Graduate Theses & Dissertations


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
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
Assessing Canada Lynx Dispersal Across an Elevation Barrier
Mountain ranges are often thought to restrict movement of wildlife, yet previous studies evaluating the role of the Rocky Mountains as a dispersal barrier for Canada lynx (Lynx canadensis) have been contradictory. Our study uses neutral microsatellite loci to evaluate the role of the Rocky Mountains as a barrier to gene flow for lynx. Although lynx exhibited low genetic differentiation, we detected a limited effect of the mountains. Furthermore, we inferred the role played by landscape variables in gene flow (genetic differentiation predicted by landscape resistance). Limited gene flow most strongly related to resistance from physical factors (low snow cover and elevation), rather than other topographic and ecological factors (high terrain roughness, low forest cover, low habitat suitability, and geographic distance). Structural connectivity was a relatively poor predictor of functional connectivity. Overall, the Rockies represent an area of reasonably high functional connectivity for lynx, with limited resistance to gene flow. Author Keywords: Canada lynx, connectivity, gene flow, genetic structure, landscape genetics, Rocky mountains
Investigating the regional variation in frequencies of the invasive hybrid cattail, Typha × glauca
Interspecific hybridization rates can vary depending on genomic compatibilities between progenitors, while subsequent hybrid spread can vary depending on hybrid performance and habitat availability for hybrid establishment and persistence. As a result, hybridization rates and hybrid frequencies can vary across regions of parental sympatry. In areas around the Laurentian Great Lakes, Typha × glauca is an invasive plant hybrid of native Typha latifolia and introduced Typha angustifolia. In areas of parental sympatry in Atlantic Canada and outside of North America, T. × glauca has been reported as either rare or non-existent. I investigated whether the low frequencies of hybrids documented in Nova Scotia, Atlantic Canada, are influenced by reproductive barriers that prevent hybrid formation or environmental factors (salinity) that reduce hybrid performance. I identified an abundance of hybrids in the Annapolis Valley (inland) and a scarcity of hybrids in coastal wetlands through preliminary site surveys throughout Nova Scotia. In Annapolis Valley populations, flowering times of progenitor species overlapped, indicating that asynchronous flowering times do not limit hybrid formation in this region. Viable progeny were created from interspecific crosses of T. latifolia and T. angustifolia from Nova Scotia, indicating that there are no genomic barriers to fertilization and germination of hybrid seeds. Typha × glauca germination in high salinity was significantly lower than that of T. latifolia, but there was no difference at lower salinities. Therefore, while germination of hybrid seeds may be impeded in the coastal wetlands where salinity is high, inland sites have lower salinity and thus an environment conducive to hybrid germination. However, I found that once established as seedlings, hybrids appear to have greater performance over T. latifolia across all salinities through higher ramet production. Moreover, I found that T. latifolia sourced from Ontario had reduced germination and lower survivorship in high salinities compared to T. latifolia sourced from Nova Scotia, which could indicate local adaptation by T. latifolia to increased salinity. These findings underline that interactions between environment and local progenitor lineages can influence the viability and the consequent distribution and abundance of hybrids. This, in turn, can help explain why hybrids demonstrate invasiveness in some areas of parental sympatry but remain largely absent from other areas. Author Keywords: flowering phenology, Hybridization, invasive species, physiology, pollen compatibility, salinity tolerance
Understanding the establishment of Typha spp. in North America using population genetics and common garden studies
There are three cattail (Typha) taxa in Canada: T. latifolia (native), T. angustifolia (introduced), and their hybrid T. x glauca. The latter is invasive in regions around the Laurentian Great Lakes, and I investigated the potential role that commercial suppliers may be playing in the introduction of non-native Typha by comparing genotypes of North American, European, and commercially available plants. I found that Ontario garden centres are importing both hybrids and non-native lineages of T. angustifolia into Canada, but was unable to identify the provenance of T. latifolia. I also investigated the possibility that the hybrid cattail leaf litter shade and leachate influences germination and early growth of the parental species of the hybrids. Using three common garden experiments, I found that T. x glauca leaf litter suppresses germination rates of the three taxa. In the early seedling growth experiment, plant performance varied by taxa, and for the competition experiment there were no intra- or interspecific competition or treatment effects on the performance of plants. Overall, my research identified a potential mechanism allowing T. x glauca to dominate wetlands, and also shows that non-native lineages are being introduced into Canada through commercial trade Author Keywords: Competition, Germination, Non-native lineages, Plant nurseries, Seedling Growth, Typha spp.
Phylogeography and Genetic Structuring of Moose (Alces alces) Populations in Ontario, Canada
Moose are an iconic species, known for their large size and impressive antlers. Eight subspecies are classified in circumpolar regions of the planet - four in North America. Two subspecies are similar in shape and size, the north-western moose (Alces alces andersoni) and the eastern moose (Alces alces americana). It was previously believed that these two subspecies meet in northern Ontario. Earlier genetic population studies used a small number of samples from Ontario, primarily in broad studies covering all of North America. A comprehensive genetic study of moose populations in Ontario has not previously been conducted. We examined the genetic diversity and population structure at 10 polymorphic loci using 776 samples from Ontario, as well as outgroups from representative populations – Manitoba/Cape Breton, representing A. a. andersoni, and New Brunswick/Nova Scotia, representing A. a. americana. Results indicated three genetic populations in the province, in north-western Ontario, north-eastern Ontario and south-central Ontario. RST values, compared against both FST and Jost’s D values for phylogenetic analyses, indicated no phylogenetic pattern which suggests no subspeciation present in the province. Population movement patterns in Ontario were studied. Gene flow was estimated using genetic and spatial data. Isolation by distance was only seen within the first distance class of 100 kilometres and then not seen again at further distances, indicating that moose display philopatry. There were very few migrants travelling across the province, with a greater number moving gradually north and west, towards better habitat and food sources. A forensic database in the form of an allele frequency table was created. Three loci showed very low levels of heterozygosity across all three populations. Probability of identity was calculated for the three populations and quantified. Samples with known geographic origins were run against the database to test for sensitivity, with identification of origin occurring at an accuracy level between 87 and 100%. Within Ontario, there are not two different subspecies, as previously believed, but two different populations of the same subspecies meeting in northern Ontario. The genetic data does not support previous research performed in Ontario. The sample sizes in our research also provide a more comprehensive view of the entire province not seen in any previous studies. The comprehensive research enabled the building of a reliable forensic database that can be used for both management and forensic purposes for the entire province. Author Keywords: Alces alces, Genetic Diversity, Moose, Ontario, Phylogeography, Subspecies
Time to adapt
To better understand species’ resilience to climate change and implement solutions, we must conserve environments that maintain standing adaptive genetic variation and the potential generation of new beneficial alleles. Coding trinucleotide repeats (cTNRs) providing high-pace adaptive capabilities via high rates of mutation are ideal targets for mitigating the decline of species at risk by characterizing adaptively significant populations. Ultimately, adaptive genetic information will inform the protection of biological diversity below the species level (i.e., “Evolutionarily Significant Units” or “ESUs”). This dissertation investigates cTNRs within candidate genes to determine their prevalence and influence under selection in North American mammals. First, I evaluated the potential for somatic mosaicism in Canada lynx (Lynx canadensis), and found that tissue-specific mosaicism does not confound cTNR genotyping success in lynx. Second, I assessed a selection of clock gene cTNRs across characterized mammals and found that these repeats are abundant and highly variable in length and purity. I also identified preliminary signatures of selection in 3 clock gene cTNRs in 3 pairs of congeneric North American mammal species, highlighting the importance of cTNRs for understanding the evolution and adaptation of wild populations. I further evaluated the influence of selection on the NR1D1 cTNR within Canada lynx sampled across Canada using environmental correlation, where I estimated the variation in NR1D1 cTNR alleles explained by environmental and spatial variables after removing the effects of neutral population structure. Although most variation was explained by neutral structure, environment and spatial patterns in eastern lynx populations significantly explained some of the variation in NR1D1 alleles. To examine the role of island populations in the generation and distribution of adaptive genetic variation, I used 14 neutral microsatellites and a dinucleotide repeat within a gene linked to mammalian body size, IGF-1, and found that both genetic drift and natural selection influence the observed genetic diversity of insular lynx. Finally, I estimated the divergence dates of peripheral lynx populations and made recommendations towards the conservation of Canada lynx; high levels of genetic differentiation coupled with post-glacial colonization histories and patterns of divergence at cTNR loci suggest at least 4 ESUs for Canada lynx across their range. Author Keywords: adaptation, Canada lynx, candidate genes, coding trinucleotide repeats, evolution, natural selection
Investigating Ecological Niche Differentiation Among Wild Candids Experiencing Hybridization in Eastern North America
Currently there are large areas of the North American landscape that are occupied by Canis spp. hybrids of several varieties, leading to the logical question as to the genetic structure and ecological function of Canis populations across the continent, and to what extent hybrids reflect contemporary landscapes. This study illustrated patterns of niche differentiation between parental canid species and their hybrids using individual high quality genetic profile and species distribution models to support the intermediate phenotype hypothesis. In general, hybrids demonstrated an intermediate habitat suitability compared to its parental species, across most environmental variables used. A similar trend was observed in the niche metric analysis, where we found that hybrids exhibit intermediate niche breadth, with eastern coyotes and eastern wolves exhibiting the broader and narrower niche, respectively. Our results demonstrate that the intermediate phenotype hypothesis is supported even at a large scale and when involving highly mobile large mammal species. Author Keywords: canid, ecological niche modelling, hybridization, intermediate phenotype, microsatellite genotype, niche differentiation
Natural antisense transcripts to nucleus-encoded mitochondrial genes are linked to Ustilago maydis teliospore dormancy
Ustilago maydis is a basidiomycete smut fungus and the causal agent of common smut of corn. Disease progression and fungal development in this pathogen occur in planta, terminating in the production of dormant teliospores. Dormant spores of many fungi are characterized by reduced metabolic activity, which is restored during spore germination. The transition out of dormancy requires the rapid translation of stored mRNAs, which may be stabilized through natural antisense transcript (NAT)-mediated mechanisms. Transcript analysis revealed that as-ssm1, a NAT to the mitochondrial seryl-tRNA synthetase (ssm1), is detected in the dormant teliospore and absent in haploid cells. Disruption of ssm1 leads to cell lysis, indicating it is essential for cellular viability. Presented data supports the hypothesis that as-ssm1 has a role in facilitating teliospore dormancy through stabilizing ssm1 transcripts, which reduces mitochondrial function. as-ssm1 expression during in planta development begins 10 days post-infection, coinciding with the first appearance of dormant teliospores. To assess the impact of as-ssm1 expression on cell division, virulence and mitochondrial function, as-ssm1 was ectopically expressed in haploid cells, leading to increased ssm1 transcript levels and the formation of double-stranded RNA. These expression mutants are characterized by attenuated growth rate, virulence, mitochondrial membrane potential and oxygen consumption. Together, these findings support a role for NATs in moderating mitochondrial function during the onset of teliospore dormancy. Author Keywords: Dormant teliospore, Mitochondria, mRNA stability, Natural antisense transcripts, Non-coding RNA, Ustilago maydis
Functional Genetic Diversity in American Mink (Neovison vison)
The release of domestic organisms to the wild is considered a threat to biodiversity because the introduction of domestic genes through interbreeding can negatively impact wild conspecifics via outbreeding and local extinction. In North America, captive American mink (Neovison vison) are frequently escaping into the wild, yet the impact of these events on the functional genetic diversity of wild mink populations is unclear. I characterized domestic and wild mink in Ontario at 17 trinucleotide microsatellites located in functional genes thought to be associated with traits affected by domestication. I found low functional genetic diversity, as only 4 of 17 genes were variable and of those four there was little evidence of allele frequency differences between domestic and wild mink. Using redundancy analysis and a spatial analysis of principal components on the four variable loci (AR, ATN1, IGF-1, and TOB1) I found no evidence to suggest domestic release events are affecting functional genetic diversity of free-ranging mink at the set of markers assessed. Author Keywords: American mink, domestication, functional gene, introgression, Neovison vison
Social discrimination by female polar bears (Ursus maritimus) when accompanied by dependent offspring during the ice-free season in southern and western Hudson Bay and James Bay
Polar bears are generally described as solitary, but features of their life cycles and habitats regularly necessitate interaction. Effective conspecific assessment, including accurate recognition and discrimination, likely confers benefits, especially to females accompanied by dependent young. Individuals in the Southern (SH) and Western (WH) Hudson Bay subpopulations are ideal for studying polar bear social behaviours because of the prolonged high densities of the ice-free season. First, I looked outside family groups to model their fine scale sociospatial organization on land. Capture locations were more likely to correspond to family groups when there were fewer neighbouring bears, when a greater proportion of neighbours were female, and when the focal individual and neighbours were significantly related. Second, I looked within the family group to assess offspring recognition. Of 288 offspring in 207 family groups captured in the SH subpopulation from 1999 through 2013, only one case of adoption (of a singleton) was observed. Author Keywords: Adoption, Kin Recognition, Logistic Regression, Maternity Analysis, Social Discrimination, Sociospatial
Development of genetic profiles for paternity analysis and individual identification of the North Atlantic right whale (Eubalaena glacialis)
The endangered North Atlantic right whale (Eubalaena glacialis) has been internationally protected from whaling since 1935 but recovery has been slow compared to the southern right whale (Eubalaena australis) due to anthropogenic mortalities and poor reproduction. Prey availability, genetic variability, and alleles of genes associated with reproductive dysfunction have been hypothesized to contribute to low calf production. The North Atlantic Right Whale DNA Bank and Database contains 1168 samples from 603 individuals. I added 115 new genetic profiles to the database which now contains profiles for 81% of individuals alive since 1980. Paternity assignments using these profiles resulted in 62% of sampled calves being assigned a father and only 38% of candidate males being assigned a paternity. This may suggest false exclusion due to genotyping errors or the existence of an unknown group of males. The use of the DNA database allowed for the identification of 10 deceased individuals which has implications for identifying cause of death and reducing mortalities. However, genetic identification is dependent on the time of post-mortem sample collection which influences DNA quantity and quality. An assessment for variations in methylenetetrahydrofolate reductase, a candidate gene associated with reproductive dysfunction, revealed six females heterozygous for a synonymous A/T variant in exon four which may influence reproductive success through changes in enzyme production, conformation or activity. Author Keywords: Eubalaena glacialis, Forensic Identification, Genetic Profiling, North Atlantic Right Whale, Paternity, Reproductive Dysfunction


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