Os efeitos da perda de hábitat e da fragmentação já estão bem estabelecidos na literatura, porém pouco se sabe sobre como o uso do habitat pode ser modificado em função de alterações na quantidade e na qualidade da mata. Este trabalho tem como objetivo compreender melhor como a perda e modificação do hábitat afeta o uso do espaço pelas aves de subosque na escala da comunidade e população. Para isso, utilizamos um banco de dados de aves, que inclui informação sobre captura e recaptura de 2.121 indivíduos, coletados em um gradiente de cobertura florestal, com fragmentos de 2,85 ha a 10.000 ha, localizados em Mata Atlântica no estado de São Paulo. As análises foram feitas por espécie, por grupos de espécies de acordo com guilda trófica e grau de sensibilidade a alterações antrópicas, e para a comunidade de forma geral. Para testar se a qualidade da vegetação influencia a abundância e frequência de uso do espaço, utilizamos dados de três áreas de florestas contínuas, com diferentes níveis de alteração (floresta secundária, mata com corte seletivo e mata madura). Observamos que, apesar de haver uma queda na abundância total da comunidade em fragmentos pequenos, há um aumento na frequência de uso do ambiente, evidenciado pelo aumento na taxa de recaptura com a perda de habitat. O mesmo padrão foi encontrado para aves com média sensibilidade, frugívoras e insetívoras. Aves com baixa sensibilidade, no entanto, mostraram maiores abundancia e taxa de recaptura em fragmentos menores e áreas mais desmatadas. Verificamos também que a frequência de uso do espaço foi maior em floresta secundária, bem como a abundância de aves. Nossos resultados sugerem que além de conduzir a uma perda de espécies e de indivíduos, a perda de hábitat também leva ao aumento na intensidade do uso do habitat. Este aumento se dá em particular para espécies de média sensibilidade, uma vez que espécies com alta sensibilidade estão ausentes de fragmentos pequenos. Observamos que, além da matriz como barreira à dispersão, a própria qualidade da mata se apresenta como um fator que modifica o uso do habitat. Esta variação no uso do habitat pode impedir que as mesmas desenvolvam seu papel de dispersores de sementes entre os fragmentos. Por fim, estudos sobre uso do espaço hoje praticamente não abordam a intensidade com que o hábitat é utilizado pelos indivíduos, sendo uma informação importante que pode ser facilmente estudada através de dados de captura e recaptura, geralmente subutilizados / The effects of habitat loss and fragmentation area well established in the literature, however not much is known about how habitat use can be modified due to alterations in habitat quantity and quality. This work aims to understand how habitat loss and changes to habitat quality affects the habitat use by understory birds at the community and population level. We analysed a database, which includes capture and recapture data from 2.121 individuals, of birds sampled along a gradient of Atlantic Forest cover and fragment size varying from 2,85 ha to 10.000 ha in the São Paulo State. We analysed data by species, by groups of species according to their trophic guilds and sensitivity to habitat change, and at the community level. To test if the quality of vegetation affects species abundance and the intensity of habitat use, we used data from three continuous forests, with different levels of habitat modification (secondary forest, forest selective logged and mature forest). Our results show that, although the total species abundance decreased in small fragments, the intensity of habitat use increases, as shown by the increase in recapture rates with habitat loss. This pattern was observed for birds with high and medium sensitivity, frugivorous and insectivorous. Species with low sensitivity, however, showed higher species abundance and recapture rate in small fragments. We also show that the frequency of habitat use was higher in secondary forest, as was the abundance of individuals. Our results suggest that habitat loss not only leads to smaller populations, but it also modifies the intensity of habitat use. This pattern was mostly observed for species with medium levels of sensitivity, as highly sensitive species were no longer present in small patches. Our results indicate that the matrix may act as a barrier for dispersal, but habitat quality may also further influence habitat use. This variation in habitat use can affect birds ability to disperse seeds between the fragments. Finally, studies of habitat use almost never focuses on the intensity of habitat use, even though this information can be easily evaluated using capture and recapture data, with the latter being usually underused

The extension of the CJS model to include individual, continuous, time-varying covariates relies on the estimation of covariate values on occasions on which individuals were not captured. Fitting this model in a Bayesian framework typically involves the implementation of a Markov chain Monte Carlo (MCMC) algorithm, such as a Gibbs sampler, to sample from the posterior distribution. For large data sets with many missing covariate values that must be estimated, this creates a computational issue, as each iteration of the MCMC algorithm requires sampling from the full conditional distributions of each missing covariate value. This dissertation examines two solutions to address this problem. First, I explore variational Bayesian algorithms, which derive inference from an approximation to the posterior distribution that can be fit quickly in many complex problems. Second, I consider an alternative approximation to the posterior distribution derived by truncating the individual capture histories in order to reduce the number of missing covariates that must be updated during the MCMC sampling algorithm. In both cases, the increased computational efficiency comes at the cost of producing approximate inferences. The variational Bayesian algorithms generally do not estimate the posterior variance very accurately and do not directly address the issues with estimating many missing covariate values. Meanwhile, the truncated CJS model provides a more significant improvement in computational efficiency while inflating the posterior variance as a result of discarding some of the data. Both approaches are evaluated via simulation studies and a large mark-recapture data set consisting of cliff swallow weights and capture histories.

Explaining spatial and temporal variation in the abundance of species is one of the primary goals of ecology. Habitat selection, the behaviour that organisms use to choose habitat patches that maximize fitness, can explain patterns in abundance between patches at small spatial scales within the dispersal capacity of the species. However, habitat selection models assume there is a reduction in individual fitness as population density increases due to increased competition between individuals. Ectotherms, which often select habitats based on temperature, a density-independent resource, may not display density-dependent responses if temperature limits energy assimilation more than finite food resources limit energy acquisition. As predicted by their dependence on environmental temperatures, some ectotherms select habitat largely independently of population density when temperatures are far from the optimal temperature for performance. But, is density-dependence prevalent in ectotherm populations when temperatures are close to the optimal temperature for performance? Habitat selection models also assume that all individuals of a population exhibit the same strategy for maximizing fitness through habitat selection. However, differences in morphology and behaviour (e.g., reproductive strategy) can modify the optimal habitat selection strategy for different phenotypes. Finally, observed patterns in habitat selection and abundance can also be modified by competition with other species. Quantifying the relative importance of these different factors that affect habitat selection behaviour will improve our ability to predict the spatial distribution and relative abundance of organisms. The objective of my thesis was to explain spatial variation in the abundance of ectotherms, using the ornate tree lizard (Urosaurus ornatus) as a study species. In chapter one, I tested whether density-dependent habitat selection explained patterns in abundance and fitness of lizards between two habitats differing in suitability. In chapter two, I tested whether density dependent habitat selection in tree lizards was caused by intraspecific competition for food that limited body size and growth. In chapter three, I tested whether variation in reproductive strategy, as indicated by throat colour phenotype, affected space use and habitat selection in male tree lizards. Finally, in chapter four, I tested whether interspecific competition with another lizard species affected habitat selection, fitness, and abundance of tree lizards. My thesis emphasizes the importance of intraspecific competition in shaping patterns of habitat selection and abundance in terrestrial ectotherms. I show that habitat selection is strongly density-dependent despite differences in thermal quality between habitats. I show that density-dependent mortality and growth lower the fitness of individuals when populations reach high densities, and this likely caused habitat selection to be density-dependent. Despite this evidence for density-dependent habitat selection, I show considerable variation between individuals in habitat selection and space use. Males with different throat colour phenotypes select habitats differently, demonstrating that variation in morphology can influence habitat selection patterns within a population. Finally, I show that interspecific competition with another lizard affects space use and how frequently tree lizards switch habitats, but this does not lead to differences in fitness or in the relative abundance of tree lizards in habitats. Therefore, intraspecific competition for resources was the dominant force shaping the relative abundance of tree lizards in different habitats.

Loggerheads (Caretta caretta) are listed as Threatened and green turtles (Chelonia mydas) are listed as Endangered under the United States Endangered Species Act. While green turtle nest production in Florida has increased markedly in recent years, loggerhead nest production has followed a more tenuous path. Reasons for these differences are unknown. Limited demographic information is available for these species of conservation concern. I used Barker models, which incorporated mark-recapture, live-resight and dead recovery data, implemented in Program MARK. These models were used to estimate apparent survival for immature loggerhead (

We propose a ratio estimator to determine population estimates using capture-recapture sampling. It's different than traditional approaches in the following ways: (1) Ordering of recaptures: Currently data sets do not take into account the "ordering" of the recaptures, although this crucial information is available to them at no cost. (2) Dependence of trials and cluster sampling: Our model explicitly considers trials to be dependent and improves existing literature which assumes independence. (3) Rate of convergence: The percentage sampled has an inverse relationship with population size, for a chosen degree of accuracy. (4) Asymptotic Attainment of Minimum Variance (Open Systems: (=population variance). (5) Full use of data and model applicability (6) Non-parametric (7) Heterogeneity: When units being sampled are hard to identify. (8) Open and closed systems: Simpler results are presented separately for closed systems. (9) Robustness to assumptions in open systems

Competition among individuals over shared resources reveals asymmetries in quality resulting in the formation of dominance hierarchies. These hierarchies act as a mechanism for social selection by partitioning resources among group-living animals. The following chapters describe my dissertation research which investigates the factors contributing to competitive asymmetries among broodmates as well as the short- and long-term consequences of the early social environment for the cooperatively breeding red-cockaded woodpecker (Picoides borealis). My research revealed that fledgling red-cockaded woodpeckers form male-biased, linear dominance hierarchies. Among fledgling males,, high relative nestling condition strongly predicted fledgling dominance, and this condition–rank relationship persisted through independence. Male nestlings are slightly larger and heavier than females; however, the sexual size dimorphism in mass is only present in mixed-sex broods, suggesting that the subtle structural size advantage gives males a competitive advantage over their sisters. Conflict rates among siblings increased with decreasing targeted feeding rates, and dominant fledglings were able to secure more food from provisioning adults through scramble competition. First-year survival favored males over females and dominant males over subordinates. Females were more dispersive overall than males, and subordinate males were more likely to disperse than dominants. The social environment prior to fledging influenced male dispersal decisions and subordinates delayed dispersal in the spring in situations where all dominants died over the winter. The probability of delayed dispersal in females was higher for females raised without brood-mates in one of two populations included in a long-term demographic data analysis. The availability of breeding vacancies may explain the differences in female dispersal behavior according to social environment between these populations. This research contributes to a greater understanding of the relative contribution of intrinsic benefits versus extrinsic constraints as an influence on delayed dispersal decisions in red-cockaded woodpeckers. Inter- and intra-sexual social rank is correlated with individual access to natal food resources and the probability of first-year survival. The intrabrood variation in dispersal strategies driven by social rank is sufficient to regularly produce both dispersal strategies among males and provides additional support that delaying natal dispersal is the preferred strategy for males in this system. / Ph. D.

The horticulture industry is facing limited water resources and public pressure to reduce non-point source pollution. In some circumstances, recapturing and recycling of irrigation water in horticultural nurseries can generate significant savings relative to the costs of alternative water sources and potentially reduce non-point source pollution. However, obtaining these savings may also incur substantial risk and capital cost outlays. Disease risk may increase in nurseries that implement recapturing and recycling if recycled water is not properly treated. These added costs must be compared with costs of alternative sources of water, such as municipal or well water. This study employed partial budgeting to compare irrigation water being extended or supplemented through recapturing and recycling against the most feasible alternative. On-site visits were conducted to obtain information for partial budgets and to clarify the reasoning of nurseries choosing to recycle irrigation water. The partial budgets were supplemented with sensitivity analysis with regard to the extraction cost of water and opportunity cost of land used for recapture of water. Six of eight nurseries obtained water from recapturing and recycling at a lower cost compared to a feasible alternative source. The regrading of land for maximum recapture, opportunity cost of land dedicated to a recapture pond, and the cost of municipal water were parameters that were critical to the irrigation choice. Sensitivity analysis indicated that water price and land cost had little effect on the least cost option. Irrigation recycling could be incentivized to motivate further water conservation within the horticulture industry. / Master of Science

Introduction: Les études populationnelles sur le cancer nécessitent un recensement de référence fiable et exhaustif, en théorie possible à partir d'un recueil histologique. Méthode: Depuis 2005, toutes les structures d'anatomopathologie des Alpes-Maritimes adressent les codes ADICAP des tumeurs malignes et invasives et identifiants patients. L'exhaustivité pour les cancers du sein et colorectaux des 50-75 ans a été évalué par méthode de capture recapture en modélisation log-linéaire et en Bayesien à partir des cas communs ou non dépistés et vus en Réunion de Concertation Pluridisciplinaire. RésultatUn programme d'assurance qualité a permis de s'assurer de la fiabilité des données recueillies.L'estimation de l'exhaustivité était de plus de 90 % pour les cancers du sein et colorectaux des 50-75 ans. Les taux observés sur le département des Alpes-Maritimes, comparés aux taux estimés en France, se sont révélés cohérents.Enfin, la base a été utilisée pour déterminer l'existant les lésions prénéoplasiques du col de l'utérus avant la vaccination anti-HPV. ConclusionCe travail conclut à l'intérêt d'un recueil histologique des cas de cancers incidents. / Introduction Cancer population studies require reliable and complete baseline data, which should theoretically be available by collecting histopathology records.Method Since 2005, all histopathology laboratories from Alpes-Maritimes address ADICAP codes for invasive cancer and patient identifiers. The completeness of such a collection was evaluated using capture-recapture analysis based on three data sources concerning breast and colorectal cancers with the number of cases which were common or not between sources recording screened, diagnosed and treated cancers in the French Alpes Maritimes districtResult Data quality for the ADICAP code database may be considered satisfactoryThe estimated completeness of cancer records collected from histopathology laboratories was higher than 90%.Rates observed in the Alpes-Maritimes, compared with estimated rates in France have proven consistent. Rates of CIN for the entire female population of the Alpes-Maritimes in 2006 has been established.Conclusion A verified and validated histopathology data collection may be useful for cancer population studies.

An island subspecies endemic to the remote St Kilda archipelago, Apodemus sylvaticus hirtensis is considered of national importance but has been little studied, despite its inclusion in the criteria for the islands’ designation as a World Heritage Site. This study expands our knowledge of the core ecology of the mice; distribution, morphology, age structure, breeding phenology, population density, range size, survival and fecundity are all described and quantified using data collected from 4462 captures of 787 individuals between 2009-2012 on three sites (Carn Mor, Glen Bay & Village Bay), 1-2km apart on the main island of Hirta. Morphological analysis confirmed the reputed gigantism the mice, with maximum body weights of 60g for males and 50.5g for a non-gravid female both being approximately double that of a mainland specimen (the heaviest gravid female caught weighed 56g). Sexual dimorphism was evident, with males >1 year old being 8.7% heavier than females on average. Significant geographical variation in size was also found; mice on the seabird breeding colony of Carn Mor were heavier, longer and in better condition than mice elsewhere. Mice were observed to have a well-defined breeding season between April and September, shorter than on the mainland, with most individuals not breeding until their second year and very few surviving two winters. No geographical differences were found in the proportion of adult mice more than a year old that were in breeding condition at any given time, although there were significant geographical differences in the proportion of individuals in breeding condition for ‘young adult’ mice entering their first spring and sub adult mice in the autumn of the year in which they were. Spatially explicit capture-recapture (SECR) methods were used to quantify population densities free from ad hoc methods of trapping area estimation. Temporal variation in population size typical of temperate small mammals was found, with densities as low as 2 mice/ha in spring, increasing through summer and autumn with juvenile recruitment until reaching a peak at the beginning of winter of up to 50 mice/ha. Geographical variation was again observed, with frequent significant differences between trapping sites and an overall trend of highest population densities on the seabird breeding site. Mean individual range sizes varied between 0.3-3.0ha and were largest in Village Bay and in males in breeding condition. Pradel robust design recruitment models were used to quantify monthly survival (0.67-1.00) and fecundity (0.03- 0.41) and overall rate of population change (0.81-1.52) between sessions. Survival varied little between grids outside of the breeding season, but tended to be greater in Carn Mor than Village Bay during the summer. Fecundity rates varied little between years and grids, with one exception where increased summer fecundity followed a severe winter decline on Carn Mor. The possible role of differences in the quality of the food supply (in particular the seabird breeding colony and spatial variation in sheep grazing pressure) on creating geographical variation in body size, condition, breeding phenology, density and population dynamics are discussed in detail, as is the overall pattern of insular traits found in the mice.

La dynamique des populations peut être définie comme l'étude des forces responsables de la taille et de la structure d'une population. Plusieurs facteurs influençant la dynamique des populations ont déjà été identifiés. Ces facteurs peuvent être classés de par leur niveau d'influence, d'une influence à l'échelle de la population toute entière, comme par exemple les changements climatiques ou la densité de population, jusqu'à des facteurs individuels comme l'âge ou le sexe. Récemment, de nombreuses études ont insisté sur l'importance de la structure en âge pour cette dynamique.Chez les espèces sociales, un niveau supplémentaire de structuration de la population est le groupe. Cependant,les conséquences de cette structuration en groupes sociaux est encore mal connue.Au cours de ma thèse, j'ai tenté de répondre a cette question de différentes manières. J'ai tout d'abord étudié comment les paramètres démographiques individuels étaient influencés par la taille et la composition du groupe. J'ai pu notamment mettre en évidence un effet négatif du nombre de juvéniles femelles présent lors du développement sur la probabilité de devenir dominant une fois à l'age adulte. Dans une deuxième temps, j'ai étudié l'importance des interactions entre groupes en quantifiant l'impact d'un changement de dominant sur la dispersion des subordonnés. Enfin, j'ai également quantifié l'influence des différents groupes au sein de la population démontrant que les grands groupes contribuent relativement moins au taux de croissance de la population. Ces différents résultats sont ensuite discuté dans un cadre de démographie évolutive et de nouvelles pistes de recherche sont proposées / Population dynamics can be defined as the study of the forces responsible for the size and structure of a population. Several factors influencing population dynamics have already been identified. These factors can be categorized according to their level of influence. Some factors have a population-wide influence, such as climate change or population density, while others affect the individual level such as age or sex. Recently, many studies have emphasized the importance of this age structure for population dynamics.In social species, an additional level of structuring of the population is the group. However, the consequences of this social group structuring are still poorly understood.In this thesis, I try to answer this question in different ways. I first studied how the individual demographic parameters were influenced by the size and composition of the group. I was able to highlight in particular a negative effect of the number of juvenile females present during development on the probability of becoming dominant once in adulthood. In a second step, I studied the importance of interactions between groups by quantifying the impact of a change of dominant on the dispersion of subordinates. Finally, I also quantified the influence of different groups within the population showing that large groups contribute relatively less to the population growth rate. These various results are then discussed in a context of evolutionary demography and new avenues of research are proposed