<p> 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 (<i>Puma concolor </i>) 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. </p><p> 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. </p><p> 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.</p>

<p> Humans introduce non-native plants to new areas at an increasing rate with the increased movement across the globe. These invasive species can become mono-cultures and extremely different from the native floral community. Amphibians, at the same time, are facing global declines with approximately one-third of all amphibians threatened or endangered. Due to the importance of amphibians as prey items for many vertebrates including small birds, mammals, and reptiles, and also predator controls over many invertebrates, including some pest species, the decline of amphibians has large implications for many environments. This study looks at a range of interactions between two invasive plants (<i> Typha angustifolia</i> and <i>Phragmites australis</i>) and two native anurans (<i>Lithobates clamitans</i> and <i>Lithobates catesbeianus</i>). </p><p> As ecosystem engineers, plants form the basis of many communities, and sculpt the physical environment by adding complexity to the earth's surface. They also add chemical constituents either actively or passively too ward off other competitors. This change in the environment on both the chemical and physical level leads to complex possibilities for a changed plant community to impact the rest of the ecosystem, including amphibians. I focus on the physical changes by looking at behavior of amphibians in these invasive plant mono-cultures and non-invaded controls, and their appearance in invaded and non-invaded wetlands, both constructed and naturally occurring. On the chemical side of the matter, I monitor water chemistry measures in natural and constructed wetlands that are either lacking invasive plants or have a substantial presence of these plants, and correlate those measures with tadpole growth and survival. </p>

<p> It is important to understand fate of nutrients like nitrogen, in streams given that anthropogenic activity, such as agriculture, have increased inputs of biologically reactive nitrogen to the environment leading to deterioration of stream health and eutrophication. Bacteria play a crucial role in the driving essential biogeochemical transformations. The purpose of this research was to improve our understanding of organic and inorganic nitrogen utilization by bacterial isolates and complex bacterial communities. Role of bacterial diversity in resource utilization is mostly neglected in biogeochemical models. Identification of bacteria based on molecular methods, like 16S rDNA sequencing, yield a wealth of information related to prokaryotic diversity and its importance in driving essential biogeochemical cycles. In this research utilization of organic and inorganic forms of nitrogen by stream heterotrophic bacterial isolates were examined. Our results reveal differences in bacterial resource utilization not as a function of the different taxa involved but of the enrichments the isolates were obtained from, as immediate environment dictate bacterial response to different nutrients and exerts a selection pressure. Carbon availability also influences nitrogen dynamics. To examine the impact of carbon on bacterial uptake of organic and inorganic nitrogen, bacterial abundance and community composition were examined in controlled, laboratory microcosms. There was a strong influence of carbon availability on bacterial nitrogen utilization, with preferential uptake of organic forms under low carbon concentrations. Carbon and nitrogen treatments likely drove changes in bacterial community composition that, in turn, affected rates of nitrogen utilization under various carbon concentrations. Metabolic functions, such as particular biogeochemical reactions are catalyzed by microbial extracellular enzymes, which are likely linked to the constituting taxa in a given microbial community. This study tracked temporal patterns of bacterial community structure and potential microbial enzyme activities in response to seasonal changes in stream organic matter pool. Differences in enzyme activities were highly correlated to nutrient (carbon and nitrogen) availability while differences in bacterial community structure were mostly driven by environmental conditions. However, the absence of link between bacterial community structure and potential enzyme activity is indicative of functional redundancy within microbial communities.</p>

<p> The abstract is not available from PDF copy and paste.</p>

<p> The goldspotted oak borer (GSOB), <i>Agrilus auroguttatus</i> Schaeffer, is an invasive wood-borer associated with tree mortality in San Diego County, California since 2008, and is believed to have been introduced via infested firewood from southeastern Arizona. From 2011-2013, I recorded GSOB emergence holes on <i>Quercus agrifolia</i> trees at eight locations within San Diego County. I evaluated the effectiveness of crown class and purple prism traps as tools to monitor GSOB populations. I also identified possible tree and site characteristics that could explain the variation in GSOB population densities. Crown class was useful in monitoring GSOB populations unlike purple prism traps. Larger trees (>50 cm diameter at breast height), trees located near a stand's edge, and trees previously infested had the greatest emergence hole densities. Sites closer to GSOB's putative original point of infestation and those with an intermediate <i>Q. agrifolia </i> density (30-50 trees per hectare) had greatest infestation levels. </p>

<p> The Nushagak River, Bristol Bay, Alaska, supports one of the largest wild sockeye salmon (<i>Oncorhynchus nerka</i>) runs in the state and also supports overlapping runs of chum (<i>O. keta</i>) and Chinook (<i>O. tshawytscha</i>) salmon. Each summer, the Alaska Department of Fish and Game deploys dual-frequency identification sonar (DIDSON) on the river to enumerate salmon to monitor escapement goals; however, salmon behavior and spawning run characteristics at the site are not incorporated into management. We investigated the feasibility of using Nushagak River DIDSON data from 2008-2011 to identify trends in run timing and compare passage rates to local environmental conditions, including tide, light intensity, and water temperature. We also used spatial analysis to examine aggregation behavior of salmon at the DIDSON site at multiple distance scales. Between all four years, run timing only varied within a few days (&lt; 1 week), regardless of water temperature. In 2009 and 2011, more salmon passed upriver during slack and ebb tides than during flood tide. Salmon were never completely spatially random, and distance scales of aggregation behavior were influenced by run period and photo period. When examining all factors together, the interaction between salmon density and run period affected distance at maximum aggregation. This research used hydroacoustics for a multi-level approach to investigating spatiotemporal patterns of Pacific salmon relative to environmental factors during their spawning migration and may help refine in-season monitoring and management of the fishery.</p>

<p> Nordihydroguaiaretic acid (NDGA) is the principal compound in the resinous leaf coating of <i>Larrea tridentata</i> (creosote bush), the dominant shrub of North American deserts. <i>L. tridentata</i> exists as three polyploid races: diploid (2X = 26), tetraploid (4X = 52), and hexaploid (6X = 78). The distributions of these ploidy levels are strongly associated with the three major deserts of the region where diploids primarily reside in the cooler, wetter Chihuahuan desert, tetraploids in the Sonoran desert, and hexaploids in the hot, dry Mojave desert. NDGA is a secondary metabolite of creosote bush that functions to protect plants from biotic and abiotic stressors such as extreme drought, harmful UV radiation, and herbivory. Here, I investigated the role of polyploidy and environmental variables on the production of NDGA by quantifying concentrations from field and greenhouse-grown polyploids. Citizen scientists were utilized to facilitate simultaneous sampling across the entire distributional range of this species, for one full year. Under natural conditions, shrubs produced significantly higher NDGA concentrations than when removed from the harsh desert environment. In field and greenhouse treatments, hexaploids exhibited higher NDGA concentrations than diploids or tetraploids. Within the diploid cytotype, I documented environmental influences on NDGA concentration based on comparisons between a field site experiencing severe drought, a watered field site, and greenhouse-grown diploids. Principal components analysis revealed that NDGA response to environmental variables successfully predicts the current ploidy distribution of this species. These observations highlight the complexity of plant-environment-genotype interactions and suggest that evolution in production of secondary metabolites may be driven by long-term changes in environmental conditions, and potentially influence species distribution regimes.</p>

<p> Despite reductions in species diversity, few studies in wetlands investigate the relationship between biodiversity and ecosystem function (BEF). My research explores the BEF relationship in a recently restored salt marsh in Long Beach, California. I hypothesized that: (1) increasing plant diversity would result in higher primary productivity and decreased recruitment of native salt marsh plants, (2) observed variation in responses would be correlated with species-specific variation in individual demographic parameters, and (3) variation in demographic parameters and resulting ecosystem processes would be correlated with functional traits. I found that while survival over one year was correlated with elevation, overall percent cover and recruit species richness were positively affected by diversity. Performance patterns reveal variation by species in photosynthetic rate, leaf mass per area and chlorophyll a/b ratios. After one year, I found that the overall diversity patterns were driven by selection effect compared to complementarity.</p>

<p> The burying beetle <i>Nicrophorus orbicollis,</i> through biparental care, raise their young on small vertebrate carrion which exposes them to microbial parasites and competitors. These interactions have led to elaborate strategies to combat microorganisms. Through the application of anal and oral secretions adults are able to preserve a carcass from which larvae feed, constituting a social immune response. Evidence suggests that larvae also contribute to this social immunity through their own secretions. Social immunity was tested through exposing larvae to an isolated food source with an experimentally elevated microbial signal, dead <i>Micrococcus luteus.</i> Larvae maintained higher lysozyme-like activity (LLA) in their oral secretions in response to the microbial signal. However, if personal immunity was compromised LLA was not maintained. Larvae and parents were tested for response to increased competition of feeding on fresh or aged carcasses with greater levels of decay. Larvae were not shown to alter LLA of their oral secretions but female parents did have a negative relationship of LLA in their oral secretions and in relation to brood size. Larvae had a negative relationship of phenoloxidase activity in their oral secretions in relation to brood size. This suggests influence of individual larval investment to social immunity affecting both parents and sibling investment. These findings show that oral secretions in <i> N. orbicollis</i> larvae, like adults, has adaptive antimicrobial activity which acts as a social immune response for defending a carrion food source and is sacrificed for personal immunity.</p>

We have coupled a 3-dimensional physical planetary geostrophic ocean general circulation model to different biological models to investigate the interaction between physical and biological processes. A 1-dimensional particle cycle model with two particle size classes has been developed and coupled to the physical model as well. / The ocean model (Zhang et al., 1992) is based on the planetary geostrophic equations in spherical coordinates. The model equations include the full prognostic temperature and salinity equations. The momentum equations are diagnostic and include geostrophic balance, and a linear friction term in order to provide a western boundary current. The wind stress is applied at the top level of the model. The temperature and salinity distributions used in the surface boundary restoring condition are taken from climatological data. The model domain consists of a flat-bottomed box of 60$ sp circ$ longitude extending between 5$ sp circ$N and 65$ sp circ$N. The horizontal resolution is 2.3$ sp circ$ in both latitude and longitude with 14 levels in the vertical. / The physical model is first coupled to a biological model where new production is given by a restoring condition of surface nitrate towards its observed concentration. The coupled model is used to examine Martin et al.'s (1987) hypothesis that lateral transport and decomposition of slow or non-sinking organic matter can cause a non-local balance between the remineralization rate and the overlying new production rate in open ocean regions. The role of the Gulf Stream in nutrient transport is examined. The model results agree well with the North Atlantic nutrient transport calculated from observed nutrients and hydrographic data. The model results suggest that the thermohaline overturning circulation and the Gulf Stream horizontal recirculation play an important role in the North Atlantic nutrient distribution. / The physical model is then tested in the seasonal mode, and coupled with a biological model which is based on nitrate limiting the rate of new production. The model simulated seasonal oxygen cycle agrees well with the results of observational studies and 1-dimensional model simulations. The oxygen utilization rate below the euphotic zone provides a useful estimate of new production. / A 1-dimensional time dependent particle cycling model with two particle size classes based on Clegg and Whitfield (1990) is then developed. The simulated total organic carbon concentration and large particle flux are consistent with observations and other 1-dimensional model simulations. The downward transport of organic carbon is mainly accomplished by the fast sinking large particles, which comprise a small fraction of the total particulate mass. The steady state version of the particle model is also coupled with the 3-dimensional physical model. The magnitudes of simulated organic carbon flux and total organic matter concentration are comparable with observations.