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This project aimed to reanalyse two large historical data sets from two different locations in New Zealand (Fiordland in the South Island and Pureora Forest Park in the North Island). The data describe populations of mice (Mus musculus), rats (Rattus rattus and R. norvegicus), and stoats (Mustela erminea) collected using standard monitoring techniques from five distinct types of forest habitat. The new analysis methods selected were an index of patchiness and Site Occupancy analysis. The objectives of the analysis were (1) to evaluate whether the patchiness index and Site Occupancy analysis methods might contribute to improved protocols for monitoring small mammal populations in the future, and (2) to use formal tests of five hypotheses to evaluate two of the assumptions made by the conventional density index often used in small mammal studies. I describe the results of the analyses for each species, including any problems encountered (such as the inability of the Site Occupancy method to analyse very sparse data sets). I also describe the results pooled from each of the two study locations and potential consequences for small mammal monitoring and control. This analysis has suggested that in most cases the density index is not a rigorous measure of small mammal populations. However, both the index of patchiness and Site Occupancy analysis provided useful, new information about these populations of rodents and stoats, despite the fact that these historical data sets were not designed for use with modern methods of analysis. Please note: some figures and tables were printed separately and added to the thesis as unnumbered pages. These can be found in the file 03Plates_and_Tables.pdf.

Effective conservation requires efficient population monitoring, which can be challenging for rare species like the desert tortoise (Gopherus agassizii). We compared two alternative survey methods that can be used to monitor tortoise populations: distance sampling and site occupancy estimation. In 2005 and 2006 combined, we surveyed 120 1-km transects to estimate density and 40 3-ha plots with five presence-“absence” surveys to estimate occupancy of Sonoran desert tortoises in two mountain ranges in southern Arizona. We found that monitoring programs based on an occupancy framework were more efficient and had greater power to detect linear trends. We also found that habitat use by Sonoran desert tortoises was influenced most by slope and aspect, contrasting with patterns observed in the Mojave Desert. Given its efficiency, power, and ability to gauge changes in distribution while accounting for variation in detectability, occupancy offers a promising alternative for long-term monitoring of Sonoran desert tortoise populations.

New thin-film solar cell materials and a greater understanding of their properties are needed to meet the urgent demand for sustainable, lower-cost and scalable photovoltaics. Computational techniques have been used to investigate Cu2ZnSnS4, CuSbS2 and CuBiS2 , which are potential absorber layer materials in thin-film photovoltaics. Their low cost, low toxicity and their constituent’s relative abundance make them suitable replacements for current thin-film absorbers, which are CdTe or Cu(In, Ga)(S, Se)2 based systems. Firstly, we have used hybrid Density Functional Theory (DFT) calculations to study CuSbS2 and CuBiS2. We calculate band gaps of 1.69 eV and 1.55 eV respectively, placing CuBiS2 within the optimal range for a viable absorber material. The density of states for both these materials indicate that formation of electron hole charge carriers will occur in the Cu d10 band. Consequently, photoexcitation leads to the oxidation of Cu(I). Secondly, we have derived interatomic potentials which describe the complex structure of Cu2ZnSnS4 accurately. We find that the Cu/Zn antisite defect represents the lowest energy form of intrinsic defect disorder. For these antisite defects, we find a preference for small neutral defect clusters, which suggests a degree of self-passivation exists. Investigations of Cu-ion transport find VCu migration is possible via a vacancy hopping mechanism. There are pathways which can be connected to give 3D long-range diffusion. Investigations of the Cu/Zn site disorder in Cu2ZnSnS4 find that configurations which are kesterite-like will dominate synthetic samples. However, perfectly ordered kesterite will not be formed due to entropic effects. The simulations indicate the stannite and stannite-like polymorphs are less favourable, and can only account for ≈2.5% of a sample. Investigations of the surfaces of Cu2ZnSnS4, suggest that the vast majority of the low index surfaces are dipolar and that only the (1 1 2), (0 1 0) and (1 0 1) surfaces have low surface energies.

Wildlife in urban settings are a management challenge because wildlife populations and their habitats are often fragmented and degraded, but natural resource managers need information concerning their spatial distribution, spatial turnover, and spatial co-occurrence while accounting for imperfect detection. Based in the Chicago Metropolitan Area during 2009-2012, my study modeled 23 species across 5 wildlife taxa concerning patterns of site occupancy, spatial turnover (i.e., colonization and extinction), and/or spatial co-occurrence at 1-2 spatial scales. In detail, I investigated: (1) detection probabilities, site occupancy, and spatial turnover as affected by habitat and anthropogenic influences at 2 spatial scales for 6 species of songbirds: field sparrows (Spizella pusilla), great crested flycatchers (Myiarchus crinitus), willow flycatchers (Empidonax traillii), bobolinks (Dolichonyx oryzivorus), marsh wrens (Cistothorus palustris), and rose-breasted grosbeaks (Pheucticus ludovicianus); (2) detection probabilities, site occupancy, and spatial turnover as affected by habitat and anthropogenic influences at 2 spatial scales for 3 species of reptiles and 4 species of amphibians: common garter snakes (Thamnophis sirtalis), painted turtles (Chrysemys picta), snapping turtles (Chelydra serpentina), blue-spotted salamanders (Ambystoma laterale), tiger salamanders (Ambystoma tigrinum), green frogs (Rana clamitans), and northern leopard frogs (Rana pipiens); (3) habitat use and landscape site occupancy and spatial turnover as affected by habitat and anthropogenic influences for 4 species of mesocarnivores: coyotes (Canis latrans), raccoons (Procyon lotor), striped skunks (Mephitis mephitis), and Virginia opossums (Didelphis virginiana); and (4) detection probabilities and spatial distributions as affected by local habitat, an interacting species (dominant or subordinate), or both for 6 species of small mammals: short-tailed shrews (Blarina brevicauda), meadow voles (Microtus pennsylvanicus), white-footed mice (Peromyscus leucopus), gray squirrels (Sciurus carolinensis), masked shrews (Sorex cinereus), and eastern chipmunks (Tamias striatus). I elucidate how managers can improve or design their survey techniques that will aid their inference of the distribution of wildlife in the Midwest. This work also provides suburban natural resource managers in the Chicago Metropolitan Area with information concerning land management and land acquisition guidelines to best conserve, attract, or deter the aforementioned wildlife on their properties.

The spatial distribution of a species is not random or uniform across all landscapes, nor is it independent of resource availability and risk of predation. A key aspect in the study of wildlife ecology is understanding how a species evaluates its surroundings and selects habitat that offers advantages to survival and reproductive success. In theory, an individual should select habitat that offers adequate resources to meet its biological requirements and allows it to adjust its use of resources based on a variety of abiotic and biotic habitat factors. Relationships between wildlife populations and habitat characteristics are difficult to assess, yet identification and characterization of these relationships can improve delineation of limiting habitat factors needed for effective conservation and management. The eastern spotted skunk (Spilogale putorius) is a small Mephitid (weasel family) that was once a fairly common furbearer throughout the central and southern United States, with annual range-wide harvests of over 100,000 individuals. In Virginia, the spotted skunk is classified as vulnerable, and anecdotal evidence suggests that this species has been rare or largely absent from the central and southern Appalachians over the last two decades. Limited knowledge of spotted skunk habitat associations in Virginia dictate the need for research on this species of concern. The aim of this study was to determine the associations of environmental characteristics ofwith spotted skunk habitat selection and genetic differentiation. I assessed first-order habitat selection by conducting an analysis of predicted occurrence at the landscape scale. Next, I assessed second- and third-order selection using resource utilization functions to determine habitat selection among, and within, home ranges. Further, I assessed fourth-order selection by identifying microhabitat selection and resource use at spotted skunk den site. Finally, I evaluated genetic diversity and population structure of spotted skunks in the Appalachian Mountains. I found that spotted skunk habitat is distributed in small, spatially disjunct patches and that movement, home range size, and resource selection are impacted by availability of habitat and the isolation and/or fragmentation of this suitable habitat. I found overall low genetic diversity and evidence of inbreeding within populations and geographic patterns of genetic differentiation with distinct subpopulations isolated by unsuitable landscape characteristics. Application of these results will contribute to more effective conservation of eastern spotted skunks throughout the Appalachian Mountains. / Doctor of Philosophy / Wildlife species do not occur throughout the landscape randomly or evenly, but rather choose their locations based on the availability of food, cover, and water. A key aspect in the study of wildlife ecology is understanding how a species chooses its natural surroundings and selects habitat that allows it to survive and reproduce. In theory, an animal should choose a location that offers enough resources, such as food, cover, and water to meet its biological needs and allows it to adjust based on access to these resources. By understanding the how the availability of these resources influences an animal's choice of location, wildlife managers can better determine the need for protection or management of the species in a given area. The eastern spotted skunk (Spilogale putorius) is a small, weasel-like animal that was once fairly common throughout the central and southern United States. In Virginia, the spotted skunk is a protected species, and experts suggest that it has been rare in the central and southern Appalachians for over several decades. Because there is limited knowledge of spotted skunk habitat needs in Virginia, research on this species is necessary. The goals of this study were to determine the type of habitat in which spotted skunks are choosing and how it affects the species genetic makeup. First, I determined in which general areas spotted skunks exist in Virginia. Next, I determined that the habitat for spotted skunks includes forests with ample bushy plants and rocks to hide from predators. I then examined the genetics of spotted skunks to determine relatedness among individuals and whether inbreeding was occurring. Finally, I compared the relatedness of pairs of spotted skunks to the distance between their locations and found that skunks that are located on the same mountain range are more closely related to each other than to skunks on different mountain ranges. These results will inform wildlife managers on how to provide spotted skunks with the habitat resources they need to survive and reproduce successfully, thus promoting skunk conservation.

In this study the effect of hydrogenation on the optical properties in the wavelength range 400-1023 nm of an ultrathin iron-vanadium superlattice is investigated. Specifically, mea- surements of transmission are performed under different states of hydrogenation, along with measurements of absolute hydrogen concentration and hydrogen site occupancy. The trans- mission measurements are used to construct pressure-concentration isotherms. Isotherms and transmission data are in turn correlated to concentration and hydrogen occupancy.  The results show a wavelength dependent decrease in transmission with hydrogenation. The decrease is greatest around 550 nm, and the wavelength of maximum decrease shifts to higher wavelengths with increasing hydrogen pressure. The non-uniform decrease will make the use of transmission as a measurement of hydrogen concentration dependent on the wavelength of the probing light.  15N resonant NRA is used to perform direct, real-space measurement of absolute hydro- gen concentration. The achieved concentrations are 0.092, 0.38 0.40 H/V. Comparing the concentrations and corresponding transmissions to the location of the plateau region in the transmission based isotherms, it appears that the system is in a single phase at 0.38 and 0.40 H/V, and in a mixed phase at 0.092 H/V. Using a combination of resonant NRA and RBS, while exploiting crystal lattice ion channeling, indirect measurements of hydrogen site occupancy are performed. At all investigated concentrations the system does not display tetrahedral site occupancy, but it remains uncertain whether the occupancy is octahedral or some dislocated octahedral-tetrahedral intermediate.  The relation of hydrogen concentration and optical transmission is investigated via a linear regression analysis. The data points generally deviate by more than one standard deviation from the fitted lines, and lie outside of the error estimation. These deviations might indicate that a linear model is inappropriate, where one possible explanation could be that the mapping from transmission to concentration is dependent on the phase of the system. / Den här studien undersöker upptag av väte i en supertunn kristallstruktur bestående av omväxlande lager av vanadin och järn, samt vätets inverkan på de optiska egenskaperna i våglängdsområdet 400-1023 nm. Specifikt genomförs mätningar av genomsläpp av ljus, under olika nivåer av väteupptag. I samband med dessa mätningar genomförs också mätningar av absolut vätekoncentration och av väteatomernas position i kristallstrukturen. Mätningarna av ljusgenomsläpp används för att skapa isotermkuror över tryck och koncentration. Isotermkurvorna och genomsläppligheten av ljus korreleras till vätekoncentration och väteatomernas position i kristallstrukturen.  Resultaten visar en våglängdsberoende minskning av ljusgenomsläppligheten med en ökande mängd väte i kristallstrukturen. Minskningen är som störst omkring 550 nm, samtidigt som våglängden för störst minskning flyttas mot högre våglängder med högre koncentration av väte. Att minskningen i genomsläpplighet är beroende av våglängd innebär att ljusgenomsläpp som metod för att mäta vätekoncentration är beroende av den ljusvåglängd som används. Metoden 15N resonant NRA används för att genomföra direkta mätningar av absolut vätekoncentration. De uppmätta koncentrationerna är 0.092, 0.38 och 0.40 H/V. När dessa koncentrationsmätningar jämförs med genomsläpplighet och tillhörande isotermkurvor, så verkar det som att systemet befinner sig i en enskild fas vid koncentrationerna 0.38 och 0.40 H/V, och i en blandad fas vid koncentrationen 0.092 H/V. Indirekta mätningar av vätets position i kristallstrukturen genomförs baserat på en kombination av resonant 15N NRA och RBS, där det utnyttjas att projektiljonerna under vissa förutsättningar kan komma att styras in i kristallstrukturen (på engelska crystal lattice ion channeling). Vid de tre uppmätta koncentrationerna så visar systemet inga tecken på att väteatomerna finns på tetrahedrala positioner. Det är inte helt uppenbart om väteatomerna istället finns på oktahedrala positioner, eller om det handlar om förskjutna positioner som är mellanliggande till oktahedrala och tetrahedrala. Relationen mellan vätekoncentration och optisk genomsläpplighet analyseras med linjär regression. Datapunkterna avviker generellt med mer än en standardavvikelse från de anpassade linjerna, och ligger utanför feluppskattningen. De här avvikelserna kan indikera att en linjär modell inte är lämplig, och en möjlig förklaring kan vara att ljusgenomsläppligheten beror av den fas i vilken systemet befinner sig.

<p>Patterns of site occupancy among boreal stream insects were studied in central Sweden with focus on sparsely distributed species and the role of dispersal and niche limitations.</p><p>In the study of dispersal limitation, I found that effects of an extraordinarily harsh winter in small to medium-sized streams were strongest in sites located in small streams and far from lake outlets. Species richness and the total abundance of macroinvertebrates and trout returned to pre-disturbance levels after three years. However, some species showed slow recolonization and the proportion of holoaquatic taxa was still reduced after three years. In a second study, I found a positive correlation between site occupancy in stream caddisflies and morphological traits associated with fast and energy-efficient flight, whereas specialized spring caddisflies showed a negative correlation to these traits compared to stream species. This suggested that streams, but not springs, select for strong dispersal ability in caddisflies. In a survey of springs in central Sweden, hydrogeology was found to be a useful predictor of the occurrence of spring specialists. Two of these, <i>Crunoecia irrorata</i> Curtis and <i>Parachiona picicornis</i> (Pictet), were found exclusively in glaciofluvial springs, characterized by a stable discharge and temperature. Less specialized members of the spring fauna (i.e. species also occurring in streams, ponds or lakes) also occurred in moraine and limestone springs characterized by more unstable conditions. </p><p>Niche limitations were studied by contrasting large-scale distributions of closely related rare and common stoneflies. Differences in temperature requirements in the juvenile stages and life cycles suggested that the rare species, <i>Isogenus nubecula</i> Newman, was restricted by a limited tolerance to low stream temperatures, whereas the two common species, <i>Isoperla grammatica</i> (Poda) and <i>Diura nanseni</i> (Kempny), appeared to have a broader tolerance to climatic conditions in the study area. In a second study of niche limitations, macroinvertebrate assemblages in 88 streams in Central Sweden showed a nested distribution pattern. Most species deviating from expected distributions occurred in small streams, indicating competitive exclusion from species-rich sites, predator avoidance, or specialization to unique habitat features of small streams. In the last paper, the longitudinal distribution of filter-feeding caddisflies in a lake-outlet stream demonstrated patterns concordant to feeding specialization. </p>

Patterns of site occupancy among boreal stream insects were studied in central Sweden with focus on sparsely distributed species and the role of dispersal and niche limitations. In the study of dispersal limitation, I found that effects of an extraordinarily harsh winter in small to medium-sized streams were strongest in sites located in small streams and far from lake outlets. Species richness and the total abundance of macroinvertebrates and trout returned to pre-disturbance levels after three years. However, some species showed slow recolonization and the proportion of holoaquatic taxa was still reduced after three years. In a second study, I found a positive correlation between site occupancy in stream caddisflies and morphological traits associated with fast and energy-efficient flight, whereas specialized spring caddisflies showed a negative correlation to these traits compared to stream species. This suggested that streams, but not springs, select for strong dispersal ability in caddisflies. In a survey of springs in central Sweden, hydrogeology was found to be a useful predictor of the occurrence of spring specialists. Two of these, Crunoecia irrorata Curtis and Parachiona picicornis (Pictet), were found exclusively in glaciofluvial springs, characterized by a stable discharge and temperature. Less specialized members of the spring fauna (i.e. species also occurring in streams, ponds or lakes) also occurred in moraine and limestone springs characterized by more unstable conditions. Niche limitations were studied by contrasting large-scale distributions of closely related rare and common stoneflies. Differences in temperature requirements in the juvenile stages and life cycles suggested that the rare species, Isogenus nubecula Newman, was restricted by a limited tolerance to low stream temperatures, whereas the two common species, Isoperla grammatica (Poda) and Diura nanseni (Kempny), appeared to have a broader tolerance to climatic conditions in the study area. In a second study of niche limitations, macroinvertebrate assemblages in 88 streams in Central Sweden showed a nested distribution pattern. Most species deviating from expected distributions occurred in small streams, indicating competitive exclusion from species-rich sites, predator avoidance, or specialization to unique habitat features of small streams. In the last paper, the longitudinal distribution of filter-feeding caddisflies in a lake-outlet stream demonstrated patterns concordant to feeding specialization.

Over the past 100–150 years Texas rangelands have dramatically changed from native open savannahs to dense woodlands. On the Edwards plateau, a major management concern is the increasing encroachment of Ashe juniper (Juniperus ashei). Preceding an anticipated brush management program, I investigated the presence, co-occurrence, and habitat relationships of 7 breeding bird species in the Leon River Watershed in central Texas, USA: black-capped vireo (Vireo atricapillus), golden-cheeked warbler (Dendroica chrysoparia), northern bobwhite (Colinus virginianus), white-eyed vireo (Vireo griseus), Bell’s vireo (Vireo bellii), painted bunting (Passerina ciris), and brown-headed cowbird (Molothrus ater). Vegetation characteristics were compared between sites occupied by each species and unoccupied sites using univariate analysis. Models for predicting species site occupancy were developed (using logistic regression) based on habitat characteristics correlated with the presence of each species. Two species of special concern, the endangered black-capped vireo and golden-cheeked warbler occupied 5.6% of sites and 13.8% of sites respectively, while the brood parasite brown-headed cowbird was the most widespread, occupying 86.8% of sites. Species co-occurrence patterns revealed significant associations between the golden-cheeked warbler and each of 5 other species. For most species, variables included in habitat models could be explained by knowledge of species known habitat associations. For example, the black-capped vireo was positively associated with increasing low-growing (<1.5 m) hardwood cover and with Low Stony Hill ecological sites. The golden-cheeked warbler was positively associated with increasing density of larger juniper trees, increasing variability in vertical vegetation structure, and decreasing midstory canopy of deciduous nonoaks (e.g., cedar elm [Ulmus crasifolia]). It also preferred Low Stony Hill and Steep Adobe ecological sites. Site occupancy seemed to be driven by variables that describe overall vegetation structure. In particular, cover of low-growing non-juniper vegetation and juniper tree density appeared to be important in determining site occupancy for several species. Although the models constructed were not very robust, resource managers can still benefit from such models because they provide a preliminary examination of important controlling variables. Managing rangelands to maintain or restore a mosaic of juniper patches and open shrublands are likely to help meet the habitat requirements of these bird communities.