<p>Drylands, comprising arid and semi-arid areas and the dry subtropics, over some 40% of the world's land area and support approximately 2 billion people, including at least 1 billion who depend on dryland agriculture and grazing. 10-20% of drylands are estimated to have already undergone degradation or desertification, and lack of monitoring and assessment remains a key impediment to preventing further desertification. Change in vegetation cover, specifically in the spatial organization of vegetation may occur prior to irreversible land degradation, and can be used to assess desertification risk. Coherent spatial structures arise in the distribution of dryland vegetation where plant growth is localized in regular spatial patterns. Such "patterned vegetation" occurs across a variety of vegetation and soil types, extends over at least 18 million ha, occurs in 5 continents and is economically and environmentally valuable in its own right.</p> <p>Vegetation patterning in drylands arises due to positive feedbacks between hydrological forcing and plant growth so that the patterns change in response to trends in mean annual rainfall. Mathematical models indicate that vegetation patterns collapse to a desertified state after undergoing a characteristic set of transformations so that the condition of a pattern at any point in time can be explicitly linked to ecosystem health. This dissertation focuses on the mathematical description of vegetation patterns with a view to improving such predictions. It evaluates the validity of current mathematical descriptions of patterning for the specific case of small-scale vegetation patterns and proposes alternative hypotheses for their formation. It assesses the significance of seed dispersal in determining pattern form and dynamics for two cases: vegetation growing on flat ground with isotropic patterning, and vegetation growing on slopes and having anisotropic (i.e. directional) patterning. Thirdly, the feedbacks between local biomass density and infiltration capacity, one of the positive feedbacks believed to contribute to patterning, are quantified across a wide range of soil and climatic conditions, and new mathematical descriptions of the biomass-infiltration relationship are proposed. Finally the influence of land surface microtopography on the partitioning of rainfall into infiltration and runoff is assessed.</p> / Dissertation

<p>Abstract</p> <p>Risky foraging is a male reproductive tactic in most polygynous mammals. It is speculated to result from intense intra-sexual reproductive competition. Consequently this behavior has been speculated to increase a male's reproductive competitiveness. However, individual males may differ in their propensity to take foraging risks. </p> <p>We therefore conducted a study on crop raiding behavior (a risky foraging strategy) in African elephants from the greater Amboseli ecosystem, in southern Kenya. We specifically examined the population sizes, gender and patterns of raiding elephants and investigated the effect of crop-raiding and genetic heterozygosity on male body size. We also examined the influence of age and genetic relatedness on observed patterns of association. Finally, we examined the role of life history milestones, association patterns and social structure on the acquisition of crop raiding behavior among wild free ranging male African elephants. With regard to the influence of association patterns on crop raiding behavior, we were specifically interested in understanding the mechanisms by which social learning might occur among male elephants.</p> <p>Our results showed that 241elephants from different populations in the ecosystem converged to raid farms. Approximately 35% of raiders were from Amboseli National Park, and the rest were other populations in the ecosystem. We observed only post-pubertal males but not females to raid. About one third of post-pubertal males from the Amboseli population were raiders. We found evidence of habitual raiding by some individuals. Crop raiding predicted post-pubertal male size, with raiders being larger than non-raiders. This result suggests that taking risks pays off for males. Our results also showed that other variables known to influence growth like genetic heterozygosity had no effect on size-for-age in male elephants, because low-heterozygosity males were rare. The probability that an individual male is a crop raider was greater for older individuals than young males. The probability that a male is a raider was greater when his two closest associates were raiders versus when they were not raiders and when a male's second closest associate was older, versus when his second closest associate was of similar age or younger. These results suggest that increasing energetic demands associated with life history milestones and social learning play a significant role in the initiation of crop raiding behavior. Raiders did not cluster into separate social units from non-raiders, probably due to the nature of social learning exhibited by this species and due to the diffuse nature of male elephant social units.</p> <p>These results have implications for understanding the evolution of risky foraging behavior in males, and for understanding the role of kin selection, dominance hierarchies and social learning in male elephant social systems. Results also have implications for understanding the spread of adaptive complex behavior in natural populations.</p> / Dissertation

<p>Speciation is a constantly ongoing process whereby reproductive isolating baririer build up over time until groups of organisms can no longer exchange genes with each other. Adaptation is thought to play a major role in the formation of these barriers, although the genetic mechanisms and geographic mode underlying the spread of barriers due to adaptive evolution is poorly understood. Critically, speciation may occur in stages through the formation of intermediate partially reproductively isolated groups. The idea of such widespread ecotypes has been the subject of great controversy over the last century. Even so, we have relatively little understanding about whether widespread ecotypes exist, wheather they are reproductively isolated, and how adaptive alleles are distributed among partially isolated groups. In this dissertation, I examined these issues in widespread coastal perennial and inland annual ecotypes of the yellow monkeyflower, Mimulus guttatus. First, I determined that coastal and inland populations comprise distinct ecotypic groups. I then determined that these ecotypes are adapted to their respective habitats through genetically based flowering time and salt tolerance differences. I assessed the genetic architecture of these adaptations through quantitative trait loci (QTL) analysis and determined the geographic distribution of the underlying alleles through latitudinally replicated mapping populations. I quantified the contribution of these loci to adaptation in the field through the incorporation of advance generation hybrids in reciprocal transplant experiments. In the process, I discovered a widespread chromosomal inversion to be involved in the adaptive flowering time and annual/perennial life-history shift among the ecotypes. Overall, the results of this study suggest that widespread reproductively isolated ecotypes can form through the spread adaptive standing genetic variation between habitats and that chromosomal rearrangements can integral to this process.</p> / Dissertation

<p>Scallops, a family of swimming bivalve mollusks, have dozens of eyes arrayed along the edges of their valves. Relatively little is known about the form and function of these unusual eyes. To learn more about them, we studied the visually influenced behavior of scallops, as well as the morphology and spectral sensitivity of their eyes. Of particular interest was whether or not the simple neural architecture of these animals constrains the number of visually-influenced behaviors they can perform. We were also interested to learn whether scallop eyes, despite providing relatively poor visual acuity, show optical refinements, such as corrections for spherical and chromatic aberration, that are known from the eyes of animals with better vision. In the following dissertation, Chapter 2 discusses the visually-influenced behaviors of scallops. It has been argued that bivalve mantle eyes only act as predator-detectors, but the behavioral trials described in this chapter suggest that vision may serve additional purposes in scallops. For example, it was found that visual cues relating to flow conditions may influence scallop feeding behavior. Chapter 3 presents a comparative study of scallop eye morphology. Here, it is found that eye morphology varies considerably between scallop species and that highly mobile scallops have better vision than less mobile or immobile species. Evidence is also presented that one of the two scallop retinas may perform tasks of similar importance to all species, such as predator detection, while the other retina may perform tasks more important to mobile species, such as those associated with the visual detection of preferred habitats. Chapter 4 investigates the spectral sensitivity of the two retinas in the mantle eyes of two scallop species. It is found that there is both inter- and intra-specific variation in scallop spectral sensitivity and that color perception in scallops may be influenced by both environmental light conditions and chromatic aberration caused by their lens. The research in this dissertation provides insight into how vision functions in animals that, like scallops, have a vast number of eyes, but a limited capacity for neural processing. Despite such limitations, it is evident that scallops display a wide range of visual behaviors and have eyes with highly-refined optics.</p> / Dissertation

<p>Whether through sea level rise, farmland abandonment, or wetland restoration, agricultural soils in coastal areas will be inundated at increasing rates, renewing connections to sensitive surface waters and raising critical questions related to environmental tradeoffs. Wetland restoration in particular is often implemented not only to promote wildlife habitat, but also to improve water quality through nutrient removal, especially in agricultural catchments. The microbial process of denitrification is the central mechanism of nitrogen removal in wetlands and flooded soils, and can be seen as a potential environmental benefit of flooding agricultural lands. While denitrification undoubtedly can remove nitrogen from soil and surface water, higher soil moisture or flooding in wetland soils can also increase the production of greenhouse gases, specifically nitrous oxide and methane, representing a potential environmental tradeoff. Understanding the likely benefits of denitrification and the likely greenhouse gas costs of wetland restoration could help inform environmental policies concerning wetland restoration. </p> <p>Determining whether restored wetlands are larger sources of greenhouse gases compared to contrasting land use types (agriculture and forested wetlands) was the first goal of this dissertation (Chapter 2). We measured gas fluxes from soil and water to the atmosphere, and related environmental variables, in four sites over two years to estimate fluxes of the three major greenhouse gases. We found that carbon dioxide was the major contributor to the radiative balance across all sites, but that in the agricultural site and one of the forested wetland reference sites, nitrous oxide was the second most important contributor. Many studies have shown that methane is more important that nitrous oxide in most freshwater wetlands, as we found in the other forested wetland reference site and in flooded parts of the restored wetland. Overall, we did not find higher greenhouse gas fluxes in the restored wetland compared to agricultural soils or forested wetlands.</p> <p>The controls over nitrous oxide are especially complex, because it can be produced by two complementary processes, nitrification and denitrification, which generally occur under different conditions in the environment. In Chapter 3, we determined the soil and environmental factors that best predicted nitrous oxide fluxes for a subset of our data encompassing gas fluxes measured in November 2007. We found that soil temperature and soil carbon dioxide flux, along with ammonium availability and denitrification potential, were good predictors of nitrous oxide (adj R<super>2</super>=0.81). Although the nitrous oxide model did not perform as well when applied to data from another sampling period, we expect to further develop our modeling efforts to include possible non-linear temperature effects and a larger range of environmental conditions. </p> <p>In Chapter 4, we present results of a stable isotope tracer experiment to determine the relative contribution of nitrification and denitrification to nitrous oxide fluxes in these different land use types, and to determine the response of these processes to changing soil moisture. We added two forms of nitrogen-15 to intact soil cores to distinguish nitrification from denitrification, and subjected the cores to drainage or to a simulated rain event. We found that across the range of soil moisture, the fraction of nitrous oxide produced by denitrification did not change, but within each soil type there was a response to the simulated rain. In mineral soils, the nitrous oxide fraction increased with increasing soil moisture, with the highest mole fraction [N₂O/(N₂+N₂O)] in the agricultural soils, while in the organic soils there was no change or even a decrease. The fraction of nitrous oxide derived from coupled nitrification-denitrification increased with increasing soil moisture, and was much higher than that from denitrification alone in the more organic soils. This suggests that, in these saturated acid-organic soils, nitrification plays an important and underappreciated role in contributing to nitrous oxide fluxes from freshwater wetlands. The results from the laboratory experiment were consistent with patterns we saw in the field and help explain the differential contribution of nitrification and denitrification to nitrous oxide fluxes in different land use types in coastal plain wetlands of North Carolina. </p> <p>Overall, we found that both nitrification and denitrification contribute to nitrous oxide fluxes in coastal plain wetlands in North Carolina, and that nitrification is an especially important source in acid-organic soils under both field-moist and saturated conditions. Although freshwater wetlands, with an average nitrous oxide mole fraction of 0.08, are generally seen as being insignificant sources of nitrous oxide, our study sites ranged from 0.10 to 0.30, placing them closer to agricultural fields (0.38; Schlesinger 2009). Although the ecosystems in our study produced more nitrous oxide than expected for freshwater wetlands, we found no significant tradeoff between the local water quality benefits conferred by denitrification and the global greenhouse gas costs in the restored wetland. These results suggest that, from a nitrogen perspective, wetland restoration in coastal agricultural lands has a net environmental benefit.</p> / Dissertation

<p>Reactive oxygen species (ROS) are produced endogenously in all aerobes and are induced by environmental stressors. ROS oxidize and disable essential cellular components such as DNA, proteins, and lipid membranes. Exposure to metals, polycyclic aromatic hydrocarbons (PAHs), and some pesticides can induce oxidative stress in marine invertebrates. All aerobic organisms have a network of antioxidants and enzymes to quench ROS and prevent oxidative damage. This dissertation examines antioxidant and oxidative stress biomarkers in endemic molluscs and crabs from two natural extreme environments: deep-sea hydrothermal vents in the Lau and North Fiji Basin, and cold seeps in the Gulf of Mexico. In addition, the acute toxicity and sub-lethal effects of four insecticides and an herbicide are examined in the estuarine blue crab, <italics>Callinectes sapidus</italics>. Blue crabs are North Carolina's most important fishery species and are frequently found in agricultural drainage ditches, an example of an anthropogenic extreme environment. </p> <p>Total glutathione, catalase, superoxide dismutase, and lipid peroxidation levels were of the same respective order of magnitude in the two vent gastropods, <italics>Alviniconcha</italics> sp. and <italics>Ifremeria nautilei</italics>, and vent mussel, <italics>Bathymodiolus brevior</italics>. These biomarkers activities were similar to those from previous reports on Mid-Atlantic Ridge mussels, except for ~100-fold higher lipid peroxidation levels among Lau molluscs. Principal component analysis (PCA) of mollusc tissue-specific biomarker levels grouped individuals by species rather than by site. </p> <p>Biomarker levels in the seep mussels <italics>Bathymodiolus childressi, B. brooksi</italics>, and <italics>B. heckerae</italics> were similar across species except for elevated foot and gill cytosolic SOD in mussels from MC-640 compared to those from AC-645. PCA of seep mussel biomarker levels differentiated by species with <italics>B. childressi</italics> isolated from <italics>B. brooksi</italics> and <italics>B. heckerae</italics>. The addition of <italics>B. brevior</italics> biomarker data to the PCA showed them grouping around <italics>B. brooksi</italics> and <italics>B. heckerae</italics>. <italics>Bathymodiolus childressi</italics> is ancestral to the other species and contains only methanotrophic endosymbionts. Whether symbionts play a role in alleviating possible toxic conditions remains unknown.</p> <p>Pesticides were acutely toxic to blue crabs in the order of Lambda-cyhalothrin > imidacloprid &#8776; aldicarb > acephate &#8776; Roundup® (glyphosate). Megalopae were almost always more sensitive to pesticides than early stage juveniles. Commercial formations of pesticides generally showed similar toxicity to active ingredients alone. Exposure to LC₂₀ levels of acephate, aldicarb, imidacloprid and Roundup significantly increased the frequency of juvenile mortality after molting. There was no significant change in total glutathione or lipid peroxidation of exposed megalopae. Lambda-cyhalothrin-, imidacloprid-, and aldicarb-based products have the potential to cause acute toxicity and molting-related mortality in shallow creeks and ditches.</p> / Dissertation

<p><p>Understanding the ecological and evolutionary responses of plant species to shifts in climate (and other rapid environmental perturbations) will require an improved knowledge of interactions between ecological and evolutionary processes as mediated by reproduction and gene flow. This dissertation research examines the processes of seed dispersal, intra- and inter-specific gene flow, and reproductive success in two red oak populations in North Carolina; the variation in these processes from site to site; and their influence on genetic structure, population dynamics, and migration potential.</p> <p><p>Using genetic and ecological data collected from two large long-term study sites, I develop a hierarchical Bayesian model to identify the parents of sampled seedlings and characterize the scale of effective seed and pollen dispersal. I examine differences in scale of dispersal between the Appalachian and Piedmont sites in light of the spatial genetic structure and ecological differences of the two sites. I then use the pedigree and dispersal estimates derived from these analyses to examine variation in reproductive success and to test hypotheses about the causes and consequences of such variation. Using parentage estimates and measures of genetic differentiation between species, I study the likely extent of hybridization in these mixed-species secondary forests. Finally, using the SLIP stand simulator, I explore the implications of new genetic dispersal estimates for migration potential in oaks.</p> <p><p>I find that effective seed dispersal distances are longer than estimated using seed trap data. While at the Piedmont site the large number of seedling found >100 m from their mother trees suggests that animal dispersers play a vital role, at the Appalachian site seedling distributions conform more closely to the original gravity-created pattern of seed density. Individual trees vary widely in their reproductive success. Seedling production was found to be positively associated with annual seed production, but exhibited hump-shaped or reversing relationships with age (suggesting the effect of senescence) and growth rate (suggesting tradeoffs in allocation). Germination fraction was negatively associated with fecundity, suggesting that density-dependent mortality may be acting on the high concentrations of seeds near highly fecund adults. Due to overlapping generations and variation in individual reproductive success, effective population size is estimated to be less than half the size that numbers of "adult" individuals would suggest, with consequences for the relative strength of drift and selection. Hybridization may boost effective population size somewhat; my analyses suggest that inter-specific gene flow is common at both study sites. Finally, simulations show that dispersal has a relatively stronger effect on migration rate and population growth than fecundity or size at maturity, and that genetic estimates of seed dispersal can yield significantly higher rates of migration and/or population persistence than seed-trap based estimates under both competitive and non-competitive conditions.</p> / Dissertation

<p>Amazonia contains the largest remaining tracts of undisturbed tropical forest on earth, and is thus critical to international nature conservation and carbon sequestration efforts. Amazonian forests are notoriously difficult to study, however, due to their species richness and inaccessibility. This has limited efforts to produce the accurate, high-resolution biodiversity maps needed for conservation and development. The aims of the research described here were to identify efficient solutions to the problems of tropical forest inventory; to use these methods to identify floristic patterns and their causes in western Amazonia; and propose new means to map floristic patterns in these forests.</p><p> Using tree inventories in the vicinity of Iquitos, Peru, I and a colleague systematically evaluated methods for rapid tropical forest inventory. Of these, inventory of particular taxonomic groups, or taxonomic scope inventory, was the most efficient, and was able to capture a majority of the pattern observed by traditional inventory techniques with one-fifth to one-twentieth the number of stems and species. Based on the success of this approach, I and colleagues specifically evaluated two plant groups, the Pteridophytes (ferns and fern allies) and the Melastomataceae (a family of shrubs and small trees), for use in rapid inventory. Floristic patterns based on inventories from either group were significantly associated with those based on the tree flora, and inventories of Pteridophytes in particular were in most cases able to capture the majority of floristic patterns identified by tree inventories. These findings indicate that Pteridophyte and Melastomataceae inventories are useful tools for rapid tropical forest inventory.</p><p> Using Pteridophyte and Melastomataceae inventories from 138 sites in northwestern Amazonia, combined with satellite data and soil sampling, I and colleagues studied the causes of vegetation patterns in western Amazonian forests. On the basis of these data, we identified a floristic discontinuity of at least 300km in northern Peru, corresponding to a 15-fold difference in soil cation concentrations and an erosion-generated geological boundary. On the basis of this finding, we assembled continent-scale satellite image mosaics, and used these to search for additional discontinuities in western Amazonia. These mosaics indicate a floristic and geological discontinuity of at least 1500km western Brasil, driven by similar erosional processes identified in our study area. We suggest that this represents a chemical and ecological boundary between western and central Amazonia.</p><p> Using a second network of 52 pteridophyte and soil inventories in northwestern Amazonia, we further studied the role of geology in generating floristic pattern. Consistent with earlier findings, we found that two widespread geological formations in western Amazonia differ eight-fold difference in soil cation concentrations and in a majority of their species. Difference in elevation, used as a surrogate for geological formation, furthermore explained up to one-third of the variation in plant species composition between these formations. Significant correlations between elevation, and cation concentrations and soil texture, confirmed that differences in species composition between these formations are driven by differences in soil properties. On the basis of these findings, we were able to use SRTM elevation data to accurately model species composition throughout our study area.</p><p> I argue that Amazonian forests are partitioned into large-area units on the basis of geological formations and their edaphic properties. This finding has implications for both the ecology and evolution of these forests, and suggests that conservation strategies be implemented on a region-by-region basis. Fortunately, the methods described here provide a means for generating accurate and detailed maps of floristic patterns in these vast and remote forests.</p> / Dissertation

<p>The Piedmont region of the southeastern United States has undergone considerable land-use change since settlement by Europeans and Africans. Forests were cleared for agriculture, followed centuries later by land abandonment. Following abandonment, natural recruitment, plantings for erosion control, and plantation forestry have resulted in a large area of the region covered by loblolly pine, Pinus taeda. Today, the Piedmont is a mosaic of farm fields, pastures, pine forests, and relic woodlots. The Calhoun Experimental Forest, located in Union County, SC, has provided a unique history of land use change's alteration of soil properties and processes, the ability of reforestation to restore or deplete soil fertility, and provided insights into the effects this change has on biological diversity.</p><p>In this work, the diversity of fungi living in soil is examined in the context of land-use change and soil biogeochemical change in and around the Calhoun Forest. This study uses molecular tools to identify fungal species from soil and to identify mycorrhizal associates of loblolly pine in a bioassay of propagule diversity, and proposes a novel use of quantitative PCR to quantify the relative abundance of major fungal families affected by land-use change.</p><p>Fungal diversity in soils is high in all land uses, but fungal communities shift from agricultural field communities largely comprised of unicellular ascomycetes and basal lineages to forest communities dominated by saprophytic and symbiotic basidiomycetes. In addition to this shift across a land use gradient, fungal communities are also responding to changes in carbon quantity and quality, biologically available nitrogen and phosphorus, pH, acidity and texture.</p><p>ECM propagule communities also differ across a land use gradient of cultivated fields, grasslands, pine forests, and mixed hardwood stands. There are few ECM propagules able to associate with loblolly pine in cultivated and grassland soils. There is a trend towards higher ECM diversity in the hardwood and pine soils, and both of those soil communities are distinct from each other as well as from soils from field treatments.</p><p>Quantitative PCR, coupled with a nested set of taxon-specific, fungal primers, is a potential way to estimate the abundance of the given taxon relative to all fungi in an environmental DNA. Primers specific to several taxonomic level of fungi were tested to confirm amplification in PCR, then were tested for taxonomic specificity by generating clone libraries with environmental DNA. Several of the successful primers were tested with soil DNA extracts in QPCR and the calculated ratios of fungal abundance varied widely by method of analysis. The results suggest that many repeated measurements and many replicates are required for a robust estimate of the relative abundance of a specific taxon.</p> / Dissertation

<p><p>Plants and their pathogens coevolve, with pathogen infection and host resistance acting in evolutionary antagonism of each other. Plant-pathogen coevolution has been shown to effect genetic divergence between populations and species, resulting in localized or specialized interactions between hosts and pathogens. Because most of the studies to date investigating plant-pathogen coevolution have been carried out in managed systems and have focused on pairwise interactions, we know little about three aspects of plant pathosystems in natural settings: 1) the role in nature of the gene-for-gene paradigm for genetic determination of resistance; 2) the relationship of host community diversity and structure, and host-pathogen interaction structure, to the coevolutionary process; and 3) the factors which underlie and drive local adaptation and specialization of interactions.</p><p><p>This dissertation constitutes the results of research in which I have begun addressing these aspects in a natural plant-fungus pathosystem comprising three <i>Ipomoea</i> host species and a single rust pathogen, <i>Coleosporium ipomoeae</i>. I have expanded previous characterization of the genetics of plant resistance in one constituent host species in the system by genetic crosses to characterize the basis of resistance in two additional species, finding support for the expectation that the gene-for-gene paradigm of interaction is important in natural systems. I conducted a cross-inoculation experiment designed to assess host and pathogen variation in infectivity and resistance, to investigate patterns of community interaction structure, and the role that antagonistic coevolution may play in structuring the communities which compose pathosystems. In these experiments I found that the coevolutionary interaction in this system leads to genetic divergence and the substantial amount of host and pathogen variation I discovered, but that it tends to preserve one pattern of community interaction structure across communities. I expanded my cross-inoculation experimental design to facilitate analysis of quantitative aspects of pathogenesis by measuring the intensity of infections, to test existing hypotheses concerning local adaptation and specialization in pathosystems. In this analysis I found strong host local adaptation and pathogen local maladaptation for the qualitative interaction trait of infectivity, and I found weak host local maladaptation and pathogen local adaptation for the quantitative interaction trait of aggressiveness. I also found host specialization among pathogens, and specialized resistance among hosts, to be common in this system. In light of these results, I hypothesize that the geographic scale of host-pathogen coevolution in this system is that of the local community, and that differences between host species result in persistent but incomplete host specialization in pathogen races.</p> / Dissertation