Ecology

Anthropogenic activities such as human activity and livestock grazing are responsible for the global rise in disturbance impacts on wildlife and may underlie regional changes in biodiversity and ecosystem dynamics. Few studies have tried to disentangle the effects of different anthropogenic activities on wildlife behaviour, leaving a major gap in our understanding of conservation and management needs in disturbed areas. Human activity and livestock grazing are increasing in spread and intensity worldwide, thereby imposing pressure on both wildlife and natural areas. In this thesis, I used a camera trapping and occupancy modeling framework to assess whether human presence and livestock grazing had different impacts on site occupancy and activity of 10 wild mammal species, and how responses differed across taxa. Specifically, I predicted that all species would be sensitive to disturbance, but the type and intensity of the response would depend on disturbance type. I detected different responses to each disturbance type across species, but response type (displacement, activity change, crepuscularity) was not associated with species characteristics such as body. Importantly, disturbance intensity had a strong effect on wildlife activity levels, with many species exhibiting marked reductions in activity at high human or livestock disturbance intensity. It remains unclear whether all species' responses are a direct consequence of disturbance versus indirect outcomes of shifts in behaviour of other species in the wildlife community (i.e., disturbance-related changes in prey activity may affect predator activity). Although on the whole disturbance intensity and effect sizes tended to be relatively low in this study, responses were exhibited across all species, implying that disturbance responses may be universal in wild mammals and largely underestimated. Ultimately, my work offers a template for the robust assessment of disturbance impacts on wildlife and provides new avenues for future research to deepen our understanding of wildlife sensitivity to anthropogenic activities.

Author Keywords: activity, anthropogenic disturbance, human activity, livestock, occupancy, wildlife

In recent decades, declining calcium concentrations have been reported throughout lakes across the southern edge of the Canadian Shield. This raises concern as Daphnia populations have shown to be decreasing as they require calcium not only for survival but to mitigate predation risks. Therefore, the purpose of my thesis was to study the adaptability of Daphnia under calcium limitation and predation risk from Chaoborus. Firstly, I examined the effects of calcium limitation and Chaobours kairomones on daphniid life-history and population growth. I found that low calcium concentrations and Chaoborus kairomones affected Daphnia calcium content, life-history traits, and survival. Next, I focused on how calcium concentrations and Chaoborus abundance affected the calcium content and abundance of daphniids. During this study, I also examined the relationship between the abundance of Daphnia and a competitor Holopedium. I found that calcium concentrations and the abundance of Chaoborus affects daphniid abundance. Overall, results from this study show the importance of considering both predation risk and calcium declines to better determine daphniid losses.

Author Keywords: anti-predator responses, Chaoborus, competition , Life-History traits, predator cues, Zooplankton

Mining and resource development are growing industries in the Arctic, resulting in increased conflict with wildlife. Best practices for mitigation require an understanding of the potential ecological effects. One such effect concerns the flooding of terrestrial bird habitat from dewatering of lakes during mining pit development. I first assessed the efficacy of bird deterrents to mitigate impacts of mining-induced flooding on arctic-nesting birds at a gold mine in Nunavut. I used a Before-After Control Impact (BACI) design to determine changes in male territory densities, between year and treatment types (Control, High and Low Deterrent Intensity). Additionally, I assessed whether deterrents impacted daily survival rates of two passerine species, and the incubation behaviour of female Lapland Longspur. Finally, I quantified nest losses during the breeding season due to direct flooding of the tundra nesting habitat caused by mining operations. Deterrents did not affect male territory densities and neither deterrent treatment nor year affected the daily survival rate of nesting passerines. Female Lapland Longspurs exposed to deterrents exhibited more incubation off-bouts than control females. I documented six flooded nests. Deterrents used in this study appear to be ineffective in mitigating nesting in potential zones of impact. Incidental take accounted for about 1.2% of all nests found in the 0.48 km2 Whale Tail Lake study area.

Author Keywords: arctic-nesting birds, audio deterrents, incidental take, mining and resource development, nest incubation, visual deterrents

Evaluating the impact of climate change is arguably one of the main goals of conservation biology, which can be addressed in part by studying the demographic history of species in the region of interest. In North America, landscape and species composition during the most recent Pleistocene epoch was primarily influenced by glaciation cycles. Glacial advance and retreat caused species ranges to shift as well, leaving signatures of past population bottlenecks in the genetic code of most species. Genomic tools have shown to be important tools for understanding these demographic events to enhance conservation biology measures in several species. In my thesis I first reviewed the state of ungulate genomics, with a focus on how such data sets can be used in understand demography, adaptation, and inform conservation and management. Importantly, the review introduces key analyses like the pairwise sequentially Markovian coalescent and features like variation in antlers and horns and selection pressures that are used throughout subsequent chapters. Using the North American mountain goat as a model species, I then explored the genomic and phenotypic variation in this alpine specialist mammal. Starting with the generation of the first genome assembly for the mountain goat, I identified genes unique to the mountain goat and modeled demographic history going back millions of years using a pairwise sequentially Markovian coalescent approach. Species' effective population size generally paralleled climatic trends over the past one hundred thousand years and severely declined to under a thousand individuals during the last glacial maximum. Given the biological importance of horns in mountain goats and the recent scientific interest in genetic basis of headgear, I analyzed over 23,000 horn records from goats harvested in British Columbia, Alaska and Northwest Territories from 1980 to 2017. Overall, variation in horn size over space and time was low; goats harvested further North had shorter horn lengths and smaller horn circumferences in one year old and 4 years and older age classes and 4 years and older age class, respectively. Proximity of roads, which was used as an indicator of artificial selection, had a small effect on horn size, with larger horns being harvested closer to major roads. Finally, I used two range-wide genomic data sets sequenced with a whole genome re-sequencing and reduced representation approaches to provide estimates of genetic diversity, contemporary effective population sizes and population structure. These insights can help inform management and will potentially make an impact in preserving the mountain goat.

Author Keywords: genome assembly, horn size, Oreamnos americanus, population demography, reduced representation sequencing, whole genome resequencing

Nitrogen is a major constituent of agricultural fertilizers, and nitrogen inputs to stream water via runoff and groundwater lead to a variety of negative environmental impacts. In order to quantify the movement of nitrogen through aquatic food webs, fourteen streams with varying land uses across South-Central Ontario were sampled for two species of fish, freshwater mussels, and water for measurement of isotope ratios of δ15N and δ13C. I found that nitrogen isotopes in fish, water, and mussels were related to the percentage of riparian monoculture, and that carbon isotopes were unrelated to monoculture. Though all species were enriched as monoculture increased, the rate of δ15N enrichment as monoculture increased did not vary between species. This study has improved our understanding of how monoculture affects nutrient enrichment in stream food webs, and assesses the validity of using nitrogen isotopes to measure trophic positions of aquatic organisms across an environmental gradient.

Author Keywords: agriculture, fish, food webs, nitrogen, stable isotopes, streams

Recent declines in growth and condition of Great Lakes' lake whitefish (Coregonus clupeaformis) have been linked to ecosystem-wide changes stemming from the invasion of dreissenid mussels. To test the influence of invasive mussels on this commercially important coregonid species, we collected archived scale samples from ten Great Lake locations and analyzed long-term changes in growth rates, delta 13C and delta 15N stable isotope ratios before and after mussel establishment. There was a decrease in pre-maturation growth after establishment in all four locations where we examined back-calculated growths. In six of the seven locations with dreissenid populations, a significant increase in delta 13C and a significant decrease in delta 15N was found. In dreissenid-absent locations of Lake Superior, we did not see changes in growth or isotope ratios indicative of a major regime shift. Observed shifts in isotopic signatures provide evidence for an increased reliance on nearshore food sources and shallower depth distribution as a result of dreissenids, which likely contributed to lowered growth of lake whitefish.

Author Keywords: Diporeia, Dreissenids, food web, Great Lakes, invasive species, lake whitefish

I implemented three hayfield management regimens in southern Ontario (a typical schedule at the farmer`s discretion, a delayed first harvest after July 14, and an early first harvest before June 1 with 65 days before second harvest), and evaluated the costs/benefits to farmers regarding hay quality and feasibility, and to Bobolinks (Dolichonyx oryzivorus) regarding reproductive activity and phenology. Typical management resulted in little to no Bobolink reproductive success, and early harvested sites were not (re)colonized. On delayed harvest sites Bobolinks experienced high reproductive success, but hay quality fell below ideal protein levels for most cattle before harvest. I also examined the habitat features Bobolinks use as the basis for establishing territories and associations between Bobolink territory size and habitat quality. I compared vegetation structure, patch size, and prey abundance between small and large territories. Small territories typically occurred on smaller fields with more preferred vegetation characteristics and greater prey abundance.

Author Keywords: agro-ecosystem, Bobolink, Dolichonyx oryzivorus, grassland birds, hayfield management

The distribution of animals is rarely random and is affected by various environmental factors. We examined space-use patterns, habitat selection and stress responses of whip-poor-wills to mining exploration activity.To the best of my knowledge, fine scale patterns such as the habitat composition within known home ranges or territories of eastern whip-poor-wills have not been investigated. Using a population at the northern edge of the distribution in an area surrounding a mining exploration site, we tested whether variations in habitat and anthropogenic disturbances influence the stress physiology of individuals. We found no effect of increased mining activity on the stress physiology of birds but found a significant scale-dependent effect of habitat on their baseline and stress-induced corticosterone levels, and we suggest that these are the result of variations in habitat quality. The importance of other factors associated with those habitat differences (e.g., insect availability, predator abundance, and microhabitat features) warrants further research.

Author Keywords: anthropogenic disturbances, Antrostomus vociferus, corticosterone, eastern whip-poor-will, habitat selection, radio-­telemetry

Changes in climate and land-use practices are leading to higher peak flows and increased transport capacity of channel substrate. Semi-alluvial streams underlain by bedrock or clay were examined to understand the potential impacts of alluvium loss on the biological community and overall productive capacity of semi-alluvial rivers. More specifically, this research investigates the productivity of gravels, bedrock, and consolidated clay, through the biomass and density of periphyton, coarse particulate organic matter, benthic invertebrates, and fish. The ecological approach undertaken demonstrates the relationships among each trophic level and linkages to productive capacity between different substrate types. Significant results were detected at the stream type level and substrate level. Bedrock-based streams were overall more productive in terms of CPOM, biomass and density of benthos in comparison to clay-based streams. Stream reaches with small to large areas of exposed bedrock or clay at the site level did not differ to areas with 100% gravel coverage in the comparison of any variable, including stream fishes. At the substrate level, gravels demonstrated the highest productive capacity in comparison to bedrock and clay substrates. CPOM biomass in gravels compared to bedrock and clay at a ratio of 30:14:1, respectively. Biomass of benthic invertebrates also demonstrated a higher productivity on gravels with a ratio of 59:19:1 in comparison to bedrock and clay, respectively. Positive relationships between CPOM and benthic invertebrate biomass were detected in both stream types.

Relationships were also detected between fish biomass and benthic invertebrate biomass. Examination of benthic fishes also demonstrated positive relationships with benthic invertebrate biomass and density. Clay substrate on all accounts supported little biota. Results indicate alluvium loss in clay bed streams could reduce productive capacity. Understanding and integration of the potential impacts of alluvium loss would aid management and No Net Loss compensation plans to protect fisheries resources in semi-alluvial streams.

Site fidelity is the behaviour of individuals to return to the same location; for female woodland caribou it may reflect reproductive success and depend on habitat quality. I investigated the influence of landscape and disturbance conditions on fidelity among three populations in Manitoba and Ontario, Canada. Habitat classifications were based on Forest Resource Inventory (FRI) and Landsat TM landcover maps. A total of 261 sites were ground-truthed to determine mapping accuracy. An amalgamated map incorporating FRI and Landsat TM data was estimated from field measurements to have an overall accuracy of 69.0%. Site fidelity was expressed as the distance between consecutive-year locations of individuals and was investigated during five week-long periods representing calving, early and late post-calving, winter, and breeding. Site fidelity was strongest during the post-calving seasons and weakest during the winter. Habitat had little influence on site fidelity in all seasons, excepting winter, even under highly disturbed conditions, suggesting maintenance of fidelity may be a maladaptive trait. Individual variation proved a strong predictor and cursory mapping indicated that caribou may return to sites visited two or more years earlier. Conservation management and policy should recognize that site fidelity may represent an ecological trap.

Author Keywords: calving, disturbance, habitat, movement, Rangifer tarandus caribou, site fidelity