Graduate Theses & Dissertations


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
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
Using automated radio-telemetry to link food availability, reproductive success, and habitat use of Barn Swallows (Hirundo rustica erythrogaster)
Drivers of North American Barn Swallow population declines are not well understood, but foraging habitat loss is thought to be a contributing factor. Determining patterns of habitat use is challenging for swallows because they move rapidly but are too small to carry GPS tags. We showed that automated radio-telemetry could be used to track the movements of swallows with enough accuracy (median error 250 m) to monitor local habitat use. We then combined information on breeding Barn Swallows habitat use, land cover, aerial insect abundance, and fledging success to test for a link between foraging habitat quality and reproductive success. Foraging activity was concentrated within 600 m of nest sites and varied with land cover; however, responses to land cover were not consistent across birds. Aerial insects were most abundant near wetlands and least abundant near open water and over cropland. Consistent with a link between foraging habitat and reproductive success, nests in barns with more wetland and less open water within 1 km, and with less field area within 2 km occupied by row crops, on average fledged more young swallows. Author Keywords: aerial insectivores, automated telemetry, habitat use, land cover, movement, nest success
Using a real-world chopping task to study motor learning and memory
Typically task interference is studied using reaching adaptation tasks (visuomotor rotation and/or force-field learning). Participants in these experiments are already experts at the base task (point-to-point, planar reaching) and their ability to adapt reaching to the imposed perturbation is studied. The pattern of data induced by the perturbation is used to make inferences about the nature and neural correlates of our learning and memory for reaching perturbations, specifically, and motor performance in general. We wanted to see if it is possible to demonstrate this same interference pattern using a novel vegetable-chopping task, where we can easily recreate natural performance settings using a task for which we can easily identify non-experts. Participants performed a chopping task in which they are asked to chop a sweet potato into 5 mm-wide slices, matching the beat of a metronome (120 bpm). Following this initial learning, participants were exposed to an interference condition. Participants then performed trials of the original task again. Interference was inferred if the second performance of the original task was impaired, compared to initial performance. Experiment 1 involved novice choppers, and either the force or frequency of chops was manipulated. Only the altered frequency task produced interference effects. In Experiment 2, competent and expert choppers had to manage either a faster or slower frequency. We found evidence for interference in competents, but not experts. These results support the idea that the vulnerability to interference of motor memory changes with practice, and so any inferences made about memory structure must take into account not only expert performance, but every level of skill. Author Keywords: expertise, interference, motor learning, reaching adaptation
Using Fluorescent Carbon Dots for Biosensing Applications of Amino Acids
Amino acids make up proteins, which are the building blocks of life. A balance of amino acids is needed to maintain a healthy state. Tyrosine (Tyr) is synthesized from the metabolism of phenylalanine, which is an essential amino acid, meaning it can only be obtained from the diet. It is related to many metabolic and neurodegenerative diseases. Tyr can undergo post-translational modifications such as phosphorylation and nitration, which are implicated in cancer and nitrative stress, respectively. Although there are many methods to detect Tyr and its analogues, phosphotyrosine (pTyr) and nitrotyrosine (nTyr), these methods are time-consuming, involve expensive instruments and involve tedious process. This research proposes a new type of nanomaterials, carbon dots (CDs), to detect these amnio acids. Data indicate that CDs can be used to detect nTyr with a limit of detection of 34 μM in the linear range of 20 - 105 μM. The amenability of CD-nTyr assay was also tested in various biological matrices and biological molecules and was shown to be sensitive to nTyr. Nitration of Tyr was carried out in the presence of sodium nitrite and hydrogen peroxide catalyzed by either Cu(II) or Fe(III) to mimic biological reactions and CDs were tested as both inhibitors and indicators of Tyr nitration. Although CDs did not inhibit the nitration reaction of Tyr, they did not serve as indicators of Tyr nitration due to the quenching of CDs by the nitrating agents. This shows the importance of using CDs to detect nTyr and further use it for biological applications to detect diseased states. Author Keywords: amino acids, carbon dots, nanomaterials, sensor, spectroscopy, tyrosine
Using DNA Barcoding to Investigate the Diet and Food Supply of a Declining Aerial Insectivote, the Barn Swallow (Hirundo rustica)
Barn Swallow (Hirundo rustica) populations have declined in North America over the past 40 years and they are listed as Threatened in Ontario, Canada. Changes in the food supply have been hypothesized as a potential cause of this population decline. I used DNA barcoding to investigate the diet and food supply of Barn Swallows and to determine if the food supply affects their reproductive performance. In two breeding seasons, I monitored nests, collected fecal samples, and monitored prey availability by collecting insects from the habitat surrounding breeding sites using Malaise traps. I used DNA barcoding to identify insect specimens collected from the habitat and to identify prey items from Barn Swallow nestling fecal samples. I found that Barn Swallow nestlings were fed a very broad range of prey items but were fed larger prey items more frequently. Prey availability was not related to the timing of reproduction, the number of nests at a breeding site, or the reproductive output of individual nests. This study provides information on the diet composition of Barn Swallows in North America and suggests that food limitation during the breeding season may not be a major factor in their population decline. Author Keywords: aerial insectivore, diet, DNA barcoding, Hirundo rustica, metabarcoding, reproductive success
Use and Utilization of Loose and Commingled Human Dental Remains in Investigations of Ancient Human Populations
Commingled teeth present a unique opportunity for a novel application of standard methodological approaches commonly utilized in dental anthropological studies. Unfortunately, little research has been conducted on loose or commingled dental assemblages to determine if they are suitable samples for reconstructing bioarchaeological narratives of ancient human populations. The lack of research on commingled dental samples is surprising, given that teeth are highly resistant to post-depositional deterioration and are often some of the only remains left in high deteriorated burials. An experimental analysis of a commingled dental assemblage recovered from four chultuns at Ka'kabish, Belize, was conducted to address this lack of research and provide a real-world example of the potential use and utilization of commingled dental assemblages in investigations of ancient human populations. Author Keywords: Anthropology, Belize, Commingled, Dental, Maya, Methods
Use Of Rapid Amygdala Kindling With Corticosterone Supplementation As A Model Of Epilepsy-Depression Comorbidity
Temporal lobe epilepsy increases risk for developing major depression, and conversely, depression increases risk for development of epilepsy. The mechanisms responsible for the widely observed bi-directional relationship between epilepsy and depression are currently poorly understood. One reason why our understanding of shared etiology has had little improvement is due to the lack of availability of a reliable animal model for inducing depression in epileptic animals. The development of a reliable model of epilepsy-depression comorbidity would greatly improve the ability to mechanistically evaluate shared pathophysiology between the conditions. Recently there has been evidence that rapid kindling of the basolateral amygdala can evoke a behavioural phenotype that is comparable to the symptoms of anxiety and depression observed in depressed epileptic patients. However, this work has yet to be replicated, leaving question as to whether or not the behavioural phenotype can be reliably evoked. In the following series of experiments we assessed rapid amygdala kindling as a potential model of epilepsy-depression comorbidity and sought to improve the model with inclusion of the glucocorticoid corticosterone. Our findings may improve our understanding of the unique relationships between epilepsy and depression. Author Keywords: animal models, depression, hippocampus, kindling, stress, temporal lobe epilepsy
Uplifting Her Voice
This thesis creates an adaptation of act five, scene three of William Shakespeare’s Titus Andronicus that reshapes the play by focusing on female empowerment through the character Lavinia. Specifically, by using other Shakespearean characters’ dialogue that can speak towards her situation, I have written a monologue and stage directions for Lavinia. The same patriarchal superstructures which existed in the West during the time of Shakespeare and at the time of the play’s setting—and which still exist today—ensure that Lavinia remains silenced. Through my adaptation, I aim to challenge these structures in a meaningful way by returning both voice and agency to Lavinia. Author Keywords: Adaptation, Agency, Metamorphosis, Patriarchy, Revenge, Voice
Untitled (dissertation 4.2)
Untitled (dissertation 4.2) offers a performative take on the political implications of digital archives. I argue that technological developments and their increasing ubiquity has not resulted in more reliable archives; it has facilitated the exacerbation of what Jacques Derrida calls mal d’archive—or archive fever—which refers to the institutionally supported passion to preserve that is perpetually threatened by the inevitably of loss. A performative perspective, specifically derived from the work of contemporary performance theorists and artists, affords a contemporary archival practice that not only accepts, but is informed by mal d’archive because it shifts the focus from what is preserved to how it has become and continues to be preservable through archival acts. This is important in our contemporary moment because the ubiquity of digital technologies has exacerbated the symptoms of mal d’archive: a rapid increase in both the formal and informal production of preservable content, and consequently, as Derrida reminds us, archival violence. Untitled (dissertation 4.2) also includes a performative engagement with mal d’archive through two interludes. The first interlude features what I am calling “glitch-utterances,” which refers to the visual representations of technological mishaps. The documents in the second interlude—an iteration of the exhibition catalogue that resulted from my 2020 artist residency at the Art Gallery of Peterborough—engage with the productive function of the archive because they performatively constitute the exhibition as having happened regardless of whether or not it actually occurred, which, significantly, it did not. I conclude Untitled (dissertation 4.2) with a look at the ecological impact of digital archives—perhaps an “ecological fever.” It is not my intention to offer a solution for this “ecological fever,” nor address its full impact. My aim is to conclude this dissertation with a supplement of sorts: a look at the ecological impact of digital archives because I feel it is irresponsible not to given their increasing ubiquity. With this in mind, the glitch-utterances featured in both interludes can perform an important role in calling attention to the technological materialities and computational processes that are rendered invisible by Big Tech companies via metaphors—the ethereal Cloud metaphor, for example. These glitch-utterances point to the very material substrates that support the virtual, and can thus act as an important reminder of the ecological consequences of digital archives, which, like archival practices, are tied to institutional agendas. Author Keywords: Archive , Curation , Digital Archive, Documentation, Multimedia performance, Performativity
Unsettling Inner Landscapes
Recent climate scientists, Indigenous resurgence scholars, and psychologists have variously indicated that we need a transformation of consciousness in order to address the cultural and spiritual forces at the root of our current environmental, interpersonal, and individual crises of disconnection. My research is in direct response to diverse calls for this paradigm shift, including the words of Elders such as the late Grandfather William Commanda who encouraged settlers such as myself to ‘remember our original instructions’. Through an anti-colonial and trauma-informed lens, my goal has been to strategically inform my roles and responsibilities in healing the disconnection and abuses in what I term the trilogy of my relationships to self, others, and Land. This study is both a critical auto-ethnography and as well as a theoretical engagement with Indigenous resurgence, settler colonialism, and sustainability discourses. I share dialogues with Anishinaabe-kweg in my community with whom I have established relationships and the results of our discussions focus on holistic models of transforming settler consciousness. What emerges is an emotional, uncertain, and yet radically hopeful narrative that points to the urgency of centering Indigenous sovereignty and Indigenous relationship models while endeavouring to reconstruct a sense of identity and belonging along more accountable lines. Recovering a sense of my Celtic epistemology and story work is offered as a strategic exemplar of how settlers might begin to remember and co-create more balanced, respectful, and reciprocal relationships with and within place. Nurturing an embodied spiritual practice of deep listening, critical self-reflection, and collective action is discussed as potentially central to sustaining a decolonizing praxis for white settler Canadians more broadly. Author Keywords: Critical auto-ethnography, Critical Spirituality, Decolonization, Indigenous-settler relations, Original Instructions, Settler colonial studies
University Aged Millennials' Attitudes and Perceptions Toward Vehicle Ownership and Car Sharing
Car-sharing may have the potential to contribute to a more sustainable transportation system. The current research sought to answer the question: what are university-aged Millennials' perceptions and attitudes toward the adoption of vehicle sharing and private vehicle ownership? The research consisted of hosting six interactive focus group sessions with Millennial students, who currently do not own vehicles. Using a qualitative approach, I analyzed the discussions through a social practice theory lens. I suggest that skills, meanings, materials, and social interactions have an influence on the way in which a transportation option is perceived by Millennials. The results revealed that social norms surrounding vehicle ownership and car sharing are being developed, shaped, changed, challenged and reconstructed. If car-sharing businesses, universities, and governments wish to progress toward a more sustainable transportation system, they should recognize the importance of marketing. Author Keywords: Car ownership, Car sharing, Millennials, Sustainability, Transportation, University


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Format: 2023/01/31