Dissertations / Theses on the topic 'Science / Ecology'

Habitat fragmentation and loss is the primary driver of mammalian carnivore extinctions across the world. In the Santa Cruz Mountains of California, native carnivores navigate daily through a landscape highly impacted by human development and activities. The puma (Puma concolor ) is the apex predator of this habitat, but it is susceptible to both direct and indirect influences of expanding human populations. Smaller predators are not only affected by anthropogenic disturbances, but also by intraguild competition with the more dominant pumas.

My dissertation utilizes new technologies to study the ecology and behavior of carnivores in a human dominated environment. In my first chapter, I catalogued puma behaviors in the wild using measurements recorded by accelerometers attached to the animals. I found that I could clearly distinguish movement from non-movement behavior, and that predation events had distinctive accelerometer signatures. The second chapter describes how I used movement data recorded by GPS (Global Positioning System) collars to evaluate puma behavioral responses to increasing development. Pumas primarily traveled nocturnally, and moved more often and further in areas of higher housing development. The increase in activity in human dominated landscapes could have major repercussions on the energetic expenditure of pumas living in fragmented areas. My third chapter addresses the impacts of human development and activities on the entire carnivore community. Combining passive and experimental observations using motion-detecting camera traps, I studied the spatiotemporal behavior of predators across a gradient of human influences. Mesopredator activity was restricted temporally in areas of high human use, and certain predators (e.g., pumas and foxes) were more sensitive to increasing development.

Lastly, education and outreach is an important component of carnivore conservation. In my fourth chapter, I describe results from a Facebook game I developed with collaborators. Players earned points by identifying wildlife species from camera trap photographs. I found that agreement among players was the most important determinant of accuracy, and that untrained Internet users could identify many wildlife species. The Internet is an emerging tool for outreach, and I hope my work encourages other ecologists to think creatively about incorporating citizen scientists into their research through social media.

With the increasing human population, it is critical to develop informed citizens with ecological perspectives and motivation to make positive contributions to the biosphere. This study investigates the impact of a place-based science elective on the development of students’ ecological identities, motivation for environmental action, and ecojustice self-efficacy. Targeted curriculum was implemented, including a campus habitat design project. Pre and post tests for three instruments were used to assess 25 high school freshmen, half of whom are members of a STEM program. There was an increase in nature relatedness, motivation and self-efficacy for STEM students but not for non-STEM students. The research study demonstrated the effectivity of using place-based curriculum within classes to encourage student connection, empowerment and involvement. Support for teachers to develop targeted mentoring of students’ abilities and interests are needed and can help develop informed, involved global citizens.

One of the least researched phenomena within the alpine regions of mountain biomes is the combination of primitive plants, algae, fungi, and lichens that are generally referred to as biological soil crusts. Sites containing well-developed biological soil crusts were examined in a variety of alpine, non-forested, vegetated landscapes in the North Cascade Mountains of Washington, USA. For each site, data were recorded for percent ground cover of biological soil crusts, slope aspect, and slope gradient of the terrain where the crust communities were located. For all of the sites, biological soil crusts were common, with a percent ground cover median of 29% and a range of 11% to 73%. The arrangement of the biological soil crusts on all sites was quite similar: all were clumped, as opposed to single, and random, as opposed to uniform. All of the soil crusts were found on soil exposed to direct sunlight. Few, if any, crusts were found in the shade of heavy forbs, or forest, or under accumulations of organic litter. When biological soil crusts were found associated with higher-order vegetation, it was with sparse graminoids, ericaceous woody shrubs, and stunted or krummholz Pinaceae trees. The biological soil crusts from this study exist on all locally undisturbed soil slope-gradients from 0% to almost 100%, and occurred on all aspects except for those in the Southwest quadrant. This study contains an extended literature review for desert and high latitude circumpolar crusts, as well as alpine biological soil crusts. Studies of biological soil crusts in subalpine and alpine environments are not common; it is hoped that this study will stimulate more research interest in these often overlooked pioneer biotic communities.

An observed 20-30% increase in forest net ecosystem exchange ( NEE) on partly cloudy days is often attributed to there being more uniform canopy illumination by diffuse radiation when clouds are present. However, the sky on such days is typically populated by fair-weather cumulus clouds, bringing dynamically changing shadow-to-light conditions on the order of minutes to the forest, with radiation alternating from 1000 W m ^-2 in the clear sky to less than 400 W m^-2 in under-cloud shadows. These dynamically changing conditions cannot be investigated by the conventional time-averaged eddy-covariance flux method, which requires nearly steady-state turbulent conditions over much longer 20-30-min periods in order for the fluxes to converge to stationary values. We examine the “true” dynamics of the whole-canopy response to the light change by using a practical ensemble-flux method applied to eddy-covariance flux measurements from two distinct forest ecosystems: Harvard Forest (HF, 42.53°N, 72.17°W), temperate mid-latitude forest near Petersham, Massachusetts, USA, and Tapajós National Forest (LBA, 2.86°S, 54.96°W), an Amazonian evergreen tropical forest near Santarem, Pará, Brazil. Using the rapid change in radiative flux that occurs during the transition from cloud-induced shadow to light as a reference starting point, we combine sets of conditional illumination-change shadow-to-light and light-to-shadow transition events characteristic of cumulus-cloud conditions and parametrize distributions of light and shadow durations and rates of light change of the radiative-flux time series for different cloud conditions reported by standard weather stations. We investigate the sensitivity of the dynamics of forest response to the illumination transitions initiated by these conditional events, and identify an unexpected transient NEE maxima when NEE increases above the clear-sky steady-state equilibrium values (NEE_eq) within the first 10 min of the light period after the shadow-to-light transition, that we hypothesize to be a physiological forest response to the abrupt light change due to presence of the intercellular CO₂ pool in the leaf tissues. Overall NEE builds up during the sunlit periods, but in shadow heat and water stresses are reduced, thus increasing the water use efficiency (WUE). To conduct this analysis, we obtain similarity criteria for realizations defined by conditional events to combine them into the ensembles. With 300 similar realizations grab-sampled at 1-s intervals, we can reliably estimate (≤ 5% standard error) dynamic ensemble fluxes resolved on a 5-s time scale. By the successful application of the first-order system of the delay differential equations with the exponential approach-to-equilibrium solutions, we are able to justify the utility of the “Big-Leaf”-model approach to describe whole-canopy fluxes and provide the dynamic parametrizations of the “Big-Leaf” Active Thermal Layer as well as of the Transient Internal Layer above both forests when the light switches on after the cloud pass. By combining results of sensitivity analysis with modelled solutions applied to the real day-long fluctuating-light time series, we show that the variable light during fair-weather clouds (Shadow period duration < 100 s, Light period duration ≥ 300 s) is responsible for an increase in NEE above the NEE _eq of 15-25% for HF and 10-15% for LBA. This indicates that there is a fluctuating-light NEE-enhancement mechanism that can be considered to be a viable alternative to the existing hypothesis of a diffuse-radiation NEE-enhancement mechanism on partly-cloudy days. We show that on such days Diffuse Fraction can be linearly-related to Cloudiness estimated using the shadow-to-light change in a conditional-event radiative-flux ratio, connecting these two NEE-enhancement mechanisms. Combination of increased NEE with the relatively high plateau in WUE allows forests to operate efficiently in partly-cloudy conditions with maxima located in the Cloudiness range [0.1-0.3] and Diffuse-Fraction range [0.35-0.6], suggesting forest adaptations to the preferred lighting conditions and fair-weather cloudiness.

The energy needs of rorqual whales (f. Balaenopteridae) govern their relationship to marine habitats during the foraging season. However, their cryptic foraging strategies and extreme feeding behaviors complicate our effort to identify and protect habitats “critical” for rorquals. What is the relationship between rorquals and their habitat, and how must that shape conservation strategies? I addressed this question in the case of sympatric humpback (Megaptera novaeangliae) and fin whales ( Balaenoptera physalus) in the marine territory of the Gitga’at First Nation in the Kitimat Fjord System of British Columbia. For three summers (2013-2015) I studied whales, their prey, and their environment aboard the RV Bangarang using oceanographic station sampling, systematic transect surveys, and opportunistic focal follows of whales (Chapter 1). Ocean sampling demonstrated the strong coupling of water features with offshore patterns in storm forcing and regional meteorology (Chapter 2). By combining these surveys with a long-term Gitga’at dataset, area humpback whales were found to practice a structured and persistent pattern in seasonal habitat use, which demonstrates how complex and habitat-specific a rorqual’s habitat use can be (Chapter 3). Both humpback and fin whales were found to respond to changes in krill supply in aggregative and behavioral thresholds that are set by a combination of intrinsic energetic needs and the context of local prey supply (Chapter 4). Associations with non-prey habitat features were markedly different in the two species (Chapter 5). Humpback distribution was more closely coupled to that of their prey and other habitat features, while fin whale distribution was driven broadly by site fidelity. Novel spatial analytics were used to identify the most probable environmental cues used by foraging whales (Chapter 6). Both species were found to be particularly sensitive to the depth of prey layers, which is governed largely by oceanographic features (Chapter 7). This coupling of habitat features and feeding performance influences the competitive dynamics of rorqual whales. The findings in this case study advance general theories on marine predator ecology and conservation, and have direct implications for the management of Gitga’at territory and the identification of fin whale critical habitat in Pacific Canada.

Empirical studies of graphs have contributed enormously to our understanding of complex systems, growing into a more scientific exploration of communities spanning the physical, biological, and social called network science. As the quantity and types of networks have grown so has their heterogeneity in quality and specificity resulting in a wealth of datasets that are not matched by existing theoretical methods. This is especially true in ecology where the majority of interactions are indirect and unobservable even in well-studied systems. As a result ecologists continue to grapple with three fundamental questions: Most basically, (i) `How do ecosystems function?' I answered this question by comparing networks to each other such that poorly-studied systems can be understood through their similarity to well-understood ones and theoretical models. To do this I created the alignment algorithm netcom which recasts ecosystem processes as statistical dynamics of diffusion kernels originating from a network's constituent nodes. Using netcom I constructed a supervised classifier which can distinguish processes in both synthetic and empirical network data. While this kind of inference works on currently available network data, I have shown how causality can serve as a more effective and unifying currency of ecological interaction. Measures of causality are even able to identify complex interactions across organizational scales of communities, answering the longstanding question (ii) `Can community structure causally determine dynamics of constituent species?' Moreover, causal inference can be readily combined with existing modeling frameworks to quantify dynamic interactions at the same scale as the underlying data. In this way we can answer the question (iii) `Which species in an ecosystem cause which other species?' These tools are part of a paradigm shift in ecology that offers the potential to make more reliable management decisions for dynamic ecosystems in real time using only observational data.

Flow regime, the magnitude, duration and timing of streamflow, controls the development of floodplain landforms on which riparian vegetation communities assemble. Streamflow scours and deposits sediment, structures floodplain soil moisture dynamics, and transports propagules. Flow regime interacts with environmental gradients like climate, land-use, and biomass-removing disturbance to shape riparian plant distributions across landscapes. These gradients select for groups of riparian plant species with traits that allow them to establish, grow, and reproduce on floodplains – riparian vegetation guilds. Here I ask, what governs the distributions of groups of similar riparian plant species across landscapes? To answer this question, I identify relationships between riparian vegetation guilds and communities and environmental gradients across the American West. In Chapter One, I discuss guild-based classification in the context of community ecology and streams. In Chapter Two, I identified five woody riparian vegetation guilds across the interior Columbia and upper Missouri River Basins, USA, based on species’ traits and morphological attributes. I modeled guild occurrence across environmental gradients, including climate, disturbance, channel form attributes that reflect hydrology, and relationships between guilds. I found guilds’ distributions were related to hydrology, disturbance, and competitive or complementary interactions (niche partitioning) between co-occurring guilds. In Chapter Three, I examine floodplain riparian vegetation across the American West, identifying how hydrology, climate, and floodplain alteration shape riparian vegetation communities and their guilds. I identified eight distinct plant communities ranging from high elevation mixed conifer forests to gallery cottonwood forests to Tamarisk-dominated novel shrublands. I aggregated woody species into four guilds based on their traits and morphological attributes: an evergreen tree guild, a mesoriparian shrub guild, a mesoriparian tree guild, and a drought and hydrologic disturbance tolerant shrub guild. Communities and guilds’ distributions were governed by climate directly, and indirectly as mediated through streamflow. In Chapter Four, I discuss the utility of guild-based assessments of riparian vegetation, current limitations to these approaches, and potential future applications of the riparian vegetation guild concept to floodplain conservation and management. The classification of vegetation into functional trait-based guilds provides a flexible, framework from which to understand riparian biogeography, complementing other models frameworks for riparian vegetation.

Technological developments in the past thirty years have transformed sequencing-based microbiology into a data-intensive field. Here, computing and efficient representations are catalyzers of insight into omnipresent and complex microbial interactions. Notably, classical ecologists have set the foundations for the way we analyze these systems, with some techniques dating back to the beginning of the twentieth century. In this thesis, we expand and where possible reuse these techniques to unravel the hidden patterns comprising the human gut microbiome.

To set an appropriate motivation and context for the rest of this work, Chapter 1 reviews recent discoveries on the human microbiome and how the communities within can influence the effectiveness of therapeutic agents. Next, in Chapter 2, we introduce EMPeror, an interactive analysis and visualization tool that is crucial to the findings presented in later chapters.

The following three chapters study concrete examples where the microbiome has been implicated as a driver or marker for dysbiosis. Chapter 3 describes how the microbial signature associated with Crohn's disease (CD) in humans, described in our previous work, is overlapping but distinct to that of dogs affected with inflammatory bowel disease (IBD). Surprisingly, unlike with humans, dog fecal samples alone are strong indicators of the disease. In Chapter 4, we study IBD from a longitudinal perspective, revealing increased volatility in the gut microbiomes of subjects with IBD, a property that does not appear to be present in unaffected controls. Furthermore, we use this as a predicting feature of the disease, and improve on the classification accuracy possible through a single fecal sample. In Chapter 5, we study the effect of fecal microbiota transplants (FMTs) to treat Clostridium difficile infection (CDI) and, using the techniques described in Chapter 2, we show the first animated visualization of this process, a dramatic microbial transformation as the subjects recover from all CDI symptoms. In addition, for CDI patients who also suffer from a subtype of IBD, a treatment with a FMT results in an increased number of relapses and decreased microbial diversity.

The closing chapter discusses these results and their possible applications, as well as future directions for computationally-centric microbiome research.

The island apple snail, Pomacea maculata, family Ampullariidae, is a large freshwater gastropod native to South America. P. maculata is known as a heavy consumer of aquatic plants. P. maculata was introduced to Florida in the 1990s and has rapidly spread throughout natural and man-made wetlands and waterways in the southeastern United States. Negative ecosystem impacts associated with P. maculata invasion include destruction of macrophyte communities via overgrazing, competitive exclusion of the native Florida apple snail Pomacea paludosa, and the potential transmission of toxins and parasites to predators.

Populations of P. maculata have been documented in freshwater tributaries of estuaries such as Mobile Bay, Alabama and the Caloosahatchee Estuary, Florida, and the snails may be moving into the estuaries themselves. The objectives of this study were: 1) to evaluate P. maculata's potential to harm macrophytes like tapegrass, Vallisneria americana, in low-salinity estuarine environments, 2) to determine how the grazer's destructiveness might by moderated by environmental context (salinity, temperature, and the presence of other macrophyte species), and 3) to identify management and restoration strategies for V. americana to minimize the harm done by P. maculata. We accomplished these objectives with feeding trials and mesocosm experiments conducted under varying conditions of salinity, temperature, and macrophyte community composition.

We found that increasing salinity lowered P. maculata grazing pressure on V. americana but increasing temperature increased grazing pressure. Herbivory on V. americana was not reduced and was sometimes intensified when other aquatic plant species were present. The results of two mesocosm experiments suggested that salinity and snail presence have a nonadditive, antagonistic, effect on V. americana. I.e., in the absence of snails the plant performed best at 0 psu, whereas when snails were present the plant did best at 5-10 psu due to reduced snail grazing. Due to the significant sub-lethal impacts of salinity on P. maculata's grazing and health it is unlikely that the snail's invasion will proceed beyond the lowest salinity portions of estuaries. These estuarine regions can therefore serve as a valuable refuge for V. americana populations, providing that effective water management keeps salinity below the approximately 10 psu threshold where significant direct harm occurs to the plants.

Bird migration is the regular seasonal movements between breeding and nonbreeding grounds. In general, birds that breed in the Northern Hemisphere tend to migrate northward in the spring to take advantage of increasing insect populations and lower predation pressures and fly south when food availability and weather conditions decline. Embarking on a journey that can stretch a thousand miles round trip is a dangerous and arduous undertaking. While en route migrants must stop and feed to replenish their depleted energy reserves, often in unfamiliar locations with unknown predation pressures. They also must react to weather conditions during flight and while on the ground. Additionally, areas of high quality habitats where birds can refuel efficiently and safely may be few and far between. Therefore, it's not surprising that mortality rates can be higher during migration than at any other period of the year. Behavioral decisions such as where and where to stop, how long to stay, and when to leave all involve costs and benefits with an ultimate goal to balance the costs and benefits on order to achieve a successful and efficient migration. Optimal migration theory, aims to explain how migrants balance behavioral and physiological parameters of migration that minimize total time spent on migration, total energy expended, or mortality risk. The eventual result of these optimization pressures is thought to be a gradient of behavioral strategies that optimize different combinations of the three currencies: time, energy, and risk. I investigated how migratory behaviors of North American songbirds in the autumn balance the three currencies. More specifically I 1) explored how stopover site selection varies across migratory strategies at the landscape (Chapter 2) and habitat-patch (Chapter 3) scale; 2) investigated the importance of wind for the evolution and maintenance of migratory routes (Chapter 4); and 3) explored how selection of wind conditions for migratory departure affects overall behavioral strategies (Chapter 5). With this research, I hope to further our predictive abilities of migratory behaviors under various environmental and geographic situations using an optimal migration framework.