Biology

Lake Huron's food web has experienced drastic changes in response to multiple stressors including declines in offshore productivity, decreased trophic transfer efficiency and a transformation of the benthic food web. However, how these changes have affected the diets and isotopic niches of predatory fish is largely unexplored. My diet study analysed stomach contents from five predatory fish species (lake trout, lake whitefish, chinook salmon, rainbow trout, and walleye) from the Ontario waters of Lake Huron. My isotopic study focused on lake trout and lake whitefish, based on community concerns that recovering lake trout are competing with or consuming lake whitefish. By contrast, I found that lake whitefish were a minimal component of lake trout diets, and the diet and isotopic overlap between these two species was low overall, but varied regionally. Both the dietary and isotope analyses reflect the high regional diversity of energy sources used by predatory fish.

Author Keywords: Food web, Isotopic Niche, Lake Huron, Predator-prey, Regime shift, Regional Energy Sources

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.

This thesis is focused on studying the population dynamics of a predator-prey system in a patchy environment, taking anti-predation responses into consideration. Firstly, we conduct mathematical analysis on the equilibrium solutions of the system. Using techniques from calculus we show that particular steady state solutions exist when the parameters of the system meet certain criteria. We then show that a further set of conditions leads to the local stability of these solutions. The second step is to extend the existing mathematical analysis by way of numerical simulations. We use octave to confirm the previous results, as well as to show that more complicated dynamics can exist, such as stable oscillations. We consider more complex and meaningful functions for nonlinear dispersal between patches and nonlinear predation, and show that the proposed model exhibits behaviours we expect to see in a population model.

Author Keywords: Anti-predation response, Asymptotic stability, Dispersal, Patch model, Population dynamics, Predator-prey

Lake whitefish (Coregonus clupeaformis) are ecologically, economically, and culturally significant across their range, yet little is documented about the species' spawning behaviour. Recruitment of lake whitefish has dramatically declined over the past two decades across many regions of the Laurentian Great Lakes, most notably in lakes Huron and Michigan, prompting research efforts to fill critical knowledge gaps in the life history of this species. Understanding the reproductive ecology of lake whitefish, including documenting aspects of spawning behaviour, may reveal clues about factors contributing to the declines. This study used fine-scale acoustic telemetry to characterize sex-specific movement patterns and habitat associations of lake whitefish during the spawning season. A VEMCO Positioning System (VPS) was deployed at an active spawning shoal in Georgian Bay (Lake Huron), with guidance provided by Saugeen Ojibway Nation members with local ecological knowledge about the shoal and the lake whitefish population. In the fall of 2020, 50 lake whitefish were captured and tagged at the spawning shoal; 28 of those fish were observed the following spawning season in 2021. A clear increase and decrease was observed in the presence of individuals in the study area over the spawning period. Both sexes moved into shallower waters at night and deeper waters during the day at rates of 0.162 m/h and 0.08 m/h, respectively. Decreased rates of movement and horizontal distance travelled were detected during the day leading up to a peak activity phase where 22 fish were present. At night during this peak activity phase, males moved 30.0% faster on average than females (0.204 ± 0.13 and 0.143 ± 0.10 m/s, respectively). This study provided a unique opportunity to work with local First Nations to understand lake whitefish spawning behaviour, providing insights into the reproductive ecology of a population undergoing concerning declines in recruitment and abundance.

Author Keywords: Coregonine restoration, Coregonus clupeaformis, Fine-scale acoustic telemetry, GLATOS, Spawning habitat, Two-Eyed Seeing

The Great Lakes represent nearly a fifth of the global freshwater surface supply, and support culturally, economically, and ecologically important fish species such as Walleye (Sander vitreus). With water temperatures projected to rise by several degrees in the coming century, understanding the energetic impacts on fishes is crucial for effective habitat and fisheries management. I measured the swimming performance, accelerometer-based activity, and metabolism of walleye in relation to body size, sex, and water temperature to assess potential responses to climate variability. Both acceleration and swim speed predicted metabolic rate with reasonable accuracy. Temperature had a positive effect on oxygen consumption whereas body mass had a negative effect. Critical swimming speed increased with temperature, and tailbeat frequency had positive relationships with swim speed and acceleration. My laboratory-based calibrations should enable remote field monitoring of energy use of walleye (via accelerometers) and help conserve an important species through bioenergetic modelling.

Author Keywords: accelerometry, bioenergetics, climate change, metabolism, respirometry, walleye

Northern flying squirrels (NFS) are mycophagous specialists (fungi-dominated diet) thatmay be displaced with southern flying squirrel (SFS) range expansion, thereby limiting fungal dispersal in forest communities. To understand the implications of squirrel species turnover on mycophagy, we investigated the home ranges of both flying squirrel species who are living in stable sympatry. We found no significant difference in home range sizes and identified spatial overlap between the two species. Through habitat selection ratios we found SFS were strongly selecting for deciduous-dominated habitats more than NFS. Lastly, we conducted microscopy on flying squirrel scat and found NFS were eating more fungi than SFS. We conclude that the squirrels are sharing the same habitat landscape but are finding ways to partition the habitat accordingly to allow for sympatry. SFS may contribute to the spore-dispersal cycle similarly to their northern counterpart through moderate fungus consumption and large home range sizes.

Author Keywords: diet, flying squirrels, Glaucomys, home range, mycophagy, sympatry

Climate change is a major conservation concern, especially for many cold-adapted species. The rate of warming due to climate change will likely outpace adaptive responses, and many populations will likely need to rely on phenotypic plasticity to cope with environmental warming. It is currently unclear whether plasticity in physiological responses to warming will be sufficient to offset the negative consequences of chronic environmental warming in ectotherms. I studied within-generation and transgenerational plasticity in two cold-adapted species of fishes, lake trout (Salvelinus namaycush) and brook trout (S. fontinalis), following temperature acclimation. Adults of both species were acclimated to either cold or warm temperatures and offspring were generated using a fully factorial breeding design, whereby the family thermal histories included crosses made within each temperature treatment and bidirectional crosses between temperatures. Offspring families were subdivided into two groups and acclimated to either warm or cold temperatures, so that offspring thermal experience matched or mismatched that of one or both parents. Offspring metabolic rate and critical thermal maximum during an acute thermal challenge were measured for both species. Limited transgenerational plasticity was detected in both species, but had a lesser effect than within-generationacclimation. In brook trout, the paternal contribution was greater than the maternal contribution. In lake trout, a mismatch in thermal acclimation, where the offspring were cold-acclimated but the parents warm-acclimated, resulted in elevated offspring metabolic rate without a corresponding increase in growth, suggesting that a mismatch in temperatures across generations could be detrimental to offspring. Using RNA-sequencing, transgenerational plasticity was linked to differential gene expression in the liver of lake trout offspring, in that genes were differentially expressed depending on the parental acclimation temperatures. Within-generation warm acclimation had the greatest effect on gene expression profile of offspring, with more genes differentially expressed under conditions of within-generation warm acclimation compared with transgenerational warm acclimation. Although it has been suggested that transgenerational plasticity may help to buffer the impact of warming due to climate change, my work implies that transgenerational plasticity, like within-generation plasticity, will be insufficient for these two species of cold-adapted salmonids to cope with climate change.

Author Keywords: Brook trout, Climate change, Lake trout, Phenotypic plasticity, Thermal tolerance, Transgenerational plasticity

Acoustic communication is vital for mediating interactions between individuals and their environment. From echolocating bats to isolated rodent pups, ultrasonic vocalizations are a useful mechanism for producing localized and cryptic acoustic signals. Flying squirrels have been demonstrated to produce almost exclusively ultrasonic calls which is rare in both squirrels and mammals, though the significance of this acoustic range is unknown. To investigate the context of ultrasonic calls in these gliding mammals, I created phylogenetic comparative analyses to compare ecological and morphological traits against call frequencies. I found that nocturnality, a trait entangled with gliding in squirrels, was related to higher-frequency calls. Furthermore, by comparing all gliding mammals and their non-gliding counterparts, I found that gliding mammals produce significantly higher frequencies than these relatives. This form of cryptic communication is likely used to avoid predation, which was further supported by behavioural experiments wherein flying squirrels used significantly higher frequencies when predation risk increased. While high frequency communication was used by most gliders, I found that ultraviolet-induced photoluminescence, another potential form of crypsis, was strongly associated with nocturnality, with half of the tested gliding mammals showing evidence of this unique colouration. While ultrasonic vocalizations are widespread in echolocating bats and echonavigating mammals, I did not find evidence to support echonavigation in flying squirrels. Instead, I found that ultrasonic vocalizations are used in a variety of social contexts and during solitary foraging and exploration. These combined results demonstrate the unique ecological and evolutionary pressures acting on small-bodied, nocturnal gliding taxa and the resulting cryptic behaviours and communication.

Author Keywords: communication, flying squirrels, gliding mammals, Sciuridae, ultrasound, ultraviolet-induced photoluminescence

Fungi are a diverse group of organisms that play crucial roles in various ecological processes and have immense economic importance. Understanding the intricate mechanisms underlying fungal growth and development is fundamental to harnessing their potential and exploring their applications in different fields. Signalling molecules, such as hormones, have been identified as key regulators in fungal physiology, orchestrating intricate processes and modulating biological responses to the environment. Phytohormones, commonly associated with plants, have been proposed as potential myco-hormones due to their production in a wide variety of fungi. Metabolomic analyses were performed via LC-MS/MS to investigate the role of phytohormones, specifically cytokinins (CKs) and indole-3-acetic acid (IAA), along with lipids and energetic metabolites such as organic acids during the growth and development of the model fungus Sordaria macrospora. The results revealed a clear switch between CK ribosides and CK free bases during the ascosporegenesis stage, with increased levels of cZ and iP and decreased levels of iPR and cZR. A similar pattern was observed in the mutant strain smgpi1 but demonstrating higher levels of CK free bases and increased fruiting body formation compared to the wild type. These findings provide insights into the regulation of phytohormones especially during fungal fruiting body development. In terms of IAA, the levels increased during the transition to sexual development in all strains, with the per5 mutant, unable to produce lipids via the cytosol, demonstrating a higher concentration than the wild type. The interplay between energetic metabolites and IAA suggests a potential role in the transition to sexual development. Additionally, the dose-dependent effects of exogenous CK application were investigated, showing the potential of low concentrations, from 1 to 10 μM, of CKs in promoting biomass accumulation or sexual development. Furthermore, gene editing in S. macrospora was proposed as a future direction to explore the functions of CKs and other metabolites during fungal development. Overall, this research contributes to our understanding of phytohormone-mediated processes in fungi and opens avenues for future investigations in fungal biology.

Author Keywords: fungi, LC-MS, metabolomics, myco-hormone, phytohormone, sexual development

I investigated the climate vulnerability of a cold-water salmonid by observing the upper thermal tolerance of brook trout (Salvelinus fontinalis) across multiple life stages. Using hatchery- and wild-ancestry fish, I assessed variation in thermal tolerances and carryover effects within and among brook trout life stages and populations that were reared under varying winter thermal regimes as embryos. Embryonic, fry, and gravid adult upper thermal tolerance were tested via CTmax. Warm acclimation was associated with an increase in embryonic upper thermal tolerance. CTmax variability was markedly higher in embryos than juvenile or adult salmonids. Effects of thermal incubation treatments varied by life stage, with incubation temperature and life stage both influencing body size and thermal tolerance. Collectively, these results suggest that brook trout only exhibit short-term carryover effects from thermal stressors during embryo incubation, with no lasting effects on phenotype beyond the first few months (10 weeks) after hatch.

Author Keywords: acclimation response, climate change, ontogeny, salmonid, stress, thermal plasticity