas. In Chapter 3, I investigated the effects of dispersal plasticity on occupancy patterns using a spatially explicit individual-based model. I showed that flexible dispersers, capable of crossing inhospitable matrix, had higher densities and a lower risk of patch extinction. In contrast, inflexible dispersers (unable to cross inhospitable matrix), were most limited by landscape connectivity, resulting in a high extinction risk in isolated patches. I developed three predictions to be explored with empirical data; (1) dispersal plasticity affects estimates of functional connectivity; (2) variation in dispersal behaviour increases the resilience of patchy populations; and (3) dispersal behaviour promotes non-random distribution of phenotypes. Finally, in Chapter 4, I examined the consequences of anthropogenic harvest on naturally cycling populations. I found that harvest mortality can exacerbate the effects of habitat fragmentation, especially when lynx densities are low. Dynamic harvest regimes maintained lynx densities and cycle dynamics while reducing the risk of population extinction. These results suggest that lynx display some flexibility to changing landscapes and that the metapopulation structure is more resilient to increasing habitat loss and fragmentation than previously understood. Future studies should focus on determining a threshold of connectivity necessary for population persistence and examining the effects of habitat loss on the fecundity of lynx. Author Keywords: Fluctuating Populations, Habitat Fragmentation, Landscape Ecology, Occupancy Dynamics, Population Ecology, Spatially Explicit Population Models
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
Evaluating the effects of landscape structure on genetic differentiation and diversity
The structure and composition of the landscape can facilitate or impede gene flow, which can have important consequences because genetically isolated groups of individuals may be prone to inbreeding depression and possible extinction. My dissertation examines how landscape structure influences spatial patterns of genetic differentiation and diversity of American marten (Martes americana) and Canada lynx (Lynx canadensis) in Ontario, Canada, and provides methodological advances useful for landscape geneticists. First, I identified the effects of map boundaries on estimates of landscape resistance, and proposed a solution to the bias: a buffer around the map boundary. Second, I assessed the sensitivity of a network-based estimate of genetic distance, conditional genetic distance, to incomplete sampling. I then used these landscape genetic tools in a pairwise, distance-based analysis of 653 martens genotyped at 12 microsatellite loci. I evaluated whether forest management in Ontario has influenced the genetic structure of martens. Although forest management practices had some impact, isolation by distance best described marten gene flow. Our results suggest that managed forests in Ontario are well connected for marten and do not impede marten gene flow. Finally, I used a site-based analysis of 702 lynx genotyped at 14 microsatellite loci to investigate spatial patterns of genetic diversity and differentiation at the trailing (contracting) edge of the lynx distribution in Ontario. I analyzed harvest records and found that the southern edge of lynx range has contracted by >175 km since the 1970s. I also found that neutral genetic diversity decreased towards the trailing edge, whereas genetic differentiation increased. Furthermore, I found strong correlations between gradients of lynx genetic structure and gradients of climate and land cover in Ontario. My findings suggest that increases in winter air temperature, decreases in snow depth, and loss of suitable habitat will result in further loss of genetic diversity in peripheral populations of lynx. Consequently, the adaptive potential of lynx populations on the southern range periphery could decline. In conclusion, my dissertation demonstrates the varying influences that contemporary landscape structure and climate gradients can have on genetic diversity and differentiation of different species. Author Keywords: Circuitscape, genetic network, landscape genetics, Lynx canadensis, Martes americana, range shift
Longitudinal trends of benthic invertebrates in regulated rivers
The Serial Discontinuity Concept describes the downstream recovery of key biophysical variables below an impoundment. With the proliferation of hydropower dams to meet increasing societal demands, further refinement and understanding of the Serial Discontinuity Concept is needed to accurately predict downstream impacts and ensure the proper management of rivers. In this study, I examine SDC predictions on physical, chemical and biological recovery in regulated rivers providing evidence from 1) a comprehensive literature review and 2) a formal test using two regulated rivers in Northern Ontario. I specifically address how these changes are reflected in benthic invertebrate abundance, diversity, and community composition. The literature review and case studies support the predicted recovery of temperature, periphyton, substrate, and drift. In addition, the study suggests that two recovery gradients exist in regulated rivers: 1) a longer, thermal gradient taking up to hundreds of kilometres downstream; and 2) a shorter, resource subsidy gradient recovering within 1-4 km downstream of an impoundment. Total benthic invertebrate abundance varies considerably and depends on the degree of flow alteration and resource subsidies from the upstream reservoir. In contrast, benthic diversity is reduced below dams irrespective of dam location and operation with little recovery observed downstream. Contrary to SDC predictions, the longitudinal gradient in regulated rivers is not a compaction of functional changes seen over several stream orders in natural rivers but a response to dam design and reservoir conditions. Stoneflies and dragonflies are particularly sensitive to regulation while filter feeding invertebrates are enhanced. Ward and Stanford's (1983) Serial Discontinuity Concept is still a useful framework for testing hypotheses. Future studies should further expand the SDC through empirical estimation within the context of the landscape to gain a better scientific understanding of regulated river ecology. Author Keywords: benthic invertebrates, dams, longitudinal, recovery, River Continuum Concept, Serial Discontinuity Concept

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Graduate student theses produced at Trent University. You may also browse theses and dissertations by year, program, or author.

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