Wildlife conservation

Animal migration is defined as the seasonal movement from one independent and non-overlapping range to another. Understanding how and why animals migrate is important not only to understand their life history processes but also for informing other important ecological processes such as the spread of wildlife disease and habitat alteration. Animal migrations have been impacted by human activity with instances of complete loss of migrations in human-altered areas. Understanding the drivers of migration can help predict responses to future environmental changes and potentially help conserve these phenomena. Seasonal movements of white-tailed deer (deer; Odocoileus virginianus; Zimmerman, 1780) have been linked to seasonal changes in environmental conditions that impact their ability to find food resources and risk of predation. The human shield hypothesis posits that prey species will select habitat close to people to use predator fear of humans to protect themselves from predation. Using global positioning system (GPS) collars, we examined the onset of deer migrations and assessed how environmental variables including snow, temperature, and plant biomass influenced migration departure dates using time-to-event models. We compared deer locations to data from GPS collared coyotes (Canis latrans; Say, 1823) within the same study area to explore daily space-use differences and examine if deer migrations were food or predation-risk driven using generalized linear mixed effects regression models. We found substantial annual and individual variation in deer migration dates. Snow depth was the strongest and most consistent predictor of deer migration, with individuals departing earlier with greater snow depth. Our regression analyses showed that deer selected for habitats closer to and with greater density of anthropogenic structures than coyotes at all times. After removing the animal locations close to areas with active supplemental feeding, these effects were diminished showing no differences in proximity or density of structures. Overall, we found more support for a food driven migration rather than a predator driven human shield. With the reduction in natural food caused by snow cover, we suggest that supplemental feeding is likely influencing the use of wintering areas by deer. The high proportion of deer migrating to human developed areas with supplemental feeders highlights the need for continued research into the impacts of human activity on animal behaviour.

Author Keywords: coyote, human shield, migration, supplemental feeding, white-tailed deer

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.

Estimation of population abundance from samples has inherent practical challenges. Moreover, analytical methods to estimate abundance may vary in statistical assumptions and prediction uncertainties. I evaluated the performance of design-based and model-based methods to estimate Canada geese (Branta canadensis) abundance based on aerial fixed-width transect surveys in the Hudson Bay Lowlands, Canada. I evaluated Empirical Bayesian Kriging (EBK), areal interpolation and a ratio estimator on the basis of accuracy and precision using spatial point simulations. Untransformed EBK was the most accurate and precise, due in part, to its inherent handling of nonstationary distributions. The ratio estimator followed the same trends as EBK and, in some cases, had higher precision. Consideration of alternative analytical methods and their strengths and weaknesses is an important step in generating reliable information for population monitoring. Geostatistical approaches such as EBK have the benefit of providing spatially explicit mapping of abundance and reliable population estimates.

Author Keywords: Areal interpolation, Design-based inference, Empirical Bayesian Kriging, Geostatistics, Model-based inference, Ratio estimator

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

Muskrat populations are declining across North America. In recent decades, hybrid cattail Typha x glauca has been invading wetlands in North America. This invasion is degrading wetland habitat, leading to reduced interspersion of water and vegetation. Muskrats are wetland-obligates and their populations are positively linked to marsh interspersion. Therefore, muskrat populations may be declining due to the invasion of T. x glauca and subsequent reduction in interspersion. To test this hypothesis, I first sampled marshes across south-central Ontario, comparing muskrat densities with the relative frequency of T. x glauca and the degree of interspersion. Second, I measured intensity of use by muskrats in a large wetland along a gradient of interspersion. My findings suggest that reduced interspersion may be contributing to muskrat population declines, but it is unclear to what degree T. x glauca is responsible. Further research is needed to understand the effects of wetland invasions on muskrat populations.

Author Keywords: invasive species, Ondatra zibethicus, Southern Ontario, Typha x glauca, wetlands, wildlife conservation

Understanding habitat needs of a species is critical, especially for species reintroduced to an area or expanding their range. I evaluated roost tree selection and survival probability of GPS-tagged eastern wild turkeys (Meleagris gallopavo silvestris) from 2017–2020 and 2022 in Peterborough County, Ontario, Canada. Fine-scale roost tree selection was associated with larger trees, with microclimate factors such as wind speed, temperature, and precipitation having little to no influence. Turkeys showed high annual survival probabilities relative to other northern regions of their range, but survival was not influenced by proximity of roost tree to a building. The behaviour of roosting in an elevated perch helps turkeys avoid ground-dwelling predators, but specific selection of one tree versus another has little additional benefit to survival. Turkeys appear to survive well in a landscape that is a mix of agricultural and urban, with forest patches intact for roosting habitat.

Author Keywords: Eastern wild turkey, habitat, Meleagris gallopavo silvestris, microclimate, roost sites, survival

Trait variation in wild populations is shaped by the interaction of genetics and the environment. Given these interactions, this thesis explored trait variation in white-tailed deer from two angles: one focused on broad-scale environmental factors, the other on fine-scale genetic mechanisms. The first chapter investigated how climate and habitat variation influence antler size, morphology, and the distribution of record-scoring deer across Ontario, Canada. Our results showed that warmer temperatures and higher percentages of rangeland and forest landcover were linked to larger antlers, while harsher winters with more precipitation had negative effects. The second chapter described the development of novel SNP assays designed to target genetic markers associated with leucism and malocclusions in an isolated island population of white-tailed deer. Together, these results highlight the importance of considering both environmental and genetic factors to understand trait variation in white-tailed deer.

Author Keywords: antlers, Odocoileus virginianus, phenotypic variation, Runs of homozygosity, white-tailed deer

Quantifying the impacts of environmental conditions on the abundance of wildlife populations is important for making informed management decisions in the face of increasing environmental threats. Managers require robust tools to estimate abundance and density of wildlife rapidly and with precision. Within the context of studying white-tailed deer, I evaluated the use of camera-traps and a recently developed spatial-mark resight model to estimate deer density and evaluate habitat and land use factors influencing deer density. The study was conducted in central Ontario, Canada on approximately 16 km2 of public land including the protected Peterborough Crown Game Preserve. Telemetry locations from 39 radio-collared deer were used and one hundred camera-traps were deployed for a total of 140 days from January 2022 to May 2022. Using telemetry locations and camera-trap photos I built a two-step spatial-mark resight model to estimate deer density. Deer density varied during the study as a portion of the population migrated to wintering areas outside of the study area. Despite fluctuations in precision, estimates improved towards the end of the study as more data became available and deer space use stabilized. The average deer density during the entire study was 3.0 deer/km2 (95% CI= 0.1, 5.8; SD= 1.7; CV= 55%; N= 238 deer). The lowest mean density was 0.2 deer/km2 (95% CI= 0.1, 0.4; SD= 0.1; CV= 50%; N= 15 deer) from February 26th to March 11th and the highest mean density was 4.8 deer/km2 (95% CI= 3.1, 6.2; SD= 0.8; CV= 17%; N= 378 deer) from May 7th to May 20th. When I incorporated spatial covariates into the model to estimate effects on deer density, higher proportions of mixed forest, deciduous forest, and road and trail density all had negative effects on deer density. While models contained some uncertainty, deer density appeared higher in the portion of the study area protected from licensed hunting. This thesis provides a framework for managers to use camera-traps and the spatial-mark resight model to monitor deer populations and link environmental covariates to spatial variation in density. As environmental threats such as habitat loss and infectious diseases increase in severity, monitoring wildlife population numbers will be vital for informed responses to these threats. The two-step spatial-mark resight model with environmental covariates provides managers with a long-term monitoring tool to evaluate management efforts and population health in forested areas.

Author Keywords: camera-trap, chronic wasting disease, landscape ecology, spatial-capture recapture, white-tailed deer, wildlife management

Climate change affects birds' reproductive ecology by altering breeding timing, distribution, and habitat suitability. Snowmelt patterns complicate these changes affecting habitat availability and suitability for birds and their arthropod prey. Snow varies as a function of both large-scale climate patterns and local-scale topography. I used elevational gradients as a proxy for local- scale snow impacts, investigating how elevation affects arthropod abundance, and nest placement, initiation, fate, and habitat for Lapland Longspur (Calcarius lapponicus) and Semipalmated Sandpiper (Calidris pusilla) north of Baker Lake, Nunavut. I found and monitored nests over multiple breeding seasons and used pitfall traps and conducted vegetation surveys. Results show that elevation significantly affects arthropod biomass and nest placement, but not nest initiation or success. Both species preferentially nested at lower elevations with higher arthropod biomass. Thus, birds in the central Arctic choose nesting sites at lower elevations with better food availability rather than higher elevations with earlier snowmelt.

Author Keywords: Arctic, arthropod biomass, Lapland Longspur, nest site selection, nest success, Semipalmated Sandpiper

Heterogeneous environments impose discordant selective pressures on natural populations, where disparate biotic/abiotic factors and variable population connectivity, yield mosaic patterns of genetic variation on the landscape. The ability to maintain or change genetic mosaics of populations becomes key to persistence, as species increasingly need to adapt to rapidly changing environmental and human-associated selective pressures. Specifically, infectious diseases can impose strong and rapid selective pressures on populations, where anthropogenic disruptions of co-evolutionary patterns and altered distributions of hosts and pathogens exacerbate disease risk. Genomic tools provide means to evaluate disease-associated impacts on the genetic landscape of host populations and facilitate implementation of informed conservation efforts. In this thesis, I evaluate disease dynamics in: 1) a long-standing arctic rabies/arctic fox (Vulpes lagopus) system affected by influxes of red fox (V. vulpes), and 2) an invasive bat pathogen system, where the North American introduction of Pseudogymnoascus destructans (Pd) has had variable impacts on bat species and populations. In these systems, signatures of host selection were estimated from temporal and spatial shifts in allelic diversity within genomic regions associated with immune response, highlighting different host mechanisms to enzootic and invasive diseases. In the arctic rabies/fox system, pathogen variants did not influence red fox local disease responses, reflecting more recent expansions of this host to Arctic regions. In contrast, arctic fox revealed genomic patterns consistent with long-term, co-evolutionary processes. In Pd/bat systems, genomic evidence supported the hypothesis that eastern small-footed bats (Myotis leibii) were inherently resistant or tolerant to Pd, the causative agent of white-nose syndrome (WNS). In contrast, WNS-impacted little brown bat (M. lucifugus) populations had varied genomic impacts subsequent to strong selective sweeps from disease. My research illustrates how immunogenetic profiling, in context of demographic processes inferred from neutral genetics, enhances understanding of the varied impacts of changing disease landscapes on host populations/species; insights relevant to other host-pathogen systems. Building on this thesis, future explorations of low coverage genomes, host-imposed reciprocal selection, and impacts on methylation, transcriptomic and proteomic patterns associated with shifts in genetic diversity, would enable more holistic understanding of the geographic mosaics within these disease systems.

Author Keywords: Disease Dynamics, High-throughput Sequencing, Immune System, Natural Selection, Population Genetics, Reduced Representation Sequencing