Electronic Thesis or Dissertation

Databases containing information such as location points, web searches and fi- nancial transactions are becoming the new normal as technology advances. Conse- quentially, searches and cross-referencing in big data are becoming a common prob- lem as computing and statistical analysis increasingly allow for the contents of such databases to be analyzed and dredged for data. Searches through big data are fre- quently done without a hypothesis formulated before hand, and as these databases grow and become more complex, the room for error also increases. Regardless of how these searches are framed, the data they collect may lead to false convictions. DNA databases may be of particular interest, since DNA is often viewed as significant evi- dence, however, such evidence is sometimes not interpreted in a proper manner in the court room. In this thesis, we present and validate a framework for investigating var- ious collisions within databases using Monte Carlo Simulations, with examples from DNA. We also discuss how DNA evidence may be wrongly portrayed in the court room, and the explanation behind this. We then outline the problem which may occur when numerous types of databases are searched for suspects, and framework to address these problems.

Author Keywords: big data analysis, collisions, database searches, DNA databases, monte carlo simulation

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

The Upper Paleolithic sequence at Vale Boi, Portugal, represents an early example of resource intensification, for which evidence of both diet diversification and intensified utilization of faunal remains has been published. The current research project tests the hypothesis that bone grease rendering was occurring throughout the Upper Paleolithic sequence at Vale Boi. As there are various issues of equifinality which makes the identification of bone grease rendering challenging, data from experimental bone grease rendering studies were utilized. The resulting analysis demonstrated limited evidence in support of a sustained use of bone grease rendering during the Upper Paleolithic sequence. However, evidence suggested that alternate bone processing activities and discard behaviours may have been occurring at the site. This suggests that the dietary behaviours of the foragers at Vale Boi were more varied than previously hypothesized.

Author Keywords: Archaeozoology, Bone Grease Rendering, Faunal Analysis, Iberia, Resource Intensification, Upper Paleolithic

Research and development activities conducted at universities and firms fuel economic growth

and play a key role in the process of innovation. Specifically, prior research has investigated the

widespread university-to-firm research development path and concluded that universities are

better suited for early stage of research while firms are better positioned for later stages. This

thesis aims to present a novel explanation for the pervasive university-to-firm research

development path. The model developed uses game theory to visualize and analyze interactions

between a firm and university under different strategies. The results reveal that as academic

research signals knowledge it helps attract tuition paying students. Generating these tuition

revenues is facilitated by university research discoveries, which, once published, a firm can build

upon to make new innovative products. In an environment of weak intellectual property rights,

moreover, the university-to-firm research development path enables firms to bypass the hefty

costs that are involved in basic research activities. The model also provides a range of solution

scenarios where a university and firm may find it viable to initiate a research line.

Author Keywords: Game theory, Intellectual property rights, Nash equilibrium, Research and development, University to-firm research path

Callousness, deceit, and manipulativeness have been identified as common characteristics of the Dark Triad. Researchers have argued that empathy and Theory of Mind underlie these characteristics. This study aimed to (a) examine the relationships between the Dark Triad, empathy, and Theory of Mind, (b) determine if empathy and Theory of Mind explain the overlap between the Dark Triad personalities, and (c) test if Theory of Mind mediated the relationship between cognitive empathy and the Dark Triad. A sample of 267 undergraduate students completed self-report scales and a film-based assessment to measure the variables of interest. The results indicated that the Dark Triad personalities were negatively associated with affective empathy but were not uniformly associated with cognitive empathy and Theory of Mind. Affective empathy did not explain the overlap between the Dark Triad personalities. Finally, Theory of Mind did not mediate the relationship between cognitive empathy and the Dark Triad.

Author Keywords: Dark Triad, Empathy, Mediation, Theory of Mind

Guidelines regarding social skills interventions for children with ASD suggest incorporating a holistic approach. This includes increasing the family's understanding of deficits associated with ASD, integrations of natural environments, and parents as active agents while supporting their well-being. The current availability of holistic parent-mediated interventions for children with ASD is limited, with no qualitative understanding of its potential benefits for either the parent or child. The current study examined qualitative parent reports on a parent-mediated social skills intervention for children with ASD (TalkAbilityTM) incorporating a longitudinal approach (i.e., 6-month follow-up). Following Braun and Clarke's model of thematic analysis, data was coded into four themes: 1) communication difficulties, frustrations and progress, 2) social relationships and concerns, 3) communication strategies, and 4) thoughts and emotions surrounding TalkAbilityTM. Results highlight the importance of considering parent experiences regarding interventions for their child's social communication skills through a qualitative viewpoint.

Author Keywords: autism spectrum disorder, parent-mediated intervention, qualitative review

This thesis uses three approaches to assess the potential of permaculture in Central Ontario. This was done using a vegetable field trial and modelling programs to determine the effectiveness of permaculture to decrease negative impacts of climate change based on projected climate values derived from regional circulation models. The first approach showed no statistical difference (P<0.05) of applying varied volumes and combinations of organic amendments on crop yields. The second approach indicated permaculture may be a sustainable production system with respect to soil erosion when compared to traditional agricultural practices. The third approach was inconclusive due to the lack of quantitative literature on permaculture management impacts on biomass yields, soil carbon or nutrient retention, which were missing from basic and scientific literature searches. The models used within this thesis include USLE, RUSLE2, AgriSuite, RothC and Holos.

Author Keywords: Agriculture, Climate Change, Computer Modelling, Permaculture, Soil Erosion and Assessment

Substance use disorder (SUD) is a pervasive psychological disorder detrimentally impacting both individuals and society on a psychological, economic, and social level. The best protocol for treating SUD as well as what defines success in treatment is often debated in the research. However, researchers agree that different psychosocial factors can influence outcomes. The literature suggests that mood, dark personality traits (narcissism and psychopathy), social supports, and state of change may be associated with treatment for SUD. The current study explored whether these factors predicted the type of treatment (abstinence-based or harm reduction) individuals with SUD were in. The sample consisted of 37 participants in a 12-step abstinence-based program and 65 in a harm reduction program at a local hospital. Results indicated that those in abstinence-based groups reported significantly fewer symptoms of anxiety and depression, lower levels of narcissism and psychopathy, more social supports, and advanced stage of change in comparison to those attending a harm reduction program. In addition, depression, narcissism, and perceived social support were significant predictors of treatment group membership. These findings suggest that those involved in abstinence-based groups appear to experience overall more wellness than those in harm reduction. Although further research is needed to specify the relations among factors, this study is a step towards understanding the difference between people who utilize one program versus another.

Author Keywords: Abstinence, Addiction, Harm Reduction, Personality, Treatment

Basic biogeographic information is lacking for many species, such as where species are found, and how they dispersed there. Using ground beetles collected during 2008-2015 from across northern Ontario and Akimiski Island, Nunavut, I present new information on ground beetle distribution in this eastern Nearctic boreal forest, including 2 first Canadian records, 9 first provincial and 48 first territorial records, as well as 74 new records that extend the known range of many large and common ground beetles several hundred kilometres. I used these distributions to redress the knowledge gap that includes fundamental distribution data, i.e. the Wallacean shortfall, and to inform later chapters in my thesis.In Chapter 3, I examine the range expansion pattern of Carabus granulatus, a non-native species, as it spread across northeastern North America and I provide a new range record. Northern Ontario is already under threat from non-native species entering the region and it is important to conduct studies in the region before more disturbance associated with development occurs. In Chapter 4, I examine the hypothesis that northern Ontario effectively acts as a climate plateau for poikilotherms, using the predictions from Bergmann's rule as my metric. The body length of ground beetles does not appear to change over the small temperature gradient that exists across northern Ontario latitudes, supporting the climate plateau hypothesis. In Chapter 5, I test hypotheses about dispersal mechanisms that contributed to post glacial re-establishment of ground beetles using predictions of geographic distribution patterns as metrics. I found that ground beetles were likely carried downstream by rivers which aided their dispersal northward from southern refugia. I infer from the current geographic distributions that flightless ground beetle species are still expanding their range in this boreal region. Finally, I argue that there is an urgent need for more basic research on species distributions while it is still possible in regions like northern Ontario, before increased industrial and agricultural development, and expanding resource extraction projects obliterate evidence of historic ecological processes.

Author Keywords: Boreal forest, Carabidae, Coleoptera, Passive dispersal, Post-glacial distribution, Range extension

Opioid drugs are among the microcontaminants that are discharged with domestic wastewater into the aquatic environment with the potential to affect the development and reproductive capacity of aquatic organisms. To study the effects of exposure of fish to opioid drugs, Japanese medaka (Oryzias latipes) were exposed over a full life cycle to environmentally relevant (i.e. ng/L) concentrations of two opioids, codeine and fentanyl. Acute exposure of early life stage (ELS) of medaka to codeine resulted in slightly extended times to hatch, but no increase in embryo mortalities or reduced hatching success. Chronic exposure to codeine at a nominal concentration of 25,000 ng/L over a full life cycle interfered with growth, reducing the weight of the fish at maturity. Life cycle treatments with codeine at all test concentrations resulted in a significant reduction in the number of eggs produced in reproductive trials, as well as a reduction in the numbers of mature oocytes in adult females. High treatments with codeine also increased the percentage of immature sperm cells in adult males. Life cycle exposures to codeine also resulted in reduced whole-body concentrations of several hypothalamic-pituitary-gonadal (HPG) axis hormones, including reduced levels of luteinizing hormone in male and female fish and a reduction in 11-ketotestosterone in males and 17β-estradiol in females. Fentanyl did not affect reproduction or HPG hormones at the exposure concentrations tested, but high fentanyl exposures increased the mortality rate among ELS's of the F1 generation offspring from life cycle exposed adults. The results of this thesis contribute to the literature on the environmental impacts of microcontaminants of wastewater origin and, the potential for effects in fish exposed to opioids.Keywords: Opioids, microcontaminants, fentanyl, codeine, sexual development, reproduction.

Author Keywords: codeine, fentanyl, microcontaminants, opioids, reproduction, sexual development