Browsing by Subject "Ecology"

Changing environmental conditions may present substantial challenges to organisms experiencing them. In animals, the fastest way to respond to these changes is often by altering behavior. This ability, called behavioral flexibility, varies among species and can be studied on several levels. First, the extent of behavioral flexibility exhibited by a species can be determined by observation of that species' behavior, either in nature or in experimental settings. Second, because the central nervous system is the substrate determining behavior, neuroanatomy can be studied as the proximate cause of behavioral flexibility. Finally, the ultimate causation can be examined by studying ecological factors that favor the evolution of behavioral flexibility. In this dissertation, I investigate behavioral flexibility across all three levels by examining the relationship between habitat structure, the size of different structures within the brain and total brain size, and behavioral flexibility in six closely-related species of Puerto Rican Anolis lizards. Anolis lizards provide an excellent taxon for this study as certain species, including those used here, are classified as belonging to different ecomorphs and are morphologically and behaviorally specialized to distinct structural habitat types.

In order to determine the presence of behavioral flexibility in Anolis, I first presented Anolis evermanni with a series of tasks requiring motor learning and a single instance of reversal learning. Anolis evermanni demonstrated high levels of behavioral flexibility in both tasks.

To address the pattern of brain evolution in the Anolis brain, I used a histological approach to measure the volume of the whole brain, telencephalon, dorsal cortex, dorsomedial cortex, medial cortex, dorsal ventricular ridge, cerebellum, and medulla in six closely-related species of Puerto Rican Anolis lizards belonging to three ecomorphs. These data were analyzed to determine the relative contribution of concerted and mosaic brain evolution to Anolis brain evolution. The cerebellum showed a trend toward mosaic evolution while the remaining brain structures matched the predictions of concerted brain evolution.

I then examined the relationship between the complexity of structural habitat occupied by each species and brain size in order to determine if complex habitats are associated with relatively large brains. I measured brain volume using histological methods and directly measured habitat complexity in all six species. Using Principal Component Analysis, I condensed the measures of habitat structure to a single variable and corrected it for the scale of each lizard species' movement, calling the resulting measurement relevant habitat complexity. I tested the relationship between relative volume of the telencephalon, dorsal cortex, dorsomedial cortex, and whole brain against both relative habitat complexity and ecomorph classification. There was no relationship between the relative volume of any brain structure examined and either relevant habitat complexity or ecomorph. However, relevant habitat complexities for each species did not completely match their ecomorph classifications.

Finally, I tested the levels of behavioral flexibility of three species of Anolis, A. evermanni, A. pulchellus, and A. cristatellus, belonging to three distinct ecomorphs, by presenting them with tasks requiring motor and reversal learning. Anolis evermanni performed well in both tasks, while A. pulchellus required more trials to learn the motor task. Only a single Anolis cristatellus was able to perform either task. Anolis evermanni displayed lower levels of neophobia than the other species, which may be related to its superior performance.

In combination, this research suggests that Anolis of different ecomorphs display different levels of behavioral flexibility. At the proximate level, this difference in behavioral flexibility cannot be explained by changes in the relative size of the total brain or brain structures associated with cognitive abilities in other taxa. At the ultimate level, the size of the brain and several constituent structures cannot be predicted by habitat complexity. However, behavioral flexibility in certain tasks may be favored by utilization of complex habitats. Flexibility in different tasks is not correlated, rendering broad comparisons to a habitat complexity problematic.

Although common knowledge dictates that the lichen thallus is formed solely by a fungus (mycobiont) that develops a symbiotic relationship with an alga and/or cyanobacterium (photobiont), the non-photoautotrophic bacteria found in lichen microbiomes are increasingly regarded as integral components of lichen thalli and significant players in the ecology and physiology of lichens. Despite recent interest in this topic, the phylogeny, ecology, and function of these bacteria remain largely unknown. The experiments presented in this dissertation employ culture-free methods to examine the bacteria housed in these unique environments to ultimately inform an assessment of their status with regard to the lichen symbiosis. Microbiotic surveys of lichen thalli using new oligonucleotide-primers targeting the 16S SSU rRNA gene (developed as part of this study to target Bacteria, but exclude sequences derived from chloroplasts and Cyanobacteria) revealed the identity of diverse bacterial associates, including members of an undescribed lineage in the order Rhizobiales (Lichen-Associated Rhizobiales 1; `LAR1'). It is shown that the LAR1 bacterial lineage, uniquely associated with lichen thalli, is widespread among lichens formed by distantly related lichen-forming fungi and is found in lichens collected from the tropics to the arctic. Through extensive molecular cloning of the 16S rRNA gene and 454 16S amplicon sequencing, ecological trends were inferred based on mycobiont, photobiont, and geography. The implications for using lichens as microcosms to study larger principles of ecology and evolution are discussed. In addition to phylogenetic and ecological studies of lichen-associated bacterial communities, this dissertation provides a first assessment of the functions performed by these bacteria within the lichen microbiome in nature through 454 sequencing of two different lichen metatranscriptomes (one from a chlorolichen, Cladonia grayi, and one from a cyanolichen, Peltigera praetextata). Non-photobiont bacterial genes for nitrogen fixation were not detected in the Cladonia thallus (even though transcripts of cyanobacterial nitrogen fixation genes from two different pathways were detected in the cyanolichen thallus), implying that the role of nitrogen fixation in the maintenance of chlorolichens might have previously been overstated. Additionally, bacterial polyol dehydrogenases were found to be expressed in chlorolichen thalli (along with fungal polyol dehydrogenases and kinases from the mycobiont), suggesting the potential for bacteria to begin the process of breaking down the fixed carbon compounds secreted by the photobiont for easier metabolism by the mycobiont. This first look at the group of functional genes expressed at the level of transcription provides initial insights into the symbiotic network of interacting genes within the lichen microbiome.

There have been few efforts to evaluate the actual and perceived effectiveness of environmental management programs created by consensus-based, multi-stakeholder negotiation or negotiated rulemaking. Previous evaluations have used perceived success among participants as a proxy for actual effectiveness, but seldom have investigated the ecological outcomes of these negotiations. Fewer still, if any, have compared the actual and perceived outcomes. Here I evaluate and compare the social and ecological outcomes of the negotiated rulemaking process of marine mammal take reduction planning. Take reduction planning is mandated by the U.S. Marine Mammal Protection Act (MMPA) to reduce the fisheries-related serious injuries and mortalities of marine mammals (bycatch) in U.S. waters to below statutory thresholds. Teams of fishermen, environmentalists, researchers, state and federal managers, and members of Regional Fisheries Management Councils and Commissions create consensus-based rules to mitigate bycatch, called Take Reduction Plans. There are six active Take Reduction Plans, one Take Reduction Strategy consisting of voluntary measures, and one plan that was never implemented. It has been 20 years since marine mammal take reduction planning was incorporated into the MMPA. Early evaluations were promising, but identified several challenges. In the past decade or more, the National Marine Fisheries Service (NMFS) has implemented measures to set up the teams for success.

I used data from formal Stock Assessment Reports to assess and rank the actual ecological success of five Take Reduction Plans (Harbor Porpoise, Bottlenose Dolphin, Atlantic Large Whale, Pelagic Longline, and Pacific Offshore Cetacean) in mitigating the bycatch of 17 marine mammal stocks. In addition, I employed social science data collection and analytical methods to evaluate Take Reduction Team participants' opinions of the take reduction negotiation process, outputs, and outcomes with respect to the ingredients required for successful multi-stakeholder, consensus-based negotiation (team membership, shared learning, repeated interactions, facilitated meetings, and consensus-based outputs). These methods included surveying and interviewing current and former Take Reduction Team participants; using Structural Equation Models (SEMs) and qualitative methods to characterize participant perceptions across teams and stakeholder groups; and identifying and exploring the reasons for similarities and differences among respondents, teams, and stakeholder groups. I also employed SEMs to quantitatively examine the relationship between actual and perceived ecological success, and contrasted actual and perceived outcomes by comparing their qualitative rankings.

Structural Equation Models provided a valid framework in which to quantitatively examine social and ecological data, in which the actual ecological outcomes were used as independent predictors of the perceived outcomes. Actual improvements in marine mammal bycatch enhanced stakeholder opinions about the effectiveness of marine mammal Take Reduction Plans. The marine mammal take reduction planning process has all of the ingredients necessary for effective consensus-based, multi-stakeholder negotiations (Chapter 2). It is likely that the emphasis that the National Marine Fisheries Service places on empirical information and keeping stakeholders informed about bycatch, marine mammal stocks, and fisheries facilitated this relationship. Informed stakeholders also had relatively accurate perceptions of the actual ecological effectiveness of the Take Reduction Plans (Chapter 3). The long timeframes over which the teams have been meeting generally have increased cooperation. The professionally trained, neutral facilitators have produced fair negotiations, in which most individuals felt they had an opportunity to contribute. Participant views of fairness significantly influenced their satisfaction with Take Reduction Plans, which significantly affected their perceptions about the effectiveness of those plans (Chapter 2). The mandate to create a consensus-based output has, for the most part, minimized defections from the negotiations and facilitated stakeholder buy-in.

In general, marine mammal take reduction planning is a good negotiated rulemaking process, but has produced mixed results (Chapters 1 and 2). Successful plans were characterized by straightforward regulations and high rates of compliance. Unsuccessful plans had low compliance with complex regulations and sometimes focused on very small stocks. Large teams and those in the northeastern U.S. (Maine to North Carolina) were least successful at reducing bycatch, which was reflected in stakeholder views of the effectiveness of these teams. Take Reduction Team negotiations have not always produced practical or enforceable regulations. Implementation of take reduction regulations is critical in determining plan success and identifying effective mitigation measures, but because of a lack of monitoring, has not been characterized consistently across most teams. Additionally, elements like the "Other Special Measures Provision" in the Harbor Porpoise Take Reduction Plan have undermined the negotiation process by allowing the National Marine Fisheries Service to alter consensus-based elements without consensus from the team, which has led to hostility, mistrust, and frustration among stakeholders.

The final chapter of this dissertation provides recommendations to improve the outcomes and make them more consistent across teams. I based these recommendations on the information gathered and analyzed in the first three chapters. They are grouped into four broad categories - team membership, social capital, fairness, and plan implementation. If the National Marine Fisheries Service implements these suggestions, both perceived and actual ecological effectiveness of marine mammal Take Reduction Teams should improve, allowing these teams to fulfill their maximum potential.

An understanding of sensory ecology, how animals receive and respond to their environment, can be a powerful tool for the conservation of endangered species because it can allow us to assess the potential success of actions designed to mitigate particular threats. We have a general understanding of how sea turtles perceive and respond to certain visual, magnetic, and chemical cues, but we understand very little about how they perceive and respond to acoustic cues. This dissertation explores the acoustic ecology of sea turtles, focusing on their auditory capabilities, responses to acoustic stimuli and the implications of this knowledge for their conservation. I measured the underwater and aerial hearing sensitivities of juvenile green (Chelonia mydas), hatchling leatherback (Dermochelys coriacea), and hatchling hawksbill (Eretmochelys imbricata) sea turtles by recording auditory evoked potential responses to tonal stimuli. Green turtles detected tonal stimuli between 50 and 1,600 Hz underwater (maximum sensitivity: 200-400 Hz) and 50 and 800 Hz in air (maximum sensitivity: 300-400 Hz), leatherbacks detected tonal stimuli between 50 and 1,200 Hz underwater (maximum sensitivity: 100-400 Hz) and 50 and 1,600 Hz in air (maximum sensitivity: 50-400Hz), and hawksbills detected tonal stimuli between 50 and 1,600 Hz in both media (maximum sensitivity: 200-400 Hz). Sea turtles were more sensitive to aerial than underwater stimuli when audiograms were compared in terms of sound pressure, but they were more sensitive to underwater stimuli when audiograms were compared in terms of sound intensity. I also examined the behavioral responses of loggerhead sea turtle (Caretta caretta) to simulated low frequency acoustic deterrent devices (ADDs) and found that these turtles exhibited a mild, aversive response to these sounds. This finding indicates that low frequency tonal ADDs have the potential to warn sea turtles of the presence of fishing gear and suggest that field tests of ADDs are warranted. Finally, I conducted a comprehensive review of our knowledge of the acoustic ecology of sea turtles, examined the sources of marine anthropogenic sound sea turtles are able to detect, evaluated the potential physiological and behavioral effects of anthropogenic sound, identified data gaps, and made recommendations for future research.

Pinniped species undergo a life history, unique among marine mammals, that includes discrete periods of occupancy on land or ice within a predominantly marine existence. This makes many pinniped species valuable sentinels of marine ecosystem health and models of marine mammal physiology and behavior. Pinniped research has often progressed hand-in-hand with advances at the technological frontiers of wildlife biology, and drones represent a leap forward in the long-established field of aerial photography, heralding opportunities for data collection and integration at new scales of biological importance. The following chapters employ and evaluate recent and emerging methods of wildlife surveillance that are uniquely enabled and facilitated by drone methods, in applied research and management campaigns with near-polar pinniped species. These methods represent advancements in abundance estimation and distribution modeling of pinniped populations that are dynamically shifting amid climate change, fishing pressure, and recovery from historical depletion.Conventional methods of counting animals from aerial imagery—typically visual interpretation by human analysts—can be time-consuming and limits the practical use of this data type. Deep learning methods of computer vision can ease this burden when applied to drone imagery, but are not yet characterized for practical and generalized use. To this end, I used a common implementation of deep learning for object detection in imagery to train and test models on a variety of datasets describing breeding populations of gray seals (Halichoerus grypus) in the northwest Atlantic Ocean (Chapter 2). I compare standardized performance metrics of models trained and tested on different combinations of datasets, demonstrating that model performance varies depending on both training and testing data choices. We find that models require careful validation to estimate error rates, and that they can be effectively deployed to aid, but not replace, conventional human visual interpretation of novel datasets for gray seal detection, location, age-classification and abundance estimation. Spatial analysis and species distribution modeling can use fine-scale drone-derived data to describe local species–habitat relationships at the scale of individual animals. I applied structure-from-motion methods to a survey of three pinniped species, pacific harbor seals (Phoca vitulina richardii), northern fur seals (Callorhinus ursinus), and Steller sea lions (Eumetopias jubatus), in adjacent non-breeding haul-outs to compare occupancy and habitat selection (Chapter 3). I describe and compare fitted occupancy models of pacific harbor seals and northern fur seals, finding that conspecific attraction is a key driver of habitat selection for each species, and that each species exhibits distinct topographic preferences. These findings illustrate both opportunities and limitations of spatial analysis at the scale of individual pinnipeds. Ease of deployment and rapid data collection make drones a powerful tool for monitoring populations of interest over time, while animal locations, revealed in high-resolution imagery, and contextual habitat products can reveal spatial relationships that persist beyond local contexts. I designed and carried out a campaign of drone surveillance over coastal habitats near Palmer Station, Antarctica, in the austral summer of 2020 to assess the seasonal abundance and habitat use of Antarctic fur seals (Arctocephalus gazella) in the Palmer Archipelago and adjacent regions (Chapter 4). I modeled abundance as a function of date, with and without additional terms to capture variance by site, and used these models to estimate peak abundance near Palmer Station in the 2020 summer season. These findings leverage the spatial and temporal advantages of drone methods to estimate species phenology, distribution and abundance. Together, these chapters describe emerging applications of drone technology that can advance pinniped research and management into new scales of analytical efficiency and ecological interpretation. These studies describe methods that have been proven in concept, but not yet standardized for practical deployment, and their findings reveal new ecological insights, opportunities for methodological advancement, and current limitations of drone methods for the study of pinnipeds in high-latitude environments.

This Doctor of Ministry thesis seeks to address the misapplication of Christian Scripture and its contribution to the climate crisis in which we find ourselves. Ellen Davis calls the Christian duty to delineate a responsible vision of what participation in the renewal of creation might mean the most essential theological task of this generation. This is but one small offering. The solution this thesis proposes is the recovery of the life, death, and resurrection of Jesus as the story of everything, a metanarrative which holds together God and all God has made. This ecological (relational) reading of Scripture finds all of Holy Scripture and reality to follow a threefold wisdom pattern of Creation/Uncreation/New Creation. Recovery of this lens allows us to name the time we are living in and imagine what faithful ecological participation in the larger story might look like.

The methodology used in this paper is narrative theology. Such a theology is advocated by Kavin Rowe and can also be seen in Richard Hays’ reading of New Testament texts as echoes of earlier narratives. NT Wright also suggests the metanarrative of the Resurrection of Christ in framing all ethical action and mission of the Church. Agrarian theological readings of Scripture, such as those offered by Ellen Davis, Wendell Berry, and Norman Wirzba, have also formed my understanding and hearing of Holy Scripture. I also have been shaped by the writing of Orthodox theologian Alexander Schmemann, who explores the liturgy of the Church in worship as the great cosmic story; Christ and the Church are offered “for the life of the world.”

It is this world which is the theme and concern of this thesis, and which much contemporary Christian theology has left behind. It is time to recover the story of a God who so loved the world to bring heaven down to dwell with us.

“American Manna: Religious Responses to the American Industrial Food System” is an investigation of the religious complexity present in religious food reform movements. I conducted ethnographic fieldwork at four field sites. These field sites are a Jewish organic vegetable farm where the farmers begin their days with meditation, a Christian raw vegan diet center run by Messianic Jews, a Christian family that raises their cattle on pastures and sends them to a halal processing plant for slaughter, and a Jewish farm where Christian and Buddhist farm staff helped to implement shmita, the biblical agricultural sabbatical year.

The religious people of America do not exist in neatly bound silos, so in my research I move with the religious people to the spaces that are less clearly defined as “Christian” or “Jewish.” I study religious food reformers within the framework of what I have termed “free-range religion” because they organize in groups outside the traditional religious organizational structures. My argument regarding free-range religion has three parts. I show that (1) perceived injustices within the American industrial food system have motivated some religious people to take action; (2) that when they do, they direct their efforts against the American food industry, and tend to do so outside traditional religious institutions; and finally, (3) in creating alternatives to the American food industry, religious people engage in inter-religious and extra-religious activism.

Chapter 1 serves as the introduction, literature review, and methodology overview. Chapter 2 focuses on the food-centered Judaism at the Adamah Environmental Fellowship at the Isabella Freedman Jewish Retreat Center in Falls Village, CT. In Chapter 3, I discuss the Hallelujah Diet as prescriptive literature and as it is put into practice at the Hallelujah Diet Retreat Center in Lake Lure, NC. Chapter 4 follows cows as they move from the grassy hills of Baldwin Family Farms in Yanceyville, NC to the meat counter at Whole Foods Markets. In Chapter 5, I consider the shmita year, the biblical agricultural sabbatical practice that was reimagined and implemented at Pearlstone Center in Baltimore, MD during 2014-2015. Chapter 6 will conclude this dissertation with a discussion of where religious food reform has been, where it is now, and a glimpse of what the future holds.

This study seeks to investigate the dynamics of dead plant carbon over fifty years of old-field forest development at the Calhoun Long Term Soil-Ecosystem Experiment (LTSE) in South Carolina, USA. Emphasis is on the transition phase of the forest, which is less well studied than the establishment and early thinning phase or the steady state phase. At the Calhoun LTSE, the biogeochemical and ecosystem changes associated with old field forest development have been documented through repeated tree measurements and deep soil sampling, and archiving of those soils, which now allow us to examine changes that have occurred over the course of forest development to date.

In this dissertation, I first quantify the accumulation of woody detritus on the surface of the soil as well as in the soil profile over fifty years, and estimate the mean residence times of that detrital carbon storage. Knowing that large accumulations of C-rich organic matter have piled onto the soil surface, the latter chapters of my dissertation investigate how that forest-derived organic carbon has been incorporated into mineral soils. I do this first by examining concentrations of dissolved organic carbon and other constituents in soil solutions throughout the ecosystem profile and then by quantifying changes in solid state soil carbon quantity and quality, both in bulk soils and in soil fractions that are thought to have different C sources, stabilities, and residence times. To conclude this dissertation, I present the 50-year C budget of the Calhoun LTSE, including live and dead plant carbon pools, to quantify the increasing importance of detrital C to the ecosystem over time.

This exceptional long term soil ecosystem study shows that 50 years of pine forest development on a former cotton field have not increased mineral soil carbon storage. Tree biomass accumulated rapidly from the time seedlings were planted through the establishment phase, followed by accumulations of leaf litter and woody detritus. Large quantities of dissolved organic carbon leached from the O-horizons into mineral soils. The response of mineral soil C stocks to this flood of C inputs varied by depth. The most surficial soil (0-7.5cm), saw a large, but lagged, increase in soil organic carbon (SOC) concentration over time, an accumulation almost entirely due to an increase of light fraction, particulate organic matter. Yet in the deepest soils sampled, soil carbon content declined over time, and in fact the loss of SOC in deep soils was sufficient to negate all of the C gains in shallower soils. This deep soil organic matter was apparently lost from a poorly understood, exchangeable pool of SOM. This loss of deep SOC, and lack of change in total SOC, flies in the face of the general understanding of field to forest conversions resulting in net increases in soil carbon. These long term observations provide evidence that the loss of soil carbon was due to priming of SOM decomposition by enhanced transpiration, C inputs, and N demand by the growing trees. These results suggest that large accumulations of carbon aboveground do not guarantee similar changes below.

Animals experience hydrodynamic forces (lift, drag, and side) and moments (pitching, yawing, and rolling) as a result of motion in an aqueous medium. Under selective pressure, most cetaceans, including porpoises, dolphins, and whales, developed a streamlined body shape and modified limbs, which delay the separation of flow, create lower drag when they swim, and therefore decrease their locomotor cost. In order to calculate the locomotor cost and propulsive efficiency of cetaceans, accurate estimates of drag on marine animals are required. However, extra momentum imparted into the fluid from lift and side forces as well as pitching, rolling, and yawing moments (here, the parasitic loads) results in extra drag force on the animal. Therefore, in addition to streaming and delaying flow separation, animals must also minimize excess fluid momentum resulting from parasitic loads. Given the endangered status of the North Atlantic right whale (Eubalaena glacialis; hereafter NARW), analyzing the hydrodynamic characteristics of the NARWs was the focus of this work. Additionally, previous studies showed that body shape of NARWs changes with life stages, reproduction status, nutritive conditions or prey abundance, and the effects of entanglement in fishing gear. Therefore, in this study, computational fluid dynamics (CFD) analysis was performed on multiple 10 m three-dimensional NARW models with different body shapes (e.g., normal condition, emaciated, and pregnant) to measure baseline measurements of flow regimes and hydrodynamic loads on the animal. Swimming speeds covering known right whale speed range (0.125 m/s to 8 m/s) were simulated in most scenarios. In addition to the hydrodynamic effects of different body shapes, drag was also considered a function of parasitic loads. The NARW models were embedded with bone segments that allowed one to manipulate the body pose of the model via adjusting the flippers or the spine of the animal before measuring hydrodynamic drag. By doing so, momentum from parasitic loads was expected to be eliminated. CFD simulations revealed that drag on NARWs is dictated by its irregular outline and that the drag coefficient (0.0071-0.0059; or dimensionless drag) of on NARWs is approximately twice that of many previous estimates for large cetaceans. It was also found that pregnant NARW model encounters the lowest drag coefficient due to delayed flow separation resulting from enlarged abdomen, whereas the emaciated NARW model experiences the highest drag coefficient possibly due to the concavity at the post-nuchal region. These results suggested that drag on NARWs and their thrust power requirements were indeed affected by its body shape but the differences between the three NARW models tested were small. Lastly, minimum drag, which corresponds to the elimination of the parasitic loads, can be obtained by adjusting the pose of the animal. Thus, minimum drag occurs at the neutral trim pose. For the static, normo-nourished NARW model, simulations revealed that by changing the angle of attack of the flippers by 4.03° (relative to the free-stream flow) and pitching the spine downward by 5° while maintaining fluke angle, the drag was lowered by approximately 11% across the flow speeds tested. This drag reduction was relative to the drag study conducted on the same animal model but without body pose adjustments. Together the studies included in the present work explored and highlighted the capability of numerical methods in investigating the hydrodynamics and energetics of cetaceans. Future studies should address how computer solutions can be used to solve problems from a wider aspect. For instance, extra parasitic loads caused by attached gear as well as possible injuries due to the encounter with fishing gear should also be considered while evaluating the energy budget of the North Atlantic right whales.

Manatees (Mammalia: Sirenia), along with the closely related dugongs, are the only herbivorous marine mammals. Manatees consume a wide variety of vascular plants and algae in both marine and freshwater habitats. However, little is known about what characteristics influence diet and food selectivity, especially in freshwater habitats, which represent a large portion of the available habitat for the endangered Antillean manatee, Trichechus manatus manatus, in Central and South America. Understanding foraging ecology is an important element of effective conservation strategies.

This dissertation investigated various aspects of the foraging ecology of the Antillean manatee in a freshwater habitat, specifically: 1) how plant availability (i.e. species richness, diversity, and abundance) varied seasonally with changes in water depths, 2) manatee food selectivity from a representative set of plant species from that freshwater habitat, and 3) the relationship of plant nutritive compounds and availability with manatee food selectivity. In addition, this dissertation describes the multiple uses of sonar technology for studying manatees and habitat characteristics in freshwater.

Plant availability to manatees was evaluated by conducting monthly plant surveys from July 2010-July 2011 in four contact lakes in the wetlands of Tabasco, Mexico. Manatee food selectivity was examined by conducting food selection experiments on a wild adult manatee during the low water season with 54 plant species representing 25+ genera. The nutritive components (i.e. crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF), hemicellulose (HC), and ash) and plant availability values for selected and non-selected plants species were evaluated to determine their relationship with manatee food selectivity. The applicability of using side-scan sonar for manatee research was tested in various freshwater and estuarine habitats in Honduras, Costa Rica, Panama, and the wetlands of Tabasco, Mexico between 2006-2011.

The major findings of this dissertation are as follows. Plant species richness, diversity, and abundance were greatest during the rising water season (July-August) and lowest during the low water season (March-June). No plants were available in April-June, which represented the majority of the low water season. The wild manatee

selected 27 (11+ genera) of the 54 species examined during the feeding experiments. Of the plant characteristics tested (i.e. nutritive components and plant availability), only digestible fiber (HC) was significantly related to manatee food selection, with manatees

selecting plants with higher HC content. Four unique applications were identified for the use of side-scan sonar to facilitate manatee research in freshwater habitats: 1) confirmation of visual sightings and determination of group size, 2) determination of mother-calf pairs, 3) habitat characterization, and 4) assisting manatee captures.

Results from this study reveal that manatees living in the freshwater wetlands of Tabasco, Mexico have to cope with a highly seasonal availability of plants and that while manatees consume plants from a wide variety of genera, they are highly selective. Unlike other herbivorous mammals, manatee food selectivity was not influenced by CP, NDF, or ADF, but rather by digestible fiber. A unique suit of anatomical and physiological characteristics suggests that manatees may be fiber digestion specialists. Both seasonal plant availability and the manatee's large dietary breadth must be considered when developing 1) conservation strategies for wild manatees in freshwater habitats and 2) protocols for captive rehabilitation of orphaned and stranded manatees that will be reintroduced into the wild.

Alien species are considered one of the primary threats to native plant populations and their control is often prominent among proposed management actions. While negative alien effects are well documented, there are also many ways that alien species can have positive effects on native plant populations that may actually contribute to their persistence. Moreover, the effect of alien species on native plants can change in magnitude and direction over varying abiotic conditions. The success of native plant populations is determined by a mix of ecological and genetic factors. Alien (and native) species and abiotic conditions could also drive selection of plant traits. In order to understand the drivers of native plant population success in the face of changing climate and increasing prevalence of alien species, it is vital to understand the relationship between genotype, phenotype, and fitness of native plants. In chapter one, I quantified the effects of neighboring alien and native plants on all demographic rates in a population of the Hawaiian endemic plant Schiedea globosa, performing biannual censuses for 4 years to encompass relatively harsh and as well as benign seasons and years. The effects of alien neighbors were mixed but most often positive across many demographic rates in both harsh and more benign abiotic conditions, suggesting that alien neighbors benefit S. globosa plants through multiple mechanisms, such as nurse plant effects and associational resistance. The effects of heterospecific native neighbors were less often positive, indicating fundamentally different effects of native and alien neighbors on the demography of the focal native. These mixed effects highlight the need to consider potential benefits of alien species in the management of threatened native plants and that those benefits may be altered by changing abiotic conditions. In chapter two, I constructed population models for multiple Schiedea species across populations and years, using demographic rate regressions driven by the effects of alien and native neighbors, integrating the mixed effects of alien and native species on demographic rates of populations to project the net effect on population growth of native populations. The effects of alien and heterospecific native plant neighbors were mixed but most often positive across many demographic rates in both harsh and more benign abiotic conditions, suggesting that alien and native neighbors benefit native plants through multiple mechanisms, such as nurse plant effects and associational resistance. The effect of alien and heterospecific native neighbors on population growth was generally positive-- the mixed, but largely positive, net effects of alien and native neighbors on population growth highlight the need to consider potential benefits of alien, as well as native, species in the management of at-risk native plant populations, and that those benefits may be altered by changing abiotic conditions, as indicated by differing effects across (and within) years and populations. In chapter 3, I used paternal half-sibship pairs to measure the heritability of morphological traits under field conditions of the critically endangered Schiedea adamantis, which were found to be heritable in prior studies in greenhouse conditions, in reintroduced populations. I also performed a selection analysis, regressing fitness components against traits of outplants that I hypothesized might influence response to climate and alien and native neighbors to study the relationship between genotype, phenotype, and fitness of plants in restoration outplantings and assessing potential for evolutionary rescue. I found no significant heritability of any of the morphological traits. I did find evidence of selection, as leaf shape, area, and whole plant morphology had significant effects on fitness components (growth, survival, and reproduction), and significant interaction effects showing traits influenced fitness components differently at different levels of shade. Together, these results suggest that while variation in traits benefit individual plants in differing field conditions, these outplantings may not have the ability to respond to selection through evolution.

Social structure is a key determinant of population biology and is central to the way animals exploit their environment. The risk of predation is often invoked as an important factor influencing the evolution of social structure in cetaceans and other mammals, but little direct information is available about how cetaceans actually respond to predators or other perceived threats. The playback of sounds to an animal is a powerful tool for assessing behavioral responses to predators, but quantifying behavioral responses to playback experiments requires baseline knowledge of normal behavioral patterns and variation. The central goal of my dissertation is to describe baseline foraging behavior for the western Atlantic short-finnned pilot whales (Globicephala macrohynchus) and examine the role of social organization in their response to predators. To accomplish this I used multi-sensor digital acoustic tags (DTAGs), satellite-linked time-depth recorders (SLTDR), and playback experiments to study foraging behavior and behavioral response to predators in pilot whales. Fine scale foraging strategies and population level patterns were identified by estimating the body size and examining the location and movement around feeding events using data collected with DTAGs deployed on 40 pilot whales in summers of 2008-2014 off the coast of Cape Hatteras, North Carolina. Pilot whales were found to forage throughout the water column and performed feeding buzzes at depths ranging from 29-1176 meters. The results indicated potential habitat segregation in foraging depth in short-finned pilot whales with larger individuals foraging on average at deeper depths. Calculated aerobic dive limit for large adult males was approximately 6 minutes longer than that of females and likely facilitated the difference in foraging depth. Furthermore, the buzz frequency and speed around feeding attempts indicate this population pilot whales are likely targeting multiple small prey items. Using these results, I built decision trees to inform foraging dive classification in coarse, long-term dive data collected with SLTDRs deployed on 6 pilot whales in the summers of 2014 and 2015 in the same area off the coast of North Carolina. I used these long term foraging records to compare diurnal foraging rates and depths, as well as classify bouts with a maximum likelihood method, and evaluate behavioral aerobic dive limits (ADLB) through examination of dive durations and inter-dive intervals. Dive duration was the best predictor of foraging, with dives >400.6 seconds classified as foraging, and a 96% classification accuracy. There were no diurnal patterns in foraging depth or rates and average duration of bouts was 2.94 hours with maximum bout durations lasting up to 14 hours. The results indicated that pilot whales forage in relatively long bouts and the ADLB indicate that pilot whales rarely, if ever exceed their aerobic limits. To evaluate the response to predators I used controlled playback experiments to examine the behavioral responses of 10 of the tagged short-finned pilot whales off Cape Hatteras, North Carolina and 4 Risso’s dolphins (Grampus griseus) off Southern California to the calls of mammal-eating killer whales (MEK). Both species responded to a subset of MEK calls with increased movement, swim speed and increased cohesion of the focal groups, but the two species exhibited different directional movement and vocal responses. Pilot whales increased their call rate and approached the sound source, but Risso’s dolphins exhibited no change in their vocal behavior and moved in a rapid, directed manner away from the source. Thus, at least to a sub-set of mammal-eating killer whale calls, these two study species reacted in a manner that is consistent with their patterns of social organization. Pilot whales, which live in relatively permanent groups bound by strong social bonds, responded in a manner that built on their high levels of social cohesion. In contrast, Risso’s dolphins exhibited an exaggerated flight response and moved rapidly away from the sound source. The fact that both species responded strongly to a select number of MEK calls, suggests that structural features of signals play critical contextual roles in the probability of response to potential threats in odontocete cetaceans.

The evolution of reproductive strategies involves a complex calculus of costs and benefits to both parents and offspring. Many marine animals produce embryos packaged in tough egg capsules or gelatinous egg masses attached to benthic surfaces. While these egg structures can protect against environmental stresses, the packaging is energetically costly for parents to produce. In this series of studies, I examined a variety of ecological factors affecting the evolution of benthic development as a life history strategy. I used marine gastropods as my model system because they are incredibly diverse and abundant worldwide, and they exhibit a variety of reproductive and developmental strategies.

The first study examines predation on benthic egg masses. I investigated: 1) behavioral mechanisms of predation when embryos are targeted (rather than the whole egg mass); 2) the specific role of gelatinous matrix in predation. I hypothesized that gelatinous matrix does not facilitate predation. One study system was the sea slug Olea hansineensis, an obligate egg mass predator, feeding on the sea slug Haminoea vesicula. Olea fed intensely and efficiently on individual Haminoea embryos inside egg masses but showed no response to live embryos removed from gel, suggesting that gelatinous matrix enables predation. This may be due to mechanical support of the feeding predator by the matrix. However, Haminoea egg masses outnumber Olea by two orders of magnitude in the field, and each egg mass can contain many tens of thousands of embryos, so predation pressure on individuals is likely not strong. The second system involved the snail Nassarius vibex, a non-obligate egg mass predator, feeding on the polychaete worm Clymenella mucosa. Gel neither inhibits nor promotes embryo predation for Nassarius, but because it cannot target individual embryos inside an egg mass, its feeding is slow and inefficient, and feeding rates in the field are quite low. However, snails that compete with Nassarius for scavenged food have not been seen to eat egg masses in the field, leaving Nassarius free to exploit the resource. Overall, egg mass predation in these two systems likely benefits the predators much more than it negatively affects the prey. Thus, selection for environmentally protective aspects of egg mass production may be much stronger than selection for defense against predation.

In the second study, I examined desiccation resistance in intertidal egg masses made by Haminoea vesicula, which preferentially attaches its flat, ribbon-shaped egg masses to submerged substrata. Egg masses occasionally detach and become stranded on exposed sand at low tide. Unlike adults, the encased embryos cannot avoid desiccation by selectively moving about the habitat, and the egg mass shape has high surface-area-to-volume ratio that should make it prone to drying out. Thus, I hypothesized that the embryos would not survive stranding. I tested this by deploying individual egg masses of two age classes on exposed sand bars for the duration of low tide. After rehydration, embryos midway through development showed higher rates of survival than newly-laid embryos, though for both stages survival rates over 25% were frequently observed. Laboratory desiccation trials showed that >75% survival is possible in an egg mass that has lost 65% of its water weight, and some survival (<25%) was observed even after 83% water weight lost. Although many surviving embryos in both experiments showed damage, these data demonstrate that egg mass stranding is not necessarily fatal to embryos. They may be able to survive a far greater range of conditions than they normally encounter, compensating for their lack of ability to move. Also, desiccation tolerance of embryos may reduce pressure on parents to find optimal laying substrata.

The third study takes a big-picture approach to investigating the evolution of different developmental strategies in cone snails, the largest genus of marine invertebrates. Cone snail species hatch out of their capsules as either swimming larvae or non-dispersing forms, and their developmental mode has direct consequences for biogeographic patterns. Variability in life history strategies among taxa may be influenced by biological, environmental, or phylogenetic factors, or a combination of these. While most prior research has examined these factors singularly, my aim was to investigate the effects of a host of intrinsic, extrinsic, and historical factors on two fundamental aspects of life history: egg size and egg number. I used phylogenetic generalized least-squares regression models to examine relationships between these two egg traits and a variety of hypothesized intrinsic and extrinsic variables. Adult shell morphology and spatial variability in productivity and salinity across a species geographic range had the strongest effects on egg diameter and number of eggs per capsule. Phylogeny had no significant influence. Developmental mode in Conus appears to be influenced mostly by species-level adaptations and niche specificity rather than phylogenetic conservatism. Patterns of egg size and egg number appear to reflect energetic tradeoffs with body size and specific morphologies as well as adaptations to variable environments. Overall, this series of studies highlights the importance of organism-scale biotic and abiotic interactions in evolutionary patterns.

Sea turtles are long lived marine species that are currently endangered because their life history and population dynamics hinder them from withstanding modern anthropogenic threats. Worldwide, fisheries bycatch in on the major threats to the survival of sea turtles and that is also the case in the Eastern Pacific. To establish regional conservation priorities for the mitigation of bycatch, it is essential to first obtain a comprehensive picture of the regional sea turtle bycatch situation. This comprehensive analysis was lacking for the Eastern Pacific; therefore one component of this dissertation (the first chapter) is focused on delivering a regional bycatch analysis for the Eastern Pacific. A literature review was conducted to obtain numbers of turtles captured, frequencies, bycatch and mortality rates per species and country in trawl, longline, and gillnet fisheries, and to compile results of mitigation measures. Moreover, estimates for current annual capture rates in trawl fisheries were obtained and compared with population numbers.

This regional bycatch used all the information compiled and synthesized to give conservation priorities at the regional level. The review underlines the high bycatch rates in trawls for Costa Rica, Guatemala, and El Salvador and the detrimental impact that these captures could have specially for hawksbill Eretmochelys imbricata due to its reduced population numbers and for green turtle Chelonia mydas due to its highest mortality rate. It also emphasizes the continuous lack of use of TEDs as a bycatch mitigation measure. In longline fisheries, the review identifies the high bycatch rates in pelagic longline fisheries of Costa Rica, Ecuador, and Nicaragua in a global context but given that olive ridley Lepidochelys olivacea is the most common species captured in these countries, it highlights the capture of loggerhead Caretta caretta and leatherback Dermochelys coriacea off Peru and Chile due to their small population numbers. Bottom longlines have high mortality rates compared with pelagic longlines in the region and the review identifies a need for further research in this area due to the scarce information but high mortality rates. The review also noted that some mitigation measures for pelagic longlines like circle hooks and hooks with appendages could bring improvements in the mitigation of bycatch in longline fisheries in the region, there is still considerable work to be done in technology transfer, sea turtle handling, and estimates of post-release mortality rates.

For gillnet fisheries, the most important highlight is how little information exists for the region given the high rates of bycatch for sea turtles in this gear. However, the difficulties of studying bycatch in highly dynamic and artisanal fisheries are recognized as the major impediment for this situation. Nevertheless, the high bycatch rates in areas where sea turtles congregate in high numbers like in foraging grounds for loggerhead in Baja California, Mexico and for greens in Paracas and Sechura, Peru, calls for either gear modifications (which has not been that successful), change of gear, or areas closed for gillnets.

The second half of the dissertation is focused on foraging ecology of oceanic sea turtles in the Southeast Pacific Ocean. Sea turtles in the oceanic stage are the least known stage due to the difficulty of accessing these individuals. However, it is a very important stage in the life cycle and can be critical for the population dynamics of sea turtles as some population models have shown. Therefore, this dissertation is filling a gap in the life cycle of sea turtle populations in the Eastern Pacific.

To study foraging ecology, we used Stable Isotope Analysis (SIA) of turtle tissues as well as potential prey items from the oceanic realm. SIA is a great tool because it gives an integrated view, from days to weeks, of prey from a consumer tissue. SIA also can be used to link consumers to habitats when elements that have spatial trends are used. In chapter two, we investigate the foraging ecology of three species of sea turtles to compare trophic status and to observe if spatial patterns were shown in the SIA signatures of sea turtles. To our knowledge this is the first study employing SIA to research the ecology of three species of sea turtles from the same time and space. Our results show that spatial patterns in delta15N and delta13C were observed in sea turtle's tissues as correlations with latitude. We also found that loggerhead's signatures differed significantly from green and olive ridleys, especially in terms of delta15N. Loggerheads had higher values of delta15N and also a wider nitrogen trophic niche. Greens and olive ridleys were similar in isotopic nitrogen values but they were significantly different in carbon. When analyzing a smaller group of animals captured in a more restricted area, nitrogen differences were not found which suggests that latitudinal spatial patterns play an important role in the nitrogen signature. On the contrary, carbon signatures still differed among turtles in the restricted area which suggest that the inshore-offshore trend is strong and made us conclude that loggerheads are restricted to oceanic areas but that greens and olive ridleys could be using both coastal and oceanic areas.

In chapter three, we conduct a mixing model analysis using the Bayesian program SIAR to identify the most important prey items for green, olive ridley, and loggerhead off Peru. Also, we wanted to identify the contribution of longline baits in the diet of oceanic turtles. The analysis was restricted to the central zone of our study area to avoid spatial trends in nitrogen. To use as sources in the model, we collected potential prey items offshore Peru during trips on longline fishing vessels and obtained their stable isotope signatures. Results from our mixing models show that for greens and olive ridleys, crustaceans, mollusks, and coastal Ulva (indicator of coastal prey) were the only important food items. In the case of greens, crustaceans had a very high proportional contribution and due to the fact that nitrogen values of crustaceans were the lowest ones among the sources it seems that greens would be eating in a lower trophic level. The importance of coastal Ulva for greens and olive ridleys is a confirmation of our findings from chapter two where we suggest that these two species could be using oceanic as well as coastal areas.

Results for loggerheads showed cnidarians, mollusks, mackerel and squid bait as foraging items and highlights the differences among this species and the other two. The lack of importance of coastal Ulva again suggests that loggerheads remain only in oceanic areas off Peru. Moreover, the importance of mackerel and squid, the most common longline baits, suggests this species is the one interacting the most with longline fisheries and that cumulative effect of multiple interactions could have a detrimental effect in this population.

Human welfare depends heavily on ecosystem services like water purification and nutrient cycling. Many of these ecosystem services, in turn, rely on reactions performed by microbes and yet remarkably little is known about how anthropogenic impacts are affecting the structure and function of microbial communities. To help address this knowledge gap, this dissertation uses field surveys and laboratory experiments to examine how watershed urbanization affects microbial communities in receiving streams. We focus on a specific functional group and its associated function - the denitrifying bacteria and denitrification. Denitrifying bacteria use reactive nitrogen and organic carbon as substrates to perform denitrification. Denitrification is one of the few ways to permanently remove reactive nitrogen from ecosystems. Since excess reactive nitrogen in water contributes to serious water quality and human health problems like toxic algal blooms and bowel cancer, denitrification in streams can be considered a valuable ecosystem service. Watershed urbanization, however, may alter the structure of denitrifying bacteria communities in ways that constrain their capacity to remove reactive nitrogen from streams.

Watershed urbanization leads to drastic changes in receiving streams, with urban streams receiving a high frequency of scouring flows, together with increased nutrient (nitrogen and carbon), contaminant (e.g., heavy metals), and thermal pollution. These changes are known to cause significant losses of sensitive insect and fish species from urban streams. Microbes like denitrifying bacteria may be similarly affected. In the first part of this dissertation, we describe results from four repeated surveys of eight central North Carolina streams affected to varying degrees by watershed urbanization. For each stream and sampling date, we characterized both overall and denitrifying bacterial communities and measured denitrification potentials. Differences in overall and denitrifying bacteria community composition were strongly associated with the urbanization gradient. Denitrification potentials, which varied widely, were not significantly associated with substrate supply. By incorporating information on the community composition of denitrifying bacteria together with substrate supply in a linear mixed-effects model, we explained 45% of the variation in denitrification potential (p < 0.001). Results suggest that 1) watershed urbanization can lead to significant changes in the composition of bacterial communities in streams and 2) such changes may have important functional consequences.

The second part of this dissertation examines how urbanization-driven changes to the structure of denitrifying bacteria communities might affect the way they respond to stress or disturbance. Some communities can resist changes to functionality in response to disturbance, potentially as a result of previous exposure and subsequent adaptation (legacy hypothesis) or high diversity (insurance hypothesis). We compare the resistance of two structurally distinct denitrifying bacteria communities to experimental disturbances in laboratory microcosms. Communities originated from either a polluted, warm urban streams or a relatively pristine, cool forest stream. In this case, the two communities had comparable compositions, but forest communities were more diverse than their urban counterparts. Urban communities experienced significant reductions in denitrification rates in response to the most severe increased pollution and temperature treatments, while forest communities were unaffected by those same treatments. These findings support the insurance, but not the legacy hypothesis and suggest that the functioning of urban streams may be more susceptible to further environmental degradation than forest streams not heavily impacted by human activities.

In the third part of this dissertation, we discuss results from a one-time survey of denitrifying bacteria communities and denitrification potentials in 49 central North Carolina streams affected to varying degrees by watershed urbanization. We use multivariate statistics and structural equation modeling to address two key questions: 1) How do different urban impacts affect the structure of denitrifying bacteria communities and 2) How do abiotic (e.g., temperature) versus biotic (denitrifying bacteria community structure) factors affect denitrification potentials in urban streams? Denitrifying bacteria community structure was strongly affected by the urban impacts measured. Community composition responded to increased temperatures, substrate supply, and contamination, while diversity responded negatively to increased temperatures and hydrologic disturbance. Moreover, increased temperatures and substrate supply had significant positive effects, while urbanization-driven changes to denitrifying bacteria community structure had significant negative effects on denitrification potential. The structural equation model captured 63% of the variation in denitrification potential among sites and highlighted the important role that microbial community structure can play in regulating ecosystem functioning. These findings provide a novel explanation for recent observations of decreasing denitrification efficiency with increasing urbanization. Ultimately, we hope findings from this dissertation will help inform more effective stream management and restoration plans and motivate ecologists to consider including microbial community structure in ecosystem models of microbe-mediated processes.