Browsing by Subject "Biology, Ecology"

Infusing models for animal movement with more behavioral realism has been a goal of movement ecologists for several years. As ecologists have begun to collect more and more data on animal distribution and abundance, a clear need has arisen for more sophisticated analysis. Such analysis could include more realistic movement behavior, more information on the organism-environment interaction, and more ways to separate observation error from process error. Because landscape ecologists and behavioral ecologists typically study these same themes at very different scales, it has been proposed that their union could be productive for all (Lima and Zollner, 1996).

By understanding how animals interact with their land- and seascapes, we can better understand how species partition up resources are large spatial scales. Accordingly I begin this dissertation with a large spatial scale analysis of distribution data for marine mammals from Nova Scotia through the Gulf of Mexico. I analyzed these data in three separate regions, and in the two data-rich regions, find compelling separation between the different communities. In the northernmost region, this separation is broadly along diet based partitions. This research provides a baseline for future study of marine mammal systems, and more importantly highlights several gaps in current data collections.

In the last 6 years several movement ecologists have begun to imbue sophisticated statistical analyses with increasing amounts of movement behavior. This has changed the way movement ecologists think about movement data and movement processes. In this dissertation I focus my research on continuing this trend. I reviewed the state of movement modeling and then proposed a new Bayesian movement model that builds on three questions of: behavior; organism-environment interaction; and process-based inference with noisy data.

Application of this model to two different datasets, migrating right whales in the NW Atlantic, and foraging monk seals in the Northwest Hawaiian Islands, provides for the first time estimates of how moving animals make choices about the suitability of patches within their perceptual range. By estimating parameters governing this suitability I provide right whale managers a clear depiction of the gaps in their protection in this vulnerable and understudied migratory corridor. For monk seals I provide a behaviorally based view into how animals in different colonies and age and sex groups move throughout their range. This information is crucial for managers who translocate individuals to new habitat as it provides them a quantitative glimpse of how members of certain groups perceive their landscape.

This model provides critical information about the behaviorally based movement choices animals make. Results can be used to understand the ecology of these patterns, and can be used to help inform conservation actions. Finally this modeling framework provides a way to unite fields of movement ecology and graph theory.

Sea turtles have experienced dramatic population declines during the last century as a consequence of direct harvest, by-catch in fisheries, and habitat loss. Despite almost 50 years of partial international protection, several populations of sea turtles are still at imminent risk of extinction. Our knowledge of their complex life histories is still far from complete; these knowledge gaps hinder our ability to provide scientific advice regarding their conservation and management. It is the very complexity of their life histories, which allows them to exploit widely separated habitats during development, often over the course of decades, which makes them inherently difficult to study. I used satellite telemetry (n=60) to investigate the movements and habitat use patterns of juvenile loggerhead (Caretta caretta), green (Chelonia mydas), and Kemp's ridley (Lepidochelys kempii) sea turtles on their summer feeding grounds in North Carolina estuaries. These turtles migrate into and out of the estuarine waters each spring and autumn, encountering a gauntlet of fishing gear on each journey. The by-catch of sea turtles is an important conservation issue in North Carolina, and throughout the world's oceans. I evaluated conservation measures established to reduce the by-catch of sea turtles in Pamlico Sound's autumnal large-mesh gill net fishery for southern flounder (Paralichthys lethostigma), using a spatially explicit predator/prey model. My findings indicated that species-specific habitat preferences contributed to a turtles' risk of encountering fishing gear and that areas of high by-catch are predictable from patterns of overlap between sea turtle habitat use and flounder fishing effort. I then examined how the behavior of green turtles affected their vulnerability to incidental capture in estuarine commercial fisheries. Individual green turtles interact with multiple gears per season as a result of strong site fidelity to habitats also preferred by fishers. Telemetry also allowed me to examine individual variation in movements, habitat use, and site fidelity patterns of juvenile loggerhead turtles, both within the estuary and as the turtles migrated out into the North Atlantic. I used these observations to test the hypothesis of a discrete ontogenetic shift in habitat and diet in juvenile loggerheads. Approximately one-third of large juvenile loggerheads tagged in North Carolina estuaries return to oceanic habitat, sometimes for several years, where they are vulnerable to by-catch in pelagic fisheries. This led me to conclude that the long held notion of a discrete ontogenetic habitat shift between the oceanic and neritic habitat was incorrect for juvenile loggerheads (and possibly also for green turtles). Finally, I explored variation in migratory destinations in these animals through multivariate analyses of carbon and nitrogen stable isotope ratios in blood plasma and red blood cells, and through analysis of sex, genetic, haplotype, body size, and remigration records, and described the trophic niche of these turtles with Bayesian isotope mixing models. Variation in migratory destination (oceanic or neritic habitat) was best described by stable isotope ratios of nitrogen and remigration tendency. Turtles that returned to the open ocean had significantly lower nitrogen ratios than those animals that remained in the neritic zone and their diets retained a substantial contribution of epipelagic prey items. The diet composition of neritic turtles, on the other hand, consisted primarily of estuarine benthic invertebrates during the summertime and autumn foraging season but shifted toward pelagic jellyfish, fish, and Sargassum during the overwintering period. Oceanic turtles likely came from open ocean regions prior to entering the summer foraging grounds while neritic turtles likely overwintered at the edge of the Gulf Stream. The agreement between the dietary compositions and migration patterns between the two groups of turtles suggest that these feeding and habitat use strategies were persistent characteristics in the turtles I sampled. My work has improved our understanding of sea turtle habitats in North Carolina estuaries and identified their migratory destinations and overwintering habitats. I hope that this work lays the groundwork for future studies that will explore how variation in habitat use and feeding strategies are manifested in life history traits that affect fitness directly, such as survivorship, growth rates, stage durations, and fecundity.

This dissertation consists of four chapters. The first three chapters examine protected areas (or parks) from multiple perspectives. Parks are the first, and often only, line of defense in efforts to conserve biodiversity. Understanding of their promise and problems is necessary to achieve conservation outcomes. Chapter One determines vegetation patterns in and around parks of differing management categories across the Amazon, Congo, South American Atlantic Coast, and West African forests. Within these forests, protected areas are the principle defense against forest loss and species extinctions. In the Amazon and Congo, parks are generally large and retain high levels of forest cover, as do their surroundings. In contrast, parks in the Atlantic Coast forest and West Africa show sharp boundaries in forest cover at their edges. This effective protection of forest cover is partially offset by their very small size: little area is deep inside park boundaries. Compared to West Africa, areas outside parks in the Atlantic Coast forest are unusually fragmented.

Chapter Two addresses a human dimension of protected areas. Given certain characteristics, parks areas may either attract or repel human settlement. Disproportionate increases in population growth near park boundaries may threaten their ability to conserve biodiversity. Using decadal population datasets, we analyze population growth across 45 countries and 304 parks. We find no evidence for population growth near parks to be greater than growth of rural areas in the same country. Furthermore, we argue that what growth does occur near parks likely results from a general expansion of nearby population centers. Parks may experience unusual population pressures near their edges; indeed, individual case studies provide examples. There is no evidence, however, of a general pattern of disproportionate population growth near their boundaries.

Chapter Three provides a review of common approaches to evaluating protection's impact on deforestation, identifies three hurdles to empirical evaluation, and notes that matching techniques from economic impact evaluation address those hurdles. The central hurdle derives from the fact that protected areas are distributed non-randomly across landscapes. Matching controls for landscape characteristics when inferring the impact of protection. Applications of matching have revealed considerably lower impact estimates of forest protection than produced by other methods. These results indicate the importance of variation across locations in how much impact protection could possibly have on rates of deforestation.

Chapter Four departs from the focus of protected areas and instead addresses a more theoretical aspect of community ecology. Ecological theories suggest that food webs might consist of groups of species forming blocks, compartments or guilds. Chapter Four considers ecological networks (subsets of complete food webs) involving species at adjacent trophic levels. Reciprocal specializations occur when (say) a pollinator (or group of pollinators) specializes on a particular flower species (or group of such species) and vice versa. We characterize the level of reciprocal specialization for various classes of networks. Our analyses include both antagonistic interactions (particularly parasitoids and their hosts), and mutualistic ones (such as insects and the flowers that they pollinate). We also examine whether trophic patterns might be palimpsests. That is, there might be reciprocal specialization within taxonomically related species within a network, but these might be obscured when these relationships are combined. Reciprocal specializations are rare in all these systems even when tested using the most conservative null model.

Plants respond to changes in their local environment and, at the same time, influence the environment at a global scale. The molecular and physiological mechanisms regulating this interaction are not completely understood and this limits our capacity to predict the response of vegetation to future environmental changes. This dissertation combined tools from genomics, physiology, and ecology to examine the response of plants to environmental change. Specifically, it focused on processes affecting carbon and water exchange in forest trees because (1) trees are long-lived species that might face repeated environmental challenges; (2) relatively little information exists about the genes and the molecular mechanisms regulating structural and physiological traits in adult, long-lived woody plants; and (3) forest trees exchange a significant amount of carbon and water with the atmosphere and are therefore major players in the global carbon and water cycles.

Water flux through forests depends both on environmental conditions (e.g., soil moisture) and on the hydraulic architecture of individual trees. Resistance to xylem cavitation is an important hydraulic trait that is often associated with drought tolerance but potentially at the cost of reduced carbon uptake. The second chapter of this dissertation evaluated the variation in resistance to xylem cavitation, hydraulic conductivity, wood anatomy traits, and leaf gas exchange across 14 co-occurring temperate tree species including both angiosperms and gymnosperms. The relationship between vulnerability to cavitation (ψ₅₀) and hydraulic conductivity within specific organs (i.e. stems and roots) was not significant when considering the phylogenetic association between species. However, even after phylogenetic correction, photosynthetic carbon uptake (A) was positively correlated with both stem and root ψ₅₀, and stomatal conductance (g_s ) was strongly correlated with root ψ₅₀ . These results suggest that there is a trade-off between vulnerability to cavitation and water transport capacity at the whole-plant level, and that this functional relationship reflects an adaptive response to the environment.

Forests are an important component of the global carbon cycle that can be directly impacted by a rise in atmospheric CO₂ concentration.. The third chapter of this dissertation investigated the effects of long-term exposure to elevated CO2 on the gene expression of mature, field-grown loblolly pine trees. Using cDNA microarrays, I compared the expression of 1784 pine transcripts in trees growing under ambient and those under elevated CO₂ at monthly intervals throughout a growing season. Overall, more genes were upregulated than downregulated by elevated CO₂, although the total number of genes differentially expressed varied throughout the season. The pattern of increasing number of differentially expressed genes until the peak of the growing season (July and August) followed by a decrease in that number, matched the seasonal trend of tree growth and photosynthetic response to elevated CO₂ in this species. The seasonal trend also reflected the interaction among multiple abiotic factors intrinsic to field conditions and emphasized the relevance of evaluating the role of genes in their natural environment. Genes consistently upregulated by elevated CO₂ were functionally associated with environmental sensing, cellular signaling, and carbon metabolism, in particular the degradation of carbohydrates through respiration. An increase in carbohydrates degradation is particularly relevant in the context of carbon balance of forest trees because of the potential for enhanced leaf and tree respiration leading to a reduced sink capacity for CO₂.

Loblolly pine produces several flushes of needles throughout the year each with an average lifespan of 19 months. Each year, two age classes of needles contribute to the annual carbon sequestration of the loblolly pine forest. To address the impact of leaf age on the effects of elevated CO₂ in carbon metabolism regulation, I compared the gene expression profiles from trees under ambient and elevated CO₂ conditions in two needle cohorts: one-year-old and current-year. Differential expression under elevated CO₂ was seven times more frequent in current-year than in one-year-old needles. Despite differences in magnitude, many of the patterns within specific groups of genes were similar across age classes. For instance, there was a trend for downregulation of genes involved in the light-reactions of photosynthesis and those in photorespiration in both age classes, while genes associated with dark respiration were largely upregulated by elevated CO₂ in both cases. The difference between the two cohorts was particularly evident in the group of genes related to energy production (ATP synthesis) and the group associated with carbon partitioning (sucrose and starch metabolism). Because sucrose and starch metabolism categories included many genes known to be important regulators of gene expression and plant physiological processes, this suggests that this stage of carbon metabolism might be an important control point in age-dependent foliar responses to elevated CO₂.

This dissertation examined both structural and physiological components of plant water and carbon relations (Chapter 2) across different biological scales of organization (whole-plant level in Chapter 2; gene-level response to ecosystem-level changes in Chapters 3 and 4) and reflecting adjustments at distinct temporal scales (life-span of the organism vs. evolutionary selection of traits). An integrative approach was used to advance our understanding of how plants acclimate and adapt to their environment, and to provide a mechanistic framework for predictive models of plant response to environmental change.

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.

This dissertation constitutes the results of research in which I have begun addressing these aspects in a natural plant-fungus pathosystem comprising three Ipomoea host species and a single rust pathogen, Coleosporium ipomoeae. 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.

A long-held assumption in animal behavior is that females and males differ fundamentally in their mating strategies. Females are thought to be more choosy because female reproduction typically is limited by parental investment. Males, on the other hand, are expected to compete among themselves for access to females or resources, since male reproduction is limited primarily by mating access. This dichotomy is challenged by the increasing realization that males can be choosy and females also compete aggressively. It remains unclear, however, if and how selection acts on aggressive behavior in the context of intrasexual competition among females (reviewed in Chapter 1). In this thesis, I use a population of free-living tree swallows (Tachycineta bicolor) to test predictions about the selective pressures shaping aggressive behavior in females. First, using an experimental manipulation of nest site availability, I demonstrate that more aggressive females have a competitive edge in acquiring nestboxes, a critical limiting resource required for breeding (Chapter 2). This result shows that more aggressive females are more likely to breed and, thus, that females experience direct selection to be aggressive in the context of competition for mating opportunities. Next, I demonstrate a fitness cost of female aggression (Chapter 3): high levels of aggression in females are not associated with the quantity of offspring, but instead, more aggressive females had offspring of lower quality (i.e. reduced mass). Using a cross-fostering approach, I explore the causal link between female aggression and offspring mass, and I find that a trade-off between female aggression and maternal care best accounts for this cost of aggression. Site differences may create variation in how selection shapes female aggression, but the overall finding that more aggressive females have lower quality offspring indicates that this cost may work counter to selection favoring aggressive behavior in the context of competition over nestboxes. Understanding the evolution of female aggressiveness in a biparental system is incomplete without examining how males may alter the selective environment shaping female behavior. In Chapter 4, I explore the potential role of a female's mate in offsetting the costs of aggression. Males appear to mitigate these costs for their female partners, but not by compensating for poor parenting by aggressive females. Instead, females invest more heavily in reproduction, laying more and larger eggs, when mated to a male that is more different from her own phenotype. If this differential investment outweighs the cost of aggressiveness in terms of offspring quality, then male phenotype may play a key role in understanding the selective pressures shaping the evolution of aggressive behavior in females. Altogether, this dissertation explores the costs and benefits of female aggressive behavior. The focus on aggressiveness as a sexually selected trait in females provides a much needed parallel to the wealth of information already known about the selective pressures shaping sexually selected traits in males.

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, Callinectes sapidus. 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.

Total glutathione, catalase, superoxide dismutase, and lipid peroxidation levels were of the same respective order of magnitude in the two vent gastropods, Alviniconcha sp. and Ifremeria nautilei, and vent mussel, Bathymodiolus brevior. 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.

Biomarker levels in the seep mussels Bathymodiolus childressi, B. brooksi, and B. heckerae 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 B. childressi isolated from B. brooksi and B. heckerae. The addition of B. brevior biomarker data to the PCA showed them grouping around B. brooksi and B. heckerae. Bathymodiolus childressi is ancestral to the other species and contains only methanotrophic endosymbionts. Whether symbionts play a role in alleviating possible toxic conditions remains unknown.

Pesticides were acutely toxic to blue crabs in the order of Lambda-cyhalothrin > imidacloprid ≈ aldicarb > acephate ≈ 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.

Under the increasing threat of climate change, it is imperative to understand the impact that environmental phenomena have on the demography and behavior of natural populations. In the last few decades an ever increasing body of research has documented dramatic changes in mortality rates and breeding phenology for a large number of species. A number of these have been attributed to the current trends in climate change, which have been particularly conspicuous in bird populations. However, datasets associated to these natural populations as well as to the environmental variables that affect their biology tend to be partial and incomplete. Thus, ecological research faces the urgent need to tackle these questions while at the same time develop inferential models that can handle the complex structure of these datasets and their associated uncertainty. Therefore, my dissertation research has focused on two main objectives: 1) to understand the relationship that demographic rates and breeding phenology of a colony of seabirds has with the environment in the context of climate change; and 2) to use and develop models that can encompass the complex structure of these natural systems, while also extending the process not only to inference but to building predictions. I divided this work in three research projects; for the first one I developed a hierarchical Bayesian model for age-specific survival for long lived species with capture-recapture data that allows the use of incomplete data (i.e. left-truncated and right-censored), and builds predictions of years of birth and death for all individuals while also drawing inference on the survivorship function. I compared this method to more traditional ones and address their limitations and advantages. My second research chapter makes use of this method to determine the age-specific survivorship of the Dry Tortugas sooty tern population, and explores the effect of changes in sea surface temperature on their cohort mortality rates. Finally, my third research chapter addresses the dramatic shift in breeding season experienced by the Dry Tortugas sooty tern colony, the most unprecedented shift reported for any bird species. I explore the role of climatic and weather variables as triggering mechanisms.

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.

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.

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 R2=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.

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.

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.

Invasive species are rapidly expanding in riparian wetlands while concurrently anthropogenic causes are increasing nitrogen (N) into these ecosystems. Microstegium vimineum (Microstegium) is a particularly abundant invasive grass in the Southeast United States. To evaluate impacts of Microstegium on both plant diversity and N cycling in a riparian floodplain, paired plots of Microstegium hand-weeded and unweeded were established for three years. Plots without Microstegium increased from 4 to 15 species m-2 and 90% of the newly establishing species were native. The Microstegium community accumulated approximately half the annual N in biomass of the diverse community, 5.04 versus 9.36 g-N m-2 year-1, respectively (p=0.05). Decomposition and release of N from Microstegium detritus was much less than in the diverse community, 1.19 versus 5.24 g-N m-2 year-1. Rates of soil N mineralization estimated by in-situ incubations were relatively similar in all plots. While Microstegium invasion appears to greatly diminish within-ecosystem circulation of N through the under-story plants, it might increase ecosystem N losses through enhanced denitrification (due to lower redox potentials under Microstegium plots). Microstegium removal ceased in the fourth growing season and formerly weeded plots increased to 59% (± 11% SE) Microstegium cover and species richness decreased to <8 species m-2.

To learn how Microstegium responds to increased N, we conducted a greenhouse competition experiment between Microstegium and four native plants across an N gradient. There was a unique competition outcome in each species combination, yet Microstegium was most dominant in the high levels of N.

Last, we disturbed a floodplain similar to wetland restoration disturbance and tracked available N. We also established a native community of plants with and without Microstegium in three levels of N. Disturbance to the floodplain dramatically increased inorganic N, especially in the form of NO₃ which was five times higher in the disturbed floodplain than the undisturbed floodplain. N levels remained elevated for over a year. Microstegium was N responsive, but did not show negative effects to the planted vegetation until the second year. Ironically, restoration activities are increasing available N, and favoring invasive species which in turn detracts from restoration success.

I examined recruitment patterns of multiple tree species in a western Amazonian floodplain forest at three ontogenetic stages: seed fall, seedling establishment, and sapling recruitment.

From analyzing a long-term seed rain dataset collected using a high-density array of seed traps, I confirmed that seed fall decreases sharply with increasing distance from fruiting trees, with disproportionately large contributions from a very small fraction of all trees. Patterns of seed fall, although idiosyncratic for individual species, tended to relate to dispersal syndrome. Intact seeds were found at significantly greater distances away from fruiting adults than ripe fruit and almost exclusively comprised the tail of the seed shadow for most species.

Saplings of all species examined recruited in areas of very low predicted seed density at significantly higher abundances than expected under a null hypothesis of "all seeds are equal". The value of a seed in terms of its potential to produce a sapling recruit - measured as sapling/seed ratio - initially increased greatly with increasing distance from reproductive conspecific adults and leveled off at farther distances, in almost all species.

A parallel experimental study employed >1000 individual seedlings of common tree species situated near and far from conspecific adults. Overall survival for all species pooled and for eight out of 11 individual species was significantly higher at sites located far from versus close to conspecific adults, with the study design controlling for seedling density at sites. Survival analysis based on multiple censuses revealed that a "distance effect" persisted and intensified over time, although the timing of onset of distance-related differential mortality differed amongst species. The role of host-specific invertebrate herbivores and microbial pathogens in causing seedling mortality near conspecific adults was confirmed by the use of mesh exclosures.

Overall, my results provide community-level support for the influence of distance-dependent processes on recruitment patterns. Seed dispersal appears critical for successful recruitment and undispersed seeds make a minimal contribution. When de-coupled from distance-dependence, effects of competition-based density-dependent processes on recruitment were weak or undetectable. I conclude that community-level tree recruitment processes and patterns in western Amazonian lowland rainforests that harbor intact floral and faunal assemblages conform closely to predictions of the Janzen-Connell hypothesis of tropical tree recruitment.

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.

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.

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.

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.

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.

Because species respond individually to climate change, understanding community assembly requires examination of multiple species from a diversity of forest niches. I present the post-glacial phylogeographic history of an understory, parasitic herb (Epifagus virginiana, beechdrop) that has an obligate and host specific relationship with a common eastern North American hardwood tree (Fagus grandifolia, American beech). The migration histories of the host and parasite are compared to elucidate potential limits on the parasite's range and to understand their responses to shared climate change. Two chloroplast DNA regions were sequenced and 9 microsatellite loci genotyped from parasite specimens collected throughout the host's range. These data were compared with available cpDNA sequences from the host (McLachlan et al. 2005) and host fossil pollen records from the last 21,000 years (Williams et al. 2004). Analyses of genetic diversity reveal high population differentiation in the parasite's southern range, a possible result of long term isolation within multiple southern glacial refuges. Estimates of migration rates and divergence times using Bayesian coalescent methods show the parasite initiating its post-glacial range expansion by migrating northward into the northeast from southern areas, then westward into the midwest, a pattern consistent with the development of high density beech forests. This result is strongly confirmed through spatial linear regression models, which show host density plays a significant role in structuring parasite populations, while the initial migration routes of the host are irrelevant to parasite colonization patterns. Host density is then used as a proxy for the parasite's habitat quality in an effort to identify the geographic locations of its migration corridors. Habitat cost models are parameterized through use of the parasite's genetic data, and landscape path analyses based on the habitat map show a major migration corridor south of the Great Lakes connecting the northeast and midwest. Host density was the major determinant controlling the parasite's range expansion, suggesting a lag time between host and parasite colonization of new territory. Parasites and other highly specialized species may generally migrate slower due to their complex landscape requirements, resulting in disassociation of forest assemblages during these times. From these results, the low migration capacities of highly specialized species may be insufficient to outrun extirpation from their current ranges.

Topography, vegetation, nutrient dynamics, soil features and hydroclimatic forcing are inherently coupled, with feedbacks occurring over a wide range of temporal and spatial scales. Vegetation growth may be limited by soil moisture, nutrient or solar radiation availability, and in turn influences both soil moisture and nutrient balances at a point. These dynamics are further complicated in a complex terrain, through a series of spatial interactions. A number of experiments has characterized the feedbacks between soil moisture and vegetation dynamics, but a theoretical framework linking short-term leaf-level to interannual plot-scale dynamics has not been fully developed yet. Such theory is needed for optimal management of water resources in natural ecosystems and for agricultural, municipal and industrial uses. Also, it complements the current knowledge on ecosystem response to the predicted climate change.

In this dissertation, the response of vegetation dynamics to unpredictable environmental fluctuations at multiple space-time scales is explored in a modeling framework from sub-daily to interannual time scales. At the hourly time scale, a simultaneous analysis of photosynthesis, transpiration and soil moisture dynamics is carried out to explore the impact of water stress on different photosynthesis processes at the leaf level, and the overall plant activity. Daily soil moisture and vegetation dynamics are then scaled up to the growing season using a stochastic model accounting for daily to interannual hydroclimatic variability. Such stochastic framework is employed to explore the impact of rainfall patterns and different irrigation schemes on crop productivity, along with their implications in terms of sustainability and profitability. To scale up from point to landscape, a probabilistic representation of local landscape features (i.e., slope and aspect) is developed, and applied to assess the effects of topography on solar radiation. Finally, a minimalistic ecosystem model, including soil moisture, vegetation and nutrient dynamics at the year time scale, is outlined; when coupled to the proposed probabilistic topographic description, the latter model can serve to assess the relevance of spatial interactions and to single out the main biophysical controls responsible for ecohydrological variability at the landscape scale.

Coral reef fish coexist in a state of high diversity that has not been successfully explained by niche diversification, larval supply, differential mortality, or a suite of other proposed factors. These processes are all occurring on a diverse substrate that would be expected to affect the abundance and distribution of fish by directing habitat preferences as well as affecting competitive and predatory success. I conducted correlational studies on healthy and degraded Caribbean reefs that addressed fish abundances at the levels of community, species, and age class. I also experimentally tested habitat preferences in two ways: choice experiments on adults of common species that determined preferences for live coral and rugosity in an isolated environment, and monitoring of artificial reefs differing in live coral cover that tested habitat selection of adults and juveniles in the field. These observations all show that live coral had no effect on community parameters such as abundance or diversity, but that rugosity was positively related to species richness. However, these measures of the community masked differences at the species and age class level. A handful of species exhibited positive or negative preferences for live coral, but these selections did not follow a taxonomic or trophic-level classification. Species within the genus Stegastes, for example, could either aggregate towards or avoid live coral. One species even reversed its habitat preference as it matured. Field distributions were not determined solely by these habitat preferences, but inclusion of competitive interactions into a multi-factorial model explained distribution of some species. Results suggest that changes in live coral cover, an increasingly common phenomenon, would not affect fish at a community level, but could affect a few species through changes to recruitment or alteration of competitive interactions.

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.