Thesis (Ph.D.)--Bowling Green State University, 2009. / Document formatted into pages; contains x, 125 p. Includes bibliographical references.

Thèse--Univ. de Paris.

Thesis (Ph. D.)--Washington State University, May 2010. / Title from PDF title page (viewed on June 11, 2010). "Department of Biological Sciences." Includes bibliographical references.

Thesis (Ph. D.)--University of Texas at Austin, 2007. / Vita. Includes bibliographical references.

Assessing how environmental change affects plants is increasingly important as terrestrial ecologists attempt to predict future patterns from current processes. However, this challenge is complicated because plant communities can respond to environmental variation at different, but overlapping scales. Additionally, both patterns and the processes that drive them are sensitive to the methods that scientists use to study them. Consequently, a variety of experimental and theoretical approaches are necessary to improve our understanding of how organisms, communities, and ecosystems will respond to future change. Collectively, the studies in this thesis employ a diverse array of approaches to test important ecological theories, including long-term observational studies, manipulative experiments, and analyses that leverage both local and global datasets. The Enquist lab has been measuring subalpine meadow carbon fluxes and climate variables at the Rocky Mountain Biological Laboratory (RMBL), for over 13 years at the time of this writing. Examining correlations between climate and carbon flux over this time has led to the identification of interesting patterns between snowmelt, precipitation events, and rates of carbon exchange. Despite the longer growing season, early snowmelt dates ultimately result in lower productivity in these systems. Pairing this study with the results of a soil moisture manipulation experiment aided in the discovery that the strength and duration of the foresummer drought was directly related to rates of carbon exchange and biomass accumulation in these systems. Thus, integrating long-term observational work with an experimental manipulation served to link pattern and process in a way that was not possible with either study alone. The studies in this thesis range in scale from sub-organismal (chapter 3), to community ecosystem (chapters 1 and 2), to continental (chapter 4). Across all scales afunctional trait ecology approach contributes a holistic view of how these changes may impact organismal, ecosystem, and evolutionary responses to environmental variation. Plants are frequently faced with fundamental performance tradeoffs, which arise due to physical, chemical, genetic/evolutionary, and/or ecological constraints. As a result, functional trait measurements can reflect ecological strategies or resource acquisition strategies. Functional ecology offers a promising approach to linking the attributes of individuals to and communities to ecosystem processes. Understanding how individuals, communities, and ecosystems will respond to environmental change is a fundamental question in ecology. I address this topic using a variety of novel experimental methods and statistical techniques. I use a functional ecology approach by considering not only the species in a community, but also the distribution of functional traits that those species represent. It is in this way that I test ecological hypotheses regarding plant responses to environmental change over physiological, ecological, and evolutionary time scales.

Spumaretrovirus, among retrovirus clades, has an extensive accumulation of evidence for an ancient origin. Recent discoveries indicate that the Spumaretrovirus ancestor could have been the first retrovirus to appear during the evolution of vertebrates. If they indeed appeared in ancient marine environments hundreds of millions of years ago, we should expect significant undiscovered diversity of foamy-like endogenous retroviruses in fish genomes. I report the discovery of these elements in 23 novel teleost hosts. These viruses have very large genomes compared to all other retroviruses, possess an unprecedented array of accessory genes, and form a robust reciprocally monophyletic sister clade with sarcopterygian host foamy viruses, with class III mammal endogenous retroviruses being the immediate sister group to both clades. I estimated that some of these viruses integrated recently into host genomes, and exogenous descendants of these viruses may be extant.

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Knowledge of how spatiotemporal environmental variation impacts ecological and evolutionary processes and contributes to genetic and phenotypic diversity of natural populations is key to understanding and protecting biological diversity. In this thesis I used pygmy grasshoppers to study how environmental conditions, population dynamics, dispersal and admixture may influence genetic structure and diversity, and to evaluate how functionally important variation may affect the ability of populations to cope with novel and changing habitats. Analyses of AFLP (Amplified Fragment Length Polymorphism) markers in Tetrix subulata individuals from 20 sampling locations in Sweden showed significant genetic structure and restricted gene flow among populations. Genetic diversity increased with population size and proportion of long-winged dispersive phenotypes on the island of Öland, but not on the mainland. A contrasting environment comparative approach (CECA) applied to 20 T. undulata populations suggested that processes associated with environmental change differently influence functional and neutral diversity. Long-winged phenotypes were more common in disturbed than in stable habitats, indicative of recent establishment. Color morph diversity was higher in disturbed environments consistent with the notion that polymorphism promotes establishment success. Conversely, neutral diversity (AFLP) was lower in disturbed habitats, pointing to a stronger eroding effect of genetic drift in disturbed compared to stable habitats. I compared genetic and morphological variation between sympatric populations of the two species. Populations of the generally dispersive T. subulata were genetically less differentiated compared with the more sedentary T. undulata, suggesting that the latter species has been less influenced by the homogenizing effects of gene flow. Non-parallel body size differences pointed to species-specific drivers of morphological change. Finally, comparisons of reproductive output of T. subulata females that had been experimentally mated with males from the same or from a different population suggested that responses to interbreeding and genetic admixture can differ in direction and magnitude even between populations within a species, and thus influence whether dispersal translates into gene flow. My thesis emphasizes the complexity of microevolution and illustrates how the effects of different ecological and evolutionary processes can vary according to disturbance regimes and geographic areas, and differ between closely related sympatric species.

Evidence suggests that human-driven changes to the earth are having clear and profound effects on many species, as well as the species with which they associate. Disruptions in the interactions between species can change the community structure, in turn changing the dynamics of entire ecosystems. The following dissertation examines how the impacts of climate change related events and invasive species may influence biotic interactions and impact orchid populations and range distributions. Here I quantify how orchid pollinators and mycorrhiza vary between species with different life histories, and between and within habitats. The results showed that orchids with wide range distributions (i.e. geographic or elevational) were more generalized in their mycorrhizal fungi requirements than co-occurring rare and/or narrow ranging species; the rarer species were also more likely to be affected by antagonistic fungal interactions. This dissertation makes a critical contribution to understanding plant and orchid ecology, to assisting ongoing orchid recovery efforts worldwide, and ultimately to developing more comprehensive management plans to mitigate future biodiversity losses.

Avian species are known to have the capacity to respond to environmental changes through physiological adjustments. The process whereby organisms adjust their phenotype without genetic change is termed phenotypic plasticity and it is mostly observed to be a phenotypic improvement to ecological challenges. Metabolic rate (MR), which is the rate of energy expenditure in a species, is a highly flexible physiological parameter which results in a great diversity of avian standardised metabolic rates. Like birds from high latitudes, Afrotropical bird species are expected to have the capacity to adjust their energy expenditure to match the availability of resources. Previous studies on the flexibility of physiological parameters in birds have focused on the magnitude of change of physiological adjustments and the cues inducing these changes. Comparative research has furthermore investigated metabolic rates across aridity, altitude, latitude and temperature gradients. Recently, a clear dichotomy has become evident with elevated metabolic rates observed in high latitude birds in winter and a down-regulation of metabolic rates observed in birds exposed to low latitude mild winters. In this study, the shape of the reaction norm, the magnitude, the reversibility, the direction and the rate of change of two physiological parameters, basal metabolic rate (BMR) and summit metabolic rate (Msum), were investigated in a coastal and an inland population of Southern Red Bishops (Euplectes orix) through seasonal acclimatisation and laboratory acclimation. Summer and winter basal metabolic rates as well as body mass, were highly flexible traits in free-ranging coastal and inland Red Bishops. Birds acclimatised to a mild coastal climate in winter exhibited reduced basal and summit metabolic rates, whereas birds originating from a more variable inland climate increased basal metabolic rate in winter, but did not show increases of Msum in winter. Red Bishops responded to short term thermal acclimation under laboratory conditions by gradually changing body mass. Acclimation periods of 21 days revealed a negative relationship between body mass and acclimation air temperature. Peak responses of basal metabolic rate to ambient temperature change were observed in both coastal and inland birds between two and eight days after the change in acclimation air temperature. The influences of seasonal acclimatisation on energy expenditure differed between coastal and inland birds, however, during laboratory acclimation individuals from the two populations showed no difference in response. Within the individuals of the coastal and inland Southern Red Bishops, phenotypic flexibility is observed in body mass, basal metabolic rate and summit metabolic rate as a response to environmental changes. This flexibility is thought to increase thermoregulatory capacities of the Southern Red Bishop in different habitats and climates.