Graduate Theses & Dissertations

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Habitat selection by sympatric Canada lynx (Lynx canadensis) and bobcat (Lynx rufus)
Range expansion by the bobcat (Lynx rufus) may be contributing to range contraction by the Canada lynx (Lynx canadensis), but interactions between them are not well understood. To investigate the potential for competition, I conducted a literature review of hierarchical habitat selection by these two species. I determined that the lynx and the bobcat select different resources at the first and second orders, and that the fourth order is under-studied compared to higher orders. I therefore conducted a snow-tracking study of fine-scale habitat selection by lynx and bobcat in an area of sympatry in northern Ontario. I found that the two species selected similar resources at the fourth order, but appeared to be allopatric at the level of the home range. These results suggest that competition is unlikely to occur between lynx and bobcat, and other factors should be considered as more probable causes of the lynx range contraction. Author Keywords: Bobcat, Canada lynx, Competition, Habitat selection, Scale, Snow tracking
Effects of Geographic Factors on the Wild Harvest of Large Mammals across North America
While the harvest of mammals is monitored in each jurisdiction across Canada and the USA, there has been no analysis of this wild harvest at a continental scale across North America. The recreational wild harvest of large mammals varies geographically across North America, and I hypothesized that this variation is influenced by both anthropogenic and other environmental factors on the landscape. I tested this hypothesis using annual harvest tallies collected by Conservation Visions Inc. for mammals for each state, provincial, and territorial jurisdiction in Canada and the USA. I built multiple additive models of the harvest, in one harvest year, 2015 – 2016, to test for landscape gradients that explain the variation in harvest levels for seven large mammal species: white-tailed deer (Odocoileus virginianus), black bear (Ursus americanus), bighorn sheep (Ovis canadensis), elk (Cervus canadensis), mule deer (Odocoileus hemionus), pronghorn (Antilocapra americana), and moose (Alces alces). I built these models from a suite of nine putative predictor variables that comprised landcover, human footprint, and evapotranspiration. For all large mammal species except for pronghorn, anthropogenic influence had a positive effect on the wild harvest density, consistent with the idea that the proximity of human populations and roads are important for fostering wild harvest activity by providing hunters access to hunting areas. The harvest of white-tailed deer, elk, and pronghorn were negatively affected by vegetation structure, urbanization, and primary productivity, respectively. Understanding the recreational wild harvest at a broad-spatial scale provides a unique perspective of the North American model of wildlife conservation and spurs future comparative analyses of the wild harvest across spatial scales. Author Keywords: Anthropogenic Influence, Hunting, Large Mammals, Primary Productivity, Vegetation Structure, Wild Harvest
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
Nutritional stoichiometry and growth of filamentous green algae (Family Zygnemataceae) in response to variable nutrient supply
In this study, I investigate the effects of nitrogen (N) and phosphorus (P) on the nutritional stoichiometry and growth of filamentous green algae of the family Zygnemataceae in situ and ex situ. I found a mean of Carbon (C):N:P ratio of 1308:66:1 for populations growing in the Kawartha Lakes of southern Ontario during the summer of 2012. FGA stoichiometry was variable, with much of the variation in algal P related to sediment P (p < 0.005, R2 = 0.58). Despite large variability in their cellular nutrient stoichiometry, laboratory analysis revealed that Mougeotia growth rates remained relatively consistent around 0.28 day-1. In addition, Mougeotia was found to be weakly homeostatic with respect to TDN:TDP supply (1/HNP = 0.32). These results suggest that FGA stoichiometry and growth rates are affected by sediment and water N and P. However, they will likely continue to grow slowly throughout the summer despite variable nutrient supply. Author Keywords: Chlorophyll concentration, Filamentous algae, Growth rate, Homeostatic regulation, Nutritional stoichiometry
MOVEMENT PARAMETERS AND SPACE USE FOR THE SOUTHERN HUDSON BAY POLAR BEAR SUBPOPULATION IN THE FACE OF A CHANGING CLIMATE
Changes to the Arctic and sub-Arctic climate are becoming increasingly evident as it warms faster than other areas of the globe, supporting evidence that predictions of future warming will be amplified due to positive feedback mechanisms. The Southern Hudson Bay polar bear (Ursus maritimus) subpopulation is one of the most southerly subpopulations in the world, putting it at increased risk due to effects of climate change. Whereas many other subpopulations have been the subject of intense research and monitoring, little research has been completed detailing the movement behaviour and space use of bears within Southern Hudson Bay. I used detailed movement data collected on female polar bears to establish a baseline of movement information for this subpopulation to which future work can be compared and effects of climate change can be assessed I evaluated the use of core areas during critical periods of the year (breeding and ice breakup) and evaluated common space use as a means of assessing site fidelity during the breeding season. Movement rates and home range sizes were comparable to those of the neighbouring Western Hudson Bay subpopulation. I also found evidence of increased occurrences of long distance, late fall movements along the coast to the northwest, presumably to gain earlier access to first ice. Though space use analysis did not reveal evidence of site fidelity to specific breeding areas in Hudson Bay, I found that core use areas are at risk of substantially shortened ice duration (x¯ =76 days shorter) using projected ice data based on the high emissions A2 climate change scenario. Author Keywords: climate change, Hudson Bay, movement, polar bear, sea ice, utilization distribution
influence of landscape features on the harvest of caribou (Rangifer tarandus) on the island of Newfoundland
Hunting represents the principal tool for managing populations of migratory caribou (Rangifer tarandus), but harvest may be affected by landscape features that govern animal distribution and hunter access. Such effects are unclear. I capitalized on an existing dataset of 21 355 caribou harvest records, 1980 – 2009, to determine the influence of landscape features on caribou harvest across the island of Newfoundland. Using a landcover map and spatial data for anthropogenic features, I modelled caribou harvest at the island scale for three phases of numerical change (growth in the 1980s, cessation of growth in the 1990s, decline in the 2000s) and harvest type (total harvest, resident harvest of males and females, resident harvest of males, resident harvest of females, and non-resident harvest of males) in relation to multiple putative predictor variables: proportion of lichen cover and distances to nearest forest cut, road, outfitter, transmission line, and town. I did the same analysis for seven individual Caribou Management Areas (CMAs). At the island scale, the number of harvested caribou increased with proximity to the nearest forest cut and with greater proportions of lichen habitat. I attribute this to landscape features that provide forage for caribou, but also access and caribou visibility for hunters. Caribou harvest increased in proximity to transmission lines for the harvest of caribou by resident hunters in the 2000s, which could be a result of more risk-prone foraging Newfoundland caribou. Non-resident hunters harvested greater numbers of male caribou further from towns, likely a result of the placement of outfitter camps and activities. At the management area scale, in most instances, more caribou harvest occurred in close proximity to transmission lines. Proximity to forest cuts and high proportions of lichen were still important landscape features leading to a greater harvest. I conclude that the caribou harvest was largely governed by hunter access and visibility of their prey, augmented by open habitats preferred by caribou. KEYWORDS Caribou, Newfoundland, Rangifer tarandus, harvest, hunting, management area, landscape, human disturbances, game species vulnerability. Author Keywords: caribou, game species vulnerability, harvest, hunting, newfoundland, rangifer tarandus
Testing for Interspecific Hybridization and a Latitudinal Cline Within the Clock Gene Per1 of the Deer Mouse (Peromyscus maniculatus) and the White-Footed Mouse (Peromyscus leucopus)
The recent northward expansion of the white-footed mouse (Peromyscus leucopus) in response to climatic changes provides a natural experiment to explore potential adaptive genetic variation within the clock gene Per1 in Peromyscus undergoing latitudinal shifts, as well as, the possibility of hybridization and introgression related to novel secondary contact with its sister species the deer mouse (Peromyscus maniculatus). Because clock genes influence the timing of behaviors critical for survival, variations in genotype may reflect an organism’s ability to persist in different environments. Hybridization followed by introgression may increase the adaptive potential of a species by quickly generating adaptive variation through novel genetic recombination or by the transfer of species-specific alleles that have evolved in response to certain environments. In chapter 2, I used microsatellite and mtDNA markers to test for hybridization and introgression between P. maniculatus and P. leucopus and found that interbreeding is occurring at a low frequency (<1%). In chapter 3, I tested for a latitudinal cline in a polyglycine repeat located within the Per1 gene of Peromyscus and discovered a putative cline in the Per1-142 and Per1-157 allele of P. leucopus and P. maniculatus, respectively. Chapter 4, further expands upon these findings, limitations, and the lack of evidence supporting introgression at the Per1 locus. Despite this lack of evidence, it is possible that novel hybridization has or could lead to adaptive introgression of other genes, allowing for the exchange of adaptive alleles or traits that could be advantageous for range expansion and adaption to future environmental changes. Author Keywords: Clock genes, Hybridization, Latitudinal gradient, Per1, Peromyscus, Range Expansion
Habitat use and community structure of grassland birds in southern Ontario agro-ecosystems.
Most grassland bird populations are in decline, so it is becoming increasingly important to understand how they use agricultural field types and form their communities. I performed point counts in cultural meadow, intensive agriculture, and non-intensive agriculture areas in 2011 and 2012. Generalized linear models were used to determine the habitat relationships of six focal species. I found that non-intensive agriculture was used most often and intensive agriculture was often avoided, but there were exceptions which indicate habitat use can be species-specific. I determined in which habitats competition was likely occurring and which species pairs were competing in 2011. In 2012, I experimentally tested these relationships by introducing artificial competitors onto sites. By comparing presence-absence data from 2011 to 2012, I found evidence of habitat-mediated interspecific and conspecific attraction involving Bobolink and Grasshopper Sparrow. This research contributes to the current understanding of grassland bird community ecology and conservation. Author Keywords: agriculture, BACI, community ecology, habitat use, species at risk, species interactions
Landscape fitness
Variation in habitat quality and disturbance levels can strongly influence a species’ distribution, leading to spatial variation in population density and influencing population dynamics. It is therefore critical to understand how density can lead to variability in demographic responses for effective conservation and recovery of species. My dissertation illustrates how density and spatial familial networks can be integrated together to gain a better understanding of the influence of density on population dynamics of boreal caribou. First, I created an analytical framework to assess results from empirical studies to inform spatially-explicit capture-recapture sampling design, using both simulated and empirical data from noninvasive genetic sampling of several boreal caribou populations in Alberta, Canada, which varied in range size and estimated population density. Analysis of the empirical data indicated that reduced sampling intensity had a greater impact on density estimates in smaller ranges, and the best sampling designs did not differ with estimated population density but differed between large and small population ranges. Secondly, I used parent-offspring relationships to construct familial networks of boreal caribou in Saskatchewan, Canada to inform recovery efforts. Using network measures, I assessed the contribution of individual caribou to the population with several centrality measures and then determined which measures were best suited to inform on the population demographic structure. I found substantial differences in the centrality of individuals in different local areas, highlighting the importance of analyzing familial networks at different spatial scales. The network revealed that boreal caribou in Saskatchewan form a complex, interconnected familial network. These results identified individuals presenting different fitness levels, short- and long-distance dispersing ability across the range, and can be used in support of population monitoring and recovery efforts. Finally, I used a spatial capture-recapture analytical framework with covariates to estimate spatial density of boreal woodland caribou across the Saskatchewan Boreal Plains, and then reconstructed parent-offspring relationships to create a familial network of caribou and determined whether spatial density influenced sex-specific network centrality, dispersal distance, individual reproductive success, and the pregnancy status of females. I show that caribou densitygreatly varied across the landscape and was primarily affected by landscape composition and fragmentation, and density had sex-specific influences on dispersal distance, reproductive success, and network centrality. The high density areas reflected good-quality caribou habitat, and the decreased dispersal rates and female reproductive output suggest that these remnant patches of habitat may be influencing demographic responses of caribou. Author Keywords: boreal caribou, density, familial networks, population dynamics, rangifer tarandus caribou, spatial capture-recapture
Temporo-spatial patterns of occupation and density by an invasive fish in streams
Since its introduction to North America in the 1990s, the Round Goby has spread throughout the Great Lakes, inland through rivers and is now moving into small tributary streams, a new environment for this species in both its native and invaded ranges. I explored density and temporal occupation of Round Gobies in four small streams in two systems in south-central Ontario, Canada in order to determine what habitat variables are the best predictors of goby density. Two streams are tributaries of Lake Ontario and two are tributaries of the Otonabee River, and all of these streams have barriers preventing upstream migration. I found that occupation and density differed between the systems. In the Otonabee River system, Round Gobies occupy the streams year round and the most important factor determining adult density is distance from a barrier to upstream movement, with the entire stream occupied but density highest next to the barriers. In the Lake Ontario system, density is highest at mid-stream and Round Gobies appear to occupy these streams mainly from spring to fall. Adult density in Lake Ontario tributaries is highest in sites with a high percentage of cobble/boulder and low percentage of gravel substrate, while substrate is less important in Otonabee River tributaries. Occupation and density patterns may differ due to contrasting environmental conditions in the source environments and distance to the first barrier preventing upstream movement. This study shows diversity in invasion strategies, and provides insight into the occurrence and movement patterns of this species in small, tributary streams. Author Keywords: biological invasion, Generalised Additive Mixed Model, habitat, Neogobius melanostomus, Round Goby, stream
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
Using genomic and phenotypic data to explore the evolution and ecology of the North American mountain goat
Evaluating the impact of climate change is arguably one of the main goals of conservation biology, which can be addressed in part by studying the demographic history of species in the region of interest. In North America, landscape and species composition during the most recent Pleistocene epoch was primarily influenced by glaciation cycles. Glacial advance and retreat caused species ranges to shift as well, leaving signatures of past population bottlenecks in the genetic code of most species. Genomic tools have shown to be important tools for understanding these demographic events to enhance conservation biology measures in several species. In my thesis I first reviewed the state of ungulate genomics, with a focus on how such data sets can be used in understand demography, adaptation, and inform conservation and management. Importantly, the review introduces key analyses like the pairwise sequentially Markovian coalescent and features like variation in antlers and horns and selection pressures that are used throughout subsequent chapters. Using the North American mountain goat as a model species, I then explored the genomic and phenotypic variation in this alpine specialist mammal. Starting with the generation of the first genome assembly for the mountain goat, I identified genes unique to the mountain goat and modeled demographic history going back millions of years using a pairwise sequentially Markovian coalescent approach. Species’ effective population size generally paralleled climatic trends over the past one hundred thousand years and severely declined to under a thousand individuals during the last glacial maximum. Given the biological importance of horns in mountain goats and the recent scientific interest in genetic basis of headgear, I analyzed over 23,000 horn records from goats harvested in British Columbia, Alaska and Northwest Territories from 1980 to 2017. Overall, variation in horn size over space and time was low; goats harvested further North had shorter horn lengths and smaller horn circumferences in one year old and 4 years and older age classes and 4 years and older age class, respectively. Proximity of roads, which was used as an indicator of artificial selection, had a small effect on horn size, with larger horns being harvested closer to major roads. Finally, I used two range-wide genomic data sets sequenced with a whole genome re-sequencing and reduced representation approaches to provide estimates of genetic diversity, contemporary effective population sizes and population structure. These insights can help inform management and will potentially make an impact in preserving the mountain goat. Author Keywords: genome assembly, horn size, Oreamnos americanus, population demography, reduced representation sequencing, whole genome resequencing

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