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  • Differential Introgression Between the Northern and Southern Extents of the Lodgepole x Jack Pine Hybrid Zone Suggests Environmentally-driven Selection and Local Adaptation.

    Resource Type:
    Thesis
    Creator:
    Yaremchuk, Danya Daria
    Abstract:
    Lodgepole and jack pine form a mosaic hybrid zone in western Canada. Introgression occurs between lodgepole and jack pine through this hybrid zone by repeated backcrossing with advanced generation hybrid progeny. Using environmentally-associated SNPs identified by redundancy analyses, we examined patterns of introgression between the northern and southern extents of this hybrid zone to identify differential introgression. Through genomic cline analyses, we found extensive introgression of these SNPs through the hybrid zone. Twenty-eight SNPs had significantly different patterns of introgression between the northern and southern extents. Fine-scale patterns revealed several SNPs that were introgressing more frequently than expected, suggesting adaptive introgression. We found that adaptive introgression is occurring more frequently in the northern hybrid extent compared to the southern hybrid extent, suggesting different environmental pressures. Using gene annotations and major allele frequency maps, we identified evidence of differing environmental pressures resulting in putative local adaptation within this hybrid zone.
    Thesis Degree:
    Master of Science (M.Sc.)
    Thesis Degree Discipline:
    Biology
    Date Created:
    2023

  • Histone Arginine Methylation in the Freeze-tolerant Wood Frog, Rana sylvatica

    Resource Type:
    Thesis
    Creator:
    Naranjo Vera, Mairelys
    Abstract:
    The wood frog, Rana sylvatica, is well known for its freeze tolerance ability. To endure winter, frozen frogs switch to a hypometabolic state via transcriptional regulation. Histone methylation is known to play a crucial role in regulating gene transcription. However, histone arginine methylation or demethylation has not previously been studied in the context of freeze tolerance. This thesis presents the first characterization of arginine methylation in a freeze tolerant vertebrate. Overall, levels of protein arginine methyltransferases (PRMTs) and methylated histone residues showed differential regulation over the freeze/thaw-cycle in wood frog liver. All PRMTs and downstream targets showed no changes during freezing, but protein levels of targets associated with transcription activation were elevated during thaw in skeletal muscle. Differential levels of histone demethylases were found in both tissues among the experimental conditions. These results indicate a role for histone methylation in supporting metabolic rate depression and tissue homeostasis during freezing.
    Thesis Degree:
    Master of Science (M.Sc.)
    Thesis Degree Discipline:
    Biology
    Date Created:
    2022

  • Application of Genomics-Based Methodologies in Genetic Toxicology to Advance In Vitro Chemical Assessment

    Resource Type:
    Thesis
    Creator:
    Cho, Eunnara
    Abstract:
    The current standard regulatory tests in genetic toxicology are inadequate for effectively addressing the growing number of chemicals needing assessment. Specifically, the standard in vitro assays do not provide sufficient mechanistic information to inform relevance to in vivo toxicity. The resulting reliance on in vivo models in regulatory toxicology has hindered efficient chemical assessment. Thus, international efforts are underway to reduce animal testing and modernize toxicity assessment by developing and promoting non-animal alternatives, or new approach methodologies (NAMs). The goal of my thesis was to develop and demonstrate the application of genomics NAMs for quantifying genotoxic hazards and obtaining information on mechanism of action to advance in vitro chemical assessment. First, the inter-platform transferability of the TGx-DDI biomarker of DNA damage-induction was investigated. TGx-DDI is a 64-gene biomarker developed using DNA microarrays in human TK6 cells that provides mechanistic support to conventional genotoxicity assays. The biomarker demonstrated a conserved performance when measured by qPCR, demonstrating that transcriptomic biomarkers can be adapted to this widely available platform. Additional chemical testing methods were explored using two next-generation sequencing-based technologies: TempO-Seq, a targeted gene expression platform, and Duplex Sequencing (DuplexSeq), an emerging technology that enables direct and accurate detection of mutations in cells. A transcriptomic biomarker of histone deacetylase inhibition, TGx-HDACi, was developed from TempO-Seq whole transcriptome profiles to address the limited assays available for detecting epigenetic mechanisms of toxicity. The availability of TGx-HDACi contributes to diversifying the transcriptomic biomarkers that can be applied in high-throughput screening of transcriptomic profiles of chemicals. Next, a comparative, inter-laboratory study in TK6 cells identified an optimal experimental design for applying DuplexSeq as a mutagenicity assay. DuplexSeq detected a robust concentration-response in cells exposed to an alkylating agent, with high sensitivity. The results also revealed strong inter-laboratory reproducibility and the power of DuplexSeq in providing a comprehensive view of chemical-induced mutagenesis. Lastly, an Adverse Outcome Pathway (AOP) describing oxidative DNA damage leading to chromosomal aberrations and mutations was developed to provide a mechanistic framework for combining NAMs in integrated testing. Collectively, my thesis lays the foundation for development and advancement of NAMs and AOPs in genetic toxicology.
    Thesis Degree:
    Doctor of Philosophy (Ph.D.)
    Thesis Degree Discipline:
    Biology
    Date Created:
    2023

  • GENETIC DIVERSITY PREDICTS POPULATION FITNESS AND PERSISTENCE: THE VALUE OF GENETIC RESCUE INCONSERVATION

    Resource Type:
    Thesis
    Creator:
    Clarke, Julia
    Abstract:
    Genetic rescue is a conservation tool that uses translocations to restore gene flow in isolated populations. Despite successes, this tool remains relatively underused, likely due to lack of understanding and long term data. Here, we review all genetic rescue attempts to date to promote a better understanding of the method. We found that the increase in genetic diversity conferred from genetic rescue was the strongest predictor of population fitness in the short-term. Further, we found no evidence for outbreeding depression among studies. To learn more about long-term effects of genetic rescue, we conducted a case study using a small, isolated, population simulating genetic rescue using a population viability analysis. We found that translocations resulted in long lasting increases in genetic diversity, however, find that increased likelihood of persistence was only evident after repeated translocations. Further, we find that without addressing underlying stressors, genetic rescue along is insufficient in the long-term.
    Thesis Degree:
    Master of Science (M.Sc.)
    Thesis Degree Discipline:
    Biology
    Date Created:
    2023

  • Time-course proteomic study of Acinetobacter baumannii after exposure to oxidative stress

    Resource Type:
    Thesis
    Creator:
    Gallo, Vanessa Giovannna
    Abstract:
    Acinetobacter baumannii is an opportunistic nosocomial Gram-negative bacterium responsible for infectious diseases. Due to its rapidly growing multidrug resistance (MDR), there is a need to improve understanding of host-pathogen interactions to identify targets for the development of novel therapeutics. Characterizing bacterial responses to a stress condition representative of a host environment was hypothesized to provide improved understanding of A. baumannii pathogenesis. To this end, an in vitro time-course proteomic study evaluating the impact of oxidative stress on two clinical strains exhibiting different levels of virulence was performed using mass spectrometry. After exposure to hydrogen peroxide, 38 proteins and 181 proteins were observed to have different abundance levels in strain Lac-4 and Lac-5, respectively. The putative localization, pathway and molecular function of these proteins were assessed. Proteins that changed abundance levels were of interest as they indicate potential response to stress and could lead to targets for future therapeutic development.
    Thesis Degree:
    Master of Science (M.Sc.)
    Thesis Degree Discipline:
    Biology
    Date Created:
    2023

  • Learnings from collaborative monitoring of remote wildlife populations: factors affecting changes in number and distribution of nesting Hudson Bay eiders ducks in the Belcher Islands

    Resource Type:
    Thesis
    Creator:
    Richard, Samuel
    Abstract:
    Anthropogenic pressures are causing a global decline in biodiversity that, in turn, impacts the human communities depending on it. In the conservation effort, efficient management requires up-to-date and accurate information about the population dynamics, habitat requirements, and distribution of organisms. There is an increasing appreciation of the benefits of coproduction and the combination of multiple knowledge systems to increase our understanding of the rapidly changing ecosystems. In this thesis, I used data from a long-term collaborative monitoring program involving Inuit and federal government researchers to study the factors affecting changes in population size and nesting distribution of a harvested sea duck in south-eastern Hudson Bay, the common eider (Somateria mollissima). I also highlight practical challenges and propose solutions related to cultural and institutional barriers that impede the delivery of respectful approaches and best practices in collaborative research programs involving large and regulated institutions and remote Indigenous communities.
    Thesis Degree:
    Master of Science (M.Sc.)
    Thesis Degree Discipline:
    Biology
    Date Created:
    2023

  • Forest Amount, Not Fragmentation or Connectivity, Increases Bird Species Richness

    Resource Type:
    Thesis
    Creator:
    Hajdasz, Adrianne Carla
    Abstract:
    Though habitat amount, fragmentation and connectivity are considered important for biodiversity, it is unclear whether fragmentation or connectivity have strong effects on biodiversity independent of habitat amount. We aimed to determine the independent effects of these variables on species richness and presence of forest birds in Eastern Ontario, Canada. We selected 70 sites where landscape habitat amount, fragmentation and structural connectivity were uncorrelated with each other. We determined bird species richness and presence by deploying autonomous recording units at each site. Only habitat amount had a significant relationship with species richness; species richness increased until forest covered ~45% of the landscape. Both habitat amount and connectivity had significant effects on the presence of some individual species, but the direction of effect (positive or negative) varied by species. We suggest that increasing habitat amount and managing connectivity for certain species may be an effective conservation strategy for birds
    Thesis Degree:
    Master of Science (M.Sc.)
    Thesis Degree Discipline:
    Biology
    Date Created:
    2023

  • Contribution of Ionophores to Clinical Antimicrobial Resistance

    Resource Type:
    Thesis
    Creator:
    Abdelgany, Amer
    Abstract:
    Antimicrobial resistance (AMR) contributes to approximately 700,000 deaths worldwide each year, and this number increases annually. The use of antimicrobials in animals is an increasing concern in the spread of AMR. Ionophores are a class of antibiotic widely used in veterinary medicine for growth promotion and disease prevention, but they are not seen as a contributor to clinical AMR. Nonetheless, mechanisms of resistance to ionophores and their relation to clinical AMR are not well understood. To address these questions, we evolved the opportunistic pathogens Staphylococcus epidermidis and Staphylococcus aureus in the presence or absence of ionophores in the lab. We then assayed resistance to ionophores and to conventional medically important antimicrobials (MIAs). Ionophore resistance was found in S.epidermidis, but not in S.aureus. Collateral sensitivity and cross-resistance were also found in S.epidermidis, while S.aureus showed only a decrease in sensitivity toward some MIAs.
    Thesis Degree:
    Master of Science (M.Sc.)
    Thesis Degree Discipline:
    Biology
    Date Created:
    2023

  • Carry-over Effects in Arctic-breeding Shorebirds: A Cross-species Perspective

    Resource Type:
    Thesis
    Creator:
    English, Willow Bernadette
    Abstract:
    Avian studies have long been limited to single populations at a single time and place. However, such studies overlook carry-over effects, where conditions in one season cause fitness consequences in subsequent seasons. As technological advances make it possible to follow individual birds over a full year, it has become clear that carry-over effects can have fitness implications, and are therefore important to consider. In this thesis, I use tracking and physiological data from 14 species of Arctic-breeding shorebirds to link reproductive and timing variation to a bird's earlier experiences. In general, carry-over effects appear to influence important metrics of breeding and timing in Arctic-breeding shorebirds. The timing of nest initiation was influenced by both carry-over effects, measured by a bird's migration timing, and local weather conditions. While patterns were generally consistent across species, variation in the influence of carry-over effects among species merits further research. Tracking data also showed that delays in one season continue into the next, although seasonally variable mitigation means that birds generally reduced the extent of delays, potentially at a physiological cost. Winter is the exception, as birds appear able to fully "reset the clock" during this period, preventing delays from accumulating across years. Winter levels of the stress hormone corticosterone (CORT) in feathers showed a positive relationship with nest success in the subsequent summer, supporting the idea that high levels of CORT may not always imply that an individual is struggling, or at least that the relationship between CORT and fitness may be complex. This thesis is one of the first multi-species studies of carry-over effects, and is unparalleled in number of species and sample size within the carry-over effect literature. It is additionally novel for the multiple methods used to assess carry-over effects across a similar group of species. The importance of carry-over effects demonstrated within this thesis highlights the need for using a whole year approach to assess what influences variation in fitness, especially in migratory species. Doing so will improve our ability to identify and understand the causes of factors affecting demographic rates and driving declines across taxa.
    Thesis Degree:
    Doctor of Philosophy (Ph.D.)
    Thesis Degree Discipline:
    Biology
    Date Created:
    2023

  • Exploration-exploitation Learning in Foraging Hummingbirds is Driven by Cumulative Experience and Energetic Costs

    Resource Type:
    Thesis
    Creator:
    Donkersteeg, Courtney Jane
    Abstract:
    Exploration is necessary to gain information about environments, but testing exploration is often overlooked. Previous studies of animal foraging have considered non-rewarded choices to be mistakes representing failure to exploit valuable resources. Here I define several ways to quantify explorative behaviour and use those metrics to test how the probability of explorative choices changes with experience and body mass. I exposed five ruby-throated hummingbirds to an artificial flower array and quantified their exploration across repeated foraging sessions with different reward positions in each session. As the birds gained experience with the experimental paradigm, explorative behaviour started higher at the beginning of each new session despite its overall decrease as the session progressed. Smaller birds were more explorative than heavier birds, consistent with previous tests of foraging success and body mass. These results show that a hummingbird's explorative behaviour changes with body mass and learning resource dynamics through experience.
    Thesis Degree:
    Master of Science (M.Sc.)
    Thesis Degree Discipline:
    Biology
    Date Created:
    2023