Graduate Theses & Dissertations

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Daphnia pulicaria responses to temperature and nutrients stress
Warming climates have had various consequences on terrestrial and aquatic food webs that are expected to persist. There is evidence suggesting that certain organisms are better equipped to handle changing climates compared to others. Therefore, the purpose of my thesis was to study the adaptability of Daphnia under temperature stress and nutrient limitation. First, to examine the effects of dietary phosphorus limitation and temperature on daphniid life-history and population growth, a series of experiments were conducted in the laboratory. In general, I found that Daphnia body growth rates and life-history traits to food carbon to phosphorus (C:P) ratios change with temperature. Next, I identified a protocol to limit the genomic DNA (gDNA) from ribonucleic acid (RNA) extractions. I found that using a modified phenol-chloroform extraction protocol was the most effective way to remove gDNA from extracted Daphnia RNA samples. Overall, results from this study show that temperature and food quality interactions are more complicated than previously thought. Furthermore, the RNA extraction protocol developed will be useful in future studies examining gene expression responses in Daphnia. Author Keywords: ecological stoichiometry, gene expression, life-history, nutrient limitation, RNA puritiy, temperature
De novo transcriptome assembly, functional annotation, and SNP discovery in North American flying squirrels (genus Glaucomys)
Introgressive hybridization between northern (Glaucomys sabrinus) and southern flying squirrels (G. volans) has been observed in some areas of Canada and the USA. However, existing molecular markers lack the resolution to discriminate late-generation introgressants and describe the extent to which hybridization influences the Glaucomys gene pool. I report the first North American flying squirrel (genus Glaucomys) functionally annotated de novo transcriptome assembly with a set of 146,621 high-quality, annotated putative species-diagnostic SNP markers. RNA-sequences were obtained from two northern flying squirrels and two southern flying squirrels sampled from Ontario, Canada. I reconstructed 702,228 Glaucomys transcripts using 193,323,120 sequence read-pairs, and captured sequence homologies, protein domains, and gene function classifications. These genomic resources can be used to increase the resolution of molecular techniques used to examine the dynamics of the Glaucomys hybrid zone. Author Keywords: annotation, de novo transcriptome, flying squirrels, high-throughput sequencing, hybridization, single nucleotide polymorphisms
Demographic history and conservation genomics of caribou (Rangifer tarandus) in Québec
Genetic variation is the raw material and basis for evolutionary changes in nature. The loss of genetic diversity is a challenge many species are facing, with genomics being a potential tool to inform and prioritize decision making. Whole genome analysis can be an asset to conservation biology and the management of species through the generation of more precise and novel metrics. This thesis uses whole genome re-sequencing to characterize the demographic history and quantify genomic metrics relevant to conservation of caribou (Rangifer tarandus) in Québec, Canada. We calculated the ancestral and contemporary patterns of genomic diversity of five representative caribou populations and applied a comparative population genomics framework to assess the interplay between demographic events and genomic diversity. When compared to the census size, NC, the endangered Gaspésie Mountain caribou population had the highest ancestral Ne:NC ratio which is consistent with recent work suggesting high ancestral Ne:NC is of conservation concern. These ratios were highly correlated with genomic signatures (i.e. Tajima’s D) of recent population declines and explicit demographic model parameters. Values of contemporary Ne, estimated from linkage-disequilibrium showed Gaspêsie having among the highest contemporary Ne:NC ratio. Importantly, classic conservation genetics theory would predict this population to be of less concern based off this metric alone. Inbreeding measures suggested nuanced patterns of inbreeding and correlated to the demographic models. This study suggests that while the Québec populations are all under decline, they harbour enough ancestral genetic variation to replenish any lost diversity, if conservation decisions are made in favour of these populations, specifically supporting NC. Author Keywords:
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)
Demography of a Breeding Population of Whimbrel (Numenius phaeopus) Near Churchill, Manitoba, Canada
I used a GIS raster layer of an area in the Churchill, Manitoba region to investigate the effect of breeding habitat on demography and density of Whimbrel from 2010 through 2013. Program MARK was used to quantify adult and daily nest survival. Apparent annual survival of 0.73 ± 0.06 SE (95% CI = 0.60-0.83) did not significantly differ between sexes or habitats and was lower than expected based on longevity records and estimates for other large-bodied shorebirds. Nest success, corrected for exposure days, was highly variable, ranging from a low of 3% (95% CI = 0-12%) in 2011 to a high of 71% (95% CI = 54-83%) in 2013. The highest rate of nest survival occurred in the spring with the warmest mean temperature. I developed a generalized linear model (GLM) with a negative-binomial distribution from random plots that were surveyed for abundance to extrapolate a local breeding population size of 410 ± 230 SE and density of 3.2 birds per square km ± 1.8 SE. The result of my study suggests that other aspects of habitat not captured by the land cover categories may be more important to population dynamics. Author Keywords: abundance, apparent survival, curlew, land cover map, nest-site fidelity, nest success
Detectability and its role in understanding upland sandpiper (Bartramia longicauda) occurence in the fragmented landscape of southern Ontario
Upland Sandpipers (Bartramia longicauda), like many grassland birds, are undergoing population decline in parts of their range. Habitat fragmentation and change have been hypothesized as potential causes of decline. I used citizen-science occurrence data from Wildlife Preservation Canada’s Adopt-A-Shrike Loggerhead Shrike (Lanius ludovicianus) program in conjunction with validation surveys, using similar point-count methods, to examine detectability and determine if landscape level habitat features could predict occupancy of Upland Sandpipers in Southern Ontario. In a single season detectability study, I used Wildlife Preservation Canada’s survey protocol to determine detectability in sites that were known to be occupied. Detectability was low, with six surveys necessary to ensure detection using a duration of at least 18 minutes early in the breeding season. The proportion of open habitat did not affect detection on the landscape. Using a larger spatial and temporal scale, with five years of citizen-science data, I showed that Annual Crop Inventory data could not effectively predict Upland Sandpiper occupancy. Model uncertainty could be attributed to survey protocol and life history traits of the Upland Sandpiper, suggesting that appropriate survey methods be derived a priori for maximizing the potential of citizen-science data for robust analyses. Author Keywords: Bartramia longicauda, citizen-science, detection, landscape, occupancy, Ontario
Detecting anti-estrogens and anti-androgens in surface waters impacted by municipal wastewater discharges and agricultural runoff
This study focused on detecting 22 target anti-estrogenic and anti-androgenic compounds in surface waters influenced by both discharges of municipal wastewater and agricultural runoff in Canada and Argentina. Polar organic chemical integrative samplers (POCIS) were used to monitor the target compounds in surface waters. The removals of the target compounds in a municipal wastewater treatment plant (WWTP) in Canada were also evaluated. In both Canada and Argentina pesticides with potential anti-estrogenic and anti-androgenic activities were detected in the surface waters. The highest concentrations were found in Argentina (up to 1010 ng L-1) in areas impacted by heavy agricultural practices. Cyproterone acetate and bicalutamide were the only two anti-cancer drugs detected only at the Canadian study site, the Speed River, ON. In the Guelph WWTP, that discharges into the Speed River, these target compounds were not all efficiently removed (>70%) during treatment. Overall, this study provides insight to possible anti-estrogenic and anti-androgenic compounds that may be contributing to endocrine disrupting activities in surface waters. Author Keywords: Anti-androgens, Anti-estrogens, Cancer Therapy Drugs, Current use pesticides, Pharmaceuticals and Personal Care Products, Polar Organic Chemical Integrative Samplers
Detection of four at-risk freshwater pearly mussel species (Bivalvia
Environmental DNA (eDNA) detection uses species-specific markers to screen DNA from bulk samples, such as water, to infer species presence. This study involved the development and testing of species-specific markers for four freshwater pearly mussels (Unionidae). The markers were applied to water samples from intensively sampled mussel monitoring sites to compare species detections from eDNA with established sampling method detections. Target species were detected using eDNA at all sites where they had previously been detected by quadrat sampling. This paired design demonstrated that eDNA detection was at least as sensitive as quadrat sampling and that high species specificity can be achieved even when designing against many sympatric unionids. Detection failures can impede species conservation efforts and occupancy estimates; eDNA sampling could improve our knowledge of species distributions and site occupancy through increased sampling sensitivity and coverage. Author Keywords: conservation genetics, cytochrome oxidase subunit I (COI), environmental DNA (eDNA), quantitative PCR (qPCR), species at risk (SAR)
Determinants of Breeding Bird Diversity in Ontario's Far North
190 species of birds are known to breed in Ontario’s far north making the region an important nursery for boreal birds. Digital point count data were collected using two different autonomous recording units (ARUs): one model with two standard microphones to detect birds and anurans, and one model with one standard microphone and one ultrasonic microphone for detecting bats. ARUs were deployed either in short or long-term plots, which were four to six days or approximately 10 weeks, respectively. I assessed differences in breeding bird richness detections between ARU and plot types. I also tested the relative impact of the habitat heterogeneity and species-energy hypotheses in relation to breeding birds and created predictive maps of breeding bird diversity for Ontario’s far north. I found no difference in species richness estimates between the two ARU models but found that long-term plots detected about 7 more bird species and 1.5 more anuran species than short-term plots. I found support for both the species-energy and habitat heterogeneity hypotheses, but support for each hypothesis varied with the resolution of the analysis. Species-energy models were better predictors of breeding bird diversity at coarser resolutions and habitat heterogeneity models were better predictors at finer resolutions. Breeding bird diversity was highest in the Ontario Shield Ecozone compared with the Hudson Bay Lowlands Ecozone, but concentrated areas of higher diversity found in the Lowlands were associated with large rivers and the associated coastlines. Author Keywords: boreal birds, breeding birds, habitat heterogeneity, Hill diversity, Ontario, species-energy hypothesis
Development and Use of Passive Samplers for Monitoring Dissolved and Nanoparticulate Silver in the Aquatic Environment
Silver nanoparticles (nAg) are the largest and fastest growing class of nanomaterials, and are a concern when released into aquatic environments even at low μg L-1+). Diffusive gradient in thin films (DGT) with a thiol-modified resin were used to detect labile silver and carbon nanotubes (CNT-sampler) were used to measure nAg. Laboratory uptake experiments in lake water provided an Ag+ DGT diffusion coefficient of 3.09 x 10 -7 cm2s-1 and CNT sampling rates of 24.73, 5.63, 7.31 mL day-1, for Ag+, citrate-nAg and PVP-nAg, respectively. The optimized passive samplers were deployed in mesocosms dosed with nAg. DGT samplers provided estimated Ag+ concentrations ranging from 0.15 to 0.98 μg L-1 and CNT-samplers provided nAg concentrations that closely matched measured concentrations in water filtered at 0.22 μm. Author Keywords: ICP-MS, mesocosms, nanoparticles, nanosilver, passive sampling
Development of genetic profiles for paternity analysis and individual identification of the North Atlantic right whale (Eubalaena glacialis)
The endangered North Atlantic right whale (Eubalaena glacialis) has been internationally protected from whaling since 1935 but recovery has been slow compared to the southern right whale (Eubalaena australis) due to anthropogenic mortalities and poor reproduction. Prey availability, genetic variability, and alleles of genes associated with reproductive dysfunction have been hypothesized to contribute to low calf production. The North Atlantic Right Whale DNA Bank and Database contains 1168 samples from 603 individuals. I added 115 new genetic profiles to the database which now contains profiles for 81% of individuals alive since 1980. Paternity assignments using these profiles resulted in 62% of sampled calves being assigned a father and only 38% of candidate males being assigned a paternity. This may suggest false exclusion due to genotyping errors or the existence of an unknown group of males. The use of the DNA database allowed for the identification of 10 deceased individuals which has implications for identifying cause of death and reducing mortalities. However, genetic identification is dependent on the time of post-mortem sample collection which influences DNA quantity and quality. An assessment for variations in methylenetetrahydrofolate reductase, a candidate gene associated with reproductive dysfunction, revealed six females heterozygous for a synonymous A/T variant in exon four which may influence reproductive success through changes in enzyme production, conformation or activity. Author Keywords: Eubalaena glacialis, Forensic Identification, Genetic Profiling, North Atlantic Right Whale, Paternity, Reproductive Dysfunction
Differences and similarities in exploration and risk-taking behaviours of two Myotis bat species.
AbstractDifferences and similarities in exploration and risk-taking behaviours of two Myotis bat species. Laura Michele Scott Behaviours that are repeatable across circumstances and time determine an individual’s personality. Personality and behavioural variation are subject to selective pressures, including risks related to the use of different habitat types. I explored the ecological and evolutionary consequences of habitat selection by comparing the behaviour of two sympatric bat species, Myotis leibii and M. lucifugus. These species display overlap in roosting preferences, however, M. leibii tend to roost in crevices on the ground, while M. lucifugus tend to roost in crevices or cavities that are raised off the ground. I hypothesized that the habitat selection patterns of these two species create behavioural reaction norms at the species level. I predicted that ground roosting behaviour favours bolder personality and more exploratory and active traits when compared with bats that do not ground roost. I examined inter- and intra-specific variation in behaviour using a modified, three-dimensional open-field test and quantified the frequency and duration of behaviours such as flying, landing, and crawling. Bats were continuously video-recorded over 1-hour nocturnal and diurnal trials. I used a priori mixed models with combinations of individual characteristics and life-history traits to select the models that best describe each species. We found that M. leibii (n = 15) displayed more exploratory and bolder behaviours than M. lucifugus while on the ground (n = 21) and higher overall activity during the trial. I also found that M. leibii displayed crawling behaviours and movements consistent with foraging while on the ground which is a rare behaviour in bats and only observed in a few species (Desmodus rotundus and Mystacina tuberculate to my knowledge). Future research should explore biomechanical adaptations associated with ground-foraging in M. leibii. Author Keywords: Bats, Behaviour, Exploration, Myotis leibii, Myotis lucifugus, Roosting

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