The aims of this thesis were to characterize the molecular ecology of the hyporheic zone – between dissolved organic matter (DOM) and microbes – and to test whether seasonal and spatial patterns existed in correlation with seasonal ecosystem processes. The hyporheic zone is an area of vertical integration between groundwater and surface water, and lateral integration between terrestrial and stream ecosystems. Colonization corers were used to collect in situ DOM and bacterial communities from the hyporheic sediments of two streams that varied in hydroperiod (i.e., permanent vs. intermittent). DOM was collected using passive samplers and analyzed using 1H NMR and fluorescence spectroscopy; bacteria were characterized using terminal-restriction fragment length polymorphism. At the permanent site, bacteria correlated significantly with seasonal environmental factors including: fall communities with DOM concentration; spring and winter communities with nitrate concentrations; and summer communities with temperature. Bacterial communities at the intermittent site were significantly correlated with flooding as a function of hydrologic connectivity. Sediment communities were discriminated between hyporheic sediments and interstitial porewaters, and shared several operational taxonomic units (OTUs). Sediment communities were more distinct when hydrologic connectivity was low, and porewater communities changed dramatically upon flooding. Fifteen out of 259 OTUs were shared across aquatic sediments, interstitial porewater and watershed soil samples. DOM was spatially and seasonally dynamic in both sites. Five key DOM groups described using 1H NMR spectroscopy revealed spatial differences between the permanent and intermittent sites. EEM-PARAFAC models confirmed that despite significantly different molecular components, the relative sources of DOM at both sites were similar, including humic-like terrestrial sources and tyrosine (microbial) sources. This study provides new knowledge on both organic matter dynamics and bacterial communities in a dynamic aquatic ecotone, and also confirmed the hypothesis that bacterial communities correlated significantly with ecosystem processes within a watershed.

In mutualisms, individuals exchange goods and services for net benefit. However, many sources of variation in these interactions remain unexplored. To examine why plantdwelling ants protect their host plants by killing herbivores, I shifted the macronutrient balance of their background diets. Providing ants with supplemental protein caused them to invest less in patrolling and defence activities, likely because the availability of lowcost protein made hunting for herbivores relatively less profitable. In contrast, supplemental sugar caused an increase in ant activity, possibly because carbohydrates serve as ‘fuel’ for patrolling. To examine a second source of variation in this interaction, I treated ants with an activator of PKG, a protein encoded by foraging, a gene with behavioural functions in other taxa. PKG activation caused ants to become more aggressive towards herbivores, causing their host plants to experience less herbivory. This suggests that an ortholog of foraging may influence cooperation in this system.

In mutualisms, individuals exchange goods and services for net benefit. However, many sources of variation in these interactions remain unexplored. To examine why plantdwelling ants protect their host plants by killing herbivores, I shifted the macronutrient balance of their background diets. Providing ants with supplemental protein caused them to invest less in patrolling and defence activities, likely because the availability of lowcost protein made hunting for herbivores relatively less profitable. In contrast, supplemental sugar caused an increase in ant activity, possibly because carbohydrates serve as ‘fuel’ for patrolling. To examine a second source of variation in this interaction, I treated ants with an activator of PKG, a protein encoded by foraging, a gene with behavioural functions in other taxa. PKG activation caused ants to become more aggressive towards herbivores, causing their host plants to experience less herbivory. This suggests that an ortholog of foraging may influence cooperation in this system.

Here I examine five non-migratory sympatric bat species that are similar in their morphology and general ecology: Eptesicus fuscus, three myotid bats, Myotis leibii, M. lucifugus, Myotis septentrionalis, and Pipistrellus (= Perimyotis) subflavus. By examining echolocation call structure, wing and jaw morphology and diet, I defined finer niche differences between species. M. lucifugus and M. septentrionalis differ in the relative abundance of moths in their diet. My results on skull morphology suggest M. lucifugus consumes harder insects than M. septentrionalis. Conversely, my data suggests M. leibii is not as efficient within a cluttered habitat but is capable of foraging in edge habitats. Eptesicus fuscus is capable of efficiently consuming larger insects whereas P. subflavus has echolocation and jaw characteristics that indicate specialization in smaller insects. Significant differences amongst these 5 species are evident based on my data of overall morphology and diet.

Here I examine five non-migratory sympatric bat species that are similar in their morphology and general ecology: Eptesicus fuscus, three myotid bats, Myotis leibii, M. lucifugus, Myotis septentrionalis, and Pipistrellus (= Perimyotis) subflavus. By examining echolocation call structure, wing and jaw morphology and diet, I defined finer niche differences between species. M. lucifugus and M. septentrionalis differ in the relative abundance of moths in their diet. My results on skull morphology suggest M. lucifugus consumes harder insects than M. septentrionalis. Conversely, my data suggests M. leibii is not as efficient within a cluttered habitat but is capable of foraging in edge habitats. Eptesicus fuscus is capable of efficiently consuming larger insects whereas P. subflavus has echolocation and jaw characteristics that indicate specialization in smaller insects. Significant differences amongst these 5 species are evident based on my data of overall morphology and diet.

Conserving biodiversity in human-dominated landscapes requires protecting networks of ecological reserves and managing the intervening matrix to maintain the potential for species to move among them. This dissertation provides original insights towards (1) identifying areas for protection in reserves that are critical to maintain biodiversity and (2) assessing the potential for species' movements among habitat patches in a reserve network. I develop and test methods that will facilitate conservation planning to promote viable, resilient populations through time. The first part of this dissertation tests and develops reserve selection strategies that protect either a single focal species in a dynamic landscape or multiple interacting species in a static landscape. Using a simulation model of boreal forest dynamics, I test the effectiveness of static and dynamic reserves to maintain spatial habitat requirements of a focal species, American Marten (Martes americana). Dynamic reserves improved upon static reserves but re-locating reserves was constrained by fragmentation of the matrix. Management of the spatial and temporal distribution of land-uses in the matrix will therefore be essential to retain options for re-locating reserves in the future. Additionally, to include essential consumer-resource interactions into reserve selection, a new algorithm is presented for American marten and its two primary prey species. The inclusion of their interaction had the benefit t of producing spatially aggregated reserves based on functional species requirements. The second part of this dissertation evaluates and synthesizes the network-theoretic approach to quantify connectivity among habitat patches or reserves embedded within spatially heterogeneous landscapes. I conduct a sensitivity analysis of network-theoretic connectivity analyses that derive least-cost movement behavior from the underlying cost surface which describes the relative ecological costs of dispersing through different landcover types. Landscape structure is shown to aff ect how sensitive least-cost graph connectivity assessments are to the quality (relative cost values) of landcover types. I develop a conceptual framework to classify network connectivity statistics based on the component of habitat connectivity that they quantify and the level within the network to which they can be applied. Together, the combination of reserve design and network connectivity analyses provide complementary insights to inform spatial planning decisions for conservation.

Competition plays a fundamental role in structuring ecological communities, and is a particularly important interaction for sessile organisms such as plants (Goldberg & Fleetwood 1987; Tilman 1994). To mitigate the negative effects of competition on fitness, plants can alter their phenotypes and reproductive traits through plastic responses. For example, decreases in the red to far-red ratio of light signal the presence of competitors, inducing a suite of responses known as shade avoidance syndrome (Franklin 2008). My thesis examines the impact of the competitive environment on reproductive output, the phenotypes Impatiens capensis produce and natural selection acting on shade avoidance responses. I found that heterospecific competitors affect both the phenotypes of I. capensis, and selection on shade avoidance traits. I also found evidence of population differentiation in hypocotyl lengths and flowering time. My thesis elucidates the influence of competition on the evolution of phenotypic plasticity in Impatiens capensis.

Long-lived individuals of the opportunistic fungal pathogen Armillaria gallica arise in single mating events, and then grow vegetatively to occupy large territories including multiple woody substrates. In effect, this leaves a spatial record of mutation, the detection of which would allow new inferences about how fungal individuals grow and infect their hosts. In this thesis, I first identified a large individual of A. gallica in eastern Ontario. I then searched for genetic variation within this individual by focusing on the tandemly repeated rRNA gene cluster and four microsatellite markers that are variable in the A. gallica population. I discovered a loss of heterozygosity (LOH) in the rRNA gene-cluster region, forming two genotypes that show significant spatial clustering in a Mantel test. My M.Sc. thesis research serves as a baseline for a genome-wide study of the mutational dynamic within the vegetative growth phase of this large and old Armillaria individual.

Habitat temperature is a major determinant of performance and activity in fish. I examined the relationships between thermal response metrics describing growth (optimal growth temperature [OGT] and final temperature preferendum [FTP]), survival (upper incipient lethal temperature [UILT] and critical thermal maximum [CTMax]), and reproduction (optimum spawning [OS] and optimum egg development temperature [OE]) for 173 North American freshwater fish species. All metrics were highly correlated and associated with thermal preference class, reproductive guild and spawning season. Controlling for phylogeny resulted in an overall decrease in correlation strength, varying with metric pair relationship. ANCOVA and Bayesian hierarchical models were utilized to assess the influence of phylogeny on metric pair relationships. For both methods, FTP based metric pairs were weakly correlated within taxonomic family. Strong within family associations were found for reproduction metrics OS-OE. These results suggest that evolutionary history plays an important role in determining species thermal response to their environment.

Long-lived individuals of the opportunistic fungal pathogen Armillaria gallica arise in single mating events, and then grow vegetatively to occupy large territories including multiple woody substrates. In effect, this leaves a spatial record of mutation, the detection of which would allow new inferences about how fungal individuals grow and infect their hosts. In this thesis, I first identified a large individual of A. gallica in eastern Ontario. I then searched for genetic variation within this individual by focusing on the tandemly repeated rRNA gene cluster and four microsatellite markers that are variable in the A. gallica population. I discovered a loss of heterozygosity (LOH) in the rRNA gene-cluster region, forming two genotypes that show significant spatial clustering in a Mantel test. My M.Sc. thesis research serves as a baseline for a genome-wide study of the mutational dynamic within the vegetative growth phase of this large and old Armillaria individual.