Graduate Theses & Dissertations

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Intra-seasonal Variation in Black Tern Nest-site Selection and Survival
Resources and risk are in constant flux and an organism’s ability to manage change may improve their likelihood of persistence. I examined intra-seasonal variation in nest-site selection and survival of a declining wetland bird, the Black Tern (Chlidonias niger surinamensis). I modelled nest site occupancy and survival of early and late-nesting birds as a function of static and dynamic factors. Early-nesting birds selected nest sites based on the degree and direction of habitat change that occurred over the nesting cycle, while late-nesting birds selected sites based on static conditions near the time of nest-site selection. Nest age had the strongest influence on daily survival rate for both early and late-nesting birds, but the shape of this relationship showed intra-seasonal differences. Additionally, early-season survival improved slightly with increasing vegetation coverage and distance between conspecific nests, while late-season survival increased with clutch size. My results suggest that intra-seasonal variation in nest-site selection and survival is driven by changing habitat conditions and predator behavior. Author Keywords: Black Tern, Chlidonias niger surinamensis, daily survival rate, intra-seasonal variation, nest-site selection
SPATIAL AND TEMPORAL GENETIC STRUCTURE OF WOLVERINE POPULATIONS
Habitat loss and fragmentation can disrupt population connectivity, resulting in small, isolated populations and low genetic variability. Understanding connectivity patterns in space and time is critical in conservation and management planning, especially for wide-ranging species in northern latitudes where habitats are becoming increasingly fragmented. Wolverines (Gulo gulo) share similar life history traits observed in large-sized carnivores, and their low resiliency to disturbances limits wolverine persistence in modified or fragmented landscapes - making them a good indicator species for habitat connectivity. In this thesis, I used neutral microsatellite and mitochondrial DNA markers to investigate genetic connectivity patterns of wolverines for different temporal and spatial scales. Population genetic analyses of individuals from North America suggested wolverines west of James Bay in Canada are structured into two contemporary genetic clusters: an extant cluster at the eastern periphery of Manitoba and Ontario, and a northwestern core cluster. Haplotypic composition, however, suggested longstanding differences between the extant eastern periphery and northwestern core clusters. Phylogeographic analyses across the wolverine's Holarctic distribution supported a postglacial expansion from a glacial refugium near Beringia. Although Approximate Bayesian computations suggested a west-to-east stepping-stone divergence pattern across North America, a mismatch distribution indicated a historic bottleneck event approximately 400 generations ago likely influenced present-day patterns of haplotype distribution. I also used an individual-based genetic distance measure to identify landscape features potentially influencing pairwise genetic distances of wolverines in Manitoba and Ontario. Road density and mean spring snow cover were positively associated with genetic distances. Road density was associated with female genetic distance, while spring snow cover variance was associated with male genetic distance. My findings suggest that northward expanding anthropogenic disturbances have the potential to affect genetic connectivity. Overall, my findings suggest that (1) peripheral populations can harbour genetic variants not observed in core populations - increasing species genetic diversity; (2) historic bottlenecks can alter the genetic signature of glacial refugia, resulting in a disjunct distribution of unique genetic variants among contemporary populations; (3) increased temporal resolution of the individual-based genetic distance measure can help identify landscape features associated with genetic connectivity within a population, which may disrupt landscape connectivity. Author Keywords: conservation genetics, Holarctic species, landscape genetics, peripheral population, phylogeography, wolverine
In situ measurements of trace metal species in the Athabasca and Mackenzie Rivers using diffusive gradient in thin films (DGT) devices
This study assesses the bioavailable metal (Cu, Ni, Zn, Pb) species in the Athabasca-Mackenzie watersheds using diffusive gradient in thin films (DGT) devices. Metal toxicity is not only based on the concentration of metal in natural waters, but also on the nature of metal species. Four main forms in aquatic systems are: free ion, inorganic species, DOM bound (humic) species and metal colloidal species. The free ion and inorganic species and very small humic species are known as DGT-labile species and, are considered to be more bioavailable to micro-organisms due to the size and thus may be toxic to microorganisms. In this study, DGT devices were applied to (1) monitor the DGT-labile metal species in the lower Athabasca River and the Mackenzie River watershed and (2) assess the DGT-labile metal concentrations on temporal and spatial scales. In the lower Athabasca River, comparison between the DGT results and the Windermere Humic Acid Model (WHAM) calculation indicated good agreements for all metals when the precipitated iron(III) hydroxide was assumed as an active binding surface. No significant variations in labile species were found over 2003-2012 (RAMP database) despite the development of oil sands. In the Mackenzie River, no significant difference in DGT-labile metal concentrations and DOC concentrations was found in yearly basis 2012-2014. Only DOC was lower in August (6.98 and 3.85 ppm, respectively; p< 0.05) due to dilution from heavy rain events. Spatially, DGT-labile Cu and Ni in the downstream Mackenzie River were higher than upstream (1.79 and 0.58 ppb for Cu, 1.68 and 0.77 ppb for Ni, 4.06 and 6.91 ppm for DOC; p < 0.05). Overall the in situ measurements of metals constitute a benchmark for future studies in water quality and be helpful in environmental management in Alberta and the Northwest Territories in Canada. Author Keywords: Athabasca River, DGT, Mackenzie River, Speciation, Trace Metal, WHAM
Novel Silica Sol-Gel Passive Sampler for Mercury Monitoring in Aqueous Systems
A novel passive sampler for mercury monitoring was prepared using organosilica sol-gel materials. It comprises a binding layer with thiol groups for mercury complexation and a porous diffusive layer through which mercury can diffuse and arrive at the binding layer. Our study demonstrated that this new sampler follows the principle of passive sampling. The mass of mercury accumulated in the binding layer depends linearly on the mercury concentration in solution, the sampling rate and the exposure time. A typical sol-gel sampler is characterized by a diffusive layer of 1.2 &mum, in which mercury ions diffuse with a coefficient of D = 0.09~10-6 cm2/s. The capacity for mercury uptake is approximately 0.64 &mug/cm2. Mercury diffusion and binding in the passive sampler are independent of the type of mercury-chloride complex. Its sampling rate increases with increasing water turbulence and decreases with increasing DOM amount. The field trial of sol-gel sampler in Miller Creek shows the concentration gained from the sol-gel passive sampler is slightly lower than that from the spot sampling. Author Keywords:
evolutionary ecology of Alaska's mountain goats with management implications
The integration of genetic and environmental information can help wildlife managers better understand the factors affecting a species’ population structure and their response to disturbance. This thesis uses genetic techniques to assess the broad and fine scale population structure of mountain goats in Alaska. The first chapter aims to determine the number of genetically distinct subpopulations and model the demographic history of mountain goats in Alaska. The second chapter investigates the population structure and demographic history of mountain goats in Glacier Bay National Park and examines the impact that climate change will have on these mountain goats. My results indicate that Alaska has eight subpopulations which diverged during the Wisconsin glaciation. In Glacier Bay, population structure is reflective of the landscape during colonization, and mountain goat population density and movement corridors are likely to decline due to future climate change. Author Keywords: Alaska, biogeography, gene flow, landscape genetics, mountain goat, population genetic structure
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
Electrochemical Characterization of Giardia Intestinalis Cytochromes b5
Giardia intestinalis is a protozoan parasite that causes waterborne diarrheal disease in animals and humans. It is an unusual eukaryote as it lacks the capacity for heme biosynthesis; nonetheless it encodes heme proteins, including three cytochrome b5 isotypes (gCYTB5s) of similar size. Homology modelling of their structures predicts increased heme pocket polarity compared to mammalian isotypes, which would favour the oxidized state and lower their reduction potentials (E°’). This was confirmed by spectroelectrochemical experiments, which measured E°’ of -171 mV, -140 mV and -157 mV for gCYTB5-I, II, III respectively, compared to +7 mV for bovine microsomal cytochrome b5. To explore the influence of heme pocket polarity in more detail, five gCYTB5-I mutants in which polar residues were replaced by nonpolar residues at one of three positions were investigated. While these substitutions all increased the reduction potential, replacement of a conserved tyrosine residue at position-61 with phenylalanine had the most significant effect, raising E°’ by 106 mV. This tyrosine residue occurs in all gCYTB5s and is likely the greatest contributor to their low reduction potentials. Finally, complementary substitutions were made into a bovine microsomal cytochrome b5 triple mutant to lower its reduction potential. These not only lowered the E°’ by more than 140 mV but also weakened the interaction of heme with the protein. The lower reduction potentials of the gCYTB5s may indicate that these proteins have different roles from their more well-known mammalian counterparts. Author Keywords:
Fish and invertebrate use of invasive Phragmites in a Great Lakes freshwater delta
Invasive Phragmites australis ssp. australis (herein “Phragmites”) has established and rapidly spread throughout many coastal areas of the Great Lakes. Known to displace native vegetation communities as it forms large, monotypic stands, Phragmites has a bad reputation when it comes to losses of biodiversity and habitat provision for wildlife. However, the extent to which Phragmites provides habitat for fish and invertebrates in coastal freshwater wetlands remains relatively unquantified. Thus, this study assessed whether fish assemblages and invertebrate communities in stands of Phragmites differ from those in stands of two native emergent vegetation communities, Typha spp. and Schoenoplectus spp. The findings showed significant differences in habitat variables among the vegetation communities in terms of water depth, macrophyte species richness, stem density and water quality. While abundance of the functional feeding group filterer-collectors was found to be significantly less in stands of Phragmites when compared to Schoenoplectus, no difference was observed in invertebrate taxa richness among vegetation communities. Lastly, no difference in fish assemblage or invertebrate community was detected when using multivariate analyses, implying that invasive Phragmites provides habitat that appears to be as valuable for fish and invertebrates as other emergent vegetation types in the St. Clair River Delta. The findings of this study will ultimately benefit the literature on invasive Phragmites and its role as fish habitat in freshwater wetlands, and aid management agencies in decisions regarding control of the invasive species. Author Keywords: aquatic invasive species, aquatic macroinvertebrates, freshwater fish, freshwater wetlands, nMDS, Phragmites
Comparison of the Optical Properties of Stratiotes aloids and the Local Plant Community
As part of a mandate to control the spread of Stratiotes aloides (WS; water soldier) in the Trent Severn Waterway, the Ministry of Natural Resources (MNR) created a management plan to eradicate WS. However, one of the biggest challenges in eradicating WS or any invasive aquatic plant is the ability to estimate the extent of its spread and detect new populations. While current detection methods can provide acceptable detection, these methods often require extensive time and effort. The purpose of this thesis was to assess the use optical properties of WS and WS exudates for detection, in order to improve on current detection methods. The optical properties of WS were sampled at three different sites during three different seasons (spring, summer, and fall) by a) randomly sampling tissue from WS and the local plant community at each site, and recording the reflectance properties in a laboratory setting b) collecting dissolved organic matter (DOM) samples from plant incubations and river water in the field. Significant differences in the reflectance properties of WS were observed among samples from different sites and different sampling times; however, changes in fluorescence properties were only seasonal. Despite spatial differences in WS reflectance; WS was detectable using both hyperspectral and multispectral reflectance. When hyperspectral reflectance was used, significant differences between WS and the local plant community were found in June using two bands (i.e. bands 525 and 535, R 2 = 0.46 and 0.48, respectively). Whereas multispectral reflectance was significant different in October using the coastal and blue band. While WS produced a unique signal using both reflectance types, multispectral reflectance had a greater potential for detection. Its greater potential for detection was due to the reduced noise produced by background optical properties in October in comparison to June. DOM derived from WS was also characterized and compared with whole-river DOM samples in order to find unique markers for WS exudates in river samples. While similarities in DOM concentrations of WS exudates to Trent River water limited the ability to detect WS using compositional data, the ratio of C4/C5 components were compared in order to find components that were proportionally similar. Based on the results of this study multispectral and fluorescence techniques are better suited for the detection of a unique WS signature. The results derived from this work are intended to have practical applications in plant management and monitoring, DOM tracing, as well as remote sensing. Author Keywords: Dissolved organic matter, Hyperspectral reflectance, Invasive species management, Multispectral reflectance, PARAFAC, Stratiotes aloides
Proximal Soil Nutrient Sensing in Croplands through Multispectral Imaging from Unmanned Aerial Vehicles (UAV) for Precision Agriculture Applications
Currently, UAVs are deployed to measure crop health in a timely manner by mapping vegetation indices. A study using two different fields was conducted in order to search for a relationship that may exist between crop health and soil fertility. A UAV equipped with sensor technology was used for mapping of vegetation indices which were then statistically compared to soil nutrient data collected via soil sampling. Elevation data was also collected which was then statistically compared to soil nutrients as well as crop health. Results of this study were unfortunately impacted by variables outside of the researcher’s control. Moisture became the greatest limiting factor in 2016 followed by an excess of rain in 2017. Results did not show any promising correlations as moisture uncontrollably became the defining variable. Further research in a more controlled setting will need to be conducted in order to explore this potential relationship. Author Keywords: Agriculture, Multispectral Imagery, Precision Agriculture, Proximal Soil Sensing, Remote Sensing, Unmanned Aerial Vehicle
Scarring, sex assignment, and sex-specific sociality of Indo-Pacific humpback dolphins (Sousa chinensis) in the Pearl River Estuary and eastern Taiwan Strait
The Pearl River Estuary (PRE) and eastern Taiwan Strait (ETS) populations of Indo-Pacific humpback dolphins (Sousa chinensis) contain ~600 and 100 catalogued individuals, respectively. Population demography is important for conservation actions but few animals have been sexed by conventional methods. Longitudinal analysis of tooth-rake scars on dorsal fins showed scars disappear within 7 months; sexing adults by scarring is likely not impacted by juvenile scarring. Using dorsal fin photographs, sex assigned for 87% of catalogued PRE adults (n=300) and for 93% of ETS adults (n=60), using scars hypothesized from male-male competition, was in concordance with sex assigned by DNA, calf association, and ventral photographs. Scarring was higher in presumed males than females and in PRE females than ETS females. Female:male sex ratios were 3:2 (PRE) and 2:1 (ETS), though this likely results from biases in photo-identification methods. Social analysis with presumed sexes showed strong female-female associations in both populations but stronger female-male and male-male associations in PRE. These results support sex differentiation by scarring, which was a non-invasive approach, and sex assignment for many PRE and ETS individuals. Author Keywords: Indo-Pacific humpback dolphins, photo-identification, scarring, sex differentiation, sexes, social structure
Population Genetics and Gut Microbiome Composition Reveal Subdivisions and Space Use in a Generalist and Specialist Ungulate
Natural populations are often difficult and costly to study, due to the plethora of confounding processes and variables present. This is of particular importance when dealing with managed species. Ungulates, for example, act as both consumers and prey sources; they also provide economic benefit through harvest, and as such, are of high ecological and economic value. I addressed conservation and management concerns by quantifying subdivision in wild populations and combined movement with non-invasive sampling to provide novel insight on the physiological drivers of space use in multiple species. This thesis explored biological patterns in ungulates using two distinct approaches: the first used molecular genetics to quantify gene flow, while the second examined the relationship between movement and the gut microbiome using high-throughput sequencing and GPS tracking. The goal of the first chapter was to quantify gene flow and assess the population structure of mountain goats (Oreamnos americanus) in northern British Columbia (BC) to inform management. I used microsatellites to generate genotype data and used a landscape genetics framework to evaluate the possible drivers behind genetic differentiation. The same analyses were performed at both a broad and fine scale, assessing genetic differentiation between populations in all of northern BC and in a case management study area northeast of Smithers BC. The results indicated panmixia among mountain goats regardless of scale, suggesting distance and landscape resistance were minimally inhibiting gene flow. Therefore, management at local scales can continue with little need for genetically informed boundaries, but regulations should be tailored to specific regions incorporating data on local access and harvest pressure. My second chapter aimed to determine the extent to which the gut microbiome drives space-use patterns in a specialist (mountain goat) and generalist (white-tailed deer, Odocoileus virginianus) ungulate. Using fecal samples, we generated genomic data using 16S rRNA high-throughput sequencing to evaluate gut diversity and gut microbiome characteristics. Additionally, individuals were fitted with GPS collars so that we could gain insight into movement patterns. Gut microbiome metrics were stronger predictors of space use and movement patterns with respect to home range size, whereas they were weaker predictors of habitat use. Notably, factors of both the gut microbiome and age of a given species were correlated with changes in space use and habitat use. Ultimately, this research linked high-throughput sequencing and GPS data to better understand ecological processes in wild ungulates. Author Keywords: gene flow, genomics, gut microbiome, home range, population genetic structure, ungulates

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