Populations in fragmented habitat patches may show ecological differentiation, which has implications for metapopulation viability. In this study we used a common garden with two watering treatments to contrast mean differences in ecophysiological traits and the relationships between traits and performance among seven populations of three alvar species. These species differ in their alvar specialization in Ontario, from almost endemic (Solidago ptarmicoides) to highly confined (Dasiphora fruticosa) to a widespread generalist (Hypericum perforatum). Populations of all species exhibited mean differences in at least one trait: photosynthesis (Amax), growth rate and specific leaf area. More surprisingly, the relationship between functional traits and performance was significantly different among populations in all species, suggesting different strategies for maximizing growth in different environments. The ecological differentiation observed affected all species regardless of distribution and is likely genetically based. This differentiation may destabilize metapopulation dynamics and reduce rates of spread if colonization is negatively impacted.

Habitat loss and disturbance due to human activity are major causes of global biodiversity decline. Beyond outright species loss, one potential outcome is modification of species interactions that are integral to ecosystem functioning. To investigate this possibility, I asked whether human activity influences avian frugivory and seed dispersal, bird-fruit interactions that facilitate plant reproduction. On Tobago (West Indies), I compared patterns of frugivory in three adjacent rainforest habitats along a gradient of increasing disturbance: primary forest in a reserve, unprotected intermediate forest outside the reserve, and nearby forest that was moderately disturbed by subsistence resource use. I assessed plant and bird community composition, seedling species, fruit removal, and bird fecal samples, to estimate human effects on seed dispersal and plant recruitment in this ecosystem. Disturbed forest had different species assemblages than primary forest, characterized by more light-demanding plants, more birds, and a shift in the relative abundance of avian feeding guilds: insectivores and frugivores declined, while nectarivores and omnivores increased. Canopy cover declined with disturbance; along with plant abundance, this explained much of the variation in bird species composition. The rate of avian fruit consumption in removal experiments varied considerably but tended to be highest in primary forest. Fecal samples showed that fruit composition of avian diets also varied with disturbance; birds captured in disturbed forest consumed more seeds from light-demanding plants. Seeds in the samples provided evidence of some seed transfer between habitats—from disturbed forest into the reserve and vice versa. Seedling composition was consistent with plant species fruiting in the same study plots, and illustrated some successful recruitment of light-demanding plants in primary forest and shade-tolerant plants in disturbed forest. Notably, the plant community of intermediate forest was more similar to disturbed than primary forest. This suggests that habitat adjacent to areas of human activity can be susceptible to ecological change, even though it does not experience the same direct disturbance. In summary, the unprotected portion of Tobago’s rainforest has a markedly different plant and bird community than the forest reserve, and my results indicate that avian frugivory and seed dispersal can be influenced by moderate human activity.

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.

Questions surrounding the causes and consequences of diversity lie at the centre of community ecology. Understanding the mechanisms by which species diversity is maintained motivates much experimental and theoretical work, but this work often focuses on fluctuation-independent mechanisms. Variability in habitat suitability is ubiquitous through space and time however, and provides another important path through which species diversity can be maintained. As a result, considering environmental variability has value for conservation and management. Finally, differences through space and time in the mechanisms that promote and maintain diversity produce spatially varying patterns of diversity. Spatial variation in different forms of diversity (species (SR), phylogenetic (PD), and functional diversity (FD)) creates difficult decisions about prioritization and reserve locations. This thesis uses experimental, observational, and theoretical methods to explore the causes and consequences of diversity. I show that variation in space and time has important implications for species coexistence and diversity maintenance. In microbial nectar communities, temperature variation through space and time alters the importance of priority effects on community assembly. Using models of warming temperatures in annual plant communities I show that considering temporal partitioning of flowering (a strategy to minimize competition) introduces constraints on phenological shifts: this has implications for phenological monitoring programs. Finally, I show that variability in the timing of fire events in Mediterranean shrublands contributes to coexistence between life forms, suggesting that it should be considered for fire management. In the final two chapters, I focus on conservation prioritization. Comparisons of species richness and evolutionary diversity through space in the Cape Floristic Region of South Africa show that existing reserves protect Proteaceae richness, but fail to capture evolutionary distinct species. More generally, in the final chapter I suggest that SR and PD should be congruent through space when species are of similar ages, regions are depauperate, or ranges are discontinuous.

Tropical freshwater ecosystems are understudied and not well understood relative to temperate systems; however, they are becoming increasingly imperiled by escalating anthropogenic impacts. The aim of this thesis was to investigate how tropical freshwater macroinvertebrate communities changed both structurally and functionally over a pristine-rural-urban land-use gradient, in relation to different spatial and temporal scales, as well as to the availability of potential food sources. Fifteen streams in the Panama Canal Watershed were sampled during the dry and wet seasons of 2007 and 2008, for macroinvertebrate communities (benthic and leaf litter), environmental variables, and potential food sources. Along the land-use gradient, in both habitat types, taxon richness, diversity, and evenness all decreased significantly; whereas, abundance increased significantly. For the benthic macroinvertebrate community, unique variation was explained equally well by local (water chemistry and sediment type) and landscape (riparian vegetation and watershed land use) characteristics in the dry season, and landscape characteristics explained slightly more variation in the wet season. Leaf-litter macroinvertebrate community unique variation was better explained by local variables than by landscape variables in both seasons. In terms of potential food resources, fine detritus and inorganic material were the most common across all streams (increased quantities in urban streams) and seasons; whereas, the availability of diatoms and leaf material increased in the dry season. Using gut content analyses, we found that collectors (gatherers and filterers) were by far the most common functional feeding group, increasing in abundance along the land-use gradient. Predators, shredders, and scrapers were all most abundant in pristine streams and decreased along the land-use gradient. Finally, using seven community metrices, a potential biomonitoring tool was developed, the Neotropical Low-land Stream Multimetric Index (NLSMI), which distinguished well among the different levels of stream impairment. This study demonstrated that tropical communities were negatively affected by human land alteration, but that community responses depended on the habitat sampled, the influence of different spatial scales varied between the seasons, and the effect of food resources appeared to be complex. These aspects must be taken into consideration for management decisions and restoration strategies to be effective.

Neotropical cichlid fishes are highly diverse and occupy diverse environments. Visual pigment evolution has been important in the diversification of African rift lake cichlids, but little is known of Neotropical cichlid visual systems. This thesis addresses the molecular evolution of rhodopsin in the Geophagini tribe of Neotropical cichlids. We use likelihood-based codon models of molecular evolution and newly isolated sequences for Neotropical cichlid rhodopsin to compare patterns of selective constraint among Neotropical, African rift lake, and African riverine cichlid rhodopsin. We provide evidence for differences in selective constraint among clades, with positive selection occurring in the Neotropical and African rift lake clades. Further, we find variation in selective constraint within geophagine cichlids. Our results suggest that Clade model C may be more appropriate than branch-site models for investigating variation in selective constraint among clades. Neotropical cichlids are emerging as an excellent system for investigating molecular evolution in visual pigments.

Neotropical cichlid fishes are highly diverse and occupy diverse environments. Visual pigment evolution has been important in the diversification of African rift lake cichlids, but little is known of Neotropical cichlid visual systems. This thesis addresses the molecular evolution of rhodopsin in the Geophagini tribe of Neotropical cichlids. We use likelihood-based codon models of molecular evolution and newly isolated sequences for Neotropical cichlid rhodopsin to compare patterns of selective constraint among Neotropical, African rift lake, and African riverine cichlid rhodopsin. We provide evidence for differences in selective constraint among clades, with positive selection occurring in the Neotropical and African rift lake clades. Further, we find variation in selective constraint within geophagine cichlids. Our results suggest that Clade model C may be more appropriate than branch-site models for investigating variation in selective constraint among clades. Neotropical cichlids are emerging as an excellent system for investigating molecular evolution in visual pigments.

Tropical freshwater ecosystems are understudied and not well understood relative to temperate systems; however, they are becoming increasingly imperiled by escalating anthropogenic impacts. The aim of this thesis was to investigate how tropical freshwater macroinvertebrate communities changed both structurally and functionally over a pristine-rural-urban land-use gradient, in relation to different spatial and temporal scales, as well as to the availability of potential food sources. Fifteen streams in the Panama Canal Watershed were sampled during the dry and wet seasons of 2007 and 2008, for macroinvertebrate communities (benthic and leaf litter), environmental variables, and potential food sources. Along the land-use gradient, in both habitat types, taxon richness, diversity, and evenness all decreased significantly; whereas, abundance increased significantly. For the benthic macroinvertebrate community, unique variation was explained equally well by local (water chemistry and sediment type) and landscape (riparian vegetation and watershed land use) characteristics in the dry season, and landscape characteristics explained slightly more variation in the wet season. Leaf-litter macroinvertebrate community unique variation was better explained by local variables than by landscape variables in both seasons. In terms of potential food resources, fine detritus and inorganic material were the most common across all streams (increased quantities in urban streams) and seasons; whereas, the availability of diatoms and leaf material increased in the dry season. Using gut content analyses, we found that collectors (gatherers and filterers) were by far the most common functional feeding group, increasing in abundance along the land-use gradient. Predators, shredders, and scrapers were all most abundant in pristine streams and decreased along the land-use gradient. Finally, using seven community metrices, a potential biomonitoring tool was developed, the Neotropical Low-land Stream Multimetric Index (NLSMI), which distinguished well among the different levels of stream impairment. This study demonstrated that tropical communities were negatively affected by human land alteration, but that community responses depended on the habitat sampled, the influence of different spatial scales varied between the seasons, and the effect of food resources appeared to be complex. These aspects must be taken into consideration for management decisions and restoration strategies to be effective.

Unraveling the relationships between organisms and patterns of diversity is a central goal of evolutionary biology, pursuant to the aim of reconstructing the history of life. I constructed a hypothesis for species relationships in the shorebird suborder Scolopaci, and mapped onto this framework behavioural and life-history traits to infer their evolutionary history. Relationships were well-resolved and well-supported, although reliable resolution of certain nodes will require additional, independent sources of information. We estimated the Scolopaci ancestor to be monogamous, and care-giving through fledging, but ancestral breeding location and migration distance reconstructions were equivocal. Tests for correlations between parental care and other traits to explain extant species’ trait diversity show that, contrary to previous reports, evolution of Scolopaci diversity was a complex process that cannot be explained by individual character correlations. This study provides important insights into Scolopaci and shorebird evolutionary history, and the general practice of inferring past processes from phylogenetic hypotheses.

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.