Agricultural crops are a food subsidy for wild ungulates that can bring animals into close proximity, facilitating disease spread. We used stable isotope analysis to reconstruct the diets of elk and white-tailed deer in three areas in the Canadian prairies and calculated their isotopic niche breadth. Isotopic niche breadth was greater for deer than elk, indicating that deer are a generalist species composed of individual specialists with varied diets, while elk are individual generalists. White-tailed deer niche breadth decreased with increasing consumption of agricultural foods in early fall, but not on an annual timescale. Elk niche breadth did not change with consumption of agricultural foods. Agricultural sources were 40-80% of the diets of both species in all areas. Agricultural feeding may increase the risk of disease in elk and deer not only by increasing their apparent density at feeding sites, but also by subsidizing increases to their overall density.

Individual variation and fitness are the cornerstones of evolution by natural selection. The trophic niche represents an important source of phenotypic variation on which natural selection can act. Although individual variation is fundamental to species-level ecological and evolutionary change, individual variation is often ignored in population-level approaches to wildlife ecology, conservation and management. Failing to link individual resource use to fitness or to biological outcomes related to fitness limits us to managing for the average resource needs of a population, which may be insufficient for protecting the diversity of resource use within populations and the underlying eco-evolutionary processes that generate that diversity. My goals were to provide insights into the mechanisms that generate and constrain intrapopulation trophic niche variation, evaluate whether linkages exist between individual biological outcomes and variation in food habits across the range of resources consumed within generalist consumer populations and examine how that variation manifests in population-level responses. I investigated the causes and physiological consequences of intrapopulation trophic niche variation in two generalist consumers, the American black bear (Ursus americanus) and brown bear (U. arctos) across three sites in British Columbia, CAN and at one site in Alaska, USA. My primary tools included stable isotope analysis to estimate diet, enzyme-linked immunoassay of hair to quantify the hormone cortisol for indexing physiological stress, and genetic analyses to identify individuals, species, and sex and to estimate ancestry. I found that individual differences in resource use can result in similar biological outcomes and that similar resource use can result in different biological outcomes. Intra- and interspecific competition, sex-based differences in nutritional and social constraints and annual variation in food availability all influenced trophic niche variation and the resultant biological outcomes. I also found evidence of a link between intrapopulation trophic niche variation and population genetic structure. My results highlight the diverse ecological drivers and diverse consequences of trophic niche variation, which further illuminates why the trophic niche is a nexus for eco-evolutionary dynamics.

Coral reefs are highly complex and also highly threatened ecosystems. Population growth and the unsustainable use of coral reefs have resulted in 55% of the world’s reefs being considered degraded. Fishing, the primary ‘local’ threat on most reefs, has altered the composition of most reef communities. As a result, very few pristine coral reefs remain. Typically, coral reef research is done via underwater visual censuses, providing abundance estimates but no indication of trophic interactions, therefore we know relatively little about the structure of intact reef food webs. Understanding how human activities affect trophic structure and feeding interactions among resident reef species may be important for coral reef conservation. Here, I apply stable isotope analysis to coral reef piscivorous fishes from Kiritimati (Republic of Kiribati), the world’s largest atoll. I examine dietary niche metrics of five focal species (Cephalopholis argus, Cephalopholis urodeta, Aphareus furca, Lutjanus bohar, and Lutjanus fulvus) and of the piscivore functional group as a whole, across an anthropogenic disturbance gradient that results from the atoll’s heavily skewed geographic population distribution. Using bootstrapped stable carbon (δ13C) and nitrogen (δ15N) isotope values, controlled for body size effects and analysed with Bayesian methods using the SIAR (Stable Isotope Analysis in R) program, I provide evidence of isotopic niche differentiation in C. argus and L. fulvus relative to other sampled species in terms of niche width metrics and mean δ13C and δ15N values. I also analyse the effect of fishing pressure at an individual level (controlling for body size effects on stable isotope signatures for each species), population level (accounting for observed differences in body size distributions across the fishing pressure gradient for each species), and the ‘community’ level (accounting for body size and relative abundance differences of the five piscivores across the fishing pressure gradient). These metrics reveal species-specific changes in niche metrics of three of the focal species at the individual level: C. urodeta, showed regionally distinct niche width metrics but no apparent correlation with fishing pressure, while A. furca and L. bohar, both had broader niche width metrics in heavily fished areas. No significant effect of fishing pressure was found at population or community levels. This study provides the first evidence using stable isotopes that fishing can alter the diets of coral reef fishes. The mechanism by which it can do so, while not entirely clear, would most likely be by expanding a given species’ dietary diversity by either forcing it to switch to non-preferred prey items or changing the diet and/or body size of its prey items, both of which would reflect significant ecological changes within a community. This thesis provides evidence of the utility of stable isotope analyses in answering important ecological questions in coral reef food webs, and reveals that fishing can affect reef communities at the most fundamental level of trophic interactions. / Graduate / 0329 / burrilladrian@gmail.com