Plant form and structure is remarkably diverse encompassing a myriad of shapes and sizes, and is a result of coordinated instances of cell growth and division. This varied form and structure represents adaptive strategies enabling plants to exploit and endure their environment maximizing fitness. Common to both cell growth and division processes, is the requirement of growth material and effectors via the secretory system. The secretory system is a dynamic pathway of organelles connected via vesicular traffic, responsible for protein modification and delivery. Challenges in studying secretion are related to its' dynamic flow between organelles, and the prevalence of redundancy and lethality, which cause difficulties in interpretation and genetic modulation. To further our understanding of the secretory process, we employed a chemical genetic approach to identify small molecule probes of secretion by first screening for inhibitors of cell expansion, followed by a microscopy based screen of GFP marker lines for perturbagens of subcellular structures. Small molecules offer the advantages of temporal and spatial application, have been shown to overcome redundancy and can be varied in concentration to control the severity of effects. We identified twenty-five small molecule probes of secretion and pursued two chemicals with striking properties, polarazine and eroonazole. Polarazine was identified as a cell division inhibitor, affecting phragmoplast structure and function, while eroonazole remodels the endoplasmic reticulum into small vesicles and is implicated in auxin signaling. This approach shows the utility of small molecule probes in furthering our understanding of secretory processes.

The transition from cross-fertilization to predominant self-fertilization is considered the most common evolutionary transition in flowering plants. This change in mating system has profound influences on the amounts and patterns of genetic diversity within and among populations, and on key genetic and demographic processes. The main goal of my thesis is to determine the molecular population genetic consequences of this transition in the annual neotropical aquatic plant Eichhornia paniculata (Pontederiaceae) using DNA sequence from individuals sampled from throughout the species’ geographic range. Populations exhibit a wide range of mating patterns associated the evolutionary breakdown of tristyly facilitating specific contrasts between outcrossing and selfing populations. Analysis of molecular variation supported the hypothesis of multiple origins of selfing, including the evolution of two morphologically distinct selfing variants from Central America and the Caribbean. A survey of 10 nuclear loci from 225 individuals sampled from 25 populations demonstrated the joint influence of mating system, population size and demographic bottlenecks in affecting patterns of nucleotide variation. Small selfing populations exhibited significantly lower genetic diversity compared with larger outcrossing and mixed mating populations. There was also evidence for higher population differentiation and a slower decay of linkage disequilibrium in predominately selfing populations from the Caribbean region. Coalescent simulations of the sequence data indicated a bottleneck associated with colonization of the Caribbean from Brazil ∼125,000 years ago. To investigate the consequences of transitions from outcrossing to selfing across the genome, I used high-throughput, short-read sequencing to assemble ~27,000 ESTs representing ∼24Mbp of sequence. Characterization of floral transcriptomes from this dataset identified 269 genes associated with floral development, 22 of which were differentially expressed in three independently derived selfing lineages compared to an outcrossing genotype. Evidence for relaxed selection in selfing lineages was obtained from an analysis of a subset of ~8000 orthologous sequences from each genotype, as predicted by theory. Selfing genomes showed an increase in the proportion of nonsynonymous to synonymous changes and relaxation of selection for codon usage bias. My thesis represents the most detailed investigation to date of the molecular population genetic consequences of intraspecific variation in the mating systems of plants.

The C3 photosynthetic pathway uses light energy to reduce CO2 to carbohydrates and other organic compounds and is a central component of biological metabolism. In C3 photosynthesis, CO2 assimilation is catalyzed by ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), which reacts with both CO2 and O2. While competitive inhibition of CO2 assimilation by oxygen is suppressed at high CO2 concentrations, O2 inhibition is substantial when CO2 concentration is low and O2 concentration is high; this inhibition is amplified by high temperature and aridity (Sage 2004). Atmospheric CO2 concentration dropped below saturating levels 25-30 million years ago (Tipple & Pagani 2007), and the C4 photosynthetic pathway is hypothesized to have first evolved in warm, low latitude environments around this time (Christin et al. 2008a). The primary feature of C4 photosynthesis is suppression of O2 inhibition through concentration of CO2 around Rubisco. This pathway is estimated to have evolved almost 50 times across 19 angiosperm families (Muhaidat et al. 2007), a remarkable example of evolutionary convergence. In several C4 lineages, there are species with photosynthetic traits that are intermediate between the C3 and C4 states, known as C3-C4 intermediates. In two eudicot genera, Flaveria (Asteraceae) and Alternanthera (Amaranthaceae), there is evidence that these species represented an intermediate state in the evolution of the C4 pathway (McKown et al. 2005; Sanchez-del Pino 2009). The purpose of this thesis is to ascertain the specific benefits to plant carbon balance and resource-use efficiencies of the C3-C4 pathway relative to C3 species, particularly at low CO2 concentrations and high temperatures, factors which are thought to have been important in selecting for C3-C4 traits (Ehleringer et al. 1991). This will provide information on the particular advantages of the C3-C4 pathway in warm, often arid environments and how these advantages may have been important in advancing the initial stages of C4 evolution in eudicots. This thesis addresses the physiological intermediacy of previously uncharacterized C3-C4 species of Heliotropium (Boraginaceae); the water- and nitrogen-use efficiencies of C3-C4 species of Flaveria; and the photosynthetic performance and acclimation of C3, C4 and C3-C4 species of Heliotropium, Flaveria and Alternanthera grown at low and current ambient CO2 levels and high temperature.

The objective of this thesis was to assess the diversity and community structure of fungi in a forest plot in Ontario using a variety of field sampling and analytical methods. Three broad questions were addressed: 1) How do different measures affect the resulting view of fungal diversity? 2) Do fruiting bodies and soil rDNA sampling detect the same phylogenetic and ecological groups of Agaricomycotina? 3) Will additional rDNA sampling resolve the phylogenetic position of unclassified fungal sequences recovered from environmental sampling? Generally, richness, abundance, and phylogenetic diversity (PD) correspond and identify the same dominant fungal groups in the study site, although in different proportions. Clades with longer branch lengths tend to comprise a larger proportion of diversity when assessed using PD. Three phylogenetic-based comparisons were found to be variable in their ability to detect significant differences. Generally, the Unifrac significance measure (Lozupone et al., 2006) is the most conservative, followed by the P-test (Martin, 2002), and Libshuff library comparison (Singleton et al., 2001) with our dataset. Fruiting body collections and rDNA sampling recover largely different assemblages of fungi at the species level; however, both methods identify the same taxonomic groups at the genus-order level as well as ectomycorrhizal fungi as the dominant functional type of Agaricomycotina. This work also shows that the Soil Clone Group I (SCGI) clade is widespread in soils of diverse origins and represents a novel subphylum of Ascomycota.

The objective of this thesis was to assess the diversity and community structure of fungi in a forest plot in Ontario using a variety of field sampling and analytical methods. Three broad questions were addressed: 1) How do different measures affect the resulting view of fungal diversity? 2) Do fruiting bodies and soil rDNA sampling detect the same phylogenetic and ecological groups of Agaricomycotina? 3) Will additional rDNA sampling resolve the phylogenetic position of unclassified fungal sequences recovered from environmental sampling? Generally, richness, abundance, and phylogenetic diversity (PD) correspond and identify the same dominant fungal groups in the study site, although in different proportions. Clades with longer branch lengths tend to comprise a larger proportion of diversity when assessed using PD. Three phylogenetic-based comparisons were found to be variable in their ability to detect significant differences. Generally, the Unifrac significance measure (Lozupone et al., 2006) is the most conservative, followed by the P-test (Martin, 2002), and Libshuff library comparison (Singleton et al., 2001) with our dataset. Fruiting body collections and rDNA sampling recover largely different assemblages of fungi at the species level; however, both methods identify the same taxonomic groups at the genus-order level as well as ectomycorrhizal fungi as the dominant functional type of Agaricomycotina. This work also shows that the Soil Clone Group I (SCGI) clade is widespread in soils of diverse origins and represents a novel subphylum of Ascomycota.

Sugars have a profound impact on plant biology, acting as structural components, signalling molecules, and sources of energy. As such, the availability of sugars has important implications for plant growth and development. Sugar levels rise and fall as part of a daily cycle, while cues from other environmental stimuli are also in flux. As sessile organisms in an ever-changing environment, plants must integrate signals from multiple pathways in order to promote the appropriate developmental responses. To uncover pathways that interact with sugars during seedling development, a chemical screen was performed in search of compounds that modify responses to sucrose. This screen identified an interaction between the folate inhibitor sulfamethoxazole (SMX) and sucrose that resulted in changes to auxin signalling and distribution. Synergy between sucrose and SMX was used to explore the effect of metabolic cues on auxin signalling during hypocotyl elongation. A second line of investigation explored whether sucrose and folates influence root meristem activity. Sucrose induced hormone signalling pathways that promote cell division and differentiation. Treatment with SMX perturbed the effect of sucrose on hormone networks that mediate growth, and resulted in a loss of meristem integrity. This study highlights the influence of metabolism on hormone signalling at the root apex, and its role in maintaining balance of a complex signalling network that drives root growth. These studies characterise an interaction between metabolic pathways that is integrated with hormone signalling during plant development. Taken together, they highlight a mechanism through which plant growth might be regulated by metabolism.

Sugars have a profound impact on plant biology, acting as structural components, signalling molecules, and sources of energy. As such, the availability of sugars has important implications for plant growth and development. Sugar levels rise and fall as part of a daily cycle, while cues from other environmental stimuli are also in flux. As sessile organisms in an ever-changing environment, plants must integrate signals from multiple pathways in order to promote the appropriate developmental responses. To uncover pathways that interact with sugars during seedling development, a chemical screen was performed in search of compounds that modify responses to sucrose. This screen identified an interaction between the folate inhibitor sulfamethoxazole (SMX) and sucrose that resulted in changes to auxin signalling and distribution. Synergy between sucrose and SMX was used to explore the effect of metabolic cues on auxin signalling during hypocotyl elongation. A second line of investigation explored whether sucrose and folates influence root meristem activity. Sucrose induced hormone signalling pathways that promote cell division and differentiation. Treatment with SMX perturbed the effect of sucrose on hormone networks that mediate growth, and resulted in a loss of meristem integrity. This study highlights the influence of metabolism on hormone signalling at the root apex, and its role in maintaining balance of a complex signalling network that drives root growth. These studies characterise an interaction between metabolic pathways that is integrated with hormone signalling during plant development. Taken together, they highlight a mechanism through which plant growth might be regulated by metabolism.

The herbivory experienced by non-native invasive plants may depend on their local environments, such as herbivore abundance. In this study, I performed a common garden experiment with plants sampled from 11 populations of Arctium minus, from southern Ontario to near its northern range limit. I also compared performance and herbivory of burdock in open and understory habitats. Finally, I conducted freezing tolerance experiments with the lepidopteran seed predator Metzneria lapella, and palatability tests with plants from different populations. Results suggested that the previously described latitudinal trends in herbivore damage among populations are due to environmental differences rather than genotypic differences among populations. At a local scale, plants of open habitat were less damaged and had better performance than understory plants. Burdock has not escaped damage by herbivores in its invaded range; instead variation among sites in herbivore populations and impacts may significantly affect the invasiveness of this species.

The herbivory experienced by non-native invasive plants may depend on their local environments, such as herbivore abundance. In this study, I performed a common garden experiment with plants sampled from 11 populations of Arctium minus, from southern Ontario to near its northern range limit. I also compared performance and herbivory of burdock in open and understory habitats. Finally, I conducted freezing tolerance experiments with the lepidopteran seed predator Metzneria lapella, and palatability tests with plants from different populations. Results suggested that the previously described latitudinal trends in herbivore damage among populations are due to environmental differences rather than genotypic differences among populations. At a local scale, plants of open habitat were less damaged and had better performance than understory plants. Burdock has not escaped damage by herbivores in its invaded range; instead variation among sites in herbivore populations and impacts may significantly affect the invasiveness of this species.

The C3 photosynthetic pathway uses light energy to reduce CO2 to carbohydrates and other organic compounds and is a central component of biological metabolism. In C3 photosynthesis, CO2 assimilation is catalyzed by ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), which reacts with both CO2 and O2. While competitive inhibition of CO2 assimilation by oxygen is suppressed at high CO2 concentrations, O2 inhibition is substantial when CO2 concentration is low and O2 concentration is high; this inhibition is amplified by high temperature and aridity (Sage 2004). Atmospheric CO2 concentration dropped below saturating levels 25-30 million years ago (Tipple & Pagani 2007), and the C4 photosynthetic pathway is hypothesized to have first evolved in warm, low latitude environments around this time (Christin et al. 2008a). The primary feature of C4 photosynthesis is suppression of O2 inhibition through concentration of CO2 around Rubisco. This pathway is estimated to have evolved almost 50 times across 19 angiosperm families (Muhaidat et al. 2007), a remarkable example of evolutionary convergence. In several C4 lineages, there are species with photosynthetic traits that are intermediate between the C3 and C4 states, known as C3-C4 intermediates. In two eudicot genera, Flaveria (Asteraceae) and Alternanthera (Amaranthaceae), there is evidence that these species represented an intermediate state in the evolution of the C4 pathway (McKown et al. 2005; Sanchez-del Pino 2009). The purpose of this thesis is to ascertain the specific benefits to plant carbon balance and resource-use efficiencies of the C3-C4 pathway relative to C3 species, particularly at low CO2 concentrations and high temperatures, factors which are thought to have been important in selecting for C3-C4 traits (Ehleringer et al. 1991). This will provide information on the particular advantages of the C3-C4 pathway in warm, often arid environments and how these advantages may have been important in advancing the initial stages of C4 evolution in eudicots. This thesis addresses the physiological intermediacy of previously uncharacterized C3-C4 species of Heliotropium (Boraginaceae); the water- and nitrogen-use efficiencies of C3-C4 species of Flaveria; and the photosynthetic performance and acclimation of C3, C4 and C3-C4 species of Heliotropium, Flaveria and Alternanthera grown at low and current ambient CO2 levels and high temperature.