Habitat modification is the primary cause of amphibian population declines worldwide. Some species survive in modified habitats whereas others become restricted to small, isolated forest patches. Although many studies compare species richness and composition between modified and intact habitats, the factors and mechanisms that maintain biodiversity in these landscapes are poorly understood. I asked how life history traits and habitat features influence interspecific variation in frog occupancy patterns in tropical pasture and forest. To identify mechanisms underlying occupancy patterns, I used experiments to examine how abiotic conditions in different habitats influence the vital rates of tadpoles. I also explored whether tadpoles use a carnivorous foraging strategy to improve performance in nutrient-poor, ephemeral pools in pasture. Although modified and intact habitats offer abiotic environments that differ in quality for frogs, pastures contribute to the maintenance of biodiversity in fragmented landscapes. I detected an equal number of species but substantially different assemblage composition in forest and pasture. Species that occurred in pasture had different traits than those in forest, including larger body sizes, larger clutch sizes, larger geographic ranges, and reproductive modes that depend on water. The occurrence of pasture-specialists was associated with habitat features at small spatial scales, whereas the occurrence of forest-specialists was associated with habitat features at small and large spatial scales. An experiment indicated that abiotic conditions in pastures may deter or facilitate adult movements to breeding sites. Behavioral selection of sites by two model species was consistent with tadpole performance. Tadpoles of a pasture-specialist performed well across the pasture-forest gradient, but abiotic conditions in pasture facilitated faster growth and development than in edge or forest. In contrast, tadpoles of a forest-specialist performed well only in edge and forest. Most tadpoles occupying ephemeral pasture pools were facultative carnivores or cannibals of eggs and hatchlings. Tadpoles may contribute to the regulation of assemblages in pasture pools, influencing the relative abundance and composition of species through differential predation on eggs and hatchlings. The study of factors and mechanisms that contribute to population growth or decline of species can facilitate understanding of assemblage-level patterns of amphibian diversity in modified landscapes.

It is an unresolved paradox that non-native species are successful in novel environments whereas native species, presumably adapted to that environment, decline. This knowledge gap has persisted because third party processes in invasion ecology have been overlooked. Ungulate densities are increasing due to the eradication of predators and landscape change and I asked how herbivory and invasion might interact to cause declines of native species. In Garry oak meadows, Canada’s most endangered ecosystem, native forbs have declined relative to non-native grasses and I tested the facilitatory role of herbivory in that degradation. My investigations, novel to the field, were conducted on islands spanning the Canada-US border. Islands served as natural experimental units in a mensurative study of abundance patterns in seven plant groups and 15 focal species along gradients of herbivory, biogeography, soil depth, and human activities. Increasing ungulate densities were related to declines in abundances of native forbs, and increasing abundances of non-native annual grasses. These regional patterns were upheld by two plot-based, 2x2 factorial experiments that contrasted the fitness of native species under manipulations of herbivory and competition for light. Specifically, I showed that ungulates limited the establishment, growth, survival and reproduction of seedlings and transplanted native forbs and shrubs and that competition from non-native species had little effect. I also calculated forage selectivity indices and tested the efficacy of fencing and cutting to reduce competition, for the restoration of native community biomass. Non-native annual grasses were rarely browsed and increased with increasing ungulate density. Non-native perennial grasses declined with herbivory, however, their regional abundances were unaffected by ungulate density despite being preferentially foraged. That non-native annual and perennial grasses differed in their responses to herbivory has consequences for restoration and illustrates the challenge of developing a comprehensive theory of invasion. Reducing ungulates, necessary for the recovery of native forbs, also benefits non-native perennial grasses and therefore their removal speed recovery of Garry oak meadows. Despite advances in invasion ecology, scientists and managers are disconnected and research is rarely implemented. I conclude by proposing seven solutions to facilitate the integration of science into management.

Because differences often exist between species in their tolerances to environmental conditions, locations characterized by extreme parameter values (i.e., high temperature, low DO, high turbidity) may provide refuges from predation or competition by altering the outcome of inter-species interactions. This thesis examined the effects and relative importance of water temperature, dissolved oxygen (DO) and turbidity on habitat use by fish species and resulting changes in community composition. The effects of abiotic factors on predator-prey interactions were tested using field surveys, laboratory experiments, field experiments and computer modeling. Field surveys were conducted in Blind Channel, Delta Marsh, Manitoba, and on Lake Winnipeg, Manitoba, to determine if small bodied forage species preferentially used high temperature, low DO or high turbidity habitats and whether predator species avoided these locations. Prey species were more abundant in these extreme locations at both small (Blind Channel) and large (Lake Winnipeg) spatial scales, but predator avoidance was only documented in Blind Channel. The tolerances of fish species to moderate hypoxia (< 3 mg/L DO) was tested in the laboratory to verify that differences did exist among species and that the observed species distributions were not solely the effect of temperature. To quantify the potential for moderately hypoxic locations to provide a refuge from predation for small fish, a field manipulation was conducted in Blind Channel; hypoxic habitats were created without altering water temperature, decoupling the natural covariation between these two factors that occurs in aquatic systems. The abundance of small forage fish was higher in the hypoxic locations compared to controls and while predators still visited the hypoxic habitats, their mean visit duration was reduced from around 300 min to less than 1 min. An individual based computer model was used to test and illustrate current understanding of the relative importance of temperature, DO and turbidity on predator habitat selection decisions and fish community composition. The model showed that DO had a stronger effect on community composition than temperature, and that reduced foraging success from high turbidity was able to overpower the other two factors. Hypoxia affects habitat selection decisions by fish species and can provide refuges from predation and competition, helping maintain higher species diversity. Water temperature appears to have a weaker effect on fish distributions than DO while turbidity primarily affects visual predators, though the strength of turbidity effects depends on the magnitude and duration of individual events. / February 2008

Approximately two thirds of the world’s land is directly supporting human population contributing to an accumulation of disturbed habitats. This dissertation investigates the impact of human mediated habitat disturbance, in introduced Eucalyptus plantations, on community diversity and population divergence using Brazilian Cerrado lizards as a model. Data was collected along a gradient from undisturbed cerrado to disturbed Eucalyptus plantations. Community diversity differences and indicator species were identified. Furthermore, the role of phenotypic divergences were determined based on populations able to persist in disturbed habitats. Dispersal, food availability (body condition), competition and predation (caudal autotomy) were tested as potential mechanisms driving phenotypic divergences. Additionally, I investigated phylogenetic community structure differences between habitats to test for a phylogenetic signal to disturbance. The evidence showed community diversity indices were significantly lower in Eucalyptus plantations with a decrease along the cerrado– Eucalyptus gradient. Furthermore, 29 % of the Cerrado species suffered local extinctions in the disturbed habitat and of these 80 % are endemic species. One indicator species was identified for the disturbed habitat and seven species were identified for the undisturbed habitat. Species able to persist in both habitats demonstrated morphological trait divergences. These species showed short dispersal distances with only two individuals dispersing between habitats indicating a mechanism driving the observed phenotypic divergences. Another mechanism is body condition, which was higher in the disturbed habitats, reflecting increased food availability possibly due to the decreased abundances. Caudal autotomy showed no difference between the habitats indicating that competition and predation are not driving phenotypic divergences. Phylogenetic community structure demonstrated a phylogenetic signal to disturbance. The undisturbed habitat consists of communities with more closely related species compared to the disturbed habitat: indicating evolutionary forces such as habitat filtering as the stronger process structuring these communities. Whereas, disturbed communities are structured by ecological forces such as competition. This research provides information for the preservation and maintenance of the Cerrado biodiversity and has an even broader impact since habitat change caused by human activities touches a plethora of ecosystems. / text

Urbanization, the creation of cities and their growth, is a process with profound implications for the diversity and community composition of local ecosystems. Urban environments are made up of a diverse patchwork of natural, seminatural and modified habitats that might harbor different plant and animal communities. Frequently, they include invasive or exotic organisms. In arid environments in particular, irrigated spaces constitute a novel habitat that contrasts heavily with natural environments. In the present study, I considered the biodiversity and composition of the ant communities in contrasting environments within the urban area of Tucson, Arizona. First, I assessed the relationship between plant productivity, measured using satellite imagery, ant abundance and ant diversity in irrigated parks, urban desert remnants and natural desert habitat. I found no significant differences in ant diversity among these habitats, despite clear differences in abundance and productivity. Next I considered the differences in ant species composition among the assemblages in the same three habitats. I found that each habitat included a distinct ant community, although those from desert remnants and natural desert were functionally similar to each other. Irrigated parks showed a potential to act as refuges for ant species threatened by the effects of climate change, but they also included a greater abundance of ants considered pests. Finally, I considered some of the characteristics behind the success of the only widespread exotic ant species found in urban habitats in Tucson: the dark rover ant (Brachymyrmex patagonicus).These ants were found in large numbers in every park sampled. As a recently introduced species, little was known of their biology. Colonies of these ants displayed aggression among each other which makes it impossible for them to form large interconnected networks of nests. Although colonies occupied nearby nests in the laboratory, under field conditions, each colony inhabited a small territory.

It is an unresolved paradox that non-native species are successful in novel environments whereas native species, presumably adapted to that environment, decline. This knowledge gap has persisted because third party processes in invasion ecology have been overlooked. Ungulate densities are increasing due to the eradication of predators and landscape change and I asked how herbivory and invasion might interact to cause declines of native species. In Garry oak meadows, Canada’s most endangered ecosystem, native forbs have declined relative to non-native grasses and I tested the facilitatory role of herbivory in that degradation. My investigations, novel to the field, were conducted on islands spanning the Canada-US border. Islands served as natural experimental units in a mensurative study of abundance patterns in seven plant groups and 15 focal species along gradients of herbivory, biogeography, soil depth, and human activities. Increasing ungulate densities were related to declines in abundances of native forbs, and increasing abundances of non-native annual grasses. These regional patterns were upheld by two plot-based, 2x2 factorial experiments that contrasted the fitness of native species under manipulations of herbivory and competition for light. Specifically, I showed that ungulates limited the establishment, growth, survival and reproduction of seedlings and transplanted native forbs and shrubs and that competition from non-native species had little effect. I also calculated forage selectivity indices and tested the efficacy of fencing and cutting to reduce competition, for the restoration of native community biomass. Non-native annual grasses were rarely browsed and increased with increasing ungulate density. Non-native perennial grasses declined with herbivory, however, their regional abundances were unaffected by ungulate density despite being preferentially foraged. That non-native annual and perennial grasses differed in their responses to herbivory has consequences for restoration and illustrates the challenge of developing a comprehensive theory of invasion. Reducing ungulates, necessary for the recovery of native forbs, also benefits non-native perennial grasses and therefore their removal speed recovery of Garry oak meadows. Despite advances in invasion ecology, scientists and managers are disconnected and research is rarely implemented. I conclude by proposing seven solutions to facilitate the integration of science into management.

Arbuscular mycorrhizal (AM) fungi are an important component of agricultural ecosystems, and can directly influence the productivity of these systems. Unfortunately, conventional agricultural practices have been shown to adversely affect AM fungi. The use of more ecologically sustainable agricultural practices such as tree-based intercropping (TBI) may have the potential to reduce the negative impact of agricultural practices on AM fungi. The objectives of this thesis were to determine (1) if trees influence the structuring of AM fungal communities, (2) if TBI systems support a more diverse AM fungal community compared to conventional monocropping (CM) systems, and (3) if differences in AM fungal richness and composition between the two cropping systems have a functional effect on the growth of crops. Molecular analysis of the AM fungal community in the TBI system revealed 17 phylotypes that all belonged to the family Glomeraceae. Differences in richness and composition among the treatments indicated that trees had an effect on the structuring of AM fungal communities. Intercropping alleys adjacent to white ash and poplar tree rows had a significantly (P < 0.05) richer and different AM fungal community compared to intercropping alleys adjacent to Norway spruce tree rows. When comparing TBI and CM systems, AM fungal abundance was not significantly (P > 0.05) different between the two cropping systems. However, differences in both richness and community composition of AM fungi were observed between the two cropping systems. The TBI system had a significantly higher AM fungal richness and contained several taxa not found in the CM system. Controlled greenhouse experiments revealed that differences in AM fungal richness and community composition between the TBI and CM systems had no functional effect on the growth of three crops (i.e. barley, canola, and soybean). The similar growth response of crops to AM fungi from the two cropping systems may be due to the lack of functional complementarity among the AM fungi. Overall, the TBI system had a more diverse AM fungal community compared to the CM system and trees appear to be a significant factor in the structuring of these communities.

Forest management practices in Ontario are required to emulate natural disturbance in an effort mitigate the anthropological impact on the environment. This is enforced by the Crown Forest Sustainability Act, initiated in 1994, yet inadequate research has been done to support management techniques that satisfy the legislation in regards to the plant diversity and community composition. A series of 435 plots on 139 sites were established in Northern Ontario, consisting of stands of various ages and disturbance origins. Plant diversity and community composition were estimated with a variety of diversity indices and multivariate community analyses. My results show that managed stands are more diverse than those with a natural disturbance origin based on multiple diversity indices. Detrended Canonical Correspondence Analyses revealed considerable variation in community composition among all stands. Plant communities differ between the stands of different disturbance origins (managed/unmanaged), and these differences are influenced by stand age. These results reject the hypothesis that current forest management practices emulate natural disturbance. / Forest Ecosystem Science Coop Inc NSERC CRD Program NSERC Strategic Grant Progam Ontario Ministry of Natural Resources Canadian Forest Service

The carboxylate biofuels platform (CBP) involves the conversion of cellulosic biomass into carboxylate salts by a mixed microbial community. Chemical engineering approaches to convert these salts to a variety of fuels (diesel, gasoline, jet fuel) are well established. However, prior to initiation of this project, little was known about the influence of inoculum source on platform performance. The studies in this dissertation test the hypothesis that microbial communities from particular environments in nature (e.g. saline and/or thermal sediments) are pre-adapted to similar industrial process conditions and, therefore, exhibit superior performances. We screened an extensive collection of sediment samples from extreme environments across a wide geographic range to identify and characterize microbial communities with superior performances in the CBP. I sought to identify aspects of soil chemistry associated with superior CBP fermentation performance. We showed that CBP productivity was influenced by both fermentation conditions and inocula, thus is clearly reasonable to expect both can be optimized to target desired outcomes. Also, we learned that fermentation performance is not as simple as finding one soil parameter that leads to increases in all performance parameters. Rather, there are complex multivariate relationships that are likely indicative of trade-offs associated within the microbial communities. An analysis of targeted locus pyrosequence data for communities with superior performances in the fermentations provides clear associations between particular bacterial taxa and particular performance parameters. Further, I compared microbial community compositions across three different process screen technologies employed in research to understand and optimize CBP fermentations. Finally, we assembled and characterized an isolate library generated from a systematic culture approach. Based on partial 16S rRNA gene sequencing, I estimated operational taxonomic units (OTUs), and inferred a phylogeny of the OTUs. This isolate library will serve as a tool for future studies of assembled communities and bacterial adaptations useful within the CBP fermentations. Taken together the tools and results developed in this dissertation provide for refined hypotheses for optimizing inoculum identification, community composition, and process conditions for this important second generation biofuel platform.

While much evidence suggests that ecosystem functioning is closely related to biodiversity, present rates of biodiversity loss are high. With the emergence of the metacommunity concept ecologists have become increasingly aware that both local processes (e.g. competition, predation), and regional processes (e.g. dispersal and regional heterogeneity) affect ecological communities at multiple spatial scales. I experimentally investigated the effects of habitat connectivity and regional heterogeneity on biodiversity, community composition, and ecosystem functioning of artificial pond metacommunities of freshwater invertebrates at the local (α), among-community (β), and regional (γ) spatial levels. There was a significant effect of habitat connectivity on mean local richness, but mean local Simpson diversity, mean local functional diversity (FD), and all the three indices of ecosystem functioning investigated (regional abundance, invertebrate biomass, and chlorophyll a concentration) were unaffected by connectivity levels. Regional heterogeneity had no effect on local diversity, but enhanced both among-community richness and among-community Simpson diversity. Conversely, connectivity reduced among-community Simpson diversity. All indices of regional diversity were unaffected by either connectivity or heterogeneity. Despite expectations that there would be strong interactions between the effects of connectivity and heterogeneity on species richness, there were no interactions for any index of biodiversity at any spatial scale. Invertebrate community composition was unaffected by either connectivity or heterogeneity, though there was a significant effect of heterogeneity on its variance. Neither connectivity nor heterogeneity had significant effects on any index of ecosystem functioning, nor among-community coefficients of variation of ecosystem functioning. Connectivity appears to act mainly as a force homogenizing habitat patches in a region, as opposed to having strong effects in and of itself on communities. Conversely, heterogeneity acts largely as a diversifying force, maintaining differences between communities within a region, but, similar to connectivity, it does not have clear effects on communities at the local scale. Despite the different processes expected to act in homogeneous and heterogeneous regions, it does not appear that connectivity and heterogeneity interact strongly. / Thesis (Master, Biology) -- Queen's University, 2008-10-16 09:06:33.103