Water is a critical resource for which plants compete in many terrestrial communities. In arid communities where water most limits plant growth, rainfall events occur in discrete, pulsed events. These pulses of water create highly variable soil moisture availabilities. Plant species respond differently to variation in soil water availabilities throughout a season and between years. How species vary in their responses to a range of water availabilities is thought to influence community and ecosystem properties. Many previously proposed hypotheses are not suitable to explain rapidly fluctuating resource availabilities or numerous input events throughout the growing season. This dissertation uses variation in water availability as a model resource to examine how species characteristics influence the process of exploitation competition within plant communities.Experiments were conducted to examine variation in growing season, exploitation competition between several pairs of co-occurring species in the Sonoran desert. Three separate studies evaluated several components of community dynamics thought to be influenced by exploitation competition. Spatial attributes of exploitation competition were assessed by measuring the performance of a deep-rooted species across the boundary of a natural expansion of a shallowly rooted species. Then, neighborhood composition was varied for species of similar growth-form to address the affects of species characteristics to shifts in abundances under field conditions. Lastly, species from the neighborhood composition study were placed under controlled, manipulated water availabilities to measure their fundamental operational conditions.Performances of plant species in all experiments were assessed using a combination of physiological and vegetative measurements, capturing the responses of the plants to both the dynamic growth conditions during the growing season, and integrated measures of plant performance post growth season. A shared preference was found for all species, where the performance of all species was greatest when water was most available in the soil profile. This work suggests the mechanism within a functional type by which plants coexist at various abundances is in part due to the variation in responses to temporal resource gradients. The variation in availability of resources and the species composition within the community should be considered in studies of competition between plant species.

All animals progress through a series of functionally discrete life stages from fertilization through adulthood and often into senescence. Reproduction in the adult stage can only occur after maturation--the final life history transition during ontogeny--from juvenile to adult. Despite a robust literature that predicts the optimal body size and development time at which this transition should occur, the ontogenetic factors that are responsible for determining metamorphosis and the manner in which they are translated into the hormonal mechanisms regulating maturation remain unresolved in most species. In this dissertation, I first review the theoretical context and importance of understanding maturation from both life history and physiological/developmental perspectives. Then I review the literature that describes various ontogenetic factors thought to determine the onset of maturation in insects. Finally, I present four studies that examine two of the major hypotheses that have been proposed to explain the onset of metamorphosis in insects using Manduca sexta larvae (Lepidoptera: Sphingidae) as a model organism. In the first study, I show that physical thresholds are unlikely to be the factor that determines maturation in larval M. sexta because larval insects do not seem to be growth constrained in the manner assumed in the literature. Next, I present three chapters that examine the possibility that attainment of a resource storage threshold is the determining factor for the onset of metamorphosis. In the first of these studies, I show that there is a hemolytic factor present after metamorphic commitment that can induce precocious metamorphosis in larval M. sexta, indicating that maturation can be coordinated at least partially from developing tissues throughout the body. The following study examines resource storage during metamorphic commitment in the final larval instar of M. sexta. I show that resource storage is of critical importance during the final period of larval growth in terms of mass allocation. Even with environmentally-induced variability in resource storage, growing M. sexta appear to have a target amount of stored resources near the body weight at which metamorphic commitment occurs. Individuals reared on reduced quality diet store proportionally more resources with a higher caloric value than individuals reared on in terms of fat growth, which is consistent with a decrease in the body weight at metamorphic commitment observed in other studies. Individuals reared at different temperatures invest differently in resource storage during growth; however, resource storage content tends to converge at the critical weight, which may explain invariance of the critical weight in response to rearing temperature found in other studies. Finally, I examine resource storage in the context of allocation tradeoffs with growth and metabolic rate. I demonstrate that storage increases substantially as growth rate declines in the final larval instar of M. sexta.

During the transitions from unicellularity to multicellularity, cells transitioned from functioning as wholes to functioning as parts of wholes. In the colonial freshwater green flagellates known as volvocine algae, living "intermediate form" species give ample evidence concerning how cells gradually lost autonomy and began functioning as dedicated parts. This dissertation concerns how and why the role of cell division changed in unicellular to colonial volvocine algae. We review a recent book on levels of selection and apply a proposed three-stage transition to the example of volvocine algae. We found that, in contrast to the previous description of "stage 1", the concept of group reproduction is potentially applicable to very early-branching colonial volvocine algae. This possibility indicates that the role of cell division could have shifted (to function in group reproduction) earlier than was previously thought (Appendix A). We show that, given some reasonable assumptions, cell- and colony-level fitness are equivalent in undifferentiated colonial volvocines (Appendix B). In spite of this, our models show that cell division number could evolve in response to specifically colony-level factors. Cell division number could be regulated indirectly via allocation to growth (Appendix B) or directly via regulation of the growth-to-first division transition (Appendix C). The extent to which group factors matter in the outcome of selection on cell division number is a matter of degree and is quantifiable (Appendix B). Colony cell number could be a genuine group-level adaptation, even in the simplest volvocine algae (Appendix B and C). Because a size-dependent growth trajectory is a substantial group-level cost of higher division numbers, our analysis highlights the potential importance of understanding how colony size affects cell growth (Appendix C). We also present data on cell-type allocation in Volvox (Appendix D). The Volvox colony is clearly the level of function for cell divisions and cell fate acquisition. However, this work indicates that the precision with which Volvox development attains these colony-level goals may be low compared to more complex multicellular organisms.

Within each leaf is an intricate network of veins. The geometry of this network shows large variation across species and environments, paralleling variation in species' functioning and geographic distributions. Here I develop theory that links leaf venation networks to 1) the worldwide leaf economics spectrum, enabling better understandings of the resource tradeoffs that are central to the terrestrial carbon and water cycles, and 2) atmospheric temperature and carbon dioxide concentrations, enabling better use of leaf fossils for paleoclimate reconstruction. I successfully test these theories across contemporary temperate and tropical sites, and apply them to paleo-sites spanning a 2Myr interval across the Cretaceous-Paleogene boundary. These theoretical and empirical results demonstrate that leaf venation networks can provide an integrative framework for understanding relationships between plant form, function, and environment.

Living organisms face a changing physical environment. A major challenge in ecology is understanding the ecological and evolutionary role that this changing physical environment has in shaping a community. One fundamental question is how environmental variation affects species coexistence. Modern understanding of environmental variation emphasized the hypothesis that possible adaptations to a fluctuating environment allow species to use different environments in different ways. Species can partition temporally their use of resources. Persistent stages in the life cycle such as prolonged longevity can buffer species through unfavorable environments. Differences in longevity will also lead to different nonlinear responses of population growth rate to fluctuating in resources. Questions arise: how do these possible adaptations to environmental fluctuations affect coexistence. Do they act through multiple coexistence mechanisms, how strong are the mechanisms, and do the mechanisms interact? A framework has been developed for quantifying coexistence mechanisms in models. Being able to quantify coexistence mechanisms in the field is critical to understand different processes contributing to species coexistence in a community: whether a process prevents species dropping out of the community (stable coexistence), or slows down species losses (unstable coexistence), or both. In many respects, applications of those techniques for quantifying coexistence mechanisms have the potential for substantial improvements. In particular, very few studies directly quantify coexistence mechanisms for perennial plants. Coexistence of plant is often puzzling because they share similar resources. Environmental variation has been suggested as an important factor for niche partitioning but challenges for studying it in perennial plants are unclear. The long generation time poses challenges to controlled experiments. Moreover, perennial plants have complex life histories. Vital rates change with size. In addition, tremendous temporal variation is observed in various life history processes. Seedling recruitment and individual growth can both be highly sensitive to fluctuation in the physical environment. Furthermore, different processes in different stages of the life history can interact with environment and competition in different ways. Using perennial plants as a specific system, our study reveals a crucial role in theory development to summarize understanding of such a complex system. I start with the simplest model for perennial plants, the lottery model, to study the relative importance of two coexistence mechanisms: the storage effect and the relative nonlinearity. Then I extend the model by showing that variation in individual growth can also lead to stable coexistence similar to the effect of variation in seedling recruitment. Species can benefit most from variable environments when the processes contributing most to capturing resources on average are also very sensitive to environmental fluctuations. New mechanisms arise through shifts in size structure, which depend on how vital rates change through ontogeny.

The majority of studies on plant biomass partitioning have focused on the effects of environment. Optimal Partitioning Theory (OPT) suggests that plants should allocate biomass to the organ that acquires the most limiting resource. Though, it has recently been disputed as to how much of this variation is due to variation in size and not environment. Additionally, while a few studies have examined differences between growth forms, the effects of evolutionary history have been largely ignored. Leaf morphology and physiology may also contribute to patterns of biomass partitioning.The role of plant size has been shown to be considerable to plant biomass allocation. Allometric biomass Partitioning Theory (APT) has recently been proposed to predict how plants should partition metabolic production based on the constraints of body size. Here, I assess the relative contribution of environment, growth form, leaf traits and phylogeny on variation in biomass allocation, after accounting for changes in size, using both an empirical and experimental approach. I use a global dataset of seed plants in addition to growing plants with differing evolutionary histories and growth forms hydroponically in two nutrient levels to examine patterns of organ partitioning while accounting for allometrically driven biomass allocation. Both the empirical and experimental interspecific analyses indicate that phylogeny accounts for the majority of the variation in biomass partitioning. Leaf biomass partitioning is partially related to growth form, however this appears to be due to differences in leaf morphology and physiology. While a strong phylogenetic signal exists, about half of the variation was not explained by any of the factors interspecifically, suggesting room for plasticity in partitioning. Intraspecifically, biomass allocation and partitioning was related to environmental factors in the directions predicted by OPT. However, the species-specific allocation response to environmental differences was not uniform, therefore obscuring interspecific patterns. These results have important implications for ecological studies; such that partitioning studies must first assess the role of plant size and evolutionary history in order to fully understand variability in biomass partitioning. Additionally, differences from environment can be incorporated with allometric changes to help understand how plants should allocate biomass.

The problem of species diversity and co-existence in hyper-diverse communities remains. Traditionally ecologists have approached this problem from examining patterns of co-occurrence, interaction matrices and abundance distributions. This work, while productive, generally has rarely explored the role of shared ancestry and species-specific quantitative function in promoting species diversity and co-existence. This has been a critical oversight as simply analyzing the list of Latin binomials in an assemblage ignores the relatedness between taxa as well as the diversity in organismal form and function--the very information relevant to evolutionary, ecological, and historical hypotheses about the distribution of diversity and community assembly. The following research is designed to investigate the role of phylogenetic and functional similarity on species diversity and co-existence through space and time in diverse tropical tree communities. Specifically, I investigate: (i) the role of phylogenetic relatedness in determining community structure from very local to large regional spatial scales; (ii) the role of phylogeny in determining the structure of tree communities at different strategraphic levels in the canopy; (iii) the power of recently developed phylogenetic analyses to detect non-random patterns of co-existence in communities when the phylogenetic tree used is not completely resolved; (iv) the role of functional similarity in promoting co-existence in a Neotropical dry forest through space and across body sizes; (v) whether decadal long trends in forest composition can be explained on the basis of species-specific function; and (vi) variability in a key functional trait across New World forest communities and along the Angiosperm phylogeny.

Mutation, recombination, selection, and demographic processes (such as gene flow and genetic drift) have shaped genetic variation, but the relative impact of these evolutionary forces remains poorly understood. This problem motivates this study which examines three regions of the genome -beta-globin, the Y-chromosome, and mtDNA- in a two part approach to assess the relative impact of evolutionary forces on human genetic variation in Africa. The first approach characterizes levels of nucleotide variability and linkage disequilibrium across thebeta-globin gene and recombinational hotspot in a sample of malarial-resistance alleles (HbC and HbS). Results suggest that the age of the HbC allele is <5,000 years and selection coefficients are 0.04-0.09 and, recombination is observed within 1-kb of the selected site on >1/3 of the chromosomes sampled. A long-standing question regarding the HbS allele is whether it originated multiple times via recurrent mutation or whether it arose once and was transferred to different haplotypic backgrounds through recombination. These results indicate that recombination played a critical role in generating haplotypic diversity at beta-globin and can explain the origins of the Bantu and Senegalese HbS haplotypes. The second approach examines Y-chromosome and mtDNA variation to disentangle the relative effects of demographic forces. A detailed characterization of the Y-chromosome and mtDNA in >1000 individuals from ~40 populations reveals that patterns of variation from these paternally- and maternally-inherited loci are remarkably different, suggesting that sex-specific demographic processes have influenced African genetic variation, particularly among agriculturalists. Hunter-gatherer populations carry a suite of Y-chromosomes that differ from those of agricultural populations. The examination of Y-SNP and Y-STR variation in eight hunter-gatherer populations reveals the presence of a very old, >50-kya, derived lineage (B2b) shared among these populations, which is absent in agricultural populations, suggesting that hunter-gatherer populations share an ancient common ancestry. Finally, the Y-chromosome results are placed into a broader evolutionary context in a phylogeographic summary as it relates to archeological and linguistic variation in Africa. Together these results underscore the vastly different effects that various evolutionary forces have had on shaping human genetic variation in Africa.

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.