Ecology

I used 31 years of Semipalmated Plover (Charadrius semipalmatus) population data to assess the effects of vital rates on a local breeding population of plovers in Churchill, Manitoba, Canada. I used three similar Bayesian Integrated Population Models (IPMs), with the last a coupled IPM population viability analysis (PVA) approach to predict the impact of changing spring temperatures on future population size. I estimated adult and juvenile apparent survival, fecundity, immigration rate, and yearly population size estimates, and I found that population growth rate was most highly correlated with immigration and adult apparent survival. Moreover, I found that the population remained relatively stationary with a slight decline in recent years. I also found a significant positive effect of spring average daily minimum temperature on juvenile apparent survival. I used this effect to inform my PVA and to evaluate the risk of quasi-extinction for 20 years after the end of the study. I found a low quasi-extinction risk and a greater probability of the population increasing in the next twenty years when informed by predicted spring temperatures from global climate models. My findings suggest some resilience of this species to one effect of climate change and emphasize the importance of continued monitoring to assess if declines in this species will change as multiple threats to their existence in the sub-arctic progress.

Author Keywords: Bayesian, Climate change, Integrated population model, Population dynamics, Population viability, Semipalmated Plover

Animal migrations are ubiquitous and one of the most threatened ecological processes globally. Because of the multifaceted nature of migration – seasonal movements between home ranges – it can be difficult to tease apart the underlying mechanisms influencing this behaviour. It is necessary to understand these mechanisms, not only to deepen our fundamental understanding of migration in animals, but also because migrations in many species are vulnerable to environmental change. In Chapter 2, I first systematically identify the broad proximate drivers of migration and offer generalities across vertebrate taxa. I quantitatively reviewed 45 studies and extracted 132 observations of effect sizes for internal and external proximate drivers that influenced migration propensity. Through this meta-analysis, I found that internal and external drivers had a medium and large effect, respectively, on migration propensity. Predator abundance and predation risk had a large effect on migration propensity, as did individual behaviour. Of the studies that examined genetic divergence between migrant and resident populations, 64% found some genetic divergence between groups. In Chapter 3, I explore the genetic basis for migration and identified genes associated with migration direction from pooled genome-wide scans on a population of 233 migrating female mule deer (Odocoileus hemionus) where I identified genomic regions including FITM1, a gene linked to the formation of lipids, and DPPA3, a gene linked to epigenetic modifications of the maternal line. These results are consistent with the underlying genetic basis for a migratory trait which contributes to the additive genetic variance influencing migratory behaviours and can affect the adaptive potential of a species. Finally, in Chapter 4 I used a pedigree-free quantitative genetic approach to estimate heritability and sources of environmental variation in migration distance, timing, and movement rate of the same population of mule deer. I found low heritability for broad patterns of migration timing, and greater variation in heritability for behaviours during migration, with low heritability for distance and duration and high heritability for movement rate along the route. Insights into the genetic and environmental sources of variation for migration are critical both for the eco-evolutionary dynamics of migration behaviour, and for the conservation of species whose migrations may be vulnerable to environmental change. My thesis reveals that broad patterns of migration are driven largely by environmental effects while within these broad patterns, migration behaviour is driven to a measurable degree by genetic variation.

Author Keywords: heritability, migration, Odocoileus hemionus, reduced representation sequencing, whole genome sequencing

Many species of shorebirds depend on stopover sites to rest and refuel during their long-distance migrations. To determine how shorebirds use migratory stopover sites, we tracked three species of shorebirds at two stopover sites in British Columbia, Canada from 2018-2021 during northward and southward migration using automated telemetry. Western Sandpipers (Calidris mauri) stayed longer at the Fraser River Estuary (4-8 days) compared to Tofino (2-6 days). We assessed habitat use of Sanderlings (Calidris alba), Semipalmated Plovers (Charadrius semipalmatus), and Western Sandpipers between beaches and mudflat at the Tofino stopover site. Time spent at the beach and mudflat habitats varied by species, tidal period, time of day, migration period, and human disturbance. This study shows that different stopover sites, and habitats within stopover sites, offer a unique set of characteristics used by birds exhibiting varying migration strategies, highlighting the importance of conserving a diversity of migration stopover locations and habitats.

Author Keywords: habitat use, human disturbance, length of stay, migration, shorebird, stopover site

In situ chlorophyll sensors are beneficial for monitoring of long-term impacts of algal blooms and accessing water quality issues in bodies of water. However, more research is needed to validate their efficacy and understand how environmental conditions can influence sensor measurements. I assessed the performance of an in situ chlorophyll sensor under controlled environmental conditions and used the same sensor to collect vertical phytoplankton patterns in south-central Ontario boreal lakes. The performance of the sensor was assessed by examining the precision of chlorophyll measurements and determining the suitable timing length that would produce precise results. In general, the sensor was relatively insensitive to conditions under lower algal concentrations and the decent of the sensor should be slowed for vertical lake profiling in lakes with higher algal biomass. Most variation resulted from the movement of particle bound algal cells. We described chlorophyll profile characteristics including surface chlorophyll levels and chlorophyll peak depth and width and investigated the relationships of these features with environmental controls. The lakes showed a typical chlorophyll profile of low phytoplankton biomass lakes. Our results showed that dissolved organic carbon was a strong predictor of epilimnetic biomass while light attenuation and dissolved organic carbon were both strong predictors of peak depth. Light attenuation and surface area were small but significant predictors of peak width. We acknowledged that any uncertainties in sensor chlorophyll readings were not an issue in our lakes due to the overall low chlorophyll biomass.

Author Keywords: chlorophyll, chlorophyll fluorescence, in situ profiling, lakes, phytoplankton biomass, water quality 

White-nose syndrome (WNS) is a skin disease of bats caused by the fungus Pseudogymnoascus destructans (Pd) that damages flight membranes during hibernation and can lead to death. The disease causes mortality of multiple bat species in eastern North America and is spreading into western North America. Future impacts of WNS on naïve bat populations are unknown. Variation in host susceptibility occurs among and within species, but mechanisms driving this variation are unclear. Multiple studies have characterized immunological responses to WNS, but skin physiology as a barrier to pathogens is understudied. The unique ability of Pd to actively penetrate the normal, intact skin of its mammalian host makes WNS an interesting study system to understand skin defenses. Aspects of the mammalian skin environment that can influence disease susceptibility include pH, sebaceous lipids, and microbiomes. I found skin mycobiomes of WNS-susceptible species had significantly lower alpha diversity and abundance compared to bat species resistant to Pd infection. Using these data, I predicted that most naïve bat species in western North America will be susceptible to WNS based on the low diversity of their skin mycobiomes. Some fungi isolated from bat wings inhibited Pd growth in vitro, but only under specific salinity and pH conditions, suggesting the microenvironment on wings can influence microbial interactions and potentially WNS-susceptibility. I measured the wing-skin pH of bats in eastern Canada and found that Eptesicus fuscus (WNS-tolerant) had more acidic skin than M. lucifugus (WNS-susceptible). Differences in sebum quantity and composition among and within mammalian species may help explain variation in skin disease susceptibility and the composition of skin microbiomes. This is due to the antimicrobial properties of sebum and the use of sebum as a nutrition source by microbes. Outcomes of this work further our understanding of inter- and intra-specific differences among bat species and individuals in skin mycobiomes and physiology, which may contribute to variation in WNS-susceptibility. Future research should focus on characterizing the physical and chemical landscape of skin as this is essential for understanding mechanisms structuring skin microbial assemblages and skin disease susceptibility in wildlife.

Author Keywords: bat, fungi, microbiome, mycology, physiology, white-nose syndrome

Increased plant size is expected to have negative consequences for mating by increasing pollen transfer among the same plant. However, recent theoretical studies have demonstrated that this may not be true for clonal plants. Instead, clonal expansion could enhance outcrossing opportunities without increasing selfing by reducing distances to potential mates. I investigated how the spatial structure of clones influences patterns of pollen dispersal, selfing rates and siring success in a natural population of Sagittaria latifolia. I found that pollen dispersal distances typically exceeded the spatial extent of clones and there was a positive association between clone size and the likelihood that clones were intermingled. Together, this resulted in a weak positive association between clone size and selfing rates, and a strong positive association between clone size and outcross siring success. This is the first empirical support for the theoretical expectation that any negative effects of selfing in large clones might be offset by increased siring success.

Author Keywords: clonal growth, fitness gain curve, geitonogamy, plant mating, plant reproductive ecology, sex allocation theory

AbstractDifferences and similarities in exploration and risk-taking behaviours of two Myotis bat species. Laura Michele Scott Behaviours that are repeatable across circumstances and time determine an individual's personality. Personality and behavioural variation are subject to selective pressures, including risks related to the use of different habitat types. I explored the ecological and evolutionary consequences of habitat selection by comparing the behaviour of two sympatric bat species, Myotis leibii and M. lucifugus. These species display overlap in roosting preferences, however, M. leibii tend to roost in crevices on the ground, while M. lucifugus tend to roost in crevices or cavities that are raised off the ground. I hypothesized that the habitat selection patterns of these two species create behavioural reaction norms at the species level. I predicted that ground roosting behaviour favours bolder personality and more exploratory and active traits when compared with bats that do not ground roost. I examined inter- and intra-specific variation in behaviour using a modified, three-dimensional open-field test and quantified the frequency and duration of behaviours such as flying, landing, and crawling. Bats were continuously video-recorded over 1-hour nocturnal and diurnal trials. I used a priori mixed models with combinations of individual characteristics and life-history traits to select the models that best describe each species. We found that M. leibii (n = 15) displayed more exploratory and bolder behaviours than M. lucifugus while on the ground (n = 21) and higher overall activity during the trial. I also found that M. leibii displayed crawling behaviours and movements consistent with foraging while on the ground which is a rare behaviour in bats and only observed in a few species (Desmodus rotundus and Mystacina tuberculate to my knowledge). Future research should explore biomechanical adaptations associated with ground-foraging in M. leibii.

Author Keywords: Bats, Behaviour, Exploration, Myotis leibii, Myotis lucifugus, Roosting

Walleye (Sander vitreus) are an ecologically and economically significant fish harvestedby recreational and commercial fisheries across Ontario. Adult Walleye are piscivores, but anecdotal evidence from anglers suggests that Walleye often target aquatic insects such as mayfly larvae (Ephemeroptera). My research examined the diet of Walleye caught from May to September in Lake St. Joseph in northern Ontario. I examined the stomach contents of angle harvested Walleye to identify the prey over two summers. Through morphological analysis of stomach contents, mayflies were found to be a significant prey source for Walleye, during larval emergence events in early summer, and to a lesser extent throughout the rest of the summer season. These findings are important for long term management of Walleye populations and associated resources. I also assess the potential and problems of Walleye management and research from my experiences of having worked with industry, government, and university partners on this project.

Author Keywords: alternative prey, Food web interactions, invertebrate, piscivore, Predator prey interactions

Rapidly changing landscapes introduce challenges for wildlife management, particularly for large mammal populations with long generation times and extensive spatial requirements. Understanding how these populations interact with heterogeneous landscapes aids in predicting responses to further environmental change. In this thesis, I profile American black bears using microsatellite loci and pooled whole-genome sequencing. These data characterize gene flow directionality and functional genetic variation to understand patterns of dispersal and local adaptation; processes key to understanding vulnerability to environmental change. I show dispersal is positively density-dependent, male biased, and influenced by food productivity gradients suggestive of source-sink dynamics. Genomic comparison of bears inhabiting different climate and forest zones identified variation in genes related to the cellular response to starvation and cold. My thesis demonstrates source-sink dynamics and local adaption in black bears. Population management must balance dispersal to sustain declining populations against the risk of maladaptation under future scenarios of environmental change.

Author Keywords: American black bear, Dispersal, Functional Genetic Variation, Gene Flow Directionality, Genomics, Local Adaptation

Organismal nutrition lies at the interface between biotic and abiotic factors in an ecosystem, dictating the transfer of energy and nutrients across trophic levels. Our ability to detect nutritional limitation in consumers is reliant on a priori knowledge of dietary history due to our inability to differentiate nutrient stress based on body-wide responses. Molecular physiological responses are increasingly being used to measure physiological stress with high levels of specificity due to the specific modes of action ecological stressors have on organismal molecular physiology. Because animal consumers respond to varying nutrient supplies by up- and down-regulating nutrient-specific metabolic pathways, we can quantify nutritional status by quantifying the expression of those pathways. Here I present an investigation into the use of transcriptomics to detect nutritional stress in the keystone aquatic herbivore, Daphnia pulex, I use RNAseq and quantitative PCR (qPCR) identify nutritional indicator genes. I found that nutritional status could be determined with 100% accuracy with just ten genes. Additionally, the functional annotation of those genes uncovered previously unidentified responses to dietary stress. Further testing and validation of the selected indicator genes is required however these findings have the potential to revolutionize our ability to measure and monitor consumer nutritional stress.

Author Keywords: Biomarkers, Daphnia, Gene expression, Nutrigenomics, Nutritional ecology, RNAseq