Graduate Theses & Dissertations

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THE EFFECTS OF ROTATIONAL GRAZING AND HAY MANAGEMENT ON THE REPRODUCTIVE SUCCESS OF BOBOLINK AND EASTERN MEADOWLARK IN EASTERN ONTARIO
I investigated the impact of beef-cattle farm management on the reproductive success of Bobolink (Dolichonyx oryzivorus) and Eastern Meadowlark (Sturnella magna) within Eastern Ontario. I monitored rotational grazing management regimes and hay cut dates while assessing breeding phenology and reproductive success of Bobolinks and Eastern Meadowlarks. In pasture paddocks the major factor determining Bobolink reproductive success was the date that cattle entered a paddock to graze, with earlier entries resulting in lower reproductive success. On a landscape scale, within a series of paddocks grazed by a single herd, as the number of paddocks grazed during the nesting season increased, the number of Bobolinks that reproduced successfully decreased. Experimental quantification of trampling showed that cattle exposure to clay pigeon targets, regardless of stocking rates, resulted in the majority of targets being trampled. In hayfields associated with beef- cattle operations, grassland birds had a higher likelihood of success when cutting occurred after 4 July. The best method to improve the reproductive success of Bobolinks and Eastern Meadowlarks is to leave some hayfields and pasture paddocks undisturbed until nesting is complete. Author Keywords: Bobolink, Dolichonyx oryzivorus, farm management, hayfield, pasture, rotational grazing
Understanding Historical and Contemporary Gene Flow Patterns of Ontario Black Bears
Consequences of habitat loss and fragmentation include smaller effective population sizes and decreased genetic diversity, factors that can undermine the long-term viability of large carnivores that were historically continuously distributed. I evaluated the historical and contemporary genetic structure and diversity of American black bears (Ursus americanus) in Ontario, where bear habitat is largely contiguous, except for southern regions that experience strong anthropogenic pressures. My objectives were to understand gene flow patterns in a natural system still largely reflective of pre-European settlement to provide context for the extent of genetic diversity loss in southern populations fragmented by anthropogenic influences. Phylogeographic analyses suggested that Ontario black bears belong to a widespread "continental" genetic group that further divides into 2 subgroups, likely reflecting separate recolonization routes around the Great Lakes following the Last Glacial Maximum. Population genetic analyses based on individual genotypes showed that Ontario black bears are structured into 3 contemporary genetic clusters. Two clusters, located in the Northwest (NW) and Southeast (SE), are geographically vast and genetically diverse. The third cluster is less diverse, and spatially restricted to the Bruce Peninsula (BP). Microsatellite analyses revealed that the NW and SE clusters are weakly differentiated from each other relative to mitochondrial DNA findings, suggesting male-biased dispersal and isolation by distance across the province. I also conducted simulations to assess competing hypotheses that could explain the reduced genetic diversity on the BP, which supported a combination of low migration and recent demographic bottlenecks. I showed that management actions to increase genetic variation in BP black bears could include restoring landscape connectivity between BP and SE; however, the irreversible human footprint in the area makes regular translocations from SE individuals a more practical alternative. Overall, my work suggests that: 1) historical genetic processes in Ontario black bears were likely predominated by isolation by distance, 2) large mammalian carnivores such as black bears can become isolated and experience reduced diversity in only a few generations, and 3) maintaining connectivity in regions under increased anthropogenic pressures could prevent populations from becoming small and geographically and genetically isolated, and should be a priority for conserving healthy populations. Author Keywords: American black bear, carnivore, conservation genetics, Ontario, phylogeography, population genetics
ECTOPARASITIC INFLUENCES OF DIPTERA ON THE ACTIVITY AND BEHAVIOUR OF WOODLAND CARIBOU (RANGIFER TARANDUS) IN A MANAGED BOREAL FOREST LANDSCAPE IN NORTHERN ONTARIO
Caribou experience direct and indirect negative effects of harassment from biting flies, influencing behavior and activity on several spatial and temporal scales. I used systematic insect collection surveys during the summers of 2011 and 2012 to examine the spatial and temporal distributions of black flies (Simuliidae), mosquitoes (Culicidae), and deer flies and horse flies (Tabanidae) in a managed boreal forest in northern Ontario. Mosquitoes had a positive association with densely treed habitats, whereas black flies more often occurred in open areas, and tabanids had a strong presence in all habitat types. Habitats in proximity to large bodies of water had fewer biting flies than inland areas. Young stands supported higher abundances of tabanids despite vegetation community type. Next, I tested for seasonal effects of biting fly abundance on caribou activity by modelling the seasonal trend in abundance for each fly family for each year and compared this to an index of daily activity for 20 radio-collared female caribou in 2011 and 10 females in 2012. I modeled this index of caribou activity for each animal in each year and extracted the set of partial correlation coefficients from multiple regressions to test for effects of biting fly abundances on caribou activity. Caribou reduced their daily activity when tabanids were more numerous, and increased activity when mosquitoes were numerous. This divergent response may reflect a difference in the efficacy of moving to reduce harassment, owing to the stronger flight capabilities of tabanids. Author Keywords: Activity, Anthropogenic Disturbance, Behaviour, Insect harassment, Temporal distribution, Woodland Caribou
Phylogeography and Genetic Structuring of Moose (Alces alces) Populations in Ontario, Canada
Moose are an iconic species, known for their large size and impressive antlers. Eight subspecies are classified in circumpolar regions of the planet - four in North America. Two subspecies are similar in shape and size, the north-western moose (Alces alces andersoni) and the eastern moose (Alces alces americana). It was previously believed that these two subspecies meet in northern Ontario. Earlier genetic population studies used a small number of samples from Ontario, primarily in broad studies covering all of North America. A comprehensive genetic study of moose populations in Ontario has not previously been conducted. We examined the genetic diversity and population structure at 10 polymorphic loci using 776 samples from Ontario, as well as outgroups from representative populations – Manitoba/Cape Breton, representing A. a. andersoni, and New Brunswick/Nova Scotia, representing A. a. americana. Results indicated three genetic populations in the province, in north-western Ontario, north-eastern Ontario and south-central Ontario. RST values, compared against both FST and Jost’s D values for phylogenetic analyses, indicated no phylogenetic pattern which suggests no subspeciation present in the province. Population movement patterns in Ontario were studied. Gene flow was estimated using genetic and spatial data. Isolation by distance was only seen within the first distance class of 100 kilometres and then not seen again at further distances, indicating that moose display philopatry. There were very few migrants travelling across the province, with a greater number moving gradually north and west, towards better habitat and food sources. A forensic database in the form of an allele frequency table was created. Three loci showed very low levels of heterozygosity across all three populations. Probability of identity was calculated for the three populations and quantified. Samples with known geographic origins were run against the database to test for sensitivity, with identification of origin occurring at an accuracy level between 87 and 100%. Within Ontario, there are not two different subspecies, as previously believed, but two different populations of the same subspecies meeting in northern Ontario. The genetic data does not support previous research performed in Ontario. The sample sizes in our research also provide a more comprehensive view of the entire province not seen in any previous studies. The comprehensive research enabled the building of a reliable forensic database that can be used for both management and forensic purposes for the entire province. Author Keywords: Alces alces, Genetic Diversity, Moose, Ontario, Phylogeography, Subspecies
Canid Predation of Domestic Sheep (Ovis aries) on Ontario Farms
Livestock predation by wild predators is a frequent and complicated issue, often cited as a significant factor in the decline of livestock production and justification for killing predators. Coyotes (Canis latrans) are the primary predators of sheep in Ontario. Some farms appear to be more susceptible to predation than others, despite the use of mitigation techniques. I explored land cover in the vicinity of farms as a potential influence on the level of predation, as coyote abundance and wild prey are correlated with certain habitat types. Using model competition, I show that landscape explains little variation in predation levels over all farms, but can explain 27% of variation in the percent of a flock killed. Total forest edge habitat and distance between forest patches were both positively associated with losses, suggesting a reduction in forest cover surrounding a farm puts the flock at greater risk. In addition, I tested four disruptive deterrents for effectiveness at protecting flocks. A matched-pairs analysis did not show a statistically significant benefit of these non-lethal mitigation tools. Author Keywords: Alternative Prey, Canis latrans, Coyote, Landscape, Predation Deterrents, Sheep
Evaulating the American Woodcock Singing-Ground Survey Protocol in Ontario using Acoustic Monitoring Devices
The breeding phenology of American Woodcocks (Scolopax minor) was evaluated in Ontario, Canada to determine if changes in dates of courtship activity have introduced negative bias into the American Woodcock Singing-ground Survey (SGS). Long-term woodcock phenology and climate data for Ontario were analysed using linear regression to determine if woodcock breeding phenology has changed between 1968 and 2014. There was no significant trend in woodcock arrival date, but arrival date was correlated with mean high temperature in March. In 2011-2013, programmable audio-recording devices (song meters) were deployed at known woodcock singing-grounds to determine if peaks in courtship activity coincided with survey dates used by the SGS. Spectrogram interpretation of recordings and data analyses using mixed-effects models indicated the SGS survey dates were still appropriate, except during the exceptionally early spring in 2012 when courtship displays were waning in one region during the survey window. The methods for interpretation of song meter recordings were validated by conducting point counts adjacent to song meters deployed at singing-grounds, and at randomly selected locations in woodcock habitat. Recommendations for the SGS protocol are included. Author Keywords: detectability, phenology, Scolopax minor, Singing-ground Survey, song meter
Yearly variation in fall movements of adult female American black bears (Ursus americanus) in central Ontario, Canada
I investigated site fidelity and habitat selection of American black bears (Ursus americanus) from 15 GPS-collared adult females in central Ontario, Canada over nine years. I used generalized linear mixed models to determine the factors affecting between-year variation in fall fidelity and the habitat selection in movement paths. I assessed second and third-order habitat preference by female bears moving between seasonal home ranges. I found that 66% of bears returned to the same fall area between years, expressed as range overlap, influenced negatively by whether they had cubs. When moving between seasonal ranges, bears selected for mixedwood, hardwood and wetlands cover but selected ridge tops over other habitat features at both scales. With increases in climatic uncertainty and habitat fragmentation, these results emphasize the need for wildlife management to consider annual variation in seasonal movements and habitat use by wide-ranging, opportunistic animals. Author Keywords: American black bear, Habitat Selection, Logistic Regression, Site Fidelity
Using automated radio-telemetry to link food availability, reproductive success, and habitat use of Barn Swallows (Hirundo rustica erythrogaster)
Drivers of North American Barn Swallow population declines are not well understood, but foraging habitat loss is thought to be a contributing factor. Determining patterns of habitat use is challenging for swallows because they move rapidly but are too small to carry GPS tags. We showed that automated radio-telemetry could be used to track the movements of swallows with enough accuracy (median error 250 m) to monitor local habitat use. We then combined information on breeding Barn Swallows habitat use, land cover, aerial insect abundance, and fledging success to test for a link between foraging habitat quality and reproductive success. Foraging activity was concentrated within 600 m of nest sites and varied with land cover; however, responses to land cover were not consistent across birds. Aerial insects were most abundant near wetlands and least abundant near open water and over cropland. Consistent with a link between foraging habitat and reproductive success, nests in barns with more wetland and less open water within 1 km, and with less field area within 2 km occupied by row crops, on average fledged more young swallows. Author Keywords: aerial insectivores, automated telemetry, habitat use, land cover, movement, nest success
Impact of Agricultural Land Use on Bobolink Occurrence, Abundance, and Reproductive Success in an Alvar Landscape
Pastures and hayfields provide surrogate habitat for many declining grassland birds. Understanding agricultural land use dynamics and habitat quality can impact conservation of grassland species. I investigated 1) patterns of land use change in protected and unprotected sites in relationship to Bobolink occurrence in Carden, Ontario, Canada and 2) whether continuous grazing at lowmoderate cattle densities provided suitable breeding habitat, using both real and artificial nests. I replicated the 2001-2005 Ontario Breeding Bird Atlas to evaluate site habitat changes and Bobolink population trends. In continuously grazed pastures and late-cut hayfields, I monitored Bobolink abundance and reproductive success and modeled daily survival rate of nests using habitat management, vegetation structure, and prey availability. Results indicated that Bobolink have declined by -15.3% since 2001 in Carden; losses were explained almost entirely by changes from suitable breeding habitat (e.g. hayfields) to tilled land or by the colonization of shrubs. For pastures, stocking densities of ≤ 1Animal Units/ha did not negatively impact Bobolink. Year and caterpillar biomass, and vegetation height were the strongest predictors of nesting success in pastures and hayfields, respectively. Focus on the preservation of suitable habitat on the breeding grounds and management on small-scale beef farms can contribute to conservation action for this declining species. Author Keywords: agricultural management, avian ecology, Bobolink, continuous grazing, grassland birds, nest success
New Interpretations from Old Data
Range contractions and expansions are important ecological concepts for species management decisions. These decisions relate not only to rare and endangered species but to common and invasive species as well. The development of the broad spatiotemporal extent models that are helpful in examining range fluctuations can be challenging given the lack of data expansive enough to cover the time periods and geographic extents needed to fit the models. Archival records such as museum databases and harvest data can provide the spatiotemporal extent needed but present statistical challenges given they represent presence-only location information. In this thesis, I used maximum entropy and Bayesian hierarchical occupancy algorithms fitted with archival presence-only records to develop spatiotemporal models covering broad spatial and temporal extents for snowshoe hare and Canada lynx. These two algorithm types are well suited for presence-only data records and can be adapted to include biological and physical processes, thus improving the ecological realism of the models. Using these modelling methods, I found the extent of occurrence (EOO) and area of occupancy (AOO) varied greatly over time and space for both snowshoe hare and Canada lynx, suggesting that management decisions for these species should include consideration of these variations. While the presence-only data were appropriate for model development and understanding changing values in EOO and AOO, it sometimes lacked the locational accuracy and precision needed to create fine scale ecological analyses, thus resulting in somewhat coarse but potentially relevant conclusions. Author Keywords: Area of occupancy, Bayesian hierarchical models, Canada lynx, Extent of occurrence, Presence-only data, Snowshoe hare
Effects of Geographic Factors on the Wild Harvest of Large Mammals across North America
While the harvest of mammals is monitored in each jurisdiction across Canada and the USA, there has been no analysis of this wild harvest at a continental scale across North America. The recreational wild harvest of large mammals varies geographically across North America, and I hypothesized that this variation is influenced by both anthropogenic and other environmental factors on the landscape. I tested this hypothesis using annual harvest tallies collected by Conservation Visions Inc. for mammals for each state, provincial, and territorial jurisdiction in Canada and the USA. I built multiple additive models of the harvest, in one harvest year, 2015 – 2016, to test for landscape gradients that explain the variation in harvest levels for seven large mammal species: white-tailed deer (Odocoileus virginianus), black bear (Ursus americanus), bighorn sheep (Ovis canadensis), elk (Cervus canadensis), mule deer (Odocoileus hemionus), pronghorn (Antilocapra americana), and moose (Alces alces). I built these models from a suite of nine putative predictor variables that comprised landcover, human footprint, and evapotranspiration. For all large mammal species except for pronghorn, anthropogenic influence had a positive effect on the wild harvest density, consistent with the idea that the proximity of human populations and roads are important for fostering wild harvest activity by providing hunters access to hunting areas. The harvest of white-tailed deer, elk, and pronghorn were negatively affected by vegetation structure, urbanization, and primary productivity, respectively. Understanding the recreational wild harvest at a broad-spatial scale provides a unique perspective of the North American model of wildlife conservation and spurs future comparative analyses of the wild harvest across spatial scales. Author Keywords: Anthropogenic Influence, Hunting, Large Mammals, Primary Productivity, Vegetation Structure, Wild Harvest
Making eDNA count
Environmental DNA (eDNA) is rapidly becoming an established method for the detection of species in aquatic systems and has been suggested as a promising tool to estimate species abundance. However, the strength of the relationship between eDNA concentrations and taxon abundance (density/biomass) can vary widely between species. I investigated the relationship between eDNA concentration and species abundance using two common and closely-related amphibians in eastern North America, the wood frog (Rana sylvatica) and northern leopard frog (Rana pipiens). I manipulated tadpole density in 80 L mesocosms and documented the relationship between tadpole density, biomass, and eDNA concentration. Species were comparable in biomass but differed in the amount of detectible genetic material produced; density and biomass were the superior abundance metric correlated with eDNA concentration for wood frogs and leopard frogs, respectively. However, increases in eDNA concentration reflected increasing tadpole biomass, therefore biomass is likely a better metric of abundance than density. Overall my findings support that eDNA concentration can be used as an index of species abundance, but that species-specific calibration may be needed before eDNA concentration can be effectively translated to an abundance metric. Future research should refine our understanding of how biotic and abiotic factors influence eDNA production, degradation, and recovery across species, before the method can receive widespread use as a monitoring tool in natural settings. Author Keywords: abundance estimates, environmental DNA, mesocosm, Rana pipiens, Rana sylvatica

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