Graduate Theses & Dissertations

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Gene flow directionality and functional genetic variation among Ontario, Canada Ursus americanus populations.
Rapidly changing landscapes introduce challenges for wildlife management, particularly for large mammal populations with long generation times and extensive spatial requirements. Understanding how these populations interact with heterogeneous landscapes aids in predicting responses to further environmental change. In this thesis, I profile American black bears using microsatellite loci and pooled whole-genome sequencing. These data characterize gene flow directionality and functional genetic variation to understand patterns of dispersal and local adaptation; processes key to understanding vulnerability to environmental change. I show dispersal is positively density-dependent, male biased, and influenced by food productivity gradients suggestive of source-sink dynamics. Genomic comparison of bears inhabiting different climate and forest zones identified variation in genes related to the cellular response to starvation and cold. My thesis demonstrates source-sink dynamics and local adaption in black bears. Population management must balance dispersal to sustain declining populations against the risk of maladaptation under future scenarios of environmental change. Author Keywords: American black bear, Dispersal, Functional Genetic Variation, Gene Flow Directionality, Genomics, Local Adaptation
Nutrigenomics of Daphnia
Organismal nutrition lies at the interface between biotic and abiotic factors in an ecosystem, dictating the transfer of energy and nutrients across trophic levels. Our ability to detect nutritional limitation in consumers is reliant on a priori knowledge of dietary history due to our inability to differentiate nutrient stress based on body-wide responses. Molecular physiological responses are increasingly being used to measure physiological stress with high levels of specificity due to the specific modes of action ecological stressors have on organismal molecular physiology. Because animal consumers respond to varying nutrient supplies by up- and down-regulating nutrient-specific metabolic pathways, we can quantify nutritional status by quantifying the expression of those pathways. Here I present an investigation into the use of transcriptomics to detect nutritional stress in the keystone aquatic herbivore, Daphnia pulex, I use RNAseq and quantitative PCR (qPCR) identify nutritional indicator genes. I found that nutritional status could be determined with 100% accuracy with just ten genes. Additionally, the functional annotation of those genes uncovered previously unidentified responses to dietary stress. Further testing and validation of the selected indicator genes is required however these findings have the potential to revolutionize our ability to measure and monitor consumer nutritional stress. Author Keywords: Biomarkers, Daphnia, Gene expression, Nutrigenomics, Nutritional ecology, RNAseq
Expression of Giardia intestinalis flavoenzyme GiOR-1 and characterization of its electron transfer properties
Giardia intestinalis possesses four isotypes of cytochrome b5 (gCYTB-I-IV) that differ from their mammalian counterparts, suggesting different functions in this protozoan parasite. Although the recently discovered Giardia flavoenzyme, GiOR-1, reduces these cytochromes, its properties have not been thoroughly studied, owing to the difficulty in its expression. Here I describe successful conditions for expression of GiOR-1 using autoinduction. GiOR-1 is obtained with flavins bound as indicated by its UV-visible spectrum. Its ability to catalyze electron transfer from donors (NADH, NADPH) to acceptors (oxygen, ferricyanide, cytochrome c, gCYTB5-III) were studied in spectrophotometric rate assays. NADPH is the preferred electron donor, while cytochromes are the preferred electron acceptors. Interestingly, the His-tag used to purify gCYTB5-III decreases its reaction rate with GiOR-1, as an untagged version has slightly faster rates. These findings establish the appropriate conditions for further studies on GiOR-1, including the identification of endogenous electron acceptors. Author Keywords: Autoinduction, Cytochrome b5, Cytochrome P450 oxidoreductase, Giardia intestinalis, GiOR-1, Polyhistidine tag
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
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:
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
Characterizing the demographic history and prion protein gene variation to infer susceptibility to chronic wasting disease in a naïve population of white-tailed deer (Odocoileus virginianus)
Assessments of the adaptive potential of natural populations are essential for understanding and predicting responses to environmental stressors like climate change and infectious disease. The range of stressors species face in a human-dominated landscape, often have contrasting effects. White-tailed deer (Odocoileus virginianus, deer) are expanding in the northern part of their range following decreasing winter severity and increasing forage availability, caused by climate change. Chronic wasting disease (CWD), a prion disease affecting cervids, is likewise expanding and represents a major threat to deer and other cervids We obtained tissue samples from free-ranging deer across their native range in Ontario, Canada which has yet to detect CWD in wild populations of cervids. High throughput sequencing was used to assess neutral genomic variation and variation in the gene responsible for the protein that misfolds into prions when deer contract CWD, known as the PRNP gene. Neutral variation revealed a high number of rare alleles and no population structure, consistent with an expanding population of deer. Functional genetic variation revealed that the frequencies of variants associated to CWD susceptibility and disease progression were evenly distributed across the landscape and the frequencies were consistent with deer populations not infected with CWD. These findings suggest that an observable shift in PRNP allele frequencies likely coincides with the start of a novel CWD epidemic. Sustained surveillance of genomic and genetic variation can be a useful tool for CWD-free regions where deer are managed for ecological and economic benefits. Author Keywords: Canadian wildlife, population genetics, prion, PRNP, RADseq, ungulate
Range dynamics of two closely related felids
Species ranges are changing and the rate at which the climate is warming is faster than anything previously seen in the past, consequently species will need to adapt quickly, track the climate or perish. Cold adapted terrestrial species are the most vulnerable, because they are limited by the availability of land at the cold edge of their range. This means that many alpine, boreal and polar species essentially have nowhere to go as the climate warms. Habitat generalists are widely distributed across the globe and are highly adaptable to anthropogenic change. Our future biodiversity may only consist of several habitat generalists. The Canada lynx (Lynx canadensis) is a boreal species that has limited range expansion potential at the cold end of its range and its range has already contracted by 40%. The lynx has nowhere to go as climate warming progresses in this current century. Therefore, understanding the causes of its range contraction could enlighten us on conservation and management strategies that we might undertake as climate warms. My analyses indicated that the Canada lynx seems to have tracked the habitat that it is adapted to in more northern homogenous boreal forests and the bobcat (Lynx rufus), a habitat generalist, has simply replaced it in the south. Author Keywords: Anthropogenic Change, Competition, Connectivity, Lynx canadensis, Lynx rufus, Range change
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
Do birds of a feather flock together
Populations have long been delineated by physical barriers that appear to limit reproduction, yet increasingly genetic analysis reveal these delineations to be inaccurate. The eastern and mid-continent populations of sandhill cranes are expanding ranges which is leading to convergence and warrants investigation of the genetic structure between the two populations. Obtaining blood or tissue samples for population genetics analysis can be costly, logistically challenging, and may require permits as well as potential risk to the study species. Non-invasively collected genetic samples overcome these challenges, but present challenges in terms of obtaining high quality DNA for analysis. Therefore, methods that optimize the quality of non-invasive samples are necessary. In the following thesis, I examined factors affecting DNA quality and quantity obtained from shed feathers and examined population differentiation between eastern and mid-continent sandhill cranes. I found shed feathers are robust to environmental factors, but feather size should be prioritized to increase DNA quantity and quality. Further, I found little differentiation between eastern and mid-continent populations with evidence of high migration and isolation-by-distance. Thus, the two populations are not genetically discrete. I recommend future population models incorporate migration between populations to enhance our ability to successfully manage and reach conservation objectives. Author Keywords: feathers, genetic differentiation, non-invasive DNA, population genetics, population management, sandhill crane (Antigone canadensis)
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
Evaluation of silver nanoparticles (AgNPs) and anti-GD2-AgNP antibody-drug conjugates as novel neuroblastoma therapies
Neuroblastoma (NB) has one of the highest mortality rates in pediatric oncology due to relapsed and refractory disease. Current aggressive multi-modal treatments are inhibited by dose-limiting toxicities and are associated with late-effects and secondary malignancies, emphasizing the necessity for novel therapeutics. Uniquely, most NB cells highly express disialoganglioside (GD2) a cell surface glycolipid that can provide a target for tumour-specific delivery. This study demonstrates a comprehensive evaluation of silver nanoparticles (AgNPs) and the first preliminary evaluation of anti-GD2-AgNP antibody-drug conjugates (ADCs) against NB in vitro. This present study validates the potential for AgNPs as an anti-cancer agent against NB as AgNPs demonstrated preferential toxicity towards NB cells through metabolic inhibition and indicative morphological alterations, while a less tumorigenic cell line demonstrated resistance to AgNP treatment. Therefore, this work identified an AgNP cell-type-dependent cytotoxicity effect. Low conjugation efficiency of the anti-GD2 monoclonal antibody, 14.G2a, to NHS-activated AgNPs failed to exert greater toxicity than the AgNPs alone. Collectively, this thesis provides novel information regarding the anti-cancer effects of AgNPs against NB with recommendations for anti-GD2-AgNP ADCs. Author Keywords: ADC, Chemotherapy, GD2, Neuroblastoma, Silver nanoparticles

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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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2004 - 2024
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