Rare species with fragmented distributions often exhibit reduced levels of genetic diversity within populations. However, life history traits such as long lived perennial habit and outcrossing mating system, are associated with high levels of within species genetic variation being partitioned within populations. Schisandra glabra (Schisandraceae) is a rare basal angiosperm with a fragmented distribution across the southeastern US and in a disjunct population in cloudforest of Mexico. The species’ clonal reproduction by rhizomes, confounds the delineation of genetically distinct individuals in the field. The patterns of genetic diversity and clonality in 10 populations of S. glabra were investigated using AFLP markers. I found a surprising number of distinct genetic individuals in the two populations sampled on 3m grids, with 31 unique genotypes out of 42 samples at Wolfpen Creek, KY, and unique genotypes in all 48 samples from Panther Creek, GA. AMOVA of 237 individuals from 10 populations revealed that the largest portion of the genetic variation is found within populations (58.0%; P<0.0001), and 27.7% (P<0.0001) of the genetic variation is partitioned between the US and Mexico S. glabra populations. Population structure was also detected between the US and Mexico populations, but no structure was detected between the majority of the US populations. The genetic differentiation of the disjunct population in Mexico, may be the result of a Pliocene or Miocene vicariance hypothesized for many species with similar distributions. The high levels of genetic diversity found within populations are evidence of historical gene flow between the US populations, and the preservation of genetic diversity by the long lived species in its present fragmented distribution.

Agroecosystems produce insects in great abundance, with episodic irruptions in time, and patchy distributions in space. In the industrial scale agroecosystems of south-central Texas, millions of Brazilian free-tailed bats (Tadarida brasiliensis) consume these insect pests. In the past decade, growers in Texas have planted transgenic Bt (Bacillus thuringiensis) crops on a large scale, which may reduce populations of target insect species by up to 95%. To investigate potential impacts of this evolving agricultural landscape on insectivorous bats, I examined the response of foraging bats to emergences of insects from replicate Bt and non-Bt fields of corn and cotton in the Winter Garden region of south-central Texas. I quantified bat activity using ultrasonic detectors deployed simultaneously in Bt and non-Bt fields. I measured insect activity using pheromone traps and video imaging. Professional crop consultants scouted fields to determine dates of insect emergence. We recorded 92% more echolocation calls, 62% more AnaBat files, and 257% more feeding buzzes over agricultural fields during periods of local insect emergence. During these insect emergence periods, bat activity was correlated with the abundance of moths and negatively related to the distance between foraging sites and roosting sites. In general, Bt crops did not have a measurable impact on the activity of bats except at one site where moths were more abundant over non-Bt crops versus Bt crops. Foraging bats showed a delayed response to moth abundance, which is consistent with the hypothesis that roosts serve as information centers that enhance foraging efficiency. The ability of millions of bats to exploit localized patches of prey across a large area provides further evidence of their pest control service. This economically important pest control service extends beyond growers in Texas, as the populations of moths produced in agroecosystems in Texas influence agricultural production on a continental scale.

Effective population size is one of the fundamental parameters in many population genetic models. It provides a common currency to compare populations by reference to an analytically tractable ideally behaving population. Different values of this parameter can have very significant effects on rates and modes of evolution. Sewall Wright's shifting balance theory stresses the importance of drift interacting with selection and dispersal in the process of evolution. For this process to work requires effective deme sizes of no more than a few hundred. Errors of only one order of magnitude can seriously distort our view of the mechanisms of evolution underlying a population structure. Methods exist for dealing with some of the obvious departures from the ideal population. Natural populations seldom conform to other assumptions about population structure made to calculate effective deme size. One such assumption is that individuals are uniformly distributed over area. Much work shows that this is often far from the case. Computer simulations were used to investigate the effects of different spatial distributions of individuals, in combination with various dispersal regimes, on the scale and degree of genetic differentiation. The model consists of diploid individuals arranged according to a spatial distribution with various dispersal regimes imposed upon them. Generations are discrete and the model is allowed to run for 120 to 200 generations. Wright's F-statistics are used as one measure of genetic differentiation. F-statistics do well at reflecting the overall level of differentiation but do not give any idea of spatial structure. Spatial autocorrelation techniques are used to examine the spatial scale and temporal continuity of gene frequency differentiation. Significant effects of the spatial distribution of individuals are found that are not visible through F-statistics. Stable features on the gene frequency surfaces are found to be much larger than the calculated neighborhood sizes. Very different scales of structure can result from different distributions of individuals even though they result in similar estimates of effective deme size. I conclude that it is necessary to have detailed information on a population's structure to be able to predict the effects of genetic drift on the scale of genetic differentiation.

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 &lt;5,000 years and selection coefficients are 0.04-0.09 and, recombination is observed within 1-kb of the selected site on &gt;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 &gt;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, &gt;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.