Graduate Theses & Dissertations

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Adaptive Genetic Markers Reveal the Biological Significance and Evolutionary History of Woodland Caribou (Rangifer tarandus caribou) Ecotypes
Migratory and sedentary ecotypes are phenotypic distinctions of woodland caribou. I explored whether I could distinguish between these ecotypes in Manitoba and Ontario using genetic signatures of adaptive differentiation. I anticipated that signatures of selection would indicate genetic structure and permit ecotype assignment of individuals. Cytochrome-b, a functional portion of the mitochondrial genome, was tested for evidence of adaptation using Tajima’s D and by comparing variations in protein physiology. Woodland caribou ecotypes were compared for evidence of contemporary adaptive differentiation in relation to mitochondrial lineages. Trinucleotide repeats were also tested for differential selection between ecotypes and used to assign individuals to genetic clusters. Evidence of adaptive variation in the mitochondrial genome suggests woodland caribou ecotypes of Manitoba and Ontario corresponded with an abundance of functional variation. Woodland caribou ecotypes coincide with genetic clusters, and there is evidence of adaptive differentiation between migratory caribou and certain sedentary populations. Previous studies have not described adaptive variation in caribou using the methods applied in this study. Adaptive differences between caribou ecotypes suggest selection may contribute to the persistence of ecotypes and provides new genetic tools for population assessment. Author Keywords: Adaptation, Cytochrome-B, Ecotype, RANGIFER TARANDUS CARIBOU, Selection, TRINUCLEOTIDE REPEAT
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
Assessing habitat suitability and connectivity for an endangered salamander complex
Habitat loss and fragmentation have significantly contributed to amphibian population declines, globally. Evaluating the state of remaining habitat patches can prove to be beneficial in identifying areas to prioritize in conservation efforts. Pelee Island, Ontario is home to a complex of salamanders including small-mouthed salamanders (Ambystoma texanum), blue-spotted salamanders (A. laterale) and unisexual Ambystoma (small-mouthed salamander dependent population). These populations have declined from intense landscape changes since the late 1800s, particularly from the historical drainage of wetlands. In this thesis, I evaluated the suitability and connectivity of habitat patches occupied by these salamanders to assess the size of, and dispersal capabilities between, remaining habitat patches. I found that there was a low amount of suitable terrestrial habitat available for this complex of salamanders, and existing habitat patches were small and isolated. Forested areas and non-breeding wetlands were considered to be suitable habitat when adjacent to existing breeding locations, suggesting that these habitats should be a focus for conservation efforts. Notably, intervention may be necessary to maintain this amphibian complex as many assemblages are isolated from one another and potential corridors currently consist of primarily unsuitable habitat. Given that much of the salamander complex is reliant on one species for reproduction, the long-term viability of this population of Ambystoma salamanders may rely on the enhancement of suitable habitat near current breeding sites by conservation organizations and local stakeholders. Ultimately, the approach used in this thesis emphasizes the value of evaluating habitat within a fragmented landscape to focus conservation efforts on imperilled species. Author Keywords: amphibians, connectivity, habitat suitability, landscape fragmentation, landscape resistance, unisexual
Assessing the population genetic structure of the endangered Cucumber tree (Magnolia acuminata) in southwestern Ontario using nuclear and chloroplast genetic markers.
Magnolia acuminata (Cucumber tree) is the only native Magnolia in Canada, where it is both federally and provincially listed as endangered.Magnolia acuminata in Canada can be found inhabiting pockets of Carolinian forest within Norfolk and Niagara regions of southwestern Ontario. Using a combination of nuclear and chloroplast markers, this study assessed the genetic diversity and differentiation of M. acuminata in Canada, compared to samples from the core distribution of this species across the United States. Analyses revealed evidence of barriers to dispersal and gene flow among Ontario populations, although genetic diversity remains high and is in fact comparable to levels of diversity estimated across the much broader range of M. acuminata in the USA. When examining temporal differences in genetic diversity, our study found that seedlings were far fewer than mature trees in Ontario, and in one site in particular, diversity was lower in seedlings than that of the adult trees. This study raises concern regarding the future viability of M. acuminata in Ontario, and conservation managers should factor in the need to maintain genetic diversity in young trees for the long-term sustainability of M. acuminata in Ontario. Author Keywords: conservation genetics, cpDNA, forest fragmentation, Magnolia acuminata, microsatellites, population genetic structure
Assessment of Potential Threats to Eastern Flowering Dogwood (Cornus florida) in Southern Ontario
In Canada, eastern flowering dogwood (Cornus florida L.) is an endangered tree that occurs only in the Carolinian forest of southern Ontario. Threats to this species include habitat fragmentation and the fungal pathogen dogwood anthracnose (Discula destructiva). I conducted a population genetic analysis using seven nuclear microsatellite markers to determine if fragmented populations are genetically isolated from one another and have low levels of genetic diversity. Genetic comparisons suggest on-going dispersal among sites and relatively high genetic diversity within most sites; however, smaller populations and younger trees were less genetically diverse. I also used linear mixed effects models to assess potential relationships between several ecological variables and the prevalence of dogwood anthracnose. Disease severity was higher in trees on shallow slopes and in larger trees; the latter also had higher likelihood of infection. Insights from this study will be important to incorporate into future management strategies. Author Keywords: Cornus florida, Discula destructiva, dogwood anthracnose, Eastern flowering dogwood, endangered, population genetics
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
Assessment of the impacts of noise and vessel traffic on the distribution, abundance and density of Chinese humpback dolphins (Sousa chinensis chinensis) in the waters of Hong Kong
Marine mammals with near-shore distributions are susceptible to human-related recreational and commercial disturbances, particularly near densely populated and industrialized coastal areas. A population of over 2,500 Chinese humpback dolphins (Sousa chinensis chinensis) occupies the Pearl River Estuary in southern China. A part of this population uses Hong Kong’s waters off of Lantau Island, where they are subjected to a number of anthropogenic threats, including vessel disturbance, fisheries interactions, and boat-based tourism. Previous research has shown that the abundance of this subspecies in Hong Kong’s waters has declined about 60% since 2003. Using a combination of acoustic recordings, dolphin distribution and abundance data, and vessel traffic information I found that: 1) Four types of vessels common to the waters on Hong Kong generate noise that is audible to Sousa chinensis chinensis; 2) The spatial distribution of underwater noise in Hong Kong’s waters does not significantly vary among the six sites sampled; 3) High-speed ferry traffic and passenger volume has increased dramatically during the study period; 4) There has been a significant decline in dolphin density in areas within and near vessel traffic; and 5) Dolphins are most at risk of vessel collisions and being exposed to vessel noise near Fan Lau and within the Urmston Road waterway just northeast of the Sha Chau and Lung Kwu Chau Marine Park . These results can inform future acoustic studies on this species and guide conservation and management efforts in Hong Kong. Author Keywords: Human impacts, Humpback dolphin, Management, Noise, Sousa chinensis chinensis, Vessel traffic
Conservation genetics of Redside Dace (Clinostomus elongatus)
Recent range reductions of endangered species have been linked to urban development, increased agricultural activities, and introduction of non-native species. I used Redside Dace (Clinostomus elongatus) as a focal species to examine the utility of novel monitoring approaches, and to understand historical and contemporary processes that have influenced their present distribution. I tested the efficacy of environmental DNA (eDNA) to detect Redside Dace, and showed that eDNA was more sensitive for detecting species presence than traditional electrofishing. Parameters such as season, number of replicates, and spatial versus temporal sampling need to be accounted for when designing an eDNA monitoring program, as they influence detection effectiveness and power. I also assessed the species’ phylogeographic structure using both mitochondrial and microsatellite DNA analysis. The data from the microsatellite markers indicate that Redside Dace populations are genetically structured, with the exception of several populations from the Allegheny River basin. Combined sequence data from three mitochondrial genes (cytochrome b, ATPase 6 and ATPase 8) indicated that Redside Dace persisted within three Mississippian refugia during the last glaciation. Secondary contact between two lineages was indicated by both mitochondrial and microsatellite data. The combined results from the eDNA and conservation genetics studies can be used to inform Redside Dace recovery efforts, and provide a template for similar efforts for other aquatic endangered species. Author Keywords: eDNA, endangered, genetics, phylogeography
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 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
Diversity, Biogeography, and Functional Traits of Native Bees from Ontario’s Far North and Akimiski Island, Nunavut
Bees (clade Anthophila), are poorly studied in northern Canada, as these regions can be difficult to access and have a short growing season. This study examined bees from two such regions: Ontario’s Far North, and Akimiski Island, Nunavut. I present this study as the largest biogeographical study of bees performed in these remote areas to enhance knowledge of northern native bees. I found 10 geographically unexpected species in Ontario and on Akimiski Island. Rarefaction and the Chao 1 Diversity Index showed that Akimiski is nearly as diverse as the Far North of Ontario, a significantly larger area. I also found, based on log femur length versus latitude, Bombus worker size was consistent with Bergmann’s rule, and there were no apparent statistical differences in the community weighted means of functional traits between the Far North’s Boreal Shield and Hudson Bay Lowlands ecozones. This work provides invaluable knowledge of the native bee species from these regions, which has implications for their future conservation. Author Keywords: Akimiski Island, Bergmann's rule, Chao 1, Community-weighted means, native bees, rarefaction
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

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