Murray, Dennis

Amphibian biodiversity is in global decline, driven primarily by habitat loss and fragmentation arising from landcover alteration. For pond-breeding amphibians, larval abundance should be governed by aquatic breeding site quality, surrounding terrestrial habitat characteristics, and proximity to neighbouring populations. If safeguarding salamander populations is a priority, conservation efforts will benefit from understanding the relative importance of each feature on salamander populations. I sought to identify the factors associated with relative abundance of Ambystoma salamander larvae across habitat patches on Pelee Island, Ontario, Canada. Larval density and a suite of environmental variables were measured at 34 breeding sites across the island. Using spatial analysis, I also determined landcover features surrounding the breeding site, including, terrestrial habitat type, terrestrial patch size, and indices of isolation (e.g., nearest neighbour distance, proximity index). The relative abundance of Ambystoma larvae was best predicted by additive effects of breeding site quality (e.g., canopy cover, submergent vegetation, and cooler water temperature) and size of surrounding terrestrial habitat patches. I did not detect any influence of agricultural land cover within 300 m of the breeding sites on larval count, implying that Ambystoma can persist within agriculture-dominated landscapes provided that high breeding habitat quality is maintained, and ponds are embedded within large forest patches. Further, I failed to detect any impact of breeding site isolation on larval numbers, indicating that local habitat quality and terrestrial patch size more strongly determine larval abundance than patch connectivity. My research highlights the critical importance of conserving high-quality aquatic breeding habitats and maintaining large contiguous patches of terrestrial habitat for amphibian

Author Keywords: Amphibian, Anthropogenic impacts, Biodiversity conservation, Habitat fragmentation, Habitat suitability, Salamanders

Population cycles are characterized by predictable temporal oscillations in population size and are influenced by densities of both predators and prey. These oscillations are influenced by the predator functional response, i.e. the influence of prey density on predator kill rate. The Canada lynx (Lynx canadensis) is a predatory mammal with cyclic northern populations driven by snowshoe hare (Lepus americanus) density. Despite some understanding of the drivers of lynx cycles, we lack understanding of how lynx hunting behaviour, including kill site selection, is influenced by the spatio-temporal distribution of prey. These concepts are explored in chapter one of this thesis.

In chapter two, we (coauthors and I) built on work in Kluane region of the Yukon where lynx and hare populations have been tracked through several population cycles. Over six winters, we deployed GPS collars on >40 individual lynx, some of which were fitted with satellite transmitters, accelerometers, and audio recorders. We validated the use of these technologies for identifying hare kills with an accuracy of >87%. This validation is the foundation for chapter three of this dissertation.

In chapter three, we investigated the drivers of spatial variation in lynx kills. Using snow track transects through four winters of declining hare density, we developed a robust model of habitat-specific hare abundance over time. Using model predictions, in combination with lynx Utilization Distributions derived from GPS locations and related habitat associations, we determined the importance of hare abundance, lynx spatial use, and landscape characteristics such as vegetation density in determining patterns of lynx kills and space use. Lynx kill sites were most strongly predicted by lynx space use, followed by the relative abundance of hares, an index of tree cover density, and elevation. Lynx space use itself was not strongly predicted by hare relative abundance, but rather by a shift to the use of more open habitats when hares were abundant to higher use of denser habitats as hare populations declined; this apparently corresponded to temporal changes in hare distribution. This thesis helps to disentangle the drivers of spatio-temporal variation in predator foraging behaviour, with important implications for understanding predator-prey dynamics.

Author Keywords: animal behaviour, biologging, foraging, habitat selection, Lynx canadensis, predator-prey dynamics

Measuring biodiversity has become increasingly complex as biologists and ecologists have gradually learned more about how biotic systems are structured and interact. Given the wide range of tools, techniques and approaches now in use to quantify biological diversity, it is useful to consider different "dimensions of diversity" to classify these measurements and provide context for their interpretation. Even within the genetic dimension of diversity alone, recent improvements in theory, technology, and statistics has generated several approaches which can provide distinct insights into natural systems. In this thesis, I use multiple "axes of diversity" to subdivide the dimension of genetic diversity to better understand a complex ecological system - the unisexual Ambystoma complex on Pelee Island, Ontario. By focusing on the genomotype axis, I found that the composition of local unisexual Ambystoma assemblages generally reflects the current relative abundance of the local sexual host populations. This suggests that sexual hosts can be thought of as a keystone species for the complex not only because they are required for unisexual Ambystoma to reproduce, but also because their relative abundance governs the composition of entire unisexual Ambystoma assemblages. Comparatively, when assessing the lineage axis of genetic diversity, unisexual Ambystoma assemblage diversity patterns primarily reflected historic landscape structure, and spatial patterns of increased lineage richness were linked to areas where both potential hosts were locally available (currently or historically). Thus, while both of the investigated axes of diversity are forms of genetic diversity, each revealed distinct factors that have shaped contemporary diversity patterns across the landscape operating at different spatial and temporal scales. Critically, our understanding of complex ecological systems is likely to be broadened by including additional axes of diversity (e.g., allelic, loci, or chromosomal structure axes), and such investigations are not limited to clonal hybrid systems. Overall, this work illustrates the importance of combining insights from distinct conceptual and analytical toolkits to generate a comprehensive understanding of the factors which have shaped the patterns of diversity we observe today.

Author Keywords: Biological diversity, Dimensions of diversity, Ecological genetics, Metacommunity ecology, Unisexual Ambystoma

Population cycles are characterized by predictable temporal oscillations in population size and are influenced by densities of both predators and prey. These oscillations are influenced by the predator functional response, i.e. the influence of prey density on predator kill rate. The Canada lynx (Lynx canadensis) is a predatory mammal with cyclic northern populations driven by snowshoe hare (Lepus americanus) density. Despite some understanding of the drivers of lynx cycles, we lack understanding of how lynx hunting behaviour, including kill site selection, is influenced by the spatio-temporal distribution of prey. These concepts are explored in chapter one of this thesis.

In chapter two, we (coauthors and I) built on work in Kluane region of the Yukon where lynx and hare populations have been tracked through several population cycles. Over six winters, we deployed GPS collars on >40 individual lynx, some of which were fitted with satellite transmitters, accelerometers, and audio recorders. We validated the use of these technologies for identifying hare kills with an accuracy of >87%. This validation is the foundation for chapter three of this dissertation.

In chapter three, we investigated the drivers of spatial variation in lynx kills. Using snow track transects through four winters of declining hare density, we developed a robust model of habitat-specific hare abundance over time. Using model predictions, in combination with lynx Utilization Distributions derived from GPS locations and related habitat associations, we determined the importance of hare abundance, lynx spatial use, and landscape characteristics such as vegetation density in determining patterns of lynx kills and space use. Lynx kill sites were most strongly predicted by lynx space use, followed by the relative abundance of hares, an index of tree cover density, and elevation. Lynx space use itself was not strongly predicted by hare relative abundance, but rather by a shift to the use of more open habitats when hares were abundant to higher use of denser habitats as hare populations declined; this apparently corresponded to temporal changes in hare distribution. This thesis helps to disentangle the drivers of spatio-temporal variation in predator foraging behaviour, with important implications for understanding predator-prey dynamics.

Author Keywords: animal behaviour, biologging, foraging, habitat selection, Lynx canadensis, predator-prey dynamics

Habitat loss and fragmentation have significantly contributed to amphibian population declines, globally. Evaluating the state of remaining habitat patches can prove to be beneficial in identifying areas to prioritize in conservation efforts. Pelee Island, Ontario is home to a complex of salamanders including small-mouthed salamanders (Ambystoma texanum), blue-spotted salamanders (A. laterale) and unisexual Ambystoma (small-mouthed salamander dependent population). These populations have declined from intense landscape changes since the late 1800s, particularly from the historical drainage of wetlands. In this thesis, I evaluated the suitability and connectivity of habitat patches occupied by these salamanders to assess the size of, and dispersal capabilities between, remaining habitat patches. I found that there was a low amount of suitable terrestrial habitat available for this complex of salamanders, and existing habitat patches were small and isolated. Forested areas and non-breeding wetlands were considered to be suitable habitat when adjacent to existing breeding locations, suggesting that these habitats should be a focus for conservation efforts. Notably, intervention may be necessary to maintain this amphibian complex as many assemblages are isolated from one another and potential corridors currently consist of primarily unsuitable habitat. Given that much of the salamander complex is reliant on one species for reproduction, the long-term viability of this population of Ambystoma salamanders may rely on the enhancement of suitable habitat near current breeding sites by conservation organizations and local stakeholders. Ultimately, the approach used in this thesis emphasizes the value of evaluating habitat within a fragmented landscape to focus conservation efforts on imperilled species.

Author Keywords: amphibians, connectivity, habitat suitability, landscape fragmentation, landscape resistance, unisexual

Species are faced with a variety of challenges in the environment, including natural challenges, such as variability in ambient temperature, and anthropogenic threats, such as habitat transformation associated with urbanisation. Understanding how animals respond to these kinds of challenges can advance the field of behavioural ecology and guide management decisions for wild species. Yet, we still have limited understanding of the extent of natural and human-caused impacts on animal behaviour and population dynamics, and lack robust assessment of behaviour in free-ranging animals. Using novel miniaturised biologging technologies, I characterised and validated behaviour in two freshwater turtle species: Blanding's turtles (Emydoidea blandingii) and Painted turtles (Chrysemys picta). Further, I investigated how these two ectothermic species navigate a thermally heterogeneous landscape near their northern range limit, by comparing selected and available ambient temperatures. I showed that turtles preferred locations that were, on average, warmer and less variable in temperature than the available environment, and that this thermal sensitivity was greatest early in the year, and at fine spatial scales that likely matched the species' perception of the environment. Lastly, I assessed whether urban development was compatible with long-term viability of a Blanding's turtle population, by monitoring habitat change and turtle survival over one decade of ongoing residential and road development. I found that Blanding's turtle habitat quantity and connectivity declined in the area, which coincided with high road mortality and severe declines in turtle survival and population size, especially in adult females. I concluded that urban development and current road mortality rates are incompatible with the long-term viability of this at-risk turtle population. Overall, my findings demonstrate the importance of variation in the thermal environment and anthropogenic impacts on habitat in shaping the behaviour and population dynamics of this species-at-risk.

Author Keywords: animal behaviour, biologging, ectotherms, habitat selection, temperature, urbanisation

Currently there are large areas of the North American landscape that are occupied by Canis spp. hybrids of several varieties, leading to the logical question as to the genetic structure and ecological function of Canis populations across the continent, and to what extent hybrids reflect contemporary landscapes. This study illustrated patterns of niche differentiation between parental canid species and their hybrids using individual high quality genetic profile and species distribution models to support the intermediate phenotype hypothesis. In general, hybrids demonstrated an intermediate habitat suitability compared to its parental species, across most environmental variables used. A similar trend was observed in the niche metric analysis, where we found that hybrids exhibit intermediate niche breadth, with eastern coyotes and eastern wolves exhibiting the broader and narrower niche, respectively. Our results demonstrate that the intermediate phenotype hypothesis is supported even at a large scale and when involving highly mobile large mammal species.

Author Keywords: canid, ecological niche modelling, hybridization, intermediate phenotype, microsatellite genotype, niche differentiation

Many emerging infectious diseases are caused by pathogens that possess free-living life stages, in which they interact with the environment directly rather than through the mediation of a host. These diseases represent major impediments to wildlife conservation; however, the dynamics of their interaction with the environment are poorly studied, often due to the difficulty of detecting these microscopic pathogens in environmental samples. One of these pathogens is Batrachochytrium dendrobatidis (Bd), a fungus that has been linked to declines in many amphibian species. In this thesis I use an emerging technique, environmental DNA detection (eDNA), to detect and quantify Bd in the water of southern Ontario (Canada) wetlands and examine its correlation with a variety of aspects of water quality, surrounding habitat, and seasonal timing. My purpose was to inform not only on potential environment-pathogen dynamics for Bd in northern environments, but to provide insight into the use of eDNA as a disease surveillance tool. I found that not only was there high geographic variation in Bd detection and intensity, but also high temporal variation within the same site on time scales as low as two weeks. While Bd prevalence was not strongly correlated with any of the variables tested, intensity showed strong correlation with canopy cover, with greater canopy cover over a waterbody correlating to lower Bd intensity. My results present several promising avenues for further examination of Bd in northern ecosystems, and indicate that, while caution is warranted in its implementation, eDNA may become an important tool in amphibian pathogen surveillance.

Author Keywords: amphibian disease, Batrachochytrium dendrobatidis, disease monitoring, environment-pathogen dynamics, environmental DNA, wildlife disease

Many facilities attempt to alleviate the risk of chronic stress in captivity by providing environmental enrichment shown to minimize behavioural disorders and stress in several species. One potential form of enrichment used in zoos is training animals to perform rides for guests, however, the effect of this activity on the welfare of individual animals has never been examined. I validated the use of saliva for assessing stress in dromedary camels (Camelus dromedarius) an animal commonly used for rides. I then measured variation in salivary cortisol in four male camels during animal rides for guests at the Toronto Zoo. The camels were sampled during the ride season (from June to August) using four treatments: 1) in their pasture, 2) at the ride area not performing rides, 3) performing a low number of rides (n=50/day) and 4) performing a high number of rides (n=150/day). Furthermore, samples were taken before and after the ride season for comparison. There was a significant difference between the post-ride season treatment and the three treatments involving guest presence during the ride season (ride area, low rides, high rides. This indicates that performing rides is not a stressful experience based on the stress metrics I used, and suggests that rides may be a form of enrichment for dromedary camels.

Author Keywords: ACTH challenge, animal welfare, camels, environmental enrichment, salivary cortisol, stress

Competition is known to impact population dynamics through both indirect and direct interactions, and direct interactions can often lead to injury in one or both parties. As such, response to injury through tissue regeneration can be important for surviving post-competitive interaction. However, the impacts of outside factors like temperature and genome size (e.g. polyploidy) are not well studied, especially in syntopic systems. We addressed this knowledge gap by comparing regeneration rates of diploid Ambystoma laterale and triploid unisexual Ambystoma at two ecologically-relevant temperatures. Environmental factors appeared to have stronger effects on regeneration than ploidy level, but overall mass was impacted more strongly by ploidy level. Interestingly, there was an interaction between temperature and time within unisexuals that was absent when comparing different ploidy levels, implying temperature has a more complex effect on polyploids. This study supports the hypothesis that polyploid organisms are better equipped to respond to shifts in their environments, which can give them a competitive advantage at the northern range limit of this species complex.

Author Keywords: Ambystoma, Genome dosage, Hybrid vigor, Polyploidy, Thermal optimum, Tissue regeneration