Graduate Theses & Dissertations

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Genomic architecture of artificially and sexually selected traits in white-tailed deer (Odocoileus virginianus)
Understanding the complex genomic architecture underlying quantitative traits can provide valuable insight for the conservation and management of wildlife. Despite improvements in sequencing technologies, few empirical studies have identified quantitative trait loci (QTL) via whole genome sequencing in free-ranging mammal populations outside a few well-studied systems. This thesis uses high-depth whole genome pooled re-sequencing to characterize the molecular basis of the natural variation observed in two sexually selected, heritable traits in white-tailed deer (Odocoileus virginianus, WTD). Specifically, sampled individuals representing the phenotypic extremes from an island population of WTD for antler and body size traits. Our results showed a largely homogenous genome between extreme phenotypes for each trait, with many highly differentiated regions throughout the genome, indicative of a quantitative model for polygenic traits. We identified and validated several potential QTL of putatively small-to-moderate effect for each trait, and discuss the potential for real-world application to conservation and management. Author Keywords: evolution, extreme phenotypes, genetics, genomics, quantitative traits, sexual selection
Assessment of an adult lake sturgeon translocation (Acipenser fulvescens) reintroduction effort in a fragmented river system
North American freshwater fishes are declining rapidly due to habitat fragmentation, degradation, and loss. In some cases, translocations can be used to reverse local extirpations by releasing species in suitable habitats that are no longer naturally accessible. Lake sturgeon (Acipenser fulvescens) experienced historical overharvest across their distribution, leading to endangered species listings and subsequent protection and recovery efforts. Despite harvest and habitat protections, many populations do not appear to be recovering, which has been attributed to habitat alteration and fragmentation by dams. In 2002, 51 adult lake sturgeon from the Mattagami River, Ontario, Canada were translocated 340 km upstream to a fragmented 35 km stretch of the river between two hydroelectric generating stations, where sturgeon were considered extirpated. This study assessed the translocation effort using telemetry (movement), demographics and genetic data. Within the first year, a portion of the radio-tagged translocated individuals dispersed out of the release area, and released radio-tagged individuals used different areas than individuals radio-tagged ten years later. Catches of juvenile lake sturgeon have increased over time, with 150 juveniles caught within the duration of this study. The reintroduced population had similar genetic diversity as the source population, with a marked reduction in effective population size (Ne). The results indicate that the reintroduction effort was successful, with evidence of successful spawning and the presence of juvenile lake sturgeon within the reintroduction site. Overall, the results suggest adult translocations may be a useful tool for re-establishing other extirpated lake sturgeon populations. Author Keywords: conservation, endangered species, lake sturgeon, reintroduction, telemetry, translocation
De novo transcriptome assembly, functional annotation, and SNP discovery in North American flying squirrels (genus Glaucomys)
Introgressive hybridization between northern (Glaucomys sabrinus) and southern flying squirrels (G. volans) has been observed in some areas of Canada and the USA. However, existing molecular markers lack the resolution to discriminate late-generation introgressants and describe the extent to which hybridization influences the Glaucomys gene pool. I report the first North American flying squirrel (genus Glaucomys) functionally annotated de novo transcriptome assembly with a set of 146,621 high-quality, annotated putative species-diagnostic SNP markers. RNA-sequences were obtained from two northern flying squirrels and two southern flying squirrels sampled from Ontario, Canada. I reconstructed 702,228 Glaucomys transcripts using 193,323,120 sequence read-pairs, and captured sequence homologies, protein domains, and gene function classifications. These genomic resources can be used to increase the resolution of molecular techniques used to examine the dynamics of the Glaucomys hybrid zone. Author Keywords: annotation, de novo transcriptome, flying squirrels, high-throughput sequencing, hybridization, single nucleotide polymorphisms
Assessing the population genetic structure of the endangered Cucumber tree (Magnolia acuminata) in southwestern Ontario using nuclear and chloroplast genetic markers.
Magnolia acuminata (Cucumber tree) is the only native Magnolia in Canada, where it is both federally and provincially listed as endangered.Magnolia acuminata in Canada can be found inhabiting pockets of Carolinian forest within Norfolk and Niagara regions of southwestern Ontario. Using a combination of nuclear and chloroplast markers, this study assessed the genetic diversity and differentiation of M. acuminata in Canada, compared to samples from the core distribution of this species across the United States. Analyses revealed evidence of barriers to dispersal and gene flow among Ontario populations, although genetic diversity remains high and is in fact comparable to levels of diversity estimated across the much broader range of M. acuminata in the USA. When examining temporal differences in genetic diversity, our study found that seedlings were far fewer than mature trees in Ontario, and in one site in particular, diversity was lower in seedlings than that of the adult trees. This study raises concern regarding the future viability of M. acuminata in Ontario, and conservation managers should factor in the need to maintain genetic diversity in young trees for the long-term sustainability of M. acuminata in Ontario. Author Keywords: conservation genetics, cpDNA, forest fragmentation, Magnolia acuminata, microsatellites, population genetic structure
Using environmental DNA (eDNA) metabarcoding to assess aquatic plant communities
Environmental DNA (eDNA) metabarcoding targets sequences with interspecific variation that can be amplified using universal primers allowing simultaneous detection of multiple species from environmental samples. I developed novel primers for three barcodes commonly used to identify plant species, and compared amplification success for aquatic plant DNA against pre-existing primers. Control eDNA samples of 45 plant species showed that species-level identification was highest for novel matK and preexisting ITS2 primers (42% each); remaining primers each identified between 24% and 33% of species. Novel matK, rbcL, and pre-existing ITS2 primers combined identified 88% of aquatic species. The novel matK primers identified the largest number of species from eDNA collected from the Black River, Ontario; 21 aquatic plant species were identified using all primers. This study showed that eDNA metabarcoding allows for simultaneous detection of aquatic plants including invasive species and species-at-risk, thereby providing a biodiversity assessment tool with a variety of applications. Author Keywords: aquatic plants, biodiversity, bioinformatics, environmental DNA (eDNA), high-throughput sequencing, metabarcoding
Detection of four at-risk freshwater pearly mussel species (Bivalvia
Environmental DNA (eDNA) detection uses species-specific markers to screen DNA from bulk samples, such as water, to infer species presence. This study involved the development and testing of species-specific markers for four freshwater pearly mussels (Unionidae). The markers were applied to water samples from intensively sampled mussel monitoring sites to compare species detections from eDNA with established sampling method detections. Target species were detected using eDNA at all sites where they had previously been detected by quadrat sampling. This paired design demonstrated that eDNA detection was at least as sensitive as quadrat sampling and that high species specificity can be achieved even when designing against many sympatric unionids. Detection failures can impede species conservation efforts and occupancy estimates; eDNA sampling could improve our knowledge of species distributions and site occupancy through increased sampling sensitivity and coverage. Author Keywords: conservation genetics, cytochrome oxidase subunit I (COI), environmental DNA (eDNA), quantitative PCR (qPCR), species at risk (SAR)
Demographic history and conservation genomics of caribou (Rangifer tarandus) in Québec
Genetic variation is the raw material and basis for evolutionary changes in nature. The loss of genetic diversity is a challenge many species are facing, with genomics being a potential tool to inform and prioritize decision making. Whole genome analysis can be an asset to conservation biology and the management of species through the generation of more precise and novel metrics. This thesis uses whole genome re-sequencing to characterize the demographic history and quantify genomic metrics relevant to conservation of caribou (Rangifer tarandus) in Québec, Canada. We calculated the ancestral and contemporary patterns of genomic diversity of five representative caribou populations and applied a comparative population genomics framework to assess the interplay between demographic events and genomic diversity. When compared to the census size, NC, the endangered Gaspésie Mountain caribou population had the highest ancestral Ne:NC ratio which is consistent with recent work suggesting high ancestral Ne:NC is of conservation concern. These ratios were highly correlated with genomic signatures (i.e. Tajima’s D) of recent population declines and explicit demographic model parameters. Values of contemporary Ne, estimated from linkage-disequilibrium showed Gaspêsie having among the highest contemporary Ne:NC ratio. Importantly, classic conservation genetics theory would predict this population to be of less concern based off this metric alone. Inbreeding measures suggested nuanced patterns of inbreeding and correlated to the demographic models. This study suggests that while the Québec populations are all under decline, they harbour enough ancestral genetic variation to replenish any lost diversity, if conservation decisions are made in favour of these populations, specifically supporting NC. Author Keywords:
Genetic Networks to Investigate Structure and Connectivity of Caribou at Multiple Spatial and Temporal Scales
Understanding genetic structure, connectivity, and movement of a species iscritical to management and conservation. Genetic network approaches allow the analysis of genetic information with flexibility and few prior assumptions. In chapter one, I tested the ability of individual-based genetic networks to detect fine-scale structure and connectivity in relation to sampling efforts. My findings revealed individual-based genetic networks can detect fine-scale genetic structure of caribou when using 15 highly variable microsatellite loci. Sampling levels less than 50% of the estimated population size resulted in highly disconnected networks which did not allow for accurate structure analysis; however community detection algorithms were robust in grouping closely related individuals despite low sampling. In chapter two, I used individual-based and population-based genetic networks to investigate structure, connectivity, and movement of caribou across a large study area in Western Canada. A community detection algorithm partitioned the population-based genetic network at multiple spatial scales which uncovered patterns of hierarchical genetic structure and highlighted patterns of gene flow. The hierarchical population structure results aligned with the known distribution of different caribou Designatable Units (DUs) and additional structure was found within each DU. Furthermore, individual-based networks that were constructed with a subset of samples from the Mackenzie Mountains region of the Northwest Territories revealed patterns of long-distance movement and high connectivity across the region. Author Keywords: Biological Conservation, Caribou, Community Detection, Connectivity, Genetic Networks, Structure
Reproductive Fitness of Smallmouth Bass (Micropterus dolomieu) Under Heterogeneous Environmental Conditions
Identifying the biotic and abiotic factors that influence individual reproductive fitness under natural conditions is essential for understanding important aspects of a species’ evolutionary biology and ecology, population dynamics, and life-history evolution. Using next generation sequencing technology, I developed five microsatellite multiplex reactions suitable for conducting large scale parentage analysis of smallmouth bass, Micropterus dolomieu, and used molecular pedigree reconstruction techniques to characterize the genetic mating system and mate selection in adult smallmouth bass nesting in Lake Opeongo, Ontario, Canada. I used multivariate spatial autocorrelation analysis to indirectly infer the occurrence and extent of natal philopatry among spawning adults, to assess the strength and direction of sex-bias in natal dispersal patterns, and to evaluate the degree of nest site fidelity and breeding dispersal of spawning adults. I also evaluated how differences in littoral zone water temperature caused by wind-induced seiche events influence the relative reproductive success of spawning adults. Lastly, I provide a synopsis of potential future research aimed at further exploring factors that influence the reproductive fitness of smallmouth bass in Lake Opeongo. This information will contribute to our understanding of the factors regulating smallmouth bass populations, and provide insight into the factors controlling the variance in individual reproductive success and thus recruitment dynamics in this species. Author Keywords: Dispersal, Fitness, Mate selection, Mating systems, Philopatry
Frog Virus 3
Understanding the maintenance and spread of invasive diseases is critical in evaluating threats to biodiversity and how to best minimize their impact, which can by done by monitoring disease occurrences across time and space. I sought to apply existing and upcoming molecular tools to assess fluctuations in both presence and strain variation of frog virus 3 (FV3), a species of Ranavirus, across Canadian waterbodies. I explored the temporal patterns and spatial distribution of ranavirus presence across multiple months and seasons using environmental DNA techniques. Results indicate that ranavirus was present in approximately 72.5% of waterbodies sampled on a fine geographical scale (<10km between sites, 7,150 km2), with higher detection rates in later summer months than earlier. I then explored the sequence variability at the major capsid protein gene (MCP) and putative virulence gene (vIF-2α) of FV3 samples from Ontario, Alberta, and the Northwest Territories, with the premise of understanding pathogen movement across the landscape. However, a lack of genetic diversity was found across regions, likely due to a lack of informative variation at the chosen genetic markers or lack of mutation. Instead, I found a novel FV3-like ranavirus and evidence for a recombinant between FV3 and a ranavirus of another lineage. This thesis provides a deeper understanding into the spatio-temporal distribution of FV3, with an idea of how widespread and threatening ranaviruses are to amphibian diversity. Keywords: ranavirus, frog virus 3, amphibians, environmental DNA, phylogenetics, wildlife disease, disease surveillance, major capsid protein, vIF-2α Author Keywords: amphibians, environmental DNA, frog virus 3, phylogenetics, ranavirus, wildlife disease
Islands, ungulates, and ice
Central to wildlife conservation and management is the need for refined, spatially explicit knowledge on the diversity and distribution of species and the factors that drive those patterns. This is especially vital as anthropogenic disturbance threatens rapid large-scale change, even in the most remote areas of the planet. My dissertation examines theinfluence of land- and sea-scape heterogeneity on patterns of genetic differentiation, diversity, and broad-scale distributions of island-dwelling ungulates in the Arctic Archipelago. First, I investigated genetic differentiation among island populations of Peary caribou (Rangifer tarandus pearyi) in contrast to continental migratory caribou (Rangifer tarandus) and evaluated whether genetic exchange among Peary caribou island populations was limited by the availability of sea ice – both now and in the future. Differentiation among both groups was best explained by geodesic distance, revealing sea ice as an effective platform for Peary caribou movement and gene flow. With future climate warming, substantial reductions in sea ice extent were forecast which significantly increased resistance to caribou movement, particularly in summer and fall. Second, I assessed genetic population structure and diversity of northern caribou and deciphered how Island Biogeography Theory (IBT) and Central Marginal Hypothesis (CMH) could act in an archipelago where isolation is highly variable due to the dynamics of sea ice. Genetic differentiation among continental and island populations was low to moderate. In keeping with IBT and CMH, island-dwelling caribou displayed lower genetic diversity compared to mainland and mainland migratory herds; the size of islands (or population range) positively influenced genetic diversity, while distance-to-mainland and fall ice-free coastlines negatively influenced genetic diversity. Hierarchical structure analysis revealed multiple units of caribou diversity below the species level. Third, I shifted my focus to the terrestrial landscape and explored the elements governing species-environment relationships. Using species distribution models, I tested the response of caribou and muskoxen to abiotic versus abiotic + biotic predictors, and included distance to heterospecifics as a proxy for competitive interactions. Models that included biotic predictors outperformed models with abiotic predictors alone, and biotic predictors were most important when identifying habitat suitability for both ungulates. Further, areas of high habitat suitability for caribou and muskoxen were largely disjunct, limited in extent, and mainly outside protected areas. Finally, I modelled functional connectivity for two genetically and spatially disjunct groups of island-dwelling caribou. For High Arctic caribou, natural and anthropogenic features impeded gene flow (isolation-by-resistance); for Baffin Island caribou we found panmixia with absence of isolation-by-distance. Overall, my dissertation demonstrates the varying influences of contemporary land- and sea-scape heterogeneity on the distribution, diversity and differentiation of Arctic ungulates and it highlights the vulnerability of island-dwelling caribou to a rapidly changing Arctic environment. Author Keywords: Circuitscape, connectivity, Island Biogeography, landscape genetics, population structure, species distribution models
Assessing Molecular and Ecological Differentiation in Wild Carnivores
Wild populations are notoriously difficult to study due to confounding stochastic variables. This thesis tackles two components of investigating wild populations. The first examines the use of niche modeling to quantify macro-scale predator-prey relationships in canid populations across eastern North America, while the second examines range-wide molecular structure in Canada lynx. The goal of the first chapter is to quantify niche characteristics in a Canis hybrid zone of C. lupus, C. lycaon, and C. latrans to better understand the ecological differentiation of these species, and to assess the impacts of incorporating biotic interactions into species distribution models. The goal of the second chapter is to determine if DNA methylation, an epigenetic marker that modifies the structure of DNA, can be used to differentiate populations, and might be a signature of local adaptation. Our results indicated that canids across the hybrid zone in eastern North America exhibit low levels of genetic and ecological differentiation, and that the importance of biotic interactions are largely lost at large spatial scales. We also identified cryptic structure in methylation patterns in Canada lynx populations, which suggest signatures of local adaptation, and indicate the utility of DNA methylation as a marker for investigating adaptive divergence. Author Keywords: Ecological Epigenetics, Ecological Genetics, SDM

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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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