Urbanization is considered one of the leading threats to biodiversity and wildlife habitat (McKinney 2002; Shochat et al. 2006). Urban environments are humandominated systems, yet they support wildlife habitat and provide meaningful ecological functions. Methods to conserve biodiversity and minimize habitat loss and fragmentation in urban environments include utilizing private residential yards and gardens to enhance habitat connectivity. Private residential yards or gardens designed to attract and support wildlife are known as backyard habitats and wildlife gardens. The City of Austin, Texas initiated Wildlife Austin in 2007. Wildlife Austin coordinates backyard habitats in Austin as a National Wildlife Federation Community Wildlife Habitat [trademark]. My research analyzes the goals of the Wildlife Austin from the perspective of landscape ecology and urban ecology; reviews research related to backyard habitats in order to identify ways of enhancing habitat connectivity for bird communities; and provides recommendations for a more scientifically grounded approach and management in the promotion of backyard wildlife habitat. / text

Understanding the factors influencing species ranges and dispersal are becoming increasingly important as climate change alters species distributions worldwide. If species are to persist, life-history strategies must rapidly evolve to accommodate shifting environments. This dissertation assesses the factors modulating dispersal in corals. First, I examined if there were any systematic differences in settlement between Indo-Pacific and Caribbean coral larvae that might explain Caribbean recruitment failures. No differences were observed, however I detected significant divergences in settlement cue preferences among coral species across both the Caribbean (Diploria strigosa, and Montastraea franksi) and the Indo-Pacific (Acropora tenuis, A. millepora, and Favia lizardensis), even for coral larvae from the same reef. Secondly, I established the extent of coral dispersal between remote reefs. I evaluated the genetic diversity and divergence across Micronesia for two coral species and investigated if these islands served as a connectivity corridor between the Indo-West-Pacific (Coral Triangle) and the Central Pacific. I found isolation-by-distance patterns whose strength depended on species, suggesting these corals are not panmictic across their ranges and that island stepping-stones facilitate gene flow to remote Pacific reefs. Next, I investigated genetic structure of symbionts in these same corals, to see if horizontally transmitted symbionts are less dispersive than their coral hosts. Symbiont genetic divergence between islands was an order of magnitude larger than host divergence and both host species and environment modulated symbiont composition. These results suggest that symbiont populations are host-specific and associating with local symbionts might be a mechanism for broadly dispersing corals to adapt locally. Lastly, I estimated heritable variation in dispersal-related traits in coral larvae. I observed strong heritable variation in gene expression, as well as parental effects on two phenotypic traits, settlement and fluorescence. I observed that patterns of differential expression in three-day-old larvae predicted variation in settlement and fluorescence two days later. Correlations between proteoglycan expression and settlement suggest that the larval extracellular matrix plays a role in settlement. Down-regulation of ribosomal proteins and differential expression of oxidative stress genes correlated with increasing fluorescence, possibly indicating reduced growth and increased stress. Overall, this dissertation contributes to our knowledge of factors affecting coral dispersal and the potential for evolution of dispersal-related traits. / text

The passage of two major hurricanes across southwest Florida (Category 5, Labor Day Hurricane of 1935; Category 4, Hurricane Donna 1960) resulted in fragmentation of mangrove forest at Big Sable Creek, Everglades National Park. Over time forest fragmentation led to forest loss and patchy conversion to unvegetated mudflats. My goal was to determine the consequence of forest fragmentation on nekton (i.e., fish and decapod crustaceans) inhabiting the intertidal zone. I used block nets across intertidal rivulets to compare nekton leaving replicate forest and unvegetated mudflat sites from October, 2002 through April 2004. Overall nekton density (individuals per 100 m3) was significantly greater (rmANOVA, p < 0.001) for mangrove (212·100 m-3) than mudflat (26·100 m-3) habitats. Biomass (g per 100 m3) was also significantly greater for mangrove (715 g·100 m-3) than mudflat (20 g·100 m-3) habitats. Composition of the nekton assemblage also differed between habitat types (ANOSIM global R=0.416, p<0.001). Structure-associated species dominated forested sites, whereas schooling species dominated mudflats. When mangrove destruction and mortality results in fragmentation (Craighead and Gilbert, 1962; Smith et al., 1994; Wanless et al., 1994), nekton density and biomass will likely decline as a consequence.

Fibrin is a biopolymer that assembles into a network during blood coagulation to become the structural scaffold of a blood clot. The precise mechanics of this network are crucial for a blood clot to properly stem the flow of blood at the site of vascular injury while still remaining pliable enough to avoid dislocation. A hallmark of fibrin's mechanical response is strain-stiffening: at small strains, its response is low and linear; while at high strains, its stiffness increases non-linearly with increasing strain. The physical origins of strain-stiffening have been studied for other biopolymer systems but have remained elusive for biopolymer networks composed of stiff filaments, such as fibrin. To understand the origins of this intriguing behavior, we directly observe and quantify the motion of all of the fibers in the fibrin networks as they undergo shear in 3D using confocal microscopy. We show that the strain-stiffening response of a clot is a result of the full network deformation rather than an intrinsic strain-stiffening response of the individual fibers. We observe a distinct transition from a linear, low-strain regime, where all fibers avoid any internal stretching, to a non-linear, high-strain regime, where an increasing number of fibers become stretched. This transition is characterized by a high degree of non-affine motion. Moreover, we are able to precisely calculate the non-linear stress-strain response of the network by using the strains on each fiber measured directly with confocal microscopy and by assuming the fibers behave like linearly elastic beams. This result confirms that it is the network deformation that causes the strain-stiffening behavior of fibrin clots. These data are consistent with predictions for low-connectivity networks with soft, bending, or floppy modes. Moreover, we show that the addition of small contractile cells, platelets, increases the low-strain stiffness of the network while the high-strain stiffness is independent of the presence of the platelets; this is also consistent with expectations for small contractile elements in a network with low connectivity. Our results elucidate the origins of strain-stiffening in fibrin networks as well as the mechanism underlying platelet-induced clot stiffening. / Physics

Neurological and psychiatric disorders reveal that the basal ganglia subserve diverse functional domains, including movement, reward, and cognitive disorders (e.g., Parkinson's disease, addiction, schizophrenia). Monkey anatomical studies show that the striatum, the input structure of the basal ganglia, receives projections from nearly the entire cerebral cortex with a broad topography of motor, limbic, and association zones. However, until recently, non-invasive methods have not been available to conduct the complete mapping of the cortex to the striatum in humans. The development of functional connectivity magnetic resonance imaging (fcMRI) now allows the identification of functional connections in humans. The present dissertation reports two studies that first create a complete map of corticostriatal connectivity and then more closely examine striatal connectivity with association networks underlying cognition.

Unconventional natural gas resources, particularly tight gas sands, constitute a significant percentage of the natural gas resource base and offer abundant potential for future reserves and production. The premise of this research is that several unique characteristics of these rocks are the consequence of post depositional diagenetic processes including mechanical compaction, quartz and other mineral cementation, and mineral dissolution. These processes lead to permanent alteration of the initial pore structure causing an increase in the number of isolated and disconnected pores and thus in the tortuosity. The objective of this research is to develop a pore scale model of the geological processes that create tight gas sandstones and to carry out drainage simulations in these models. These models can be used to understand the flow connections between tight gas sandstone matrix and the hydraulic fractures needed for commercial production rates. We model depositional and diagenetic controls on tight gas sandstones pore geometry such as compaction and cementation processes. The model is purely geometric and begins by applying a cooperative rearrangement algorithm to produce dense, random packings of spheres of different sizes. The spheres are idealized sand grains. We simulate the evolution of these model sediments into low-porosity (3% to 10%) sandstone by applying different amount of ductile grains and quartz precipitation. A substantial fraction of the original pore throats in the sediment are closed by the simulated diagenetic alteration. Thus, the pore space in typical tight gas sandstones is poorly connected, and is often close to being completely disconnected, with significant effect on flow properties. The drainage curves for model rocks were computed using invasion percolation in a network taken directly from the grain-scale geometry and topology of the model. The drainage simulations show clear percolation behavior, but experimental data frequently do not. This implies that either network models based on intergranular void space are not a good tool for modeling of tight gas sandstone or the experiments are not correctly done on tight gas samples. In addition to reducing connectivity, the porosity-reducing mechanisms change pore throat size distributions. These combined effects shift the drainage water relative permeability curve toward higher values of water saturation, and gas relative permeability shifts toward smaller values of gas. Comparison of simulations with measured relative permeabilities shows a good match although same network fail to match drainage curves. This could happens because the model gives the right fluid configuration but at the wrong values of curvature and saturation. The significance of this work is that the model correctly predicts the relative permeabilities of tight gas sandstones by considering the microscale heterogeneity. The porosity reduction due to ductile grain deformation is a new contribution and correctly matches with experimental data from literature. The drainage modeling of two-phase flow relative permeabilities shows that the notion of permeability jail, a range of saturations over which both gas and water relative permeabilities are very small, does not occur during drainage. / text

Landscape connectivity models aim to map the links or corridors that wildlife would or do use between patches of habitat. Migratory species such as elk traverse between such patches which serve as seasonal ranges. The goal of this study was to compare and contrast the suitability of several landscape connectivity models for describing and predicting migration in a long-distance migrant. We measured the suitability of connectivity models for covering and predicting the migratory movements of elk in the Greater Yellowstone Ecosystem. GPS point data was converted to sequential networks for multiple populations of elk. GPS data was also used to delineate the summer and winter ranges of each population. The kernel density of routes in the networks was measured for comparison to connectivity models. The ranges served as the patches to be connected by such models. A resistance surface was produced using reclassified landcover data for mapping habitat suitability and linear road data for human presence or obstruction to movement. Landscape connectivity was measured for eleven migratory elk populations using three distinct models. The first measured connectivity using circuit theory; the second, agent based modeling; the third, least cost corridors. The model results were compared to the migratory network density by measuring correlation. This was followed by a new method of measuring the influence of autocorrelation between the models and networks. Some of the models were then altered to test for suspected influences. This study shows that least cost corridors and circuit theory can are limited in their ability to predict the migratory movements between summer and winter ranges but only so much. They lack the ability to predict exploratory movements that do not link conspicuous ranges to each other. They also lack the ability to account for all avoidance behaviors in the landscape. Our results suggest that connectivity models need improvement by accounting for exploration outside of prime habitat. It also suggests connectivity models are not adequate predictors of migratory movements and not suited to conservation planning of migratory networks. This supports Sawyer's (et al. 2009) ungulate conservation planning of considering connectivity but basing priority on migratory landscape usage. It is assumed that fragmentation or loss in connectivity impedes seasonal migration, cutting off wildlife from resources (Rudnick et al. 2012). This study shows that migratory elk are actually using less than prime and supposedly fragmented habitat in migration and that there is more than connectivity at play.

Die Untersuchung von Zuverlässigkeitsnetzwerken geht bis zum frühen 20. Jahrhundert zurück. Diese Arbeit beschäftigt sich hauptsächlich mit der Zweifach-Kantenzusammenhangswahrscheinlichkeit. Zuerst werden einfache Algorithmen, die aber für allgemeine Graphen nicht effizient sind, gezeigt, zusammen mit Reduktionen. Weiterhin werden Charakterisierungen von Kanten bezogen auf Wegemengen gezeigt. Neue strukturelle Bedingungen für diese werden vorgestellt. Neue Ergebnisse liegen ebenfalls für Graphen hoher Dichte und Symmetrie vor, genauer für vollständige und vollständig bipartite Graphen. Naturgemäß sind Graphen von geringer Dichte hier einfacher in der Untersuchung. Die Arbeit zeigt Ergebnisse für Kreise, Räder und Leiterstrukturen. Graphen mit beschränkter Weg- beziehungsweise Baumweite haben polynomiale Algorithmen und in Spezialfällen einfache Formeln, die ebenfalls vorgestellt werden. Der abschließende Teil beschäftigt sich mit Schranken und Approximationen.

Because American black bears (Ursus americanus) are an important game species in Arizona and are endangered in México, an understanding of the population structure, gene flow, and connectivity are important for effective management. Black bears inhabit coniferous and broadleaf deciduous woodlands in southern Arizona and northern México, usually in sky islands (sky islands are mountains that rise from the desert and are isolated from each other). Because a single sky island is too small to support a viable bear population, black bears move through desert lowlands to reach other sky islands. My objective was to assess genetic structure, connectivity, and conservation implications for sky island black bears in southern Arizona and northern México. I addresses 4 components of bear ecology and genetics: a literature review of genetic information available for black bears in North America; the use of 2 mitochondrial DNA genes (Control Region and ATP synthase protein 8) to study the phylogenetic relationship of black bears from the sky islands of southern Arizona and northern México relative to all North America; the use of 10 microsatellite loci to detect the current genetic structure of black bears in the sky islands in Arizona and northern México; and the use of noninvasive samples collected from the field to determine bear density and population size for black bear in Sierra San Luis, Sonora, México. These studies provide information that can be used by biologists, land managers, and others to assist in the conservation of black bears and their habitat.

<p>Genetic diversity, population structure, and connectivity influence interactions among communities and populations. At hydrothermal vents in the western pacific, population structure in vent-associated species could occur at spatial scales ranging from vent sites separated by a few hundred meters to oceanic basins separated by more than 3000 kilometers. The spatial scale of population structure has important conservation implications; species that are well-connected across large geographic regions are more resilient to natural and anthropogenic disturbance. This dissertation examines the genetic diversity, population structure, and connectivity of 3 vent-associated species in the western Pacific. It first presents results from the development of microsatellite primers for Ifremeria nautilei, a deep-sea vent associated snail, then uses mitochondrial COI sequences and a suite of microsatellite markers to examine the broader connectivity of three vent-associated species, Ifremeria nautilei, Chorocaris sp. 2, and Olgasolaris tollmanni, across three back-arc basins in the western Pacific. </p><p>Within Manus Basin, no significant genetic differentiation was detected in populations of Ifremeria nautilei (based on COI and microsatellite), Chorocaris sp. 2 (based on COI and microsatellite), or Olgasolaris tollmanni (based on COI). A previously documented low-abundance cryptic species, Chorocaris sp. 1, was detected from a single site, South Su (based on COI). The population of I. nautilei in Manus Basin was found to be significantly differentiated from a second population that appeared to be panmictic across North Fiji and Lau Basin (based on COI and microsatellites). Chorocaris sp. 2 was also found to be significantly differentiated between Manus and North Fiji Basin (based on COI). Both I. nautilei and Chorocaris sp. 2 showed signs of potential low-level migration between Manus and other southwestern Pacific basins. O. tollmanni was undifferentiated between Manus and Lau Basin (based on COI). It is likely that a variable impedance filter exists that limits the realized dispersal of some, but not all species between Manus Basin and other western Pacific back-arc basins. The presence of a variable filter has implications for the conservation and management of hydrothermal vents in Manus Basin, as it is unclear what effects sustained anthropogenic disturbance will have on isolated populations of I. nautilei and Chorocaris sp. 2.</p> / Dissertation