Ecology

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

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

Animals are essential to freshwater biogeochemistry and productivity. Through their excretion, aquatic consumers release bioavailable nutrients and carbon that can vary with animal taxonomic rank, trophic position, and abiotic factors such as light and nutrient supply. In fresh waters, light and nutrient supply is often modulated by dissolved organic matter (DOM), a "murky" component in the water that gives it a brown color and that may indirectly affect animal nutrient and carbon excretion. Additionally, contaminants can impact animal physiology, altering metabolism and inducing stress, further affecting nutrient and contaminant excretion. The size and structure of the ecosystem, including community composition and biomass, can also impact the contribution of aquatic animals to the elemental pool. To understand these dynamics, I examined animal‐mediated elemental cycling in freshwater ecosystems across gradients of DOM concentration and composition and under contaminant exposure. I tested fish and invertebrate nitrogen, phosphorus, and DOM excretion across trophic positions during two sampling events in Lake Erie and in naturally DOM-variable streams and lakes. I also investigated the effects of chronic exposure to silver nanoparticles (AgNP) under environmentally relevant conditions on fish nutrient and silver (Ag) release. I found that aquatic animals can be a substantial nutrient contributor to the nutrient pool, particularly when their population biomass is high and ambient nutrient concentrations are low. I also detected nonlinear relationships between animal nutrient excretion and DOM characteristics that varied with taxonomic rank and trophic position and that dampened at larger ecological scales. Importantly, I identified several fish DOM excretion signatures that differed relative to ambient DOM and reported the first fish Ag excretion rates under AgNPs exposure. My results underscore the context-dependency and variability inherent in animal-mediated elemental cycling, highlighting the critical role of animals as both modifiers and conduits of nutrients, DOM, and contaminants in aquatic ecosystems.

Author Keywords: carbon, consumer-nutrient driven dynamics, ecological stoichiometry, nitrogen, phosphorus, silver nanoparticles

We studied the physiological and molecular responses of lab-grown Daphnia pulex to shifts in dietary (carbon, nitrogen, phosphorus, and cyanobacteria) and growth media (calcium) nutrient supply using a set of potential biomarkers via qPCR. Each examined nutrient had a strong effect on Daphnia mass-specific growth rate, and we found significant dose-dependent effects of treatment level (medium and low) on the gene expression of selected indicator genes. Furthermore, linear discriminant analysis models using different combinations of treatment levels could separate the animals between nutritional treatments with 86-100% prediction accuracy. This would suggest that Daphnia appear able to respond to nutrient limitation by adjusting their growth rate and associated molecular pathways to deal with an insufficient supply of nutrients. While this study provides valuable information regarding Daphnia's ability to adjust physiological and molecular processes under controlled laboratory conditions, more validation needs to be conducted before applying these potential biomarkers to wild populations to assess the type and intensity of nutritional stress.

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

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

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