Made available in DSpace on 2016-06-02T20:06:11Z (GMT). No. of bitstreams: 1 DissMP.pdf: 748309 bytes, checksum: b6a638a5f9ec09f6622480b42f13d699 (MD5) Previous issue date: 2006-02-22 / Financiadora de Estudos e Projetos / This work has as main objective to insert covariates in the capture probability of the multiple capture-recapture method for closed animal population. Factors like climate, seasons of the year, animal size, could a¤ect the animal capture probability. We revise the methodology concepts, we make a study about the posteriori parameters sensibility, we present new parameters for the capture probability in specific situations and we insert covariates in the model used by Castledine (1981) through bayesian methods. The bayesian analysis was made through several studies of stochastic simulation through MCMC (Monte Carlo Markov Chain) with simulated and real data to obtain the population size posteriori results. / Este trabalho tem como objetivo principal a inserção de covariáveis nas probabilidades de captura do método de captura-recaptura múltipla para população fechada. No caso de população animal, por exemplo, fatores como clima, época do ano, tamanho do animal, podem afetar a probabilidade de captura do animal. Revisamos os conceitos da metodologia, fazemos um breve estudo sobre a sensibilidade das estimativas a posteriori em relação a escolha dos hiperparâmetros, apresentamos uma reparametrização para a probabilidade de captura em situações específicas e, motivados nessa reparametrização, inserimos covariáveis no modelo proposto por Castledine (1981) por meio de métodos bayesianos. A análise bayesiana foi feita através de vários estudos de simulação estocástica via MCMC (Monte Carlo Markov Chain) com dados simulados e reais para obter os resultados a posteriori do tamanho populacional.

Pour comprendre l'origine des variations d'histoire de vie des organismes, il fautétudier et mettre en évidence les stratégies d'histoire de vie et les processus évolutifsqui les gouvernent. Ce travail de thèse a pour objectif d'étudier les stratégiesd'histoire de vie et leur conditionnement par les caractéristiques individuellesen conditions naturelles. Les stratégies d'histoire de vie sont vues comme un agencementde normes de réactions et de compromis évolutifs. Cependant, l'étude desprocessus évolutifs en milieu naturel se heurte à des problèmes d'ordre méthodologique.En effet, le suivi exhaustif au cours du temps d'individus d'une populationest difficilement réalisable, voire impossible en conditions naturelles. Les méthodesde capture-marquage-recapture permettent une observation partielle des histoires devie et des traits d'histoire de vie. Ce travail se base sur l'idée que nos observationsne sont que la partie visible de processus sous-jacents qu'il est nécessaire de prendreen compte pour ne pas biaiser nos inférences statistiques. J'utilise la modélisation àstructure cachée pour 1) séparer le processus d'observation du processus dynamiqued'intérêt, 2) modéliser les histoires de vie complètes des individus, 3) intégrer dansun cadre unique et cohérent les décisions d'histoire de vie et les compromis évolutifset 4) représenter explicitement les mécanismes sous-jacents qui génèrent nos observations.Dans ce cadre, on peut alors intégrer les théories et concepts de la biologieévolutive dans l'analyse statistique des données d'observations. J'illustre ce travailpar l'étude du conditionnement des stratégies d'histoire de vie dans une populationnaturelle de saumon Atlantique sur le Scorff (Morbihan) à partir de données de CMR.Mes résultats mettent en évidence des décisions d'histoire de vie statut-dépendanteset des compromis évolutifs qui n'auraient pas pu être mis en évidence hors du cadrede modélisation proposé. / Understanding the origin of life history variations of organisms requires studying life historystrategies and evolutionary processes that drive them. This thesis aims at studying life historystrategies under natural conditions and how they are conditioned by individual characteristics.Life history strategies are seen as a combination of reaction norms and evolutionarytrade-offs. The study of evolutionary processes in the wild faces to methodological issues.Indeed, the exhaustive monitoring of individuals over time is often impossible in the wild.Capture-mark-recapture methods allow a partial observation of life histories and life historytraits. This work was based on the idea that our observations are only the visible part ofunderlying processes that need to be accounted for to limit the risk of flawed statistical inferences.I resort to hidden structure modeling to 1) separate the observation process fromthe dynamic process of interest, 2) model the full life histories of individuals, 3) integratewithin a single and coherent framework life history decisions and evolutionary trade-offs and4) explicitly represent the underlying mechanisms that generate our observations. Withinthis framework, one can confront theories and concepts in evolutionary biology with observationaldata through appropriate statistical tools. Finally, I illustrate this work by studying theconditioning of life-history strategies in a natural population of Atlantic salmon on the Scorffriver (Morbihan) using CMR data. My results highlight status-dependent life history decisionsand evolutionary trade-offs that could not be identified without our proposed modelingframework.

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.

Ecological inquiry is rooted fundamentally in understanding population abundance, both to develop theory and improve conservation outcomes. Despite this importance, estimating abundance is difficult due to the imperfect detection of individuals in a sample population. Further, accounting for space can provide more biologically realistic inference, shifting the focus from abundance to density and encouraging the exploration of spatial processes. To address these challenges, Spatial Capture-Recapture (“SCR”) has emerged as the most prominent method for estimating density reliably. The SCR model is conceptually straightforward: it combines a spatial model of detection with a point process model of the spatial distribution of individuals, using data collected on individuals within a spatially referenced sampling design. These data are often coarse in spatial and temporal resolution, though, motivating research into improving the quality of the data available for analysis. Here I explore two related approaches to improve inference from SCR: sampling design and data integration. Chapter 1 describes the context of this thesis in more detail. Chapter 2 presents a framework to improve sampling design for SCR through the development of an algorithmic optimization approach. Compared to pre-existing recommendations, these optimized designs perform just as well but with far more flexibility to account for available resources and challenging sampling scenarios. Chapter 3 presents one of the first methods of integrating an explicit movement model into the SCR model using telemetry data, which provides information at a much finer spatial scale. The integrated model shows significant improvements over the standard model to achieve a specific inferential objective, in this case: the estimation of landscape connectivity. In Chapter 4, I close by providing two broader conclusions about developing statistical methods for ecological inference. First, simulation-based evaluation is integral to this process, but the circularity of its use can, unfortunately, be understated. Second, and often underappreciated: statistical solutions should be as intuitive as possible to facilitate their adoption by a diverse pool of potential users. These novel approaches to sampling design and data integration represent essential steps in advancing SCR and offer intuitive opportunities to advance ecological learning about spatial processes.

Coyote (Canis latrans) range expansion in the Central Appalachian Mountains has stimulated interest in ecology of this predator and potential impacts to prey populations. This is particularly true in the Ridge and Valley Region in western Virginia where white-tailed deer (Odocoileus virginianus) populations are restricted by low nutritional carrying capacity and are subject to two other predators, bobcats (Lynx rufus) and American black bears (Ursus americanus), in addition to an active hunter community. I address two primary objectives of the Virginia Appalachian Coyote Study: to investigate 1) spatial ecology and 2) population dynamics of coyote populations in Bath and Rockingham counties. I deployed 21 GPS satellite collars on 19 coyotes over 32 months. I estimated home range size (mean = 13.46 km², range = 1.23 km² - 38.24 km²) across months using biased-random bridges and second-order habitat selection at four scales using eigenanalysis of selection ratios. I developed a metric to classify social status of individuals as either resident or transient based on stability of home range centers over time. I found evidence for class substructure for selection of territories where adult residents had a higher probability of mortality in high productivity/high risk habitats, compared to subadults and transients that were restricted to less productive habitats. I collected scat samples over five scat surveys across 2.5 years and extracted fecal DNA to identify individual coyotes in a mark-recapture framework. I estimated coyote densities in Bath (5.53 – 9.04 coyotes/100 km²) and Rockingham Counties (2.41 – 8.53 coyotes/100 km²) using a spatial capture-recapture model. Six-month apparent survival was lower in Bath County (Φ_Bath = 0.442, 0.259 – 0.643; Φ_Rockingham = 0.863, 0.269 – 0.991). The Bath County population demonstrated persistence despite high mortality and the Rockingham population demonstrated boundedness with recruitment inverse of changes in density. Findings at both sites suggest density-dependence, and tests of territoriality, presence of transients, and territory turnover demonstrate a capacity for immediate local immigration in response to high mortality in Bath County. I suggest that landscape-level habitat management may be a viable strategy to reduce potential conflicts with coyotes in the region. / Ph. D.

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.

The ranging behaviour, habitat preferences, genetic structure, and demographic parameters of bottlenose dolphins living in the Azores were studied using data collected from 1999 to 2004. Only 44 dolphins out of 966 identified were frequently sighted within and between years and showed strong site fidelity. The remaining individuals were either temporary migrants from within or outside the archipelago, or transients. Estimates of home range size were three times larger than previously reported for this species, possibly as a result of the lower availability of food resources. Mitochondrial DNA sequences showed very high gene and nucleotide diversity. There was no evidence of population structuring within the Azores. The Azorean population was not differentiated from the pelagic population of the Northwest Atlantic, suggesting the "unproductive" waters of the Atlantic do not constitute a barrier to dispersal. Population size, survival and temporary emigration rates were estimated using open-population models and Pollock's robust design. A few hundreds of dolphins occur in the area on a given year, though the majority should use it temporarily, as suggested by the high emigration rates. Bottlenose dolphins preferentially used shallow areas with high bottom relief. Temporal and spatial persistence of dolphin-habitat associations documented in this study further supports the idea of a close relationship between certain bathymetric features and important hydrographic processes and suggests the occurrence of prey aggregations over these areas may be, to some extent, predictable. Several results of this study suggest there are no reasons for concern about the status of this population. Yet, the resident group may be negatively affected by increasing pressure from the whale watching activity. Although the proposed Marine Park constitutes important habitat for resident dolphins, at present, the area is clearly insufficient to satisfy their spatial requirements and its conservation value may be limited.

Cette étude se place dans le contexte des maladies infectieuses émergentes maintenant reconnues comme une menace majeure de la biodiversité. Engendrant un taux de mortalité atteignant 95 %, les épidémies à virus Ebola ayant affecté les populations de gorilles de plaine de l'Ouest (Gorilla gorilla gorilla) conduisirent à la classification de ce taxon comme " En danger critique d'extinction ". Cette étude s'intéresse aux capacités de récupération de ses populations. Grâce à des données uniques d'observation en phase pré- et post-épidémique, nous avons évalué l'impact de l'épidémie sur la structure et la dynamique sociale d'une population et estimé son potentiel de récupération au cours des six ans qui ont suivi. Nos résultats de démographie et de dynamique, couplés à des approches statistique et de modélisation démographique détaillée au niveau des classes d'âge et de sexe, et intégrant l'immigration, nous ont permis de mettre en évidence 1) un impact délétère sur le potentiel reproducteur, du fait de l'organisation sociale du gorille ; 2) les atouts de la flexibilité et de l'organisation sociale dans la récupération de la structure de la population ; 3) le rôle de l'immigration pour la récupération à long-terme des effectifs. La mise en évidence de caractéristiques structurelles typiques d'une population affectée par Ebola nous a permis de montrer qu'une population voisine étudiée était indemne. Ceci met en évidence l'impact hétérogène des épidémies au niveau régional, induisant probablement un certain degré de fragmentation des populations. Ce nouvel élément permet de discuter les hypothèses d'émergence et de propagation du virus, et pose la question de l'impact de la fragmentation de la population sur sa dynamique globale et sur la récupération des populations locales affectées. Nos résultats suggèrent une faible résilience des populations de gorilles de plaine face à Ebola et la menace de ce virus pour la persistance des populations. Cependant, une meilleure connaissance du potentiel de flux d'individus au niveau régional et le développement de modèles démographiques prenant en compte cette dimension permettrait de mieux préciser cette résilience.

Made available in DSpace on 2016-06-02T20:04:52Z (GMT). No. of bitstreams: 1 6306.pdf: 1062380 bytes, checksum: de31a51e2d0a59e52556156a08c37b41 (MD5) Previous issue date: 2014-05-30 / Financiadora de Estudos e Projetos / In this work, we make a study of the Bayes sequential decision procedure applied to capture-recapture with fixed sample sizes, to estimate the size of a finite and closed population process. We present the statistical model, review the Bayesian decision theory, presenting the pure decision problem, the statistical decision problem and the sequential decision procedure. We illustrate the theoretical methods discussed using simulated data. / Neste trabalho, fazemos um estudo do procedimento de decisão sequencial de Bayes aplicado ao processo de captura-recaptura com tamanhos amostrais fixados, para estimação do tamanho de uma população finita e fechada. Apresentamos o modelo estatístico, revisamos a teoria de decisão bayesiana, apresentando o problema de decisão puro, o problema de decisão estatística e o procedimento de decisão sequencial. Ilustramos os métodos teóricos discutidos através de dados simulados.

Made available in DSpace on 2016-06-02T20:05:58Z (GMT). No. of bitstreams: 1 DissKBRS.pdf: 617246 bytes, checksum: 9436ee8984a49f5df072023b717747c6 (MD5) Previous issue date: 2006-02-24 / In this work we present the methodology of capture-recapture, under the classic and bayesian approach, to estimate the number of errors of software through inspection by distinct reviewers. We present the general statistical model considering independence among errors and among reviewers and consider the particular cases of equally detectable errors (homogeneous) and reviewers not equally e¢ cient (heterogeneous) and of errors not equally detectable (heterogeneous) and equally e¢ cient reviewers (homogeneous). After that, under the assumption of independence and heterogeneity among errors and independence and homogeneity among reviwers, we supposed that the heterogeneity of the errors was expressed by a classification of these in easy and di¢ cult of detecting, admitting known the probabilities of detection of an easy error and of a di¢ cult error. Finally, under the hypothesis of independence and homogeneity among errors, we presented a new model considering heterogeneity and dependence among reviewers. Besides, we presented examples with simulate and real data. / Nesta dissertação apresentamos a metodologia de captura-recaptura, sob os enfoques clássico e bayesiano, para estimar o número de erros de um software através de sua inspeção por revisores distintos. Apresentamos o modelo estatístico geral considerando independência entre erros e entre revisores e consideramos os casos particulares de erros igualmente.detectáveis (homogêneos) e revisores não igualmente eficientes (heterogêneos) e de erros não igualmente detectáveis (heterogêneos) e revisores igualmente eficientes (homogêneos). Em seguida, sob a hipótese de heterogeneidade e independência entre erros e homogeneidade e independência entre revisores, supusemos que a heterogeneidade dos erros era expressa por uma classificação destes em fácil e difícil de detectar, admitindo conhecidas as probabilidades de detecção de um erro fácil e de um erro difícil. Finalmente, sob a hipótese de independência e homogeneidade entre erros, apresentamos um novo modelo considerando heterogeneidade e dependência entre revisores. Além disso, apresentamos exemplos com dados simulados e reais.