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

Rares, discrets, fascinants et sanguinaires sont autant d'adjectifs utilisés en Europe pour qualifier les grands carnivores qui arpentent nos forêts. La dégradation de leur habitat et la raréfaction de leurs proies, associées au folklore qui les entoure, ont engendré de nombreux conflits avec l'Homme et les ont menés à disparaître de la plupart de leurs aires historiques de répartition. Depuis, ces espèces ont le statut d'espèces protégées dans la plupart des pays européens. Ce statut est notamment garanti pour la plupart par la Directive Habitat et la convention de Berne. Ces textes législatifs ont permis d'instaurer un contexte favorable pour un retour progressif de ces espèces au sein de nos écosystèmes. Afin de remplir les exigences instaurées par ces différents textes législatifs, il était nécessaire d'améliorer les connaissances scientifiques sur l'écologie de ces espèces et la dynamique de leurs populations. Les pays européens ont ainsi déployé des efforts considérables afin de contribuer à une connaissance globale et à une gestion durable des grands carnivores. Ces efforts ne sont clairement pas homogènes entre l'ours, le loup et le lynx. Le premier enjeu de cette thèse était donc d'évaluer les facteurs pouvant expliquer l'hétérogénéité d'investissement dans la conservation de ces espèces en Europe. Ce chapitre repose à la fois sur des critères écologiques des populations locales et sur des critères économiques des pays considérés. Le premier résultat fort de cette étude montre que l'ours et le lynx auraient un même profil et bénéficieraient du même intérêt pour les scientifiques européens, le loup différant de ces deux espèces. Le second résultat probant révèle que les travaux de recherche seraient davantage orientés vers les populations à forts effectifs plutôt que vers les petites populations. L'investissement scientifique dans ce premier chapitre est en partie quantifié par l'effort investi dans le suivi des populations, qui reste un véritable défi pour les grands carnivores. En effet, le comportement discret de ces espèces, leur faible densité et leur besoin de grands espaces sont autant de contraintes pour leur suivi qui requiert alors d'importants moyens humains et financiers. Le suivi des effectifs du lynx boréal (Lynx lynx), en France, est un exemple révélateur de ces contraintes. Il reposait jusqu'à récemment sur la collecte d'indices de présence indirects. Motivés par la mise en place d'un protocole de suivi non-invasif mais coûteux par piégeage photographique dans le massif jurassien français, nous avons évalué dans un deuxième chapitre une nouvelle méthode d'estimation des effectifs de cette population qui permet d'inclure l'information spatiale dans l'analyse. Cette méthode a permis de fournir la première estimation fiable des effectifs de lynx en France. Cette estimation est fournie néanmoins avec une précision toute relative au vu du peu de données collectées lors de ce suivi. L'écart entre le budget nécessaire pour obtenir un recensement de la population et le budget disponible pour le suivi de l'espèce étant considérable, il a fallu dans un troisième chapitre développer un nouvel outil pour optimiser l'utilisation des données disponibles. La combinaison des données de présence-absence et des données de piégeage photographique a permis d'améliorer considérablement les estimations d'effectifs qui sont, dans le Jura français, plutôt en hausse ces dernières années. La situation n'est pas aussi favorable pour l'espèce dans la région des Vosges. Cette population, issue d'une réintroduction, semble décliner de manière drastique depuis les 5 dernières années. Dans un quatrième chapitre, nous avons donc étudié l'efficacité de deux stratégies de conservation visant d'une part à favoriser la connectivité entre les populations vosgienne et jurassienne et d'autre part à réintroduire des individus dans la forêt Palatine allemande, située en continuité du massif vosgien. / Rare, discrete, fascinating and bloodthirsty are all adjectives used in Europe to describe the large carnivores that roam our forests. Degradation of their habitat and depletion of their prey, combined with these wild and "bloodthirsty" aspects, have led to numerous conflicts with humans and led them to disappear from most of their historical range. Since then, most of them have a protected status in most European countries. This status is guaranteed for most of these countries by the Habitats Directive and the Berne Convention. These laws created a favorable context for a gradual return of these species in our ecosystems. To fulfill the requirements established by these laws, it was necessary to improve scientific knowledge of the ecology of these species and to develop methodological tools to understand the dynamics of their populations. European countries then made considerable efforts to contribute to global knowledge and sustainable management of large carnivores. These efforts, in the case of the bear, wolf and lynx, are clearly not homogenous within Europe. The first challenge of this thesis was to evaluate the factors that might explain the heterogeneity of investment in the conservation of large carnivores in Europe. This chapter is based both on ecological criteria of local species and economic criteria of the countries of interest. The first strong result of this study revealed that the bear and lynx have the same profile and receive the same interest from European scientists, wolf differing from the two other species. The second convincing result revealed that the research would be more oriented towards abundant populations rather than small populations as previously assumed by the scientific community. The scientific investment in this first chapter is partly quantified by the amount of effort invested in monitoring populations. It turns out to be a real challenge for large carnivores. The secretive behavior of these species, their low density and their need for large spaces are all constraints to monitoring requiring substantial human and financial resources. Eurasian lynx (Lynx lynx) monitoring in France is a typical example of these constraints. Until now, monitoring was based on the collection of indirect presence signs. Recently, a non-invasive but expensive camera-trapping protocol has been settled in the French Jura Mountains. We then evaluated in a second chapter a new method for estimating the size of this population. This method has provided the first reliable estimate of the abundance of lynx in France. This estimate, however, came with a relative precision given the limited quantity of data collected during this session. The gap between the needs for a census of the population and the budget available for the monitoring of the species is huge so we had to develop a new modeling tool to achieve our goal. In the third chapter, the objective was to improve these estimates, optimizing the use of the available data. The combination of presence-absence data and camera trapping data has greatly improved the French Jura population estimates that go rising in recent years. The situation is not as favorable for the species on the Vosges part. This population, after reintroduction, appears to be declining drastically over the last 5 years. In a fourth chapter, we therefore investigated the effectiveness of two conservation strategies: the first one was to instate some connectivity between the Vosges and Jura populations and the second one to reintroduce individuals in the German Palatinate Forest, situated in continuity with the Vosges.

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

The black caiman (Melanosuchus niger) and the yacare caiman (Caiman yacare) have in the past been exposed to overexploitation due to the economic profit for their hides, and therefore suffered from great declines in population sizes, especially black caimans. Legal regulation efforts made it possible for these two species to recover and today they are widely distributed in South America. Evaluation of protection and management of populations of top predators like these caimans depend on the ability to detect the animals. The probability of detecting a crocodile, or any animal, is affected by several factors such as habitat complexity and behaviour why it is of importance to acknowledge such matter in order to obtain reliable results for further implications. This study aims to investigate the detection probability and abundances in these two species as a contribution to the monitoring efforts at a local scale. Night counts were performed in Cedral lagoon located in the Beni region in Bolivia. By using the relation between marked animals and resightings of them, as well as the abundance estimate produced by the Lincoln-Petersen estimator, estimates of detection probabilities could be accounted for the total caiman population (black plus yacare caimans) and the black caiman population. Very low sighting probabilities (p = 0.03) were obtained when based on marked animals who tend to be more wary after a capture event. Those based on the L-P output were higher (total caiman population p = 0.15, black caimans p = 0.15). Population sizes were estimated to 25 ± 8.5 black caimans and 34 ± 12 caimans in total. The population size based on marked animals was 12 ± 25.4 caimans.

Master of Science / Department of Statistics / Paul I. Nelson / Capture-Recaputre (CR) experiments stemmed from the study of wildlife and are widely used in areas such as ecology, epidemiology, evaluation of census undercounts, and software testing, to estimate population size, survival rate, and other population parameters. The basic idea of the design is to use “overlapping” information contained in multiple samples from the population. In this report, we focus on the simplest form of Capture-Recapture experiments, namely, a two-sample Capture-Recapture design, which is conventionally called the “Petersen Method.” We study and compare the performance of three methods of constructing confidence intervals for the population size based on a Capture-Recapture design, asymptotic normality estimation, Chapman estimation, and “inverting a chi-square test” estimation, in terms of coverage rate and mean interval width. Simulation studies are carried out and analyzed using R and SAS. It turns out that the “inverting a chi-square test” estimation is better than the other two methods. A possible solution to the “zero recapture” problem is put forward. We find that if population size is at least a few thousand, two-sample CR estimation provides reasonable estimates of the population size.

Nesta tese propomos dois modelos espaciais de captura-recaptura para estimação da abundância populacional em população aberta. Os modelos estatísticos propostos ajustam-se a dados obtidos via amostragem de captura-recaptura com marcação individual realizada em diferentes locais dentro do habitat, levando em consideração as taxas de nascimentos e mortes durante o período de estudo e as localizações geográficas das capturas. No primeiro modelo, propomos uma modelagem hierárquica para os tamanhos populacionais locais a fim de obter a distribuição preditiva da abundância populacional para regiões não visitadas pela amostragem. Nesta etapa, uma estrutura para dados zero-inflacionados foi adotada para acomodar situações quando realizam-se amostragens em locais sem a presença da espécie. O segundo modelo proposto leva em consideração o deslocamento dos animais entre os diferentes locais de amostragem, generalizando o primeiro modelo no qual consideramos a permanência dos animais em um mesmo local. Neste caso, tornou-se possível estimar o tamanho da área de vida (movimentação) da espécie além de predizer locais com maiores abundâncias de animais. Em ambos modelos, propomos uma abordagem bayesiana para o processo inferencial e derivamos algoritmos de simples implementação computacional, a partir do uso de técnicas de dados aumentados. As propriedades frequentistas dos estimadores bayesianos foram avaliadas por meio de estudos de simulação e, por fim, estas propostas de modelagem foram aplicadas a três conjuntos de dados reais de aracnídeos. / In this thesis we propose two spatial capture-recapture models for estimation of population abundance in the open population. The proposed statistical models conform to data obtained through individual tag capture-recapture sampling performed in different areas within the habitat, taking into account the rates of births and deaths during the study period and the geographical locations of the catches. In the first model, we propose a hierarchical modeling for local population sizes in order to obtain the predictive distribution of population abundance for regions not visited by sampling. In this step, a structure for zero-inflated data was adopted to accommodate situations when sampling is performed in areas without the presence of the species. The second proposed model takes into account the movement of the animals among the different sampling areas, generalizing the first model in which we consider the permanence of the animals in the same area. In this case, it became possible to estimate the size of the area of movement of the species and to predict areas with higher abundances of animals. In both models, we propose a Bayesian approach to the inferential process and derive algorithms from simple computational implementation, from the use of augmented data techniques. The frequentist properties of the Bayesian estimators were evaluated by simulation studies and, finally, these modeling proposals were applied to three real data sets of arachnids.

Introdução - O método de captura-recaptura vem sendo empregado em Epidemiologia desde meados do século XX, e se consolidou a partir dos anos 1990, quando se nota grande número de publicações sobre sua aplicação e desenvolvimento nesta área. O sub-registro de eventos vitais ainda se revela um entrave para o cálculo direto de indicadores como os de fecundidade e mortalidade infantil, forçando seu cálculo indireto através de métodos demográficos, cujos procedimentos não permitem estimação em níveis geográficos menores do que unidade da federação, em períodos intercensitários. Objetivo Estimar o sub-registro de nascidos vivos, aplicando o método de captura-recaptura para populações fechadas. Métodos - As bases de dados do Sistema Nacional de Informação sobre Nascidos Vivos (SINASC) e do Registro Civil do IBGE, nos segundo e terceiro trimestres de 2006 do estado de Sergipe, foram pareadas por relacionamento determinístico a partir do número da Declaração de Nascido Vivo. As desagregações geográficas adotadas foram as de microrregião e regional de saúde de residência da mãe. Os modelos de Huggins para populações fechadas foram aplicados para estimar as probabilidades de captura em cada uma das bases e o total de nascidos vivos ocorrido no período, dentro de cada desagregação geográfica O aplicativo utilizado para as estimações foi o Software MARK®. Resultados A aplicação do método de captura e recaptura para estimar sub-registro de nascidos vivos é factível, inclusive para desagregações geográficas menores do que unidade da federação. O relacionamento determinístico foi prejudicado em quatro microrregiões e em uma regional de saúde, devido à falta de preeenchimento do número da Declaração de Nascido Vivo na base do IBGE. O aplicativo MARK® apresenta interface amigável, o que facilitou a construção e seleção dos modelos estatísticos, permitindo identificar que a idade da mãe afeta a probabilidade de captura pelo Registro Civil, característica de heterogeneidade na população de nascidos vivos. Conclusões O relacionamento determinístico destas duas bases de dados oficiais viabiliza ações localizadas, porque acaba por identificar onde e quantas vidas mantêm-se no anonimato jurídico, devido ao sub-registro e registro tardio. O método de captura e recaptura mostrou-se uma alternativa acessível e barata para a estimação de sub-registro de nascidos vivos / Introduction Capture-recapture method has been used in Epidemiology since the middle of twentieth century and from the 1990s on, huge number of publications about applying and developing the method on this area have been noted. Underreporting of vital events is still a drawback for the direct calculation of health indicators like fertility and infant mortality, forcing indirect calculation with demographic methods, wich procedures do not allow estimation in geographic levels smaller than States, in intercensuses periods. Objective To estimate underreporting of live births, using the capture-recapture method for closed populations. Methods The National Live Birth Information System (SINASC) and the Civil Registry databases, in the second and third trimesters of 2006 of the State of Sergipe, Brazil, were linked through deterministic linkage using the Live Birth Declaration number as the connection key. Mothers micro-regions and health regions of residence were adopted as geographical subdivisions. Huggins closed capture models were used to estimate the capture probabilities for each database as well as the derived estimation of the total of live births in the selected time interval, at each of geographical subdivisions. MARK® Software was used to get all estimations. Results The capture-recapture method is feasible for estimation of live birth underreporting, even for geographical subdivisions smaller than States. Deterministic linkage was damaged due to lack of filling of the Live Declaration number in some of the Civil Registry databases registries, mainly at four mother residences micro-regions and at one health region. Program MARK® shows friendly interface, which favoured models building and selection, and allowed to point out mother ages influence in Civil Registry database capture probability, characterisc heterogeneity of live born population. Conclusions Deterministic linkage of these two official databases makes possible local actions, because it allows do identify where and how many lives are neglected legal registrations duty, due to underreporting and to late reporting. Capture-recapture method appears as an accessible and cheap alternative for live birth underreporting estimation

Distance sampling and spatial capture-recapture are statistical methods to estimate the number of animals in a wild population based on encounters between these animals and scientific detectors. Both methods estimate the probability an animal is detected during a survey, but do not explicitly model animal movement. The primary challenge is that animal movement in these surveys is unobserved; one must average over all possible paths each animal could have travelled during the survey. In this thesis, a general statistical model, with distance sampling and spatial capture-recapture as special cases, is presented that explicitly incorporates animal movement. An efficient algorithm to integrate over all possible movement paths, based on quadrature and hidden Markov modelling, is given to overcome the computational obstacles. For distance sampling, simulation studies and case studies show that incorporating animal movement can reduce the bias in estimated abundance found in conventional models and expand application of distance sampling to surveys that violate the assumption of no animal movement. For spatial capture-recapture, continuous-time encounter records are used to make detailed inference on where animals spend their time during the survey. In surveys conducted in discrete occasions, maximum likelihood models that allow for mobile activity centres are presented to account for transience, dispersal, and heterogeneous space use. These methods provide an alternative when animal movement causes bias in standard methods and the opportunity to gain richer inference on how animals move, where they spend their time, and how they interact.

Estimates of population abundance and survival are critical for effective wildlife management. Obtaining estimates of these kind using traditional wildlife monitoring techniques (i.e. ground and aerial surveys) has proven to be difficult, especially for species that are wide ranging and exist in small, patchily distributed populations. My objective was to implement fecal DNA-based capture-recapture surveys to estimate abundance and survival of two different ungulate populations that inhabit the deserts of southeastern California. I also compared fecal DNA-based capture-recapture techniques to traditional methods by evaluating the costs and precision associated with both methods. Using artificial water sources as focal sampling sites, I performed sampling during the summers of 2015, 2016, and 2017 in the Mojave and Sonoran Deserts of California. I was able to obtain reasonably precise estimates of abundance and survival for both species. To my knowledge, my study provides the first abundance and survival estimates of desert mule deer in California in over 13 years. Additionally, my study shows that when compared to traditional methods, fecal DNA-based capture recapture techniques can achieve much higher precision at a fraction of the cost.

Résumé : Les méthodes de capture-recapture servent à décrire l'état d'une population et les processus qui en sous-tendent la dynamique, lorsque les méthodes d'observation et de détection de cette population sont imparfaites. En surveillance des maladies infectieuses, elles peuvent simplement être utilisées pour estimer la taille totale de la population infectée par un pathogène et estimer quantitativement la sensibilité du système de surveillance de ce pathogène. Bien qu'exploitées très largement dans le domaine de la santé publique pour répondre à cet objectif, l'utilisation des méthodes de capture-recapture (CR) en surveillance des maladies infectieuses animales peut être considérée comme récente. Parce que le contexte de surveillance des maladies animales est nettement différent de celui de la surveillance des maladies humaines, des questions demeurent quant à l'intérêt et aux limites de ces méthodes pour estimer la sensibilité des systèmes de surveillance des maladies animales. Pour tenter de répondre à ces questions, nous avons identifié quatre systèmes de surveillance différents par leur complexité, leur efficacité et leur maladie d'intérêt : nous avons retenu les systèmes de surveillance de la fièvre aphteuse au Cambodge, de l'influenza aviaire hautement pathogène (IAHP) H5N1 en Egypte, de la tremblante ovine en France et de l'IAHP H5N1 en Thaïlande. Pour chacun de ces systèmes de surveillance, nous avons déterminé le modèle de CR le plus adapté compte tenu des données générées (respectivement le modèle de CR à deux sources, le modèle log-linéaire à 4 sources, le modèle de comptage tronqué en zéro et le modèle de comptage enflé en zéro). Pour chaque application, nous avons donc estimé le nombre total d'unités épidémiologiques non détectées par les systèmes de surveillance considérés ce qui nous a permis d'apprécier la sensibilité de chaque système de surveillance considéré. Il est ressorti de ces applications que les méthodes de capture-recapture sont relativement faciles à conduire et qu'elles permettent à faible coût d'estimer l'importance réelle d'une maladie sur un territoire quand celle-ci est surveillée de manière imparfaite. Il semble cependant que les pratiques de surveillance et de contrôle des maladies animales limitent les applications à l'échelle de l'animal, et nécessitent d'élargir l'unité épidémiologique à une échelle supérieure (troupeau, commune, etc...). Cet élargissement introduit de nouvelles contraintes (notamment l'hétérogénéité d'abondance) qu'il est nécessaire de prendre en compte pour ne pas biaiser les estimations finales. Ce travail propose des perspectives d'application en épidémiologie descriptive, ainsi que des perspectives méthodologiques de recherche en statistique et en modélisation.