Wilson, Paul

Globally, wildlife populations are experiencing increasing rates of range loss, population decline, and extinction. Caribou (Rangifer tarandus) have experienced dramatic declines in both range and population size across Canada over the past century. Boreal caribou (R. t. caribou), one of twelve Designatable Units, have lost approximately half of their historic range in the last 150 years, particularly along the southern edge of their distribution. Despite this northward contraction, some populations have persisted at the trailing range edge, over 150 km south of the boreal continuous range (BCR) in Ontario, along the coast and near-shore islands of Lake Superior. Better understanding the population structure and evolutionary history of caribou in the Lake Superior range (LSR) could help to inform conservation and management actions, such as the delineation of conservation or management units or translocations between populations. In this thesis, I use whole genome sequences from boreal, eastern migratory and barren-ground caribou sampled in Manitoba, Ontario, and Quebec to investigate evolutionary history and population structure. I discovered that the LSR caribou form a distinct group but also some evidence of gene flow with the BCR. Notably, caribou from the LSR demonstrated relatively high levels of inbreeding (measured as Runs of Homozygosity; ROH) and genetic drift, which may contribute to the differentiation observed between caribou occupying the two ranges. Despite inbreeding, the LSR caribou retained Heterozygosity Rich Regions (HRR). I found genomic structure among caribou populations from the LSR and BCR but found these two ranges had similar demographic histories. My analyses indicate that the LSR caribou display distinct genomic characteristics but share ancestry with the BCR, with historical gene flow between these two ranges. Collectively, this dissertation characterizes the population structure and evolutionary history of caribou from the southernmost range in Ontario, providing key insights for the conservation and management of these small and isolated populations.

Access to human blood for forensic research and training in bloodstain pattern analysis (BPA) can be difficult due to many ethical, safety and cost concerns. Mammalian blood alternatives can be sourced, especially from local and willing abattoirs, but some concerns remain, and the added difficulties of high variation and species-specific differences in cellular components pose other issues. Therefore, synthetic alternatives to human blood provide practical options for the BPA community. This thesis explores the use of alginate hydrogels as a base material for forensic blood substitute (FBS) development. Hydrogels are first explored as a suitable environment for DNA stability and functionality and compared to other polymer systems. The ability of DNA to remain intact while undergoing electrospray ionization (ESI) is also investigated. The FBS design focuses on mimicking the fluid properties and genetic capabilities of whole human blood – a material not developed in FBSs previously. ESI was used to develop microparticles (MPs) that serve as cellular components of human blood (the red blood cells – RBCs, and white blood cells – WBCs). The microparticles were ionically crosslinked using calcium to provide small MPs (RBCs) or covalently crosslinked with functional DNA to provide larger WBC-like functional particles. The integration of these novel MPs into alginate-based materials is optimized and their use in BPA scenarios is explored. The FBS is tested in BPA scenarios of dripping experiments, impact patterns, and the ability to extract and amplify the contained DNA. In addition, the stability (or shelf-life) of the FBS was also assessed. The FBS exhibited similar spreading ratios to blood and demonstrated feasibility in use for impact angle (a) determination and impact pattern creation. Importantly, the DNA contained within the FBS could be processed with analogous protocols used in DNA evidence processing, enhancing its applicability to BPA research and training.

Author Keywords: Alginate hydrogels, Bloodstain pattern analysis, Electrospray ionization, Forensic blood substitutes, Forensic materials, Synthetic DNA design

Hybridization contributes to the genetic diversity and can impact speciation. This study investigates the genetic evidence of recent hybridization under climate change in sympatric populations of northern and southern flying squirrels in Ontario. Using low-coverage whole-genome sequences, my research examines the existing population structure and measures the genomic variation of the Glaucomys species. The global estimates of FST (0.308) and DXY (0.141) are indicative of substantial differentiation between the species. Measures of genetic diversity (π), differentiation (FST), and divergence (DXY) across the genome reveal insights into the divergent selection driving speciation. Results indicate an absence of contemporary hybridization or introgression at a site with longstanding sympatry. Across both species' genomes, signatures of selection align with four different scenarios for the formation of genomic landscapes of differentiation, shedding light on the complex speciation history of these flying squirrels. These findings enhance understanding of evolutionary dynamics, adaptation, speciation, and genetic differentiation.

Author Keywords: Genomic differentiation, Glaucomys, northern flying squirrel, southern flying squirrel, speciation

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

The ability of animal populations to compensate for harvest mortality provides the basis for sustainable harvesting. Coyote populations are resilient to exploitation, but the underlying mechanisms of compensation and how they inter-relate are not fully understood. Moreover, deficiencies in the quality and quantity of information about eastern coyotes preclude effective management. I combined field work, laboratory work, and genetic profiling to investigate the population dynamics of eastern coyotes in southeastern Ontario. Specifically, I conducted research on coyotes during 2010–2013 in Prince Edward County where coyote hunting and trapping seasons were open all year. First, I investigated their social status dynamics and space-use patterns. Transients exhibited extensive space-use relative to residents, potentially encountering vacant territories and/or breeding positions, and some transients became residents, potentially filling vacant territories and/or breeding positions. Accordingly, the study population demonstrated the potential to compensate for harvest mortality via source-sink dynamics and/or buffering reproductive capacity. Second, I investigated their survival and cause-specific mortality. Residents exhibited greater survival than transients, probably partly because of the benefits of holding a territory, and transients seemingly exhibited greater vulnerability to harvest than residents, probably partly because their movements exposed them to greater cumulative mortality risks over time. Accordingly, harvest mortality disproportionately impacted the non-reproductive segment of the study population and thus may have failed to substantially limit reproduction, and thus recruitment. Third, I investigated their reproduction and breeding histories. Females in the study population exhibited age-specific reproductive rates and litter sizes generally typical of those in exploited coyote populations. Accordingly, increased reproductive rates and increased litter sizes may have offset losses due to harvest mortality. There was at least some breeder turnover in the study population due to harvest mortality, but many breeders survived to reproduce for multiple years and those that died were quickly replaced. My findings have important management implications for eastern coyotes and contribute significantly to better understanding of their resilience to harvest. Indiscriminate killing of coyotes through liberal harvest is unlikely to be effective in reducing their abundance. Management strategies should consider non-lethal alternatives and/or targeted lethal control for dealing with problem coyotes.

Author Keywords: Canis latrans var., eastern coyotes, population dynamics, Prince Edward County, southeastern Ontario

The length of photoperiod can alter circadian rhythms and change fat depot mass whencombined with environmental temperatures below thermoneutral. To isolate photoperiod effects, we compared the effects of long and short photoperiod exposure at thermoneutrality in photoperiod sensitive, F1 generation adult male white-footed mice (P. leucopus). Mice were housed in long-day or short-day photoperiod conditions at thermoneutrality for 4 weeks. Short photoperiod decreased vWAT mass without changing body weight, scWAT or iBAT mass, or calorie consumption. Short photoperiod increased Adrβ3 and Lpl mRNA expression in vWAT with no change in Ucp1, Pgc1a or Hsl. vWAT Per1, Per2 and Nr1d1 mRNA expression were aligned to the onset of dark and food intake, while Bmal1 and Clock were misaligned. These findings suggest that short photoperiod per se can decrease visceral fat accumulation, without activating thermogenesis, reinforcing that environmental photoperiod should be considered when researching cause and prevention of obesity.

Author Keywords: adiposity, circadian rhythm, clock genes, obesity, Peromyscus, photoperiod

Across vertebrate taxa, the hypothalamic-pituitary-adrenal axis (or the stress axis) is highly conserved, and is central to vertebrate survival because it allows appropriate responses to psychological stressors. Habitat shapes successful physiological and ecological strategies, and to appreciate how individual species respond to stressors in their environment, it is essential to have a thorough knowledge of the basic stress physiology of each species. In this dissertation, I studied the functioning and evolution of the stress physiology of New World flying squirrels. I showed that baseline, circulating cortisol levels in northern (Glaucomys sabrinus) and southern (G. volans) flying squirrels are some of the highest ever reported for mammals, indicating that their stress axes operate at a higher set point than most other species. I also assessed other aspects of their acute stress response, including free fatty acid and blood glucose levels, and indices of immune function, and showed that the flying squirrels' physiological reaction to stressors may differ from that of other mammals. Using immunoblotting, I found that corticosteroid-binding globulin (CBG) expression levels in flying squirrels appeared to be higher than previously reported using alternative methods. I also concluded however, that these levels did not appear to be high enough to provide their tissues with the protective CBG-bound buffer from their high circulating cortisol concentrations experienced by the majority of vertebrates. Thus, this arm of cortisol regulation within the flying squirrel stress axes may be weak or non-existent. Following this, I focused on southern flying squirrels and showed evidence that the second arm of cortisol regulation — the negative feedback mechanism at the level of the brain — functions effectively, but that this species is glucocorticoid resistant. Their tissue receptors appear to have a reduced affinity for cortisol, and this affinity may change seasonally to allow for the onset of other biological processes required for survival and reproduction. Due to their distinctive stress physiology, northern and southern flying squirrels may provide comparative physiologists with model systems for further probing of the function and evolution of the stress axis among vertebrates.

Author Keywords: corticosteroid-binding globulin, flying squirrel, Glaucomys, glucocorticoids, physiological ecology, stress physiology

Range contractions and expansions are important ecological concepts for species management decisions. These decisions relate not only to rare and endangered species but to common and invasive species as well. The development of the broad spatiotemporal extent models that are helpful in examining range fluctuations can be challenging given the lack of data expansive enough to cover the time periods and geographic extents needed to fit the models. Archival records such as museum databases and harvest data can provide the spatiotemporal extent needed but present statistical challenges given they represent presence-only location information. In this thesis, I used maximum entropy and Bayesian hierarchical occupancy algorithms fitted with archival presence-only records to develop spatiotemporal models covering broad spatial and temporal extents for snowshoe hare and Canada lynx. These two algorithm types are well suited for presence-only data records and can be adapted to include biological and physical processes, thus improving the ecological realism of the models. Using these modelling methods, I found the extent of occurrence (EOO) and area of occupancy (AOO) varied greatly over time and space for both snowshoe hare and Canada lynx, suggesting that management decisions for these species should include consideration of these variations. While the presence-only data were appropriate for model development and understanding changing values in EOO and AOO, it sometimes lacked the locational accuracy and precision needed to create fine scale ecological analyses, thus resulting in somewhat coarse but potentially relevant conclusions.

Author Keywords: Area of occupancy, Bayesian hierarchical models, Canada lynx, Extent of occurrence, Presence-only data, Snowshoe hare

Chemical presumptive tests are used as the primary detection method for latent bloodstain evidence. This work focuses on developing a forensic blood substitute which mimics whole blood reactivity to a luminol solution commonly used in presumptive testing. Designing safe and accessible materials that mimic relevant properties of blood is a recognized research need in forensic science. Understanding the whole blood dynamics related to reactivity with presumptive testing chemicals is important for developing accurate analogues. Provided in this thesis is a quantitative and qualitative characterization of photoemission from the reaction of a luminol solution to ovine blood. Luminol reactivity of a horseradish peroxidase encapsulated sol-gel polymer was validated against this ovine blood standard. This material, the luminol-reactive forensic blood substitute, is a key deliverable of this research. An optimized protocol for implementing this technology as a reagent control test, and as a secondary school chemistry experiment are presented. This thesis outlines the research and development of a forensic blood substitute as it relates to presumptive testing in bloodstain pattern analysis.

Author Keywords: bloodstain pattern analysis, forensic science, luminol, presumptive testing, secondary school education, sol-gel chemistry

The research and development of synthetic blood substitutes is a reported need within the forensic community. This work contributes to the growing body of knowledge in bloodstain pattern analysis by offering a materials science approach to designing, producing and testing synthetic forensic blood substitutes. A key deliverable from this research is the creation of a robust silicon-based material using the solution-gelation technique that has been validated for controlled passive drip and spatter simulation. The work investigates the physical properties (viscosity, surface tension and density) of forensic blood substitute formulations and describes the similarity in the spreading dynamics of the optimized material to whole human blood. It then explores how blood and other fluids behave in impact simulation using high-speed video analysis and supports the use of the optimized material for spatter simulation. Finally, the work highlights the practical value of the material as an educational tool for both basic and advanced bloodstain experimentation and training.

Author Keywords: bloodstain pattern analysis, forensic blood substitutes, high-speed video analysis, silicon solution-gelation chemistry, thin-film deposition, training and education