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 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
Characterizing the demographic history and prion protein gene variation to infer susceptibility to chronic wasting disease in a naïve population of white-tailed deer (Odocoileus virginianus)
Assessments of the adaptive potential of natural populations are essential for understanding and predicting responses to environmental stressors like climate change and infectious disease. The range of stressors species face in a human-dominated landscape, often have contrasting effects. White-tailed deer (Odocoileus virginianus, deer) are expanding in the northern part of their range following decreasing winter severity and increasing forage availability, caused by climate change. Chronic wasting disease (CWD), a prion disease affecting cervids, is likewise expanding and represents a major threat to deer and other cervids We obtained tissue samples from free-ranging deer across their native range in Ontario, Canada which has yet to detect CWD in wild populations of cervids. High throughput sequencing was used to assess neutral genomic variation and variation in the gene responsible for the protein that misfolds into prions when deer contract CWD, known as the PRNP gene. Neutral variation revealed a high number of rare alleles and no population structure, consistent with an expanding population of deer. Functional genetic variation revealed that the frequencies of variants associated to CWD susceptibility and disease progression were evenly distributed across the landscape and the frequencies were consistent with deer populations not infected with CWD. These findings suggest that an observable shift in PRNP allele frequencies likely coincides with the start of a novel CWD epidemic. Sustained surveillance of genomic and genetic variation can be a useful tool for CWD-free regions where deer are managed for ecological and economic benefits. Author Keywords: Canadian wildlife, population genetics, prion, PRNP, RADseq, ungulate
Cytokinin Oxidase/Dehydrogenase (CKX) Gene Family in Soybeans (Glycine max)
Glycine max (soybean) is an economically important plant species that registers a relatively low yield/seed weight compared to other food and oil seed crops due to higher rates of flower and pod abortion. Alleviation of this abortion rate can be achieved by altering the sink strength of the reproductive organs of soybeans. Cytokinin (CK) plays a fundamental role in promoting growth of sink organ (flowers and seeds) by increasing the assimilate demand. Cytokinin oxidase/dehydrogenase (CKX) is an enzyme that catalyses the irreversible breakdown of active CKs and hence reduce the cytokinin content. The current thesis uncovers the members of CKX gene family in soybeans and the natural variations among CKX genes within soybean varieties with different yield characteristics. The identification of null variants of OsCKX2 that resulted in large yield increases by Ashikari et al. (2005) provided a rationale for current thesis. The soybean CKX genes along with the ones from Arabidopsis, Rice and Maize were used to construct a phylogenetic tree. Using comparative phylogeny, protein properties and bioinformatic programs, the potential effect of the identified natural variations on soybean yield was predicted. Five genes among the seventeen soybean CKXs identified, showed polymorphisms. One of the natural variations, A159G, in the gene GmCKX16 occurred close to the active site of the protein and was predicted to affect the activity of enzyme leading to higher accumulation of CKs and hence increased seed weight. Use of such natural variations in marker assisted breeding could lead to the development of higher yielding soybean varieties. Author Keywords: CKX, Cytokinins, Seed weight, Seed Yield, SNPs, Soybeans
Cytokinin biosynthesis, signaling and translocation during the formation of tumors in the Ustilago maydis-Zea mays pathosystem
Cytokinins (CKs) are hormones that promote cell division. During the formation of tumors in the Ustilago maydis-Zea mays pathosystem, the levels of CKs are elevated. Although CK levels are increased, the origins of these CKs have not been determined and it is unclear as to whether they promote the formation of tumors. To determine this, we measured the CK levels, identified CK biosynthetic genes as well as CK signaling genes and measured the transcript levels during pathogenesis. By correlating the transcript levels to the CK levels, our results suggest that increased biosynthesis and signaling of CKs occur in both organisms. The increase in CK biosynthesis by the pathosystem could lead to an increase in CK signaling via CK translocation and promote tumor formation. Taken together, these suggest that CK biosynthesis, signaling and translocation play a significant role during the formation of tumors in the Ustilago maydis-Zea mays pathosystem. Author Keywords: Biosynthesis, Cytokinins, Signaling, Translocation, Ustilago maydis, Zea mays
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:
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)
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
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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Graduate student theses produced at Trent University. You may also browse theses and dissertations by year, program, or author.

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