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The thesis begins with a general introduction to population genetics in chapter 1. I review the fundamental processes of evolution - mutation, recombination, selection, gene flow and genetic drift - and give an overview of Bayesian inference in statistical population genetics. Later, I introduce the studied species, Alpine ibex (Capra ibex ), and its recent history. This history is intimately linked to the structured population in the Swiss Alps that provides the source of genetic data for this thesis. A particular focus is devoted to approximate Bayesian computation (ABC) in chapter 2, a method of inference that has become important over the last 15 years and is convenient for complex problems of inference. In chapter 3, the biological focus is on estimating the distribution of mutation rates across neutral genetic variation (microsatellites), and on inferring the proportion of male ibex that obtain access to matings each breeding season. The latter is an important determinant of genetic drift. Methodologically, I compare different methods for the choice of summary statistics in ABC. One of the approaches proposed by collaborators and me and based on boosting (a technique developed in machine learning) is found to perform best in this case. Applying that method to microsatellite data from Alpine ibex, I estimate the scaled ancestral mutation rate (THETA anc = 4Neu) to about 1:288, and find that most of the variation across loci of the ancestral mutation rate u is between 7.7*10 -4 and 3.5*10 -3. The proportion of males with access to matings per breeding season is estimated to about 21%. Chapter 4 is devoted to the estimation of migration rates between a large number of pairs of populations. Again, I use ABC for inference. Estimating all rates jointly comes with substantial methodological problems. Therefore, I assess if, by dividing the whole problem into smaller ones and assuming that those are approximately independent, more accuracy may be achieved overall. The net accuracy of the second approach increases with the number of migration rates. Applying that approach to microsatellite data from Alpine ibex, and accounting for the possibility that a model without migration could also explain the data, I find no evidence for substantial gene flow via migration, except for one pair of demes in one direction. While chapters 3 and 4 deal with neutral variation, in chapter 5 I investigate if an allele of the Major Histocompatibility Complex (MHC) has been under selection over the last ten generations. Short- and medium-term methods for detecting signals of selection are combined. For the medium-term analysis, I adapt a matrix iteration approach that allows for joint estimation of the initial allele frequency, the dominance coefficient, and the strength of selection. The focal MHC allele is shared with domestic goat, and an interesting side issue is if this reflects an ancestral polymorphism or is due to recent introgression via hybridization. I find most evidence for asymmetric overdominance (selection coefficient s: 0.974; equilibrium frequency: 0.125) or directional selection against the `goat' allele (s: 0.5) with partial recessivity. Both scenarios suggest a disadvantage of the `goat' homozygote, but differ in the relative fitness of the heterozygotes. Overall, two aspects play a dominating role in this thesis: the biological questions and the process of inference. They are linked, yet while the proximate motivation for the biological component is given by a specific system - the structured population of Alpine ibex in the Swiss Alps - the methods used and advanced here are fairly general and may well be applied in different contexts.

We studied the dynamic of nine populations of Alpine ibex ( Capra ibex ibex ) in five protected areas. We showed a strong effect of age on demographic parameters, with a marked decrease of survival after 10-12 years of age. We also found a high variability of old females' reproduction between populations. Contrary to what is expected for a highly dimorphic species like ibex, males survived as well as females except for old individuals. Winter harshness had a negative impact on survival of old individuals but not on reproduction and survival of young. We conclude that ibex have evolved a highly conservative life-history tactic compared to other ungulates studied to now. From a management viewpoint we also showed that under some circumstances ground counts might provide reliable estimates of ibex population trends.

La gestion des maladies infectieuses dans la faune sauvage se heurte à de nombreuses limites, et le développement de stratégies efficaces représente un défi de taille. Pour atteindre cet objectif, une compréhension fine des facteurs influençant la transmission et la persistance de l’infection est nécessaire. Parmi ces facteurs, l’hétérogénéité de transmission est une caractéristique importante des populations sauvages. En effet, la diversité des comportements, des structures sociales et spatiales, ou encore des espèces peut conduire à des contributions très variables au nombre de nouvelles infections. Par conséquent, quantifier l’hétérogénéité de transmission pourrait permettre d’améliorer l’efficacité des mesures de gestion sanitaire dans la faune sauvage, en ciblant les individus ou les unités de population qui sont responsables de la majorité des évènements de transmission. L’objectif de cette thèse était d’améliorer les connaissances sur la gestion des maladies infectieuses dans des populations sauvages hétérogènes, en utilisant la brucellose à Brucella melitensis dans une population de bouquetin des Alpes (Capra ibex) comme modèle d’étude. En effet, la biologie de la brucellose et l’écologie de l’espèce hôte se prêtent bien à l’existence et donc à l’étude d’une hétérogénéité de transmission à différentes échelles. A l’aide de cultures bactériennes, nous avons tout d’abord montré que seulement 58 % des individus séropositifs sont à risque d’excréter la brucellose, et que ce risque diminue avec l’âge. Ensuite, mettant à profit l’existence d’informations détaillées sur la dynamique de population et le comportement du bouquetin, et de données épidémiologiques dans la population d’étude, nous avons développé un modèle individu-centré afin de quantifier l’hétérogénéité individuelle et spatiale de la transmission. Nous avons démontré que la transmission de la brucellose était hétérogène entre individus, les femelles provoquant environ 90% des nouvelles infections, et entre unités spatiales, plus de 80% des cas de transmission ayant lieu dans les trois sous-unités socio-spatiales qui forment la zone cœur du massif. Nous avons également estimé l’évolution temporelle de la séroprévalence et de la force d’infection, en utilisant différents modèles statistiques. Les résultats suggèrent que l’importante opération de capture menée en 2015, avec test systématique et élimination des individus séropositifs, a permis de diminuer la transmission de la brucellose dans la population. Sur la base de l’ensemble de ces résultats, nous avons évalués une série de stratégies de gestion sanitaire qui pourraient être utilisées à l’avenir dans la population. Les résultats, issus du modèle individu-centré, confirment que la stratégie prioritaire devrait être d’éliminer le plus d’individus séropositifs, et que cibler les femelles et/ou la zone cœur permet d’améliorer l’efficacité des mesures. Bien qu’il n’y ait pas de solution évidente pour la gestion de la brucellose dans notre cas d’étude, les stratégies de gestion ciblées sont très prometteuses et permettent de raffiner les mesures sanitaires classiquement utilisées. Il est donc primordial de bien comprendre l’hétérogénéité de transmission dans les populations sauvages infectées, et de rechercher des stratégies ciblées qui peuvent permettre d’améliorer la gestion en termes d’efficacité et d’acceptabilité / The management of infectious diseases in wildlife reservoirs is particularly challenging and faces several limitations. The development of appropriate management strategies requires a detailed understanding of the factors affecting the transmission and persistence of the infectious agent in the population. Among these factors, heterogeneity of transmission is a common characteristic in natural host-pathogen systems. Indeed, wild animals express a broad range of behaviours, are organised in a variety of social and spatial structures, occupy many areas with very different characteristics and belong to a large diversity of species. Such heterogeneities, from between-individuals to between-species, may result in different contributions to the overall number of new cases of infections. Thus, understanding transmission heterogeneity could provide valuable insights on how to effectively manage these systems, by targeting the individuals or areas that are responsible for most transmissions. The aim of this thesis was to provide insights on the monitoring and management of infectious diseases in heterogeneous wild populations, using Brucella melitensis infection in a French population of wild Alpine ibex (Capra ibex) as a case study. The biology of brucellosis and the ecology of Alpine ibex makes this case study a good candidate for transmission heterogeneity at several levels. Using bacterial examinations, we first established that only 58% of seropositive individuals were at risk to excrete Brucella, and that this risk decreased with increasing age. Then, we took advantage of detailed information available on ibex population dynamics, behaviour, and habitat use, and on epidemiological surveys, to build an individual-based model in order to quantify heterogeneity at the individual and spatial levels. The transmission is extremely heterogeneous between individuals, with females generating around 90% of the new cases of brucellosis infection, and between spatial units, three of the five socio-spatial units (the core area) accounting for more than 80% of brucellosis transmission. Using statistical models to estimate the temporal dynamics of the seroprevalence and of the force of infection in the population, we found evidence that the massive captures with test-and-remove operations that were conducted in 2015 managed to reduce brucellosis transmission in the population. Based on these results, we evaluated several predictive disease management strategies in the individual-based model. Our results confirmed that the primary strategy should be to remove as many seropositive individuals as possible, and that strategies targeting females and/or the core area are more effective than untargeted management. Although there is no silver bullet for the management of brucellosis in the population of study, targeted strategies offer a wide range of promising refinements to classical sanitary measures. We therefore encourage to look for heterogeneity in other infection-wildlife systems and to evaluate potential targeted strategies for improving management schemes in terms of efficiency and acceptability

Tesis-Universidad de Valladolid, 2000. / Incluye referencias bibliográficas e índices.

Comprendre l'impact des changements globaux sur la dynamique des populations animales représente un enjeu sociétal majeur pour favoriser le maintien de la biodiversité. Le milieu de montagne permet de travailler sur de petites communautés d'herbivores à forte valeur patrimoniale, cynégétique ou emblématique. Il s'agit en effet d'un milieu en pleine mutation depuis plusieurs décennies à cause de la déprise agricole et du développement récent de l'écotourisme et des activités humaines récréatives. Ces changements ont conduit à l'aménagement et à la modification de nombreux habitats. Par ailleurs, le milieu montagnard est fortement saisonnier et semble particulièrement sensible au changement global actuel. L'effet des changements climatiques récents reste pourtant encore mal évalué. L'augmentation de la température moyenne des 30 dernières années est susceptible de modifier la dynamique des ressources disponibles pour les herbivores, mais aussi la chronologie d'accès à ces ressources, notamment à travers la diminution du couvert neigeux en hiver et sa fonte accélérée au printemps. L'objectif de cette thèse est donc d'évaluer l'effet des variables climatiques locales et globales sur les traits d'histoire de vie des herbivores de montagne, principalement à travers l'exemple de la marmotte alpine (Marmota marmota), un mammifère social et hibernant. Ce travail a permis de mieux appréhender les mécanismes d'action du climat sur la démographie des espèces de montagne, mais aussi de mettre en évidence le déclin continu d'une population de marmottes Alpines, dans les Alpes françaises, depuis les années 1990. Il pourrait ainsi servir de base pour établir les règles de gestion de cette espèce emblématique, et maintenir une forte biodiversité dans les écosystèmes de montagne / Natural systems responses to global change are of major concern for human societies to maintain high species diversity. Mountains, and particularly alpine climate, offer the opportunity to work with small mammalian herbivore communities, with a strong patrimonial, hunting or emblematic value. Since the last decades, mountains are indeed facing major changes, due to the loss of agricultural lands and the recent development of ecotourism and human recreational activities. Those changes have modified natural habitats and their management planning a lot. Additionally, alpine climate is strongly seasonal and seem particularly sensitive to the actual global change. However, the recent impact of climate change on species and natural habitats is still under-evaluated. The increase in the average global temperature of the last 30 years could modify resources dynamics for a wide variety of species. The availability of resources, but also the chronology of access to these resources, for example through the decrease of snow cover in winter and its accelerated thaw in spring, is of crucial importance for herbivore populations. The aim of this thesis is therefore to evaluate the potential role of local and global climatic factors on life history traits of mountain herbivores, mostly through the example of the alpine marmot (Marmota marmota), a social and hibernating mammal. This work allowed us to better understand the mechanisms underlying the effect of climate change on mountain mammal population dynamics and demography; but also to highlight the continuous decline of an alpine marmot population in the French Alps since the 90s. Conservation strategies and practices could thus arise from this work, in order to maintain biodiversity in mountainous ecosystems