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.

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

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

Understanding the spatial ecology of large carnivores in increasingly complex, multi-use landscapes is critical for effective conservation and management. Complementary to this need are robust monitoring and statistical techniques to understand the effect of bottom-up and top-down processes on wildlife population densities. However, for wide-ranging species, such knowledge is often hindered by difficulties in conducting studies over large spatial extents to fully capture the range of processes influencing populations. This thesis addresses research gaps in the above themes in the context of the American black bear (Ursus americanus) in the multi-use landscape of Ontario, Canada. First, I assess the performance of a widely adopted statistical modelling technique – spatially explicit capture-recapture (SECR) – for estimating densities of large carnivores (Chapter 2). Using simulations, I demonstrate that while SECR models are generally robust to unmodeled spatial and sex-based variation in populations, ignoring high levels of this variation can lead to bias with consequences for management and conservation. In Chapter 3, I investigate fine-scale drivers of black bear population density within study areas and forest regions by applying SECR models to a large-scale, multi-year black bear spatial capture-recapture dataset. To identify more generalizable patterns, in Chapter 4 I then assess patterns of black bear density across the province and within forest regions as a function of coarse landscape-level factors using the same datasets and assess the trade-offs between three different modeling techniques. Environmental variables were important drivers of black bear density across the province, while anthropogenic variables were more important in structuring finer-scale space use within study areas. Within forest regions these variables acted as both bottom-up and top-down processes that were consistent with ecological influences on black bear foods and intensity of human influences on the species' avoidance of developed habitats. Collectively, this thesis highlights the opportunities and challenges of working across multiple scales and over expansive landscapes within a SECR framework. Specifically, the multi-scale approach of this thesis allows for robust inference of the mechanisms structuring fine and broad scale patterns in black bear densities and offers insight to the relative influence of top-down and bottom-up forces in driving these patterns. Taken together, this thesis provides an approach for monitoring large carnivore population dynamics that can be leveraged for the species conservation and management in increasingly human-modified landscapes.

Author Keywords: animal abundance, black bear, capture-recapture, density estimation, statistical ecology, wildlife management

Roosts offer bats protection from predators, shelter from external environmental conditions, and a space where sociality, mating, and the rearing of young can occur. However, knowledge gaps still remain for many forest roosting species, such as the little brown bat (Myotis lucifugus) surrounding what roosts are selected, and what variables are influential at differing scales of selection. As a species-at-risk, identifying and predicting roost habitat selection may aid conservation and management. I identified forest roosts in a previously unexamined area of this species' range using radio-telemetry, and measured tree-scale characteristics of located roosts. I then used a logistic model selection process with stand-scale variables to predict roost presence across forest stands. Height of trees in a given stand was the best predictor of roost presence - which may be linked to solar exposure and other thermal benefits. I then examined roost-level variables effecting the abundance of roosting bats in an artificial roosting environment (bat boxes). I found that temperature and social effects were both significant predictors of bat abundance, with warmer minimum temperatures in the box having a positive effect. These results suggest maternal bats may select roosts with higher minimum temperatures, likely due to the energetic benefits that may be gained over the course of reproduction.

Author Keywords: forest roost, habitat selection, little brown bat, Myotic lucifugus, roost choice, stand selection

I used the Motus Wildlife Tracking System to monitor the fall migration behaviour and assess the underlying drivers of migration strategy in a small shorebird, the Semipalmated Plover (Charadrius semipalmatus), breeding at two subarctic sites: Churchill, Manitoba and Burntpoint Creek, Ontario, Canada. Semipalmated Plovers from both sites departed breeding areas between mid-July and early August, with females preceding males and failed breeders preceding successful breeders. Migrants showed between and within-population variation in migration behaviour, though birds from both sites tended to follow interior or coastal routes and congregated in three major stopover regions along the mid-Atlantic coast of North America. I found that later-departing birds had initial flight tracks oriented more toward the south, faster overall ground speeds, were less likely to stopover in North America, and stopped at lower latitudes, suggesting that later-departing individuals use aspects of a time-minimizing strategy on fall migration. My findings emphasize the importance of the mid-Atlantic coast for Semipalmated Plovers and establish connectivity between sites used during breeding and migration.

Author Keywords: Breeding, Migration, Motus, Semipalmated Plover, Shorebird, Stopover

Habitat loss and fragmentation can disrupt population connectivity, resulting in small, isolated populations and low genetic variability. Understanding connectivity patterns in space and time is critical in conservation and management planning, especially for wide-ranging species in northern latitudes where habitats are becoming increasingly fragmented. Wolverines (Gulo gulo) share similar life history traits observed in large-sized carnivores, and their low resiliency to disturbances limits wolverine persistence in modified or fragmented landscapes - making them a good indicator species for habitat connectivity. In this thesis, I used neutral microsatellite and mitochondrial DNA markers to investigate genetic connectivity patterns of wolverines for different temporal and spatial scales. Population genetic analyses of individuals from North America suggested wolverines west of James Bay in Canada are structured into two contemporary genetic clusters: an extant cluster at the eastern periphery of Manitoba and Ontario, and a northwestern core cluster. Haplotypic composition, however, suggested longstanding differences between the extant eastern periphery and northwestern core clusters. Phylogeographic analyses across the wolverine's Holarctic distribution supported a postglacial expansion from a glacial refugium near Beringia. Although Approximate Bayesian computations suggested a west-to-east stepping-stone divergence pattern across North America, a mismatch distribution indicated a historic bottleneck event approximately 400 generations ago likely influenced present-day patterns of haplotype distribution. I also used an individual-based genetic distance measure to identify landscape features potentially influencing pairwise genetic distances of wolverines in Manitoba and Ontario. Road density and mean spring snow cover were positively associated with genetic distances. Road density was associated with female genetic distance, while spring snow cover variance was associated with male genetic distance. My findings suggest that northward expanding anthropogenic disturbances have the potential to affect genetic connectivity. Overall, my findings suggest that (1) peripheral populations can harbour genetic variants not observed in core populations - increasing species genetic diversity; (2) historic bottlenecks can alter the genetic signature of glacial refugia, resulting in a disjunct distribution of unique genetic variants among contemporary populations; (3) increased temporal resolution of the individual-based genetic distance measure can help identify landscape features associated with genetic connectivity within a population, which may disrupt landscape connectivity.

Author Keywords: conservation genetics, Holarctic species, landscape genetics, peripheral population, phylogeography, wolverine

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