Biology

Ustilago maydis (D.C.) Corda is a biotrophic pathogen that secretes effectors to establish and maintain a relationship with its host, Zea mays. In this pathosystem, the molecular function of effectors is well-studied, but the regulation of effector gene expression remains largely unknown. This study characterized Zfp1, a putative U. maydis Zn(II)2Cys6 transcription factor, as a modulator of effector gene expression. The amino acid sequence of Zfp1 indicated the presence of a GAL4-like zinc binuclear cluster as well as a fungal specific transcription factor domain. Nuclear localization was confirmed by tagging Zfp1 with enhanced green fluorescent protein. Deletion of zfp1 resulted in attenuated hyphal growth, reduced infection frequency, an arrest in pathogenic development, and decreased anthocyanin production. This phenotype can be attributed to the altered transcript levels of genes encoding predicted and confirmed U. maydis effectors in the zfp1 deletion strain during pathogenic growth. Complementation of zfp1 deletion strain with tin2, an effector involved in anthocyanin induction, suggested this effector is downstream of Zfp1 and its expression is influenced by this transcription factor during in planta growth. When wild-type zfp1 was ectopically inserted in the zfp1 deletion strain, pathogenesis and virulence were partially restored. This, coupled with zfp1 over-expression strains having a similar phenotype as the deletion strains, suggested Zfp1 may interact with other proteins for full function. These findings show that Zfp1, in conjunction with one or more binding partners, contributes to U. maydis pathogenesis, virulence, and anthocyanin production through the regulation of effector gene expression.

Author Keywords: effector, pathogenesis, transcription factor, Ustilago maydis, Zea mays, zinc finger

Coldwater streams are becoming increasingly impacted due to urbanization. Using environmental surveys, mark-recapture and telemetry, I assessed factors influencing seasonal brook trout (Salvelinus fontinalis) habitat use and movement in urban headwater streams in central Ontario between 2017-18. Generalized additive models were used to assess which habitat variables best explained seasonal yearling and older brook trout abundance, while generalized least squares models were used to assess overall trends in radio-tagged brook trout movement. My research demonstrated dynamic patterns in habitat use and movement by urban stream-dwelling brook trout. Yearlings were primarily influenced by water quality (stream temperature, conductivity), while older brook trout were most strongly influenced by stream morphology (depth, undercut bank). Movement occurred disproportionately around the spawning season and was more limited in the smaller, more altered stream. These findings may be used to inform fisheries managers on crucial timing and location of brook trout habitat refugia within urbanized environments.

Author Keywords: Brook trout, coldwater stream, groundwater, habitat use, radiotelemetry, urbanization

Invasive Phragmites australis ssp. australis (herein "Phragmites") has established and rapidly spread throughout many coastal areas of the Great Lakes. Known to displace native vegetation communities as it forms large, monotypic stands, Phragmites has a bad reputation when it comes to losses of biodiversity and habitat provision for wildlife. However, the extent to which Phragmites provides habitat for fish and invertebrates in coastal freshwater wetlands remains relatively unquantified. Thus, this study assessed whether fish assemblages and invertebrate communities in stands of Phragmites differ from those in stands of two native emergent vegetation communities, Typha spp. and Schoenoplectus spp. The findings showed significant differences in habitat variables among the vegetation communities in terms of water depth, macrophyte species richness, stem density and water quality. While abundance of the functional feeding group filterer-collectors was found to be significantly less in stands of Phragmites when compared to Schoenoplectus, no difference was observed in invertebrate taxa richness among vegetation communities. Lastly, no difference in fish assemblage or invertebrate community was detected when using multivariate analyses, implying that invasive Phragmites provides habitat that appears to be as valuable for fish and invertebrates as other emergent vegetation types in the St. Clair River Delta. The findings of this study will ultimately benefit the literature on invasive Phragmites and its role as fish habitat in freshwater wetlands, and aid management agencies in decisions regarding control of the invasive species.

Author Keywords: aquatic invasive species, aquatic macroinvertebrates, freshwater fish, freshwater wetlands, nMDS, Phragmites

Syrphids, also known as hover flies (Diptera: Syrphidae) are a diverse and widespread family of flies. Here, I report on their distributions from a previously understudied region, the far north of Ontario, as well as Akimiski Island, Nunavut. I used samples collected through a variety of projects to update known range and provincial records for over a hundred species, bringing into clearer focus the distribution of syrphids throughout this region. I also analysed a previously un-tested trap type for collecting syrphids (Nzi trap), and report on results of DNA analysis for a handful of individuals, which yielded a potential new species.

Author Keywords: Diptera, Ontario, range extension, Syrphidae

Competition is known to impact population dynamics through both indirect and direct interactions, and direct interactions can often lead to injury in one or both parties. As such, response to injury through tissue regeneration can be important for surviving post-competitive interaction. However, the impacts of outside factors like temperature and genome size (e.g. polyploidy) are not well studied, especially in syntopic systems. We addressed this knowledge gap by comparing regeneration rates of diploid Ambystoma laterale and triploid unisexual Ambystoma at two ecologically-relevant temperatures. Environmental factors appeared to have stronger effects on regeneration than ploidy level, but overall mass was impacted more strongly by ploidy level. Interestingly, there was an interaction between temperature and time within unisexuals that was absent when comparing different ploidy levels, implying temperature has a more complex effect on polyploids. This study supports the hypothesis that polyploid organisms are better equipped to respond to shifts in their environments, which can give them a competitive advantage at the northern range limit of this species complex.

Author Keywords: Ambystoma, Genome dosage, Hybrid vigor, Polyploidy, Thermal optimum, Tissue regeneration

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

Populations have long been delineated by physical barriers that appear to limit reproduction, yet increasingly genetic analysis reveal these delineations to be inaccurate. The eastern and mid-continent populations of sandhill cranes are expanding ranges which is leading to convergence and warrants investigation of the genetic structure between the two populations. Obtaining blood or tissue samples for population genetics analysis can be costly, logistically challenging, and may require permits as well as potential risk to the study species. Non-invasively collected genetic samples overcome these challenges, but present challenges in terms of obtaining high quality DNA for analysis. Therefore, methods that optimize the quality of non-invasive samples are necessary. In the following thesis, I examined factors affecting DNA quality and quantity obtained from shed feathers and examined population differentiation between eastern and mid-continent sandhill cranes. I found shed feathers are robust to environmental factors, but feather size should be prioritized to increase DNA quantity and quality. Further, I found little differentiation between eastern and mid-continent populations with evidence of high migration and isolation-by-distance. Thus, the two populations are not genetically discrete. I recommend future population models incorporate migration between populations to enhance our ability to successfully manage and reach conservation objectives.

Author Keywords: feathers, genetic differentiation, non-invasive DNA, population genetics, population management, sandhill crane (Antigone canadensis)

This thesis investigated the role of the neuronal ceroid lipofuscinosis protein, Cln5, during autophagy. This was accomplished by performing well-established assays in a Dictyostelium cln5 knockout model (cln5-). In this study, cln5- cells displayed a reduced maximum cell density during growth and impaired cell proliferation in autophagy-stimulating media. cln5- cells had an increased number of autophagic puncta (autophagosomes and lysosomes), suggesting that autophagy is induced when cln5 is absent. cln5- cells displayed increased amounts of ubiquitin-positive proteins but had no change in proteasome protein abundance. During the development of cln5- cells, fruiting bodies developed precociously and cln5- slug size was reduced. Lastly, when cln5- cells were developed on water agar containing ammonium chloride (NH4Cl), a lysosomotropic agent, the formation of multicellular structures was impaired, and the small slug phenotype was exaggerated. In summary, these results indicate that Cln5 plays a role in autophagy in Dictyostelium. The cellular processes that regulate autophagy in Dictyostelium are similar to those that regulate the process in mammalian cells. Thus, this research provides insight into the undefined pathological mechanism of CLN5 disease and could identify cellular pathways for targeted therapeutics.

Author Keywords: Autophagy, Batten disease, Cln5, Dictyostelium discoideum, NCL

The primary method used to maintain white-tailed deer (Odocoileus virginianus) populations at densities that are ecologically, economically, socially, and culturally sustainable is hunter harvest. This method considers only the removal of animals from the population (the direct effect) and does not conventionally consider the costs imposed on deer as they adopt hunter avoidance strategies (the risk effect). The impact of risk effects on prey can exceed that of direct effects and there is interest in applying this concept to wildlife management. Deer are potential candidates as they have demonstrated behavioural responses to hunters. I explored the potential of such a management practice by quantifying how human decisions around hunting create a landscape of fear for deer and how deer alter their space use and behaviour in response. I used a social survey to explore the attitudes of rural landowners in southern and eastern Ontario towards deer and deer hunting to understand why landowners limited hunting on their property. I used GPS tracking devices to quantify habitat selection by hunters and hunting dogs (Canis familiaris) to better understand the distribution of hunting effort across the landscape. I used GPS collars to quantify the habitat selection of deer as they responded to this hunting pressure. I used trail cameras to quantify a fine-scale behavioural response, vigilance, by deer in areas with and without hunting. Human actions created a highly heterogeneous landscape of fear for deer. Landowner decisions excluded hunters from over half of the rural and exurban landscape in southern and eastern Ontario, a pattern predicted by landowner hunting participation and not landcover composition. Hunter decisions on whether to hunt with or without dogs resulted in dramatically different distributions of hunting effort across the landscape. Deer showed a high degree of behavioural plasticity and, rather than adopting uniform hunter avoidance strategies, tailored their response to the local conditions. The incorporation of risk effects into white-tailed deer management is feasible and could be done by capitalizing on a better understanding of deer behaviour to improve current management practices or by designing targeted hunting practices to elicit a landscape of fear with specific management objectives.

Author Keywords: Brownian bridge movement models, hunting, landscape of fear, resource utilization functions, risk effects, white-tailed deer

The ability of animal populations to compensate for harvest mortality provides the basis for sustainable harvesting. Coyote populations are resilient to exploitation, but the underlying mechanisms of compensation and how they inter-relate are not fully understood. Moreover, deficiencies in the quality and quantity of information about eastern coyotes preclude effective management. I combined field work, laboratory work, and genetic profiling to investigate the population dynamics of eastern coyotes in southeastern Ontario. Specifically, I conducted research on coyotes during 2010–2013 in Prince Edward County where coyote hunting and trapping seasons were open all year. First, I investigated their social status dynamics and space-use patterns. Transients exhibited extensive space-use relative to residents, potentially encountering vacant territories and/or breeding positions, and some transients became residents, potentially filling vacant territories and/or breeding positions. Accordingly, the study population demonstrated the potential to compensate for harvest mortality via source-sink dynamics and/or buffering reproductive capacity. Second, I investigated their survival and cause-specific mortality. Residents exhibited greater survival than transients, probably partly because of the benefits of holding a territory, and transients seemingly exhibited greater vulnerability to harvest than residents, probably partly because their movements exposed them to greater cumulative mortality risks over time. Accordingly, harvest mortality disproportionately impacted the non-reproductive segment of the study population and thus may have failed to substantially limit reproduction, and thus recruitment. Third, I investigated their reproduction and breeding histories. Females in the study population exhibited age-specific reproductive rates and litter sizes generally typical of those in exploited coyote populations. Accordingly, increased reproductive rates and increased litter sizes may have offset losses due to harvest mortality. There was at least some breeder turnover in the study population due to harvest mortality, but many breeders survived to reproduce for multiple years and those that died were quickly replaced. My findings have important management implications for eastern coyotes and contribute significantly to better understanding of their resilience to harvest. Indiscriminate killing of coyotes through liberal harvest is unlikely to be effective in reducing their abundance. Management strategies should consider non-lethal alternatives and/or targeted lethal control for dealing with problem coyotes.

Author Keywords: Canis latrans var., eastern coyotes, population dynamics, Prince Edward County, southeastern Ontario