Graduate Theses & Dissertations

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Genomic architecture of artificially and sexually selected traits in white-tailed deer (Odocoileus virginianus)
Understanding the complex genomic architecture underlying quantitative traits can provide valuable insight for the conservation and management of wildlife. Despite improvements in sequencing technologies, few empirical studies have identified quantitative trait loci (QTL) via whole genome sequencing in free-ranging mammal populations outside a few well-studied systems. This thesis uses high-depth whole genome pooled re-sequencing to characterize the molecular basis of the natural variation observed in two sexually selected, heritable traits in white-tailed deer (Odocoileus virginianus, WTD). Specifically, sampled individuals representing the phenotypic extremes from an island population of WTD for antler and body size traits. Our results showed a largely homogenous genome between extreme phenotypes for each trait, with many highly differentiated regions throughout the genome, indicative of a quantitative model for polygenic traits. We identified and validated several potential QTL of putatively small-to-moderate effect for each trait, and discuss the potential for real-world application to conservation and management. Author Keywords: evolution, extreme phenotypes, genetics, genomics, quantitative traits, sexual selection
Assessing Connectivity of Protected Area Networks and the Role of Private Lands in the United States
Forestalling biodiversity loss through the establishment of protected areas is a universally accepted conservation strategy, yet despite established guidelines for protected area coverage and placement, much of the world is currently failing to meet its commitments to conservation planning and landscape protection. Calls for the United States to protect more land usually focus on the need for strategic selection of land parcels to bolster protected area coverage and network functionality, but to date there lacks focused research on either the role of private protected areas in conservation planning or the factors affecting individual protected area selection and importance. We determined gaps in conservation planning in the contiguous United States by analyzing the connectivity of protected area networks by state, and assessing the importance of private protected areas in improving linkages in protected area connectivity. We found that all states had low coverage from protected areas (average <8.4% of total land mass), and especially private protected areas (average <1.1% of total land mass), and that the overall contribution of such areas to protected area network connectivity also was low. Terrain ruggedness was identified as the main factor affecting the current location of protected areas, and that protected area spatial layout is a primary influence on landscape connectivity. We conclude that establishment of private protected areas could offer a viable conservation tool for increasing protected area coverage and connectivity, but that current efforts are inadequate to either adequately link existing protected areas or to meet established land protection guidelines. Author Keywords: Aichi Target 11, conservation planning, graph theory, network theory, private conservation, protected areas
Demography and habitat selection of Newfoundland caribou
The objective of this thesis is to better understand the demography and habitat selection of Newfoundland caribou. Chapter 1 provides a general introduction of elements of population ecology and behavioural ecology discussed in the thesis. In Chapter 2, I examine the causes of long-term fluctuations among caribou herds. My findings indicate that winter severity and density-dependent degradation of summer range quality offer partial explanations for the observed patterns of population change. In Chapter 3, I investigate the influence of climate, predation and density-dependence on cause-specific neonate survival. I found that when caribou populations are in a period of increase, predation from coyotes and bears is most strongly influenced by the abiotic conditions that precede calving. However, when populations begin to decline, weather conditions during calving also influenced survival. I build on this analysis in Chapter 4 by determining the influence of climate change on the interplay between predation risk and neonate survival. I found that the relative equilibrium between bears and coyotes may not persist in the future as risk from coyotes could increase due to climate change. In Chapter 5, I investigate the relationships in niche overlap between caribou and their predators and how this may influence differential predation risk by affecting encounter rates. For coyotes, seasonal changes in niche overlap mirrored variation in caribou calf risk, but had less association with the rate of encounter with calves. In contrast, changes in niche overlap during the calving season for black bears had little association with these parameters. In Chapter 6, I examine broad-level habitat selection of caribou to study trade-offs between predator avoidance and foraging during the calving season. The results suggest that caribou movements are oriented towards increased access to foraging and the reduction of encounter risk with bears, and to a lesser extent, coyotes. Finally, I synthesize the major findings from this thesis and their relevance to caribou conservation in Chapter 7, to infer that Newfoundland caribou decline is ultimately driven by extrinsic and intrinsic elements related to density-dependence. Reduction in neonate survival emerged from nutritionally-stressed caribou females producing calves with lower survival. Author Keywords: Behavioural ecology, Black bear (Ursus americanus), Coyote (Canis latrans), Population ecology, Predator-prey interactions, Woodland caribou (Rangifer tarandus)
Sex-Specific Graphs
Sex-specific genetic structure is a commonly observed pattern among vertebrate species. Facing differential selective pressures, individuals may adopt sex-specific life historical traits that ultimately shape genetic variation among populations. Although differential dispersal dynamics are commonly detected in the literature, few studies have investigated the potential effect of sex-specific functional connectivity on genetic structure. The recent uses of Graph Theory in landscape genetics have demonstrated network capacities to describe complex system behaviors where network topology intuitively represents genetic interaction among sub-units. By implementing a sex-specific network approach, our results suggest that Sex-Specific Graphs (SSG) are sensitive to differential male and female dispersal dynamics of a fisher (Martes pennanti) metapopulation in southern Ontario. Our analyses based on SSG topologies supported the hypothesis of male-biased dispersal. Furthermore, we demonstrated that the effect of the landscape, identified at the population-level, could be partitioned among sex-specific strata. We found that female connectivity was negatively affected by snow depth, while being neutral for males. Our findings underlined the potential of conducting sex-specific analysis by identifying landscape elements that promotes or impedes functional connectivity of wildlife populations, which sometimes remains cryptic when studied at the population level. We propose that SSG approach would be applicable to other vagile species where differential sex-specific processes are expected to occur. Author Keywords: genetic structure, Landscape Genetics, Martes pennanti, Population Graph, sex-biased dispersal, Sex-Specific Graphs
Assessment of an adult lake sturgeon translocation (Acipenser fulvescens) reintroduction effort in a fragmented river system
North American freshwater fishes are declining rapidly due to habitat fragmentation, degradation, and loss. In some cases, translocations can be used to reverse local extirpations by releasing species in suitable habitats that are no longer naturally accessible. Lake sturgeon (Acipenser fulvescens) experienced historical overharvest across their distribution, leading to endangered species listings and subsequent protection and recovery efforts. Despite harvest and habitat protections, many populations do not appear to be recovering, which has been attributed to habitat alteration and fragmentation by dams. In 2002, 51 adult lake sturgeon from the Mattagami River, Ontario, Canada were translocated 340 km upstream to a fragmented 35 km stretch of the river between two hydroelectric generating stations, where sturgeon were considered extirpated. This study assessed the translocation effort using telemetry (movement), demographics and genetic data. Within the first year, a portion of the radio-tagged translocated individuals dispersed out of the release area, and released radio-tagged individuals used different areas than individuals radio-tagged ten years later. Catches of juvenile lake sturgeon have increased over time, with 150 juveniles caught within the duration of this study. The reintroduced population had similar genetic diversity as the source population, with a marked reduction in effective population size (Ne). The results indicate that the reintroduction effort was successful, with evidence of successful spawning and the presence of juvenile lake sturgeon within the reintroduction site. Overall, the results suggest adult translocations may be a useful tool for re-establishing other extirpated lake sturgeon populations. Author Keywords: conservation, endangered species, lake sturgeon, reintroduction, telemetry, translocation
Effects of Hydroelectric Corridors on the Distribution of Female Caribou (Rangifer tarandus) on the Island of Newfoundland
A species of concern is caribou (Rangifer tarandus), a species in decline across most of the circumpolar North, including the island of Newfoundland. Resource exploitation across caribou ranges is projected to accelerate in the coming decades as oil extraction, roads, forest harvesting, and mining encroach upon their habitat. Hydroelectric corridors, in particular, are anticipated to expand significantly. The effects of these linear developments on caribou habitat remain unclear. I capitalized on an existing dataset of nearly 700 radio‐tracked female caribou, 1980‐2011, to determine the long‐term effects of hydroelectric corridors on their seasonal distributions. Using an island-wide landcover map, I tested for preference or avoidance hydroelectric corridors in each of 4 seasons using the Euclidean Distance habitat selection technique at the extent of the population ranges (broad scale) for each decade (1980s, 1990s, 2000s). I also examined the distribution of caribou ≤10 km and ≤20 km from corridors (narrow scale) for five herds. At the broad scale, the response was highly variable. Female caribou were most likely to avoid corridors during the 1980s, but they often exhibited little aversion, even preference for corridors, particularly in the 1990s and 2000s. Hydroelectric corridors, therefore, did not appear to be limiting at this scale. I surmise that these long-term shifts reflect the heightened density-dependent food limitation for Newfoundland caribou. At the narrow scale, avoidance of corridors was common – typically, a 50% reduction in use within 2-5 km of the corridor. Consistent with the broad scale, caribou exhibited the strongest tendency for avoidance in the 1980s compared to subsequent decades. Understanding space-use remains central to the study of caribou ecology. Hydroelectric lines in Newfoundland tended to coincide with other anthropogenic features. Cumulative effects must be considered to understand the full range of effects by human developments on caribou. Author Keywords: Caribou, distribution, habitat, hydroelectric, Newfoundland, Rangifer tarandus
Habitat Characteristics, Density Patterns and Environmental Niches of Indo-Pacific Humpback Dolphins (Sousa chinensis) of the Pearl River Estuary and Eastern Taiwan Strait
The purpose of this thesis is to quantify the habitat characteristics, density patterns and environmental niches of two groups of Indo-Pacific humpback dolphins: Chinese white dolphins (CWD) of the Pearl River estuary (PRE), and Taiwanese white dolphins (TWD, =Taiwanese humpback dolphin, THD) found in the eastern Taiwan Strait (ETS). Much work has already been done on the habitat use of CWDs in parts of the PRE, so the purpose of my first two chapters was to advance knowledge of the TWD to a comparable level. Chapter 2 contains the first published description of the relatively shallow, inshore, estuarine habitat of the TWD. General environmental characteristics and observed group sizes were consistent with other populations of humpback dolphins, and group sizes were not correlated with the environmental variables measured during surveys. Chapter 3 investigated density patterns of TWDs, finding spatiotemporal heterogeneity across the study area. Humpback dolphin densities fluctuated from year to year, but some parts of the study area were consistently used more than others. Environmental characteristics again did not influence dolphin densities, though more dolphins than expected were sighted in waters adjacent to major land reclamations, which may be related to the location of these areas close to major rivers. In Chapter 4, niches of the TWD and CWDs found in the PRE were compared using species distribution models, which indicated significant niche overlap. This may be due to niche conservatism maintaining similar fundamental niches between the two groups since their historical split >10,000 years ago, or a result of the intrinsic biotic factors that influence occurrence data affecting the hypervolume dimensions of each realized niche in similar ways. Geographic predictions indicate that most of the TWD’s range has likely been surveyed, and that there may be connectivity between PRE humpback dolphins and at least one neighbouring putative population due to continuous predicted suitable habitat in waters that remain poorly surveyed. Overall, my thesis demonstrates that density patterns may vary over time, but on a broad temporal scale, these two allopatric groups of Indo-Pacific humpback dolphins have similar habitat requirements in geographically isolated, but environmentally similar locations. Author Keywords: density, habitat, Indo-Pacific humpback dolphin, niche overlap, Sousa chinensis, species distribution model
EVALUATION OF HAYFIELD MANAGEMENT STRATEGIES AND BOBOLINK TERRITORIAL HABITAT IN SOUTHERN ONTARIO
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
Habitat use within and among roosts of chimney swifts (Chaetura pelagica)
Chimney swifts are listed as Threatened nationally and in many provinces within Canada due to rapid population declines. I examined large-scale spatial variation in the maximum size of chimney swift roosts at the northern edge of their range to identify where larger roosts occur. I used multi-sourced data collected across Ontario and Quebec between 1998 and 2013. I found that larger roosts were found at more northerly latitudes, and that very large roosts (>1000 birds) only occurred north of 45°. I also investigated fine-scale patterns of chimney swift positioning inside one of the largest roosts in Ontario. Using digitally recorded images, I calculated the angular position of swifts inside the roost relative to ambient and roost temperature. I found that swifts showed a strong preference for clinging to the south facing wall and clustered more when ambient air temperature was warmer. Thus, huddling in swifts provides additional or alternate benefits, other than serving purely to reduce costs of thermoregulation at low ambient temperatures. This research contributes to the understanding of chimney swift roosting ecology and identifies large roosting sites that should be retained for conservation. Author Keywords: chimney swift, communal roosting, conservation, group size, social thermoregulation, species-at-risk
Environmental structure, morphology and spatial ecology of the five-lined skink (Plestiodon fasciatus) at high latitude range limits
Detecting relevant and meaningful patterns from the complex, interconnected network of relationships between organisms and their environment is a primary objective of ecology. Ecological patterns occur across multiple scales of space and time. In this dissertation, I examine aspects of environmental structure that influence a species’ distribution and are expressed in that species’ population dynamics. I compare the morphology of the five-lined skink (Plestiodon fasciatus) near its high latitude range limits with a lower latitude population and evaluate the economics of their behaviour in the context of its reproductive strategy. I tested the conformity of this species to biogeographical rules postulated by MacArthur, Bergmann, and Rensch. Spatial ecology was investigated in the context of the environmental potential for polygamy proposed by Emlen and Oring (1977) The five-lined skink, Plestiodon fasciatus, conformed to these biogeographic rules. Specifically, abiotic factors were the primary limiting factors affecting distribution at the high latitude range limits of the species; body size was larger in high latitude populations; and the degree of sexual size dimorphism was greater at high latitude than at low latitude. Spatial ecology at the individual scale was influenced by sites with suitable thermal conditions which facilitate the polygynandrous mating system documented in P. fasciatus in high latitude populations. My results confirm the importance of microsites with suitable thermal profiles as key habitat for ectothermic vertebrates at high latitudes. The influence of temperature as a limiting abiotic factor is expressed in population density, body size, spatial ecology, and reproductive strategy of P. fasciatus. Conservation and restoration of high latitude populations of ectothermic vertebrates should focus on ensuring thermal requirements of the species of concern are met before other factors are addressed, as temperature is likely the single most important limiting factor at high latitude range limits. Author Keywords: biogeography, lizard, Plestiodon fasciatus, range limits, sexual size dimorphism, spatial ecology
Mixed methods approaches in marine mammal science
This thesis explored the contribution of mixed methods approaches to marine mammal science through the use of concurrent and sequential designs to study distribution and feeding ecology of bowhead whales (Balaena mysticetus) in the Arctic region of Nunavik, Quebec, Canada. The study combines Inuit knowledge (IK), collected through semi-directed interviews with Inuit harvesters, and analyses of stable isotopes and trace elements (SI/TE) in baleen plates. A systematic literature review found that mixed methods are increasingly used in marine mammal ecology studies in remote locations, yet are still relatively rare and face a number of challenges. Both IK and SI/TE, indicated that bowhead whales have a seasonal pattern in their distribution and feeding ecology. They are most commonly present in productive nearshore areas in summertime, feeding in areas of great prey diversity, and moving to offshore areas in winter to fast. Mixed methods approaches used in this case study enabled the collection of complementary knowledge about bowhead whale ecology important for local management in a changing climate. This study also shows the value of mixed methods approaches for future marine mammal studies in Nunavik and elsewhere. Author Keywords: Arctic, bowhead whale, distribution, feeding ecology, mixed methods, traditional ecological knowledge
Evaluating the Effects of Habitat Loss and Fragmentation on Canada Lynx
Current major issues in conservation biology include habitat loss, fragmentation and population over-exploitation. Animals can respond to landscape change through behavioural flexibility, allowing individuals to persist in disturbed landscapes. Individual behaviour has only recently been explicitly included in population models. Carnivores may be sensitive to changing landscapes due to their wide-ranging behaviour, low densities and reproductive rates. Canada lynx (Lynx canadensis) is a primary predator of snowshoe hares (Lepus americanus). Both species range throughout the boreal forests of North America, however lynx are declining in the southern range periphery. In this dissertation, I developed new insights into the effects of habitat loss and fragmentation on lynx. In Chapter 2, I created a habitat suitability model for lynx in Ontario and examined occurrence patterns across 2 regions to determine if habitat selection is flexible when different amounts of habitat are available. Although lynx avoided areas with <30% suitable habitat where suitable land cover is abundant, I found that they have flexible habitat selection patterns where suitable land cover is rare and occurred in low habitat areas. In Chapter 3, I investigated the effects of dispersal plasticity on occupancy patterns using a spatially explicit individual-based model. I showed that flexible dispersers, capable of crossing inhospitable matrix, had higher densities and a lower risk of patch extinction. In contrast, inflexible dispersers (unable to cross inhospitable matrix), were most limited by landscape connectivity, resulting in a high extinction risk in isolated patches. I developed three predictions to be explored with empirical data; (1) dispersal plasticity affects estimates of functional connectivity; (2) variation in dispersal behaviour increases the resilience of patchy populations; and (3) dispersal behaviour promotes non-random distribution of phenotypes. Finally, in Chapter 4, I examined the consequences of anthropogenic harvest on naturally cycling populations. I found that harvest mortality can exacerbate the effects of habitat fragmentation, especially when lynx densities are low. Dynamic harvest regimes maintained lynx densities and cycle dynamics while reducing the risk of population extinction. These results suggest that lynx display some flexibility to changing landscapes and that the metapopulation structure is more resilient to increasing habitat loss and fragmentation than previously understood. Future studies should focus on determining a threshold of connectivity necessary for population persistence and examining the effects of habitat loss on the fecundity of lynx. Author Keywords: Fluctuating Populations, Habitat Fragmentation, Landscape Ecology, Occupancy Dynamics, Population Ecology, Spatially Explicit Population Models

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