Over the 21st century, climate change and wetland habitat loss will pose major threats to the Eastern Massasauga (Sistrurus catenatus), a federally threatened and Great Lakes region endemic rattlesnake. I collected capture-recapture data from sites across the range and modeled the effect of climatic variables on growth rate and asymptotic size. I found that high snow residence time was associated with larger asymptotic sizes but slower growth, while high spring precipitation increased growth rate. I then projected future growth and size under different carbon emission scenarios. Given the threat posed by successional encroachment of woody vegetation, I used spatially explicit capture-recapture models to examine the effects of landscape characteristics and phenology on the spatial distribution of density for a population in Michigan. I found highest density in areas close to a stream and with low vegetation intensity, which can inform prescribed burn programs and give additional insights into life history.

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Semiparametric modeling is a hybrid of the parametric and nonparametric modelings where some function forms are known and others are unknown. In this dissertation, we have made several contributions to semiparametric modeling based on the single index model related to the following three topics: the first is to propose a model for detecting change points simultaneously with estimating the unknown function; the second is to develop two models for spatially correlated data; and the third is to further develop two models for spatially-temporally correlated data. To address the first topic, we propose a unified approach in its ability to simultaneously estimate the nonlinear relationship and change points. We propose a single index change point model as our unified approach by adjusting for several other covariates. We nonparametrically estimate the unknown function using kernel smoothing and also provide a permutation based testing procedure to detect multiple change points. We show the asymptotic properties of the permutation testing based procedure. The advantage of our approach is demonstrated using the mortality data of Seoul, Korea from January, 2000 to December, 2007. On the second topic, we propose two semiparametric single index models for spatially correlated data. One additively separates the nonparametric function and spatially correlated random effects, while the other does not separate the nonparametric function and spatially correlated random effects. We estimate these two models using two algorithms based on Markov Chain Expectation Maximization algorithm. Our approaches are compared using simulations, suggesting that the semiparametric single index nonadditive model provides more accurate estimates of spatial correlation. The advantage of our approach is demonstrated using the mortality data of six cities, Korea from January, 2000 to December, 2007. The third topic involves proposing two semiparametric single index models for spatially and temporally correlated data. Our first model has the nonparametric function which can separate from spatially and temporally correlated random effects. We refer it to "semiparametric spatio-temporal separable single index model (SSTS-SIM)", while the second model does not separate the nonparametric function from spatially correlated random effects but separates the time random effects. We refer our second model to "semiparametric nonseparable single index model (SSTN-SIM)". Two algorithms based on Markov Chain Expectation Maximization algorithm are introduced to simultaneously estimate parameters, spatial effects, and times effects. The proposed models are then applied to the mortality data of six major cities in Korea. Our results suggest that SSTN-SIM is more flexible than SSTS-SIM because it can estimate various nonparametric functions while SSTS-SIM enforces the similar nonparametric curves. SSTN-SIM also provides better estimation and prediction. / Ph. D.

Fluid dynamicists are always in need of innovative instruments for flow velocity measurements. An ideal instrument would be non-intrusive, have a very fine spatial resolution as well as a very fine temporal resolution, be able to measure three-components of velocity, and be compact. Through recent advancements, laser Doppler velocimetry can now meet all of those requirements making it an important part of aerodynamicist's research toolbox. The first paper presented in this manuscript style thesis explains the development of an advanced three-velocity component, spatially-resolving laser-Doppler velocimetry (LDV) system for highly resolved velocity measurements in situations with limited optical access. The new instrument, a next generation version of the previously developed 'comprehensive' LDV technology, enables measurements of three components of velocity and particle position in the axial direction all through a single transceiving lens. Described here is the design process and the final design for the 'compact, comprehensive' LDV (Comp²LDV). The probe was designed to achieve ± 10 micron root-mean-square uncertainties in axial particle position, which combined with the long measurement volume, allow researchers to obtain a three-velocity-component velocity statistics profiles over a span of approximately 1.5mm without the need for traversing. Results from measurements in a flat plate turbulent boundary layer very near the wall have compared favorably to data from previous studies. The second paper focuses on the motion and evolution of coherent structures in supersonic jet flows and how that relates to the intense noise the flows generate. As a preliminary study to experimentally address these relationships, novel non-intrusive measurements using two-component laser Doppler velocimetry (LDV) have been conducted at exceptionally high data rates to lend insight into the statistical behavior of noise-generating flow structures. A new heated supersonic jet facility has been constructed to provide supersonic flow at total temperatures ratios (T₀/Tₐ) up to 3. In the present work, the instrumentation is validated via comparison of LDV measurements along the centerline of a screeching cold jet with microphone and high-speed shadowgraph results. Reynolds stress spectra are presented for an over-expanded case (nozzle pressure ratio of 3.2) of a design Mach number 1.65 nozzle operated cold (T₀/Tₐ = 1). A preliminary study was then conducted in the near-nozzle shear layer, up to x/d = 4.0, at design nozzle pressure ratio (4.58) and total temperature ratio of 2.0. Results are presented for Reynolds stress time-delay correlations and power spectra at Re_d = 1.1M for this case. The stream-wise Reynolds normal stress spectra are compared with published spectral behavior reported by other researchers, indicating a similar spectral shape in the downstream stations as previously measured with LDV and hot wire anemometry for cold jets, but which differ in shape from density-based techniques. / Master of Science

Tigers (Panthera tigris tigris) can be viewed as a proxy for intact and healthy ecosystems. Their wild populations have plummeted to fewer than 3,200 individuals in the last four decades and threats to these apex predators are mounting rather than diminishing. Global conservation bodies (Global Tiger Initiative, World Wildlife Fund, Wildlife Conservation Society, Panthera etc.) have recently called for solidarity and scaling up of conservation efforts to save tigers from extinction. In South Asia, tiger habitat ranges from tropical evergreen forests, dry arid regions and sub-tropical alluvial floodplains, to temperate mixed deciduous forest. The churia habitat is relatively unstudied and is considered a young and geologically fragile mountain range in Nepal. The contribution of the churia habitat to tiger conservation has not been considered, since modern conservation started in 1970's. This study focuses on the ecology of the tiger with respect to population density, habitat use, and prey occupancy and density, in the churia habitat of Chitwan National Park. This study also includes the first assessment of genetic diversity, genetic structure, and gene flow of tigers across the Terai Arc Landscape- Nepal. The Terai Arc Landscape harbors the only remaining tiger population found across the foothills of the Himalayas in Nepal and northwest India. I used a combination of camera-trapping techniques, which have been a popular and robust method for monitoring tiger populations across the landscape, combined with a noninvasive genetic approach to gain information on tigers, thus adding new information relevant to global tiger conservation. I investigated tiger, leopard (Panthera pardus fusca), and prey densities, and predicted the tiger density across the Churia habitat in Chitwan National Park. I used a camera-trap grid with 161 locations accumulating 2,097 trap-nights in a 60 day survey period during the winter season of 2010-2011. Additionally, I used distance sampling techniques for estimating prey density in the churia habitat by walking 136 km over 81 different line transects. The team photographed 31 individual tigers and 28 individual leopards along with 25 mammalian species from a sampling area of 536 km² comprising Churia and surrounding areas. Density estimates of tigers and leopards were 2.2 (SE 0.42) tigers and 4.0 (SE 1.00) leopards per 100 km². Prey density was estimated at 62.7 prey animals per 100 km² with contributions from forest ungulates to be 47% (sambar Rusa unicolor, chital Axis axis, barking deer Muntiacus muntjak, and wild pigs Sus scrofa). Churia habitat within Chitwan National Park is capable of supporting 5.86 tigers per 100 km² based on applying models developed to predict tiger density from prey density. My density estimates from camera-traps are lower than that predicted based on prey availability, which indicates that the tiger population may be below the carrying capacity. Nonetheless, the churia habitat supports 9 to 36 tigers, increasing estimates of current population size in Chitwan National Park. Based on my finding, the Churia habitat should no longer remain ignored because it has great potential to harbor tigers. Conservation efforts should focus on reducing human disturbance to boost prey populations to potentially support higher predator numbers in Churia. I used sign surveys within a rigorous occupancy framework to estimate probability of occupancy for 5 focal prey species of the tiger (gaur Bos gaurus, sambar, chital, wild pig, and barking deer); as well as probability of tiger habitat use within 537 km² of churia habitat in Chitwan National Park. Multi-season, auto-correlation models allowed me to make seasonal (winter versus summer) inferences regarding changes in occupancy or habitat use based on covariates influencing occupancy and detection. Sambar had the greatest spatial distribution across both seasons, occupying 431-437 km² of the churia habitat, while chital had the lowest distribution, occupying only 100-158 km². The gaur population showed the most seasonal variation from 318- 413 km² of area occupied, with changes in occupancy suggesting their migration out of the lowland areas in the summer and into the churia in the winter. Wild pigs showed the opposite, moving into the churia in the summer (444 km² area occupied) and having lower occupancy in the winter (383 km²). Barking deer were widespread in both seasons (329 - 349 km²). Tiger probability of habitat use Ψ SE(Ψ) was only slightly higher in winter 0.63 (SE 0.11) than in summer 0.54 (SE 0.21), but confidence intervals overlapped and area used was very similar across seasons, from 337 - 291 km². Fine-scale variation in tiger habitat use showed that tigers intensively use certain areas more often than others across the seasons. The proportion of available habitat positively influenced occupancy for the majority of prey species and tigers. Human disturbance had a strong negative influence on the distribution of the majority of prey species but was positively related to tiger habitat use. Tigers appear to live in areas with high disturbance, thus increasing the risk of human-tiger conflict in the churia habitat. Thus, efforts to reduce human disturbance would be beneficial to reducing human wildlife conflict, enriching prey populations, and would potentially support more tigers in churia habitat of Nepal. Overall, I found high prey occupancy and tiger habitat use, suggesting that the churia is highly valuable habitat for tigers and should no longer be neglected or forgotten in tiger conservation planning. Thirdly, I assessed genetic variation, genetic structure, and gene flow of the tigers in the Terai Arc Landscape, Nepal. I opportunistically collected 770 scat samples from 4 protected areas and 5 hypothesized corridors across the Terai Arc Landscape. Historical landuse change in the Terai Arc was extracted from Anthrome data sets to relate landuse change to potential barriers and subsequent hypothesized bottleneck events in the landscape. I used standard genetic metrics (allelic diversity and heterozygosity) to estimate genetic variation in the tiger population. Using program Structure (non-spatial) and TESS (spatial), I defined the putative genetic clusters present in the landscape. Migrant analysis was carried out in Geneclass and Bayesass for estimating contemporary gene flow. I tested for a recent population bottleneck with the heterozygosity test using program Bottleneck. Of the 700 samples, 396 were positive for tiger (57% success). Using an 8 multilocus microsatellite assay, I identified 78 individual tigers. I found large scale landuse changes across the Terai Arc Landscape due to conversion of forest into agriculture in last two centuries and I identified areas of suspected barriers. I found low levels of genetic variation (expected heterozygosity = 0.61) and moderate genetic differentiation (F_ST = 0.14) across the landscape, indicative of sub-population structure and potential isolation of sub-populations. I detected three genetic clusters across the landscape consistent with three demographic tiger sub-populations occurring in Chitwan-Parsa, Bardia, and Suklaphanta protected areas. I detected 10 migrants across all study sites confirming there is still some dispersal mediated gene flow across the landscape. I found evidence of a bottleneck signature, especially around the lowland forests in the Terai, likely caused by large scale landuse change in last two centuries, which could explain the low levels of genetic variation detected at the sub-population level. These findings are highly relevant to tiger conservation indicating that efforts to protect source sites and to improve connectivity are needed to augment gene flow and genetic diversity across the landscape. Finally, I compared the abundance and density of tigers obtained using two non-invasive sampling techniques: camera-trapping and fecal DNA sampling. For cameras: I pooled the 2009 camera-trap data from the core tiger population across the lowland areas of Chitwan National Park. I sampled 359 km² of the core area with 187 camera-trap locations spending 2,821 trap-nights of effort. I obtained 264 identifiable photographs and identified a total of 41 individual tigers. For genetics, I sampled 325 km² of the core area along three spatial routes, walking a total of 1,173 km, collecting a total of 420 tiger fecal samples in 2011. I identified 36 tigers using the assay of 8 multilocus genotypes and captured them 42 times. I analyzed both data types separately for estimating density and jointly in an integrated model using both traditional, and spatial, capture-recapture frameworks. Using Program MARK and the model averaged results, my abundance estimates were 46 (SE 1.86) and 44 (SE 9.83) individuals from camera and genetic data, respectively. Density estimates (tigers per 100 km²) via traditional buffer strip methods using half of the Mean Maximum Distance Moved (½ MMDM) as the buffer surrounding survey grids, were 4.01 (SE 0.64) for camera data and 3.49 (SE 1.04) for genetic data. Spatially explicit capture recapture models resulted in lower density estimates both in the likelihood based program DENSITY at 2.55 (SE 0.59) for camera-trap data and 2.57 (SE 0.88) for genetic data, while the Bayesian based program SPACECAP estimates were 2.44 (SE 0.30) for camera-trap data and 2.23 (SE 0.46) for genetic data. Using a spatially explicit, integrated model that combines data from both cameras and genetics, density estimates were 1.47 (SD 0.20) tigers per 100 km² for camera-trap data and 1.89 (SD 0.36) tigers per 100 km² for genetic data. I found that the addition of camera-trap data improved precision in genetic capture-recapture estimates, but not visa-versa, likely due to low numbers of recaptures in the genetic data. While a non-invasive genetic approach can be used as a stand-alone capture-recapture method, it may be necessary to increase sample size to obtain more recaptures. Camera-trap data may provide a more precise estimates, but genetic data returns more information on other aspect of genetic health and connectivity. Combining data sets in an integrated modeling framework, aiding in pinpointing strengths and weaknesses in data sets, thus ultimately improving modeling inference. / Ph. D.

Carnivore are undoubtedly among the most threatened of the mammal species in Africa because of the low density at which they occur and their large home range requirements that do not match with human propensity to develop and alter wildlife habitat. However, the degree of threat is unevenly distributed within the continent, with western and central African carnivores being the most threatened and the least studied. I estimated population size, density, and proportion of area occupied in relation to environmental factors of one medium-size (serval – Leptailurus serval) and two large carnivores (lion – Panthera leo and leopard – P. pardus) in the Niokolo Koba National Park, Senegal, West Africa, using remote camera surveys and both traditional (CR), spatially explicit capture-recapture (SECR) techniques for servals and leopards, and non-spatial (MR) and spatial mark resight (SMR) methods for lions. Lions selected optimal sites with both high tree density and prey activity; leopards occupied areas with high tree density but with less prey activity; and servals selected habitats with more dense canopy cover where leopards were absent. The presence of lions was favorable to serval presence, as we presume leopards avoid lions, although we did not have strong evidence to support it. Moreover, the half mean maximum distance moved (½ MMDM) method under CR methods appeared to overestimate leopard and serval density while full MMDM estimates were close to SECR methods density estimates. For lions, both ½ MMDM and full MMDM methods in MR framework overestimated density whereas the SMR method resulted in more reasonable estimates, especially in light of previous assessments of lion densities in West Africa.. These results are of high importance for conservation and management purposes of the imperiled Niokolo Koba carnivore community. / Master of Science

Although it has been well established that abnormal group delay is a real physical phenomenon and is not in violation of Einstein causality, there has been little investigation into whether or not such abnormal behaviour can be used to reduce signal latency in practical communication systems in the presence of noise. In this thesis, we use time-varying probability of error to determine if abnormal group delay “channels” can offer reduced signal latency. Since the detection system plays a critical role in the analysis, three important detection systems are considered: the correlation, matched filter and envelope detection systems. Our analysis shows that for both spatially negligible microelectronic systems and spatially extended microwave systems, negative group delay “channels” offer reduced signal latency as compared to conventional “channels”. The results presented in the thesis can be used to design a new generation of electronic and microwave interconnects with reduced or eliminated signal latency.

Although it has been well established that abnormal group delay is a real physical phenomenon and is not in violation of Einstein causality, there has been little investigation into whether or not such abnormal behaviour can be used to reduce signal latency in practical communication systems in the presence of noise. In this thesis, we use time-varying probability of error to determine if abnormal group delay “channels” can offer reduced signal latency. Since the detection system plays a critical role in the analysis, three important detection systems are considered: the correlation, matched filter and envelope detection systems. Our analysis shows that for both spatially negligible microelectronic systems and spatially extended microwave systems, negative group delay “channels” offer reduced signal latency as compared to conventional “channels”. The results presented in the thesis can be used to design a new generation of electronic and microwave interconnects with reduced or eliminated signal latency.

Estimates of animal abundance or density are fundamental quantities in ecology and conservation, but for many species such as rare, small mammals, obtaining robust estimates is problematic. In this thesis, I combine elements of two standard abundance estimation methods, capture-recapture and distance sampling, to develop a method called trapping point transects (TPT). In TPT, a "detection function", g(r) (i.e. the probability of capturing an animal, given it is r m from a trap when the trap is set) is estimated using a subset of animals whose locations are known prior to traps being set. Generalised linear models are used to estimate the detection function, and the model can be extended to include random effects to allow for heterogeneity in capture probabilities. Standard point transect methods are modified to estimate abundance. Two abundance estimators are available. The first estimator is based on the reciprocal of the expected probability of detecting an animal, ^P, where the expectation is over r; whereas the second estimator is the expectation of the reciprocal of ^P. Performance of the TPT method under various sampling efforts and underlying true detection probabilities of individuals in the population was investigated in a simulation study. When underlying probability of detection was high (g(0) = 0:88) and between-individual variation was small, survey effort could be surprisingly low (c. 510 trap nights) to yield low bias (c. 4%) in the two estimators; but under certain situations, the second estimator can be extremely biased. Uncertainty and relative bias in population estimates increased with decreasing detectability and increasing between-individual variation. Abundance of the Key Largo woodrat (Neotoma floridana smalli), an endangered rodent with a restricted geographic range, was estimated using TPT. The TPT method compared well to other viable methods (capture-recapture and spatially-explicit capture-recapture), in terms of both field practicality and cost. The TPT method may generally be useful in estimating animal abundance in trapping studies and variants of the TPT method are presented.