Graduate Theses & Dissertations

Nutrigenomics of Daphnia
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
Islands, ungulates, and ice
Central to wildlife conservation and management is the need for refined, spatially explicit knowledge on the diversity and distribution of species and the factors that drive those patterns. This is especially vital as anthropogenic disturbance threatens rapid large-scale change, even in the most remote areas of the planet. My dissertation examines theinfluence of land- and sea-scape heterogeneity on patterns of genetic differentiation, diversity, and broad-scale distributions of island-dwelling ungulates in the Arctic Archipelago. First, I investigated genetic differentiation among island populations of Peary caribou (Rangifer tarandus pearyi) in contrast to continental migratory caribou (Rangifer tarandus) and evaluated whether genetic exchange among Peary caribou island populations was limited by the availability of sea ice – both now and in the future. Differentiation among both groups was best explained by geodesic distance, revealing sea ice as an effective platform for Peary caribou movement and gene flow. With future climate warming, substantial reductions in sea ice extent were forecast which significantly increased resistance to caribou movement, particularly in summer and fall. Second, I assessed genetic population structure and diversity of northern caribou and deciphered how Island Biogeography Theory (IBT) and Central Marginal Hypothesis (CMH) could act in an archipelago where isolation is highly variable due to the dynamics of sea ice. Genetic differentiation among continental and island populations was low to moderate. In keeping with IBT and CMH, island-dwelling caribou displayed lower genetic diversity compared to mainland and mainland migratory herds; the size of islands (or population range) positively influenced genetic diversity, while distance-to-mainland and fall ice-free coastlines negatively influenced genetic diversity. Hierarchical structure analysis revealed multiple units of caribou diversity below the species level. Third, I shifted my focus to the terrestrial landscape and explored the elements governing species-environment relationships. Using species distribution models, I tested the response of caribou and muskoxen to abiotic versus abiotic + biotic predictors, and included distance to heterospecifics as a proxy for competitive interactions. Models that included biotic predictors outperformed models with abiotic predictors alone, and biotic predictors were most important when identifying habitat suitability for both ungulates. Further, areas of high habitat suitability for caribou and muskoxen were largely disjunct, limited in extent, and mainly outside protected areas. Finally, I modelled functional connectivity for two genetically and spatially disjunct groups of island-dwelling caribou. For High Arctic caribou, natural and anthropogenic features impeded gene flow (isolation-by-resistance); for Baffin Island caribou we found panmixia with absence of isolation-by-distance. Overall, my dissertation demonstrates the varying influences of contemporary land- and sea-scape heterogeneity on the distribution, diversity and differentiation of Arctic ungulates and it highlights the vulnerability of island-dwelling caribou to a rapidly changing Arctic environment. Author Keywords: Circuitscape, connectivity, Island Biogeography, landscape genetics, population structure, species distribution models
Using genomic and phenotypic data to explore the evolution and ecology of the North American mountain goat
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
Range dynamics of two closely related felids
Species ranges are changing and the rate at which the climate is warming is faster than anything previously seen in the past, consequently species will need to adapt quickly, track the climate or perish. Cold adapted terrestrial species are the most vulnerable, because they are limited by the availability of land at the cold edge of their range. This means that many alpine, boreal and polar species essentially have nowhere to go as the climate warms. Habitat generalists are widely distributed across the globe and are highly adaptable to anthropogenic change. Our future biodiversity may only consist of several habitat generalists. The Canada lynx (Lynx canadensis) is a boreal species that has limited range expansion potential at the cold end of its range and its range has already contracted by 40%. The lynx has nowhere to go as climate warming progresses in this current century. Therefore, understanding the causes of its range contraction could enlighten us on conservation and management strategies that we might undertake as climate warms. My analyses indicated that the Canada lynx seems to have tracked the habitat that it is adapted to in more northern homogenous boreal forests and the bobcat (Lynx rufus), a habitat generalist, has simply replaced it in the south. Author Keywords: Anthropogenic Change, Competition, Connectivity, Lynx canadensis, Lynx rufus, Range change
Reproductive Fitness of Smallmouth Bass (Micropterus dolomieu) Under Heterogeneous Environmental Conditions
Identifying the biotic and abiotic factors that influence individual reproductive fitness under natural conditions is essential for understanding important aspects of a species’ evolutionary biology and ecology, population dynamics, and life-history evolution. Using next generation sequencing technology, I developed five microsatellite multiplex reactions suitable for conducting large scale parentage analysis of smallmouth bass, Micropterus dolomieu, and used molecular pedigree reconstruction techniques to characterize the genetic mating system and mate selection in adult smallmouth bass nesting in Lake Opeongo, Ontario, Canada. I used multivariate spatial autocorrelation analysis to indirectly infer the occurrence and extent of natal philopatry among spawning adults, to assess the strength and direction of sex-bias in natal dispersal patterns, and to evaluate the degree of nest site fidelity and breeding dispersal of spawning adults. I also evaluated how differences in littoral zone water temperature caused by wind-induced seiche events influence the relative reproductive success of spawning adults. Lastly, I provide a synopsis of potential future research aimed at further exploring factors that influence the reproductive fitness of smallmouth bass in Lake Opeongo. This information will contribute to our understanding of the factors regulating smallmouth bass populations, and provide insight into the factors controlling the variance in individual reproductive success and thus recruitment dynamics in this species. Author Keywords: Dispersal, Fitness, Mate selection, Mating systems, Philopatry
SPATIAL AND TEMPORAL GENETIC STRUCTURE OF WOLVERINE POPULATIONS
Habitat loss and fragmentation can disrupt population connectivity, resulting in small, isolated populations and low genetic variability. Understanding connectivity patterns in space and time is critical in conservation and management planning, especially for wide-ranging species in northern latitudes where habitats are becoming increasingly fragmented. Wolverines (Gulo gulo) share similar life history traits observed in large-sized carnivores, and their low resiliency to disturbances limits wolverine persistence in modified or fragmented landscapes - making them a good indicator species for habitat connectivity. In this thesis, I used neutral microsatellite and mitochondrial DNA markers to investigate genetic connectivity patterns of wolverines for different temporal and spatial scales. Population genetic analyses of individuals from North America suggested wolverines west of James Bay in Canada are structured into two contemporary genetic clusters: an extant cluster at the eastern periphery of Manitoba and Ontario, and a northwestern core cluster. Haplotypic composition, however, suggested longstanding differences between the extant eastern periphery and northwestern core clusters. Phylogeographic analyses across the wolverine's Holarctic distribution supported a postglacial expansion from a glacial refugium near Beringia. Although Approximate Bayesian computations suggested a west-to-east stepping-stone divergence pattern across North America, a mismatch distribution indicated a historic bottleneck event approximately 400 generations ago likely influenced present-day patterns of haplotype distribution. I also used an individual-based genetic distance measure to identify landscape features potentially influencing pairwise genetic distances of wolverines in Manitoba and Ontario. Road density and mean spring snow cover were positively associated with genetic distances. Road density was associated with female genetic distance, while spring snow cover variance was associated with male genetic distance. My findings suggest that northward expanding anthropogenic disturbances have the potential to affect genetic connectivity. Overall, my findings suggest that (1) peripheral populations can harbour genetic variants not observed in core populations - increasing species genetic diversity; (2) historic bottlenecks can alter the genetic signature of glacial refugia, resulting in a disjunct distribution of unique genetic variants among contemporary populations; (3) increased temporal resolution of the individual-based genetic distance measure can help identify landscape features associated with genetic connectivity within a population, which may disrupt landscape connectivity. Author Keywords: conservation genetics, Holarctic species, landscape genetics, peripheral population, phylogeography, wolverine
Evaluating the effects of landscape structure on genetic differentiation and diversity
The structure and composition of the landscape can facilitate or impede gene flow, which can have important consequences because genetically isolated groups of individuals may be prone to inbreeding depression and possible extinction. My dissertation examines how landscape structure influences spatial patterns of genetic differentiation and diversity of American marten (Martes americana) and Canada lynx (Lynx canadensis) in Ontario, Canada, and provides methodological advances useful for landscape geneticists. First, I identified the effects of map boundaries on estimates of landscape resistance, and proposed a solution to the bias: a buffer around the map boundary. Second, I assessed the sensitivity of a network-based estimate of genetic distance, conditional genetic distance, to incomplete sampling. I then used these landscape genetic tools in a pairwise, distance-based analysis of 653 martens genotyped at 12 microsatellite loci. I evaluated whether forest management in Ontario has influenced the genetic structure of martens. Although forest management practices had some impact, isolation by distance best described marten gene flow. Our results suggest that managed forests in Ontario are well connected for marten and do not impede marten gene flow. Finally, I used a site-based analysis of 702 lynx genotyped at 14 microsatellite loci to investigate spatial patterns of genetic diversity and differentiation at the trailing (contracting) edge of the lynx distribution in Ontario. I analyzed harvest records and found that the southern edge of lynx range has contracted by >175 km since the 1970s. I also found that neutral genetic diversity decreased towards the trailing edge, whereas genetic differentiation increased. Furthermore, I found strong correlations between gradients of lynx genetic structure and gradients of climate and land cover in Ontario. My findings suggest that increases in winter air temperature, decreases in snow depth, and loss of suitable habitat will result in further loss of genetic diversity in peripheral populations of lynx. Consequently, the adaptive potential of lynx populations on the southern range periphery could decline. In conclusion, my dissertation demonstrates the varying influences that contemporary landscape structure and climate gradients can have on genetic diversity and differentiation of different species. Author Keywords: Circuitscape, genetic network, landscape genetics, Lynx canadensis, Martes americana, range shift

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