An efficient three-dimensional structured solver for the Euler and Navier-Stokes equations is developed based on a finite volume upwind algorithm using Roe fluxes. Multigrid and optimal smoothing multi-stage time stepping accelerate convergence. The accuracy of the new solver is demonstrated for inviscid flows in the range 0.675 :5M :5 25. A comparative grid convergence study for transonic turbulent flow about a wing is conducted with the present solver and a scalar dissipation central difference industrial design solver. The upwind solver demonstrates faster grid convergence than the central scheme, producing more consistent estimates of lift, drag and boundary layer parameters. In transonic viscous computations, the upwind scheme with convergence acceleration is over 20 times more efficient than without it. The ability of the upwind solver to compute viscous flows of comparable accuracy to scalar dissipation central schemes on grids of one-quarter the density make it a more accurate, cost effective alternative. In addition, an original convergencea cceleration method termed shock acceleration is proposed. The method is designed to reduce the errors caused by the shock wave singularity M -+ 1, based on a localized treatment of discontinuities. Acceleration models are formulated for an inhomogeneous PDE in one variable. Results for the Roe and Engquist-Osher schemes demonstrate an order of magnitude improvement in the rate of convergence. One of the acceleration models is extended to the quasi one-dimensiona Euler equations for duct flow. Results for this case d monstrate a marked increase in convergence with negligible loss in accuracy when the acceleration procedure is applied after the shock has settled in its final cell. Typically, the method saves up to 60% in computational expense. Significantly, the performance gain is entirely at the expense of the error modes associated with discrete shock structure. In view of the success achieved, further development of the method is proposed.

abstract: Urban riparian corridors have the capacity to maintain high levels of abundance and biodiversity. Additionally, urban rivers also offer environmental amenities and can be catalysts for social and economic revitalization in human communities. Despite its importance for both humans and wildlife, blue space in cities used by waterbirds has received relatively little focus in urban bird studies. My principal objective was to determine how urbanization and water availability affect waterbird biodiversity in an arid city. I surveyed 36 transects stratified across a gradient of urbanization and water availability along the Salt River, a LTER long-term study system located in Phoenix, Arizona. Water physiognomy (shape and size) was the largest factor in shaping the bird community. Connectivity was an important element for waterbird diversity, but not abundance. Urbanization had guild-specific effects on abundance but was not important for waterbird diversity. Habitat-level environmental characteristics were more important than land use on waterbird abundance, as well as diversity. Diving and fish-eating birds were positively associated with large open bodies of water, whereas dabbling ducks, wading birds, and marsh species favored areas with large amounts of shoreline and emergent vegetation. My study supports that Phoenix blue space offers an important subsidy to migrating waterbird communities; while alternative habitat is not a replacement, it is important to consider as part of the larger conservation picture as traditional wetlands decline. Additionally, arid cities have the potential to support high levels of waterbird biodiversity, heterogeneous land use matrix can be advantageous in supporting regional diversity, and waterbirds are tolerant of urbanization if proper resources are provided via the habitat. The implications of this study are particularly relevant to urban planning in arid cities; Phoenix alone contains over 1,400 bodies of water, offering the opportunity to design and improve urban blue space to optimize potential habitat while providing public amenities. / Dissertation/Thesis / Masters Thesis Applied Biological Sciences 2016

<p> Southern flying squirrels (SFS; <i>Glaucomys volans</i>) are known kleptoparasites on the endangered red-cockaded woodpecker&rsquo;s (RCW; <i> Picoides borealis</i>) cavities and cost land managers time and money to control, and the ecology of SFS in habitats managed for RCWs is poorly understood. This study is designed to obtain a better understanding of the general ecology of SFSs surrounding RCW habitat and provide possible non-lethal deterrent methods to prevent harmful interactions between SFSs and RCWs. Spatially-explicit capture-recapture showed generally higher SFS densities and habitat associations outside of RCW cluster partitions. Stable isotope analysis of SFS diets across Mississippi and Alabama revealed a narrow dietary breath relative to food items, thus habitat management may still be viable option to control SFSs. Lastly, investigation of odor deterrents resulted in the greatest avoidance of cavities containing gray rat snake (<i>Pantherophis spiloides </i>) feces and warrants further investigation.</p><p>

No description available.

<p> Habitat loss and the resulting fragmentation can alter animal movements and disrupt animal seed dispersal mutualisms; however, these effects on spatial patterns of seed dispersal are not well understood. To explore the effects of habitat loss and fragmentation on seed dispersal distances and seed dispersion (aggregation), I created a spatially-explicit, individual-based model of an animal dispersing seeds (SEADS &ndash; Spatially-Explicit Animal Dispersal of Seeds). For Chapter 1, I ran SEADS in a theoretical landscape of 0-90% habitat loss to determine the effects of habitat loss on three animal traits relevant to seed dispersal: movement distance, gut retention time, and time between movements. SEADS results revealed a complex interaction involving all animal traits and habitat loss on dispersal distances and dispersion, driven by a novel underlying mechanism of fragment entrapment. Unexpectedly, intermediate habitat loss could increase dispersal distances and dispersion relative to low and high habitat loss for some combinations of animal traits. In Chapter 2, I developed a new method (TriAD) to estimate animal locations from triangulation data to improve triangulations for toucans. Location estimates calculated with TriAD averaged 23-63 m closer to true locations for three of four distance classes compared to the traditional method (Lenth&rsquo;s maximum likelihood estimator, LMLE). Additionally, over 99% of 570 triangulations converged for TriAD compared to 85.8% for the LMLE. For toucan data, 98.0% of 4445 triangulations converged in TriAD compared to 88.6% for the LMLE. In Chapter 3, I parameterized SEADS with data from toucan movements and gut retention trials collected in Costa Rica to evaluate the effects of landscape, body size, and social organization on seed dispersal. The larger, less social species dispersed seeds 17-28% farther and in less aggregated patterns than the smaller, social species. This pattern was driven by longer movements in the larger species, suggesting that body size is more important than social organization for seed dispersal in our system. Habitat use and home range sizes limited dispersal distance and dispersion for both species. Findings from our simulations illustrate the importance of separating and quantifying the effects of disperser behaviors and landscape effects that shape seed deposition in fragmented areas.</p><p>

<p> The United States Fish and Wildlife service declared an unusual mortality event (UME) in 2006 when a high number of northern sea otters in Alaska were found dead beginning in 2002. Necropsies revealed the cause of death in 30% of cases to be septicemia with meningoencephalitis and/or vegetative valvular endocarditis (VVE) colonized by gram positive cocci, later determined to be primarily <i>Streptococcus infantarius</i> ss <i>coli</i> and <i>Streptococcus phocae</i>. While much work has been done to uncover the pathogenic agents responsible for these deaths in northern sea otters, the ecology of <i>S. infantarius</i> ss <i>coli</i> and <i>S. phocae</i> in the environment remains poorly understood. This study investigated the presence of <i>S. infantarius</i> ss <i> coli</i> and <i>S. phocae</i> in the marine environment by 1) developing a molecular method to detect <i>S. infantarius</i> ss <i>coli</i> 2) examining potential microbe-habitat associations in Kachemak Bay and Resurrection Bay, Alaska, and 3) determining the competency of otter prey species to act as reservoirs for these pathogens. A PCR assay was developed to detect the <i>sodA</i> gene of <i> S. infantarius</i> ss <i>coli</i> in both environmental and clinical samples. Water and bay mussels were collected from sites in Kachemak and Resurrection Bays and pathogen presence was determined using PCR. Habitat attributes were recorded onsite and determined using ShoreZone. Prey competency was determined via a dosing experiment in the lab. Our primer set for the <i> S. infantarius</i> ss <i>coli</i> <i>sodA</i> gene, as well as a previously published primer set for the <i>S. phocae</i> <i> sodA</i> gene, successfully identified our targets in clinical and environmental samples using conventional PCR. Primer sets we designed successfully quantified the <i>sodA</i> gene of <i>S. infantarius</i> ss <i> coli</i> and/or <i>S. phocae</i> in environmental samples and in dosed prey samples using qPCR. <i>S. infantarius</i> ss <i> coli</i> and/or <i>S. phocae</i> were present in water or mussels at 61 of 162 sites. Statistical analyses to determine bacterial correlations with habitat attributes revealed some correlations between habitat parameters selected and presence of our target bacteria in the environment. Prey competency experiments showed that bivalves were the most competent pathogen reservoirs. Results of this study will inform microbial ecologists and wildlife managers of the potential environmental risk factors for <i>S. infantarius</i> ss <i>coli</i> and <i>S. phocae</i> infection as well as provide information about pathogenic bacterial presence in the marine environment. </p><p>

<p> Apple snails are in the Family Ampullariidae, a family of freshwater gastropods. Some species in the genus <i>Pomacea</i> have gained considerable notoriety as very destructive invasive species. Ampullariids have a gill and breathe water; in some species, the mantle cavity is modified into an air sack that may function as a lung or flotation device. Apple snails definitively identified as <i>Pomacea maculata</i> have successfully invaded numerous localities in Louisiana, and studies of the physiology of these animals may enhance our understanding of the biology of highly invasive species and suggest effective approaches to controlling the invasive populations. This study investigated respiration of <i>P. maculata</i> in water and in air and the ability of the animals to survive long-term emersion in a state of aestivation. The ability of the animals to disperse over dry ground was studied. Finally, the anatomy of the gill and lung were examined. The results of the study indicate that the gill and the lung in <i>P. maculata</i> are vascularized, capable of gas exchange, and fully functional, which permits survival and respiration in water and during long- and short-term exposure to air. Both the capacity to sustain travel over dry land and the ability to survive long term aerial exposure in an aestivated state were demonstrated by <i>P. maculata</i>. The major physiological changes observed during aestivation include a decrease in heart rate, a reduction in VO2, and the use of discontinuous respiration. A review of published literature suggests that extensive physiological variation exists among populations of native and invasive <i>P. maculata</i>. In conclusion, <i>P. maculata </i> in Louisiana is well-adapted to life in both water and air, can move overland, and can survive emersion for over a year. These physiological adaptations suggest that controlling the further spread of <i>P. maculata </i> will be very difficult.</p><p>

No description available.

No description available.

Vancouver Island marmots (M. vancouverensis) rank among the world's most critically endangered mammals. There were probably fewer than 100 marmots in 1998, with 90% distributed south of Alberni Inlet, and the remainder on or near Mount Washington. This represents a 60–70% decline in numbers during the past 10 years, and a considerably reduced geographic range during the past several decades. I used data from marked animals, radio-telemetry and population counts to test whether population dynamics were consistent with predictions made under five hypotheses: habitat tracking, sink-connectivity, weather, predators and disease. Estimates of demographic rates from intensive mark-recapture work and population counts were generally consistent, although estimation of adult survival from counts was problematic because of the difficulty of distinguishing surviving marmots from immigrants. There was no apparent influence of mark-recapture on survival or reproduction, and intensively studied colonies showed similar dynamics to colonies that were visited infrequently. There was little evidence for habitat tracking in natural habitats. Few colonies showed chronically low reproduction or survival, which would be the predicted result of a gradually deteriorating environment. Declines were more often abrupt and catastrophic. Marmots did not colonize clearcuts in proportion to their temporal or spatial availability, and ultimately colonized only a minuscule fraction of the potential habitat. However, marmots already inhabiting clearcuts represent a special case of habitat tracking; survival rates were significantly lower at clearcuts of more advanced seral age (i.e., >11 years after harvest). Evidence for source-sink and landscape connectivity processes was relatively strong. Marmots inhabiting clearcuts had chronically lower survival rates (by 5–10%). Per female reproductive contribution in clearcuts was half that of females inhabiting natural environments. However not all clearcuts acted as sinks, or acted as sinks in all years. Colonizations of clearcuts were spatially concentrated and none occurred at distances greater that 5 km from an existing natural colony. Apparent adult survival was significantly associated with isolation but juvenile survival was not, which is consistent with the prediction that isolated colonies should receive fewer immigrants. However the spatial pattern of extinctions was unexpected. Isolated and closely-clustered colonies had similar probabilities of extinction. Weather significantly influenced marmot survival and reproduction but explained only small amounts of variation. Survival was significantly associated with rainfall, temperature and snowpack depth. Reproduction was negatively associated with snowpack and temperature. Slope aspect was significantly associated with survival, perhaps suggesting the importance of snowmelt patterns. Natural and clearcut colonies responded differently to weather. Indices of wolf and cougar abundance were inconsistent and probably do not reflect true population sizes. Deer abundance was weakly associated with marmot survival in natural habitats, which could suggest switching of predator hunting effort. Marmot survival was spatially correlated, which is consistent with the idea that a few individual predators may focus hunting efforts at adjacent colonies. Field observations and radio-telemetry corroborated the importance of predators. In natural habitats, disappearances were uniformly distributed throughout summer, as predicted. In clearcuts, disappearances, were more heavily skewed towards late summer, suggesting that winter mortality was more important. Spatial correlation of survival is also consistent with the disease hypothesis. Survival was lower in colonies with high relative density of adults, which is a predicted result given the prediction of increased risk of disease transmission. The incidence of high mortality events increased during the 1990s, and the degree of spatial correlation also increased despite a more fragmented population structure. These trends are consistent with a hypothesis of a new disease organism or increased risk of infection. Forestry appears to be the primary cause of recent population dynamics in the Nanaimo Lakes region. Logging reduced overall marmot survival, inhibited their ability to re-colonize sites, and concentrated the population, making colonies more susceptible to predators and disease. The prognosis for continued survival remains hopeful provided that current plans for captive-breeding and captive-breeding and reintroduction are pursued aggressively. / Graduate