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

Le sanglier (Sus scrofa) est une espèce chassée emblématique en Europe. Comme la plupart des ongulés de zones tempérés, l'espèce sanglier s'est étendue en Europe au cours des dernières décennies. Le nombre de sangliers tués chaque année en France est passé de 36429 en 1973 à 526709 en 2011. Cette situation unique du sanglier parmi les ongulés est pourtant très commune en Europe, et a conduit à une augmentation du montant des indemnisations des dégâts occasionnés par le sanglier. Les indemnisations sont alors passées de 2 à 18 millions d'euros entre 1973 et 2001. Contrôler les populations de sangliers est donc devenu un objectif majeur pour les gestionnaires. Évaluer les paramètres démographiques qui pilotent les dynamiques de populations est nécessaire afin d'améliorer notre connaissance du sanglier. Mais s'intéresser à l'évolution des traits d'histoire de vie du sanglier est également indispensable pour mieux comprendre cette espèce. Par conséquent, contrôler les populations de sangliers en intégrant des considérations évolutives est essentiel pour permettre une gestion durable de cette espèce. Le temps est donc venu de mieux comprendre cette espèce dans un contexte de démographie évolutive, grâce à un suivi à long-terme unique d'une population de sangliers fortement chassée dans la forêt de Châteauvillain-Arc-en-barrois, France. Tout d'abord, d'un point de vue démographique, nous proposons un outil de gestion afin de contrôler le taux de croissance des populations de sangliers. Ensuite, nous replaçons le sanglier au sein des mammifères en nous intéressant plus particulièrement à des comparaisons inter spécifiques de tactiques d'histoire de vie, grâce à de récents développements méthodologiques en dynamique de population. Nous trouvons alors que le sanglier présente une stratégie d'histoire de vie plus proche de celle de petits mammifères (comme l'écureuil) que de celle d'un ongulé de taille similaire. Puis, nous trouvons que, en réponse aux variations de disponibilité alimentaire, les femelles sangliers présentent différentes stratégies de reproduction afin de maximiser le nombre de petits viables / Wild boar (Sus scrofa) is an emblematic game species in Europe. As most ungulate populations in temperate areas, wild boar abundance and distribution has increased in most European countries over the last decades. The number of wild boar shot annually in France has increased from 36,429 in 1973 to 526,709 in 2011. This unique situation is common throughout Europe and has led to higher costs to agriculture because of damage to crops. Compensation for damage caused by wild boar in France rose from 2 to 18 million Euros between 1973 and 2001, a nearly tenfold increase. Controlling wild boar populations has thus become an important target for managers. Evaluating the vital rates that drive the population dynamics is necessary to improve our understanding of wild boar. But investigating the evolution of life history traits in wild boar is also required to improve our understanding of this species. As a consequence, controlling wild boar populations incorporating evolutionary considerations is essential to allow a sustainable management of this species. The time has thus come to better understand this species is an evolutionary demography context, taking advantage of a unique long-term monitoring of a heavily hunted wild boar population located in the Châteauvillain-Arc-en-barrois forest, France. First, from a demographic viewpoint, we provide a management tool to control population growth rate of wild boar population. Second, we put back the wild boar among mammals by focusing on inter-specific comparisons of life history tactics among mammals using recent developments in population dynamics. We found that wild boar exhibits a life history strategy close to small mammals such as squirrel rather than the life history strategy observed in similar-sized ungulates. Then, we found that, in response to changes in food availability, wild boar females are able to display different reproductive tactics to maximize the number of recruits at a given breeding event

The biological diversity of the planet is at great risk as a direct result of an ever-expanding human population and its associated activities. Landscape transformation to accommodate such activities leads to habitat loss and habitat fragmentation, often creating patches of relatively undisturbed habitat within a matrix of transformed areas that are often too small too support most species previously occupying the area and as a result loses its ecological integrity. A century ago the escarpment region of Mpumalanga consisted of large open plains covered with montane grassland dissected by montane forests and riparian vegetation alongside mountain streams. Today the grasslands and forests have almost disappeared from the area, the remaining patches mostly small fragments within a matrix of exotic tree plantations which have also dried up many of the rivers and streams in the area. The natural grassland areas persisting in the region are unique in habitat characteristics and floral species composition. It is also high in plant species richness, diversity and endemicity. The high degree of isolation experienced by these floral communities poses serious threats to both the floral and faunal species that currently exits within these isolated ‘islands’, many of which are endemic to the area and at great risk of extinction. These risks call for serious collaboration between the land owners (mostly forestry companies) and conservationists to assure the practical and necessary preservation and management of this unique and crucially valuable natural resource. This study aims to provide the first step into understanding the ecological principles associated with habitat fragmentation related specifically to the mountain grassland fragments within the afforestation matrix of the escarpment region of Mpumalanga, and to create a platform for the process of collaboration between land owners and conservation agencies to assess and manage these grassland patches. The aims of Chapter 2 included: 1 To determine if any marked human-induced disturbance to the plant communities in the grassland fragments has occurred. I do this in three ways: a) To compare the plant community composition of eighteen fragments with those of six control plots outside of the plantations where no marked disturbance to the grassland can be observed. b) To determine whether the plant assemblages in the fragments can be assigned to any of the natural and intact plant communities that Matthews (1993) described from a large-scale survey of undisturbed mountain areas. c) To determine the presence of any known intruder plant species within the fragments. 2 To assign conservation priorities to the remaining grassland fragments. The results obtained from the TWINSPAN analysis revealed six alliances of plant communities grouped hierarchically into four orders and two major classes of montane grassland. The DECORANA supported these results, indicating clear differences between communities 1.1 (Eriosema salignum – Loudetia simplex grassland of the wetter North region), 1.2 (Lobelia erinus – Panicum natalense grassland of the Transitional region), 2.1 (Parinari capensis – Eragrostis racemosa grassland) and 2.2 (Helichrysum rugulosum – Eragrostis racemosa grassland). Different plant communities revealed different combinations of geological characteristics, slope, aspect and elevation. The sample plots of isolated grassland fragments and those of large unfragmented areas compare well with each other - the species richness of experimental and control plots do not differ significantly. Also, the species composition of plots from the Wetter North, Transitional and Drier South regions show more variation than is evident between experimental and control plots. There was also good qualitative comparisons (quantitative comparisons were not possible as a results of sampling and analytic discrepancies) between the sample plots used in this study and the plant communities described by Graham Deall and Wayne Matthews. Some evidence of exotic invader plants was found within the sample plots, notably Pteridium aquilinum. Fortunately such species were localized in their distribution and restricted to community 1.1.2.2. The aims of Chapter 3 included the following: 1. To compare the faunal biodiversity in grassland fragments within afforested areas to that of control plots in large, relatively undisturbed grassland areas. 2. To determine to which degree the Coleoptera, Orthoptera, Lepidoptera and bird communities reflect recognized plant communities, and are restricted to specific plant communities. 3. To compare the habitat specificity (degree of stenotopy) of the different taxonomic groups and trophic levels of animals. 4. To make recommendations for the conservation of the Afromontane grassland fauna in the remaining grassland fragments in afforested areas. The sampling of 15602 beetles, grasshoppers and crickets were collected, with an average of 3900 per sampling period, revealed unique combinations of animal species linked to the different plant communities mentioned above. Significant differences were evident from the one-way analyses of similarity (ANOSIM) used to compare the faunal community structures of sample plots of the Wetter North, Transitional and Dryer South regions. The faunal community structures of the experimental and control plots of the Wetter North and Transitional regions did not differ significantly. The indexes of habitat specificity (fractions of species constricted to certain plant communities) indicated that the plants and butterflies were more habitat-specific than the Coleoptera, Orthoptera and Birds. The carnivorous insects showed a surprisingly high level of habitat specificity compared to the relatively low level of the phytophagous insects. This surprising trend was also evident in various insect families – Acrididae, Scarabaeidae and Nymphalidae had relatively high levels of habitat specificity compared to that of the Curculionidae and the Chrysomelidae. Chapter 4 has the following aims: 1. To quantify the effect of several environmental characteristics (slope, rainfall, geology, etc) on the faunal community structure of the grassland fragments. 2. To quantify the effects of degree of isolation on species richness, species diversity and assemblage structure of plants, insects and birds in grassland remnants. 3. To test for the effects of edges on the extant insect biodiversity in the grassland fragments inside plantations. 4. To quantify the effects of fragment size on species richness, species diversity and assemblage structure of plants, insects and birds. 5. To rank the grassland fragments in an order of conservation importance using factors such as biodiversity and uniqueness of the floral community. No clear relationship between fragment size and area sampled and species richness and/or – diversity was evident from the results. Indeed, the smallest area sampled had the fourth highest species richness and the largest area sampled had the fourth lowest species richness and species diversity. Regressions results did not show any significant effects of the geographical area sampled on the biodiversity estimates of the fragments. Therefore I assume that the estimates arrived at for the area sampled within each fragment is representative of that of the complete fragment. The Detrended correspondence analysis (DCA - using square root transformed abundance data) used, indicated the need to perform a gradient analysis using a redundancy analysis (RDA). The permutation test resulting from this analysis revealed a non-significant value for the first canonical axis, but a significant value for the first four canonical axes together. The ten species contributing the most to above-mentioned result include two Scarabs (Scarabaeidae – Aphodius sp 1 and Melolonthinae sp 2), two weevils (Curculionidae – Eudraces sp 1 and Curculionidae sp 42), one leaf beetle (Chrysomelidae – Asbecesta near capensis), one darkling beetle (Tenebrionidae – Lagria sp 1), one longhorn beetle (Cerambycidae – Anubis scalaris), one jewel beetle (Buprestidae – Buprestidae sp 1), one ladybird (Coccinellidae – Coccinellidae sp 4) and one Dor beetle (Bolboceratidae – Mimobolbus maculicollis). Of these ten beetles only three are not restricted to the Drier South Region (Anubis scalaris – Wetter North and Drier South, Lagria sp 1 – throughout and Eudraces sp 1 – throughout). The associated stepwise multivariate regression showed distance to the nearest grassland to be the only environmental characteristic to significantly influence the faunal community structure of the fragments. Slope was the environmental characteristic with the smallest effect. In contrast with the results from redundancy analysis, the analysis of similarity (ANOSIM) and t-tests did not reveal significant differences in the faunal community structure of fragments closer to – and further than one kilometre from the nearest grassland neighbour. This trend was the most evident for fragments of the Transitional region and the least obvious for the fragments of the study area as a whole. The SIMPER analysis showed that of the ten species contributing most to the dissimilarity between insect communities of fragments closer/further than one kilometre from the nearest grassland neighbour, eight were also in the group of ten species characterizing the faunal communities of either/both groups (contributing towards similarity). The insect communities found at 10, 20 and 50 metres from the edge of the grassland fragments did not differ significantly, nor did an ANOSIM performed separately for each of the three major plant communities reveal any significant edge-related differences. The ANOVA results for the individual species revealed only one (of 57 - in the Transitional region) having a distribution that differs significantly with respect to distance from the habitat edge:Eremnus sp. 2 was only found at 10 metres from the edge of the fragment, close to the plantations. Of all the groups, only bird diversity, bird richness and general faunal diversity showed significant relationships with fragment size. There was a non-significant trend for insects to biodiversity to be reduced in very small fragments. Most of the botanical data exhibited no significant relationship with fragment size. The species composition of control sites were not found to be significantly different from that of experimental fragments for all the faunal groups pooled together or for the fragments of the Transitional Region and the Wetter North Region. Using the four separate scores for birds, butterflies, beetles and grasshoppers, each fragment was assigned a total conservation score. The twenty-four fragments were then ranked in order of conservation importance. Fragments of the Wetter North had an average score of 65.3, fragments of The Transitional Region 66.6 and fragments of the Drier South 52.3. The results relating to this study has lead to the following conclusions: o It is concluded that afforestation and habitat fragmentation have not significantly impacted on the flora of the montane grassland of the study area since many of the grassland fragments surrounded by plantations are still easily identifiable as natural communities, described by Matthews and Deall in broader-scale surveys in the past. Also, no obvious invader – or disturbed plant communities are discernible even though some of them have been isolated for as long as 40 years. o The plant communities of conservation importance described by Matthews coincide with the important communities recognized in this study. Rare and endangered plant species, as well as species endemic to the region, are more often than not found on the scarce Black Reef quartzite of the region, which is more evident to the Northern part of the study area. Communities 1.1 and 1.2.2 are therefore of particular conservation importance, not only as a result of their scare geological base, but also because of the high risk associated with the few grassland examples left of these communities. o The high levels of habitat specificity of many of the taxonomic and trophic faunal groups indicate that many of the invertebrate taxa are probably endemic to the region, and that the plant endemicity encountered in the Afromontane grasslands is reflected by a similar degree of animal endemicity. o The similarity in faunal assemblages and diversity between isolated fragments and large areas of grassland emphasizes the conservation importance of the fragments, even when smaller than 5 Ha in extent. o Appropriate management of the grassland fragments within the plantations is therefore important for the conservation of the plant and animal taxa encountered there. Experimental management involving grazing, mechanical cutting, grazing and burning is needed to decide on an efficient management regime, so that the grassland biodiversity can be conserved in a planned way. Such work will also allow empirical testing the efficiency of the indicator species suggested above. o Isolated grassland fragments in this study represent largely unaffected natural plant and insect communities, differing little from large unfragmented grasslands in the study area. o Fragments found within afforested areas therefore have a high conservation importance, since they represent ‘natural’ grassland areas and are often the only representative of a particular plant community left in the area. o No significant edge effects on the faunal communities 10, 20 and 50 metres from the fragments’ edges exist as a result of afforestation in the area. o Birds (and probably other vertebrates in these grasslands) are affected by fragment size, while invertebrates are much less affected and plants do not show any measurable effect of fragment size. o Fragments in the wetter northern part of the study area, characterized by high levels of plant endemicity, have a higher conservation importance as judged by faunal biodiversity. / Dissertation (MSc (Zoology and Entomology))--University of Pretoria, 2005. / Zoology and Entomology / unrestricted

Fluctuations, or "noise", can play a key role in determining the behaviour of living systems. The molecular-level fluctuations that occur in genetic networks are of particular importance. Here, noisy gene expression can result in genetically identical cells displaying significant variation in phenotype, even in identical environments. This variation can act as a basis for natural selection and provide a fitness benefit to cell populations under stress. This thesis focuses on the development of new conceptual knowledge about how gene expression noise and gene network topology influence drug resistance, as well as new simulation techniques to better understand cell population dynamics. Network topology may at first seem disconnected from expression noise, but genes in a network regulate each other through their expression products. The topology of a genetic network can thus amplify or attenuate noisy inputs from the environment and influence the expression characteristics of genes serving as outputs to the network. The main body of the thesis consists of five chapters: 1. A published review article on the physical basis of cellular individuality. 2. A published article presenting a novel method for simulating the dynamics of cell populations. 3. A chapter on modeling and simulating replicative aging and competition using an object-oriented framework. 4. A published research article establishing that noise in gene expression can facilitate adaptation and drug resistance independent of mutation. 5. An article submitted for publication demonstrating that gene network topology can affect the development of drug resistance. These chapters are preceded by a comprehensive introduction that covers essential concepts and theories relevant to the work presented.

Les polychlorobiphényles (PCB) et les polybromodiphényléthers (PBDE) sont deux familles de composés hydrophobes partageant certaines propriétés physico-chimiques. Des travaux antérieurs ont montré que ces composés pouvaient affecter les traits d’histoire de vie des poissons. Il s’avère cependant que les études approchant des situations environnementales sont rares. Cette thèse se divise en trois parties. La première partie s’est attachée à évaluer les effets d’une exposition à un mélange réaliste de PCB et de PBDE sur les traits d’histoire de vie du poisson-zèbre. Les résultats ont montré une taille asymptotique plus élevée, une probabilité de ponte retardée chez les individus exposés et une faible survie des larves F1 en situation de jeûne issues des pontes précoces des individus exposés. La seconde partie a cherché à identifier, sur la base d’un modèle bioénergétique (DEB), les modes d’action physiologique (PMoA) de PCB et PBDE. Deux PMoAs probables ont été révélés: le premier est lié à l’augmentation de la fraction d’énergie allouée à la maintenance et la croissance somatique et le deuxième est lié à l’augmentation des coûts de production d’un œuf. La troisième partie de la thèse s’est intéressée à évaluer les conséquences de la contamination sur la dynamique de population de poissons. Les résultats ont montré une réduction de l’abondance numérique, une augmentation de la biomasse et un grand risque de surexploitation chez la population exposée, Les résultats de cette thèse pourraient constituer un outil d’aide à une gestion durable des stocks halieutiques qui prennent en compte les effets de multiples contaminations qui se surajoutent à la pression de pêche. / Polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) are two families of hydrophobic compounds sharing some similar environmental properties. Previous studies have demonstrated that these compounds could affect fish life-history traits. However, few studies have focused on environmental situations. This thesis is divided into three parts. The first part aimed to evaluate the effects of a realistic mixture of PCBs and PBDEs on the life-history traits of zebrafish. The results showed a slower growth, but to a larger asymptotic length, and delayed spawning probability in exposed fish. In addition, offspring issued from early spawning events of exposed fish exhibited a lower larval survival under starvation condition. The second part aimed to identify, on the basis of a bioenergetic model (DEB), the physiological modes of action (PMoA) of PCBs and PBDEs. Two potential PMoAs have been revealed: the first one was through an increase of the fraction of energy allocated to somatic maintenance and growth and the second one was through an increase of the cost of production of an egg. The third part focused on the population dynamical consequences of the individual life-history effects of PCBs and PBDEs. The results showed a lower abundance, a higher biomass and a higher risk of overexploitation in exposed population compared to control population. The results of this thesis could be a helpful tool for sustainable management of fish stocks that take into account the effects of multiple contaminations that are added to the fishing pressure.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2016-01-13T12:47:04Z No. of bitstreams: 1 elizamariaferreira.pdf: 2774756 bytes, checksum: 61a94ee557cce6b0fb63b18f2d57e8e4 (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2016-01-25T17:29:48Z (GMT) No. of bitstreams: 1 elizamariaferreira.pdf: 2774756 bytes, checksum: 61a94ee557cce6b0fb63b18f2d57e8e4 (MD5) / Made available in DSpace on 2016-01-25T17:29:48Z (GMT). No. of bitstreams: 1 elizamariaferreira.pdf: 2774756 bytes, checksum: 61a94ee557cce6b0fb63b18f2d57e8e4 (MD5) Previous issue date: 2015-02-27 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / O objetivo deste trabalho é estudar algumas aplicações da teoria de controle ótimo para problemas biológicos. Assim, apresentamos inicialmente o estudo de dois modelos diferentes: “Optimal Control of Biological Invasions in Lake Network”, proposto por Potapov et al. [13], e “Simulating Optimal Vaccination Times during Cholera Outbreaks” proposto por Modnak et al. [9]. Os modelos têm suas dinâmicas baseadas em equações diferenciais ordinárias e neles foi minimizado um funcional, com uma única e com várias restrições, respectivamente. No primeiro modelo a teoria de controle ótimo é usada para minimizar os custos com a prevenção juntamente com os custos gerados pelos danos da invasão biológica em estudo, e no segundo modelo aplica-se o controle ótimo para minimizar os custos da vacinação e tratamento dos indivíduos infectados durante um surto de cólera. Com base nos modelos propostos por Vieira e Takahashi em “A Sobrevivência do Vírus varicelazoster”, [16], e por Shulgin et al. em “Pulse vaccination strategy in the SIR epidemic model”, [14], propomos um modelo matemático que considera a vacinação da população como uma estratégia de controle da varicela. Nós usamos a teoria de controle ótimo para definir as condições necessárias para minimizar os custos da vacinação e tratamento dos indivíduos infectados com catapora ou com herpes zoster. A dinâmica é baseada em equações diferenciais ordinárias, que são as restrições sob as quais queremos minimizar o funcional utilizando a teoria de controle ótimo. / The goal of this work is to study some applications of the theory of optimal control for biological problems. Thus, initially we present the study of two different models: “Optimal Control of Biological Invasions in Lake Network” proposed by Potapov et al. [13], and “Simulating optimal Vaccination Times During Cholera Outbreaks” proposed by Modnak et al. [9]. The models have their dynamics based on ordinary differential equations and are minimizing the functional with a single and with several restrictions, respectively. The first model uses optimal control theory to minimize costs with prevention and together with the costs generated by the damage of the invasion, the second model applies optimal control to minimize costs in the vaccination and treatment of infected individuals during cholera outbreak. Based on models proposed by Vieira and Takahashi on “The Virus Survival varicella-zoster”, [16], and by Shulgin et al. in “Pulse vaccination strategy in the SIR epidemic model”, [14], we propose a mathematical model that considers a vaccination of the population as a varicella control strategy. We use the optimal control theory to define necessary conditions to minimize the costs of vaccination and treatment of infected individuals with chickenpox or with herpes zoster. The dynamics is based on ordinary differential equations which are the constraints under which we want to minimize the functional in the optimal control theory.

Cette thèse porte sur la modélisation de la dynamique des populations et de ses applications, à la démographie et l’actuariat d’une part, et à l’étude des processus de Hawkes d’autre part. Ces travaux de thèse proposent d’explorer à travers différents points de vue comment se déforme la structure d’une population, tant concernant la répartition des âges que sa composition en terme de caractéristiques. À travers cinq chapitres, nous déclinons une même philosophie qui, pour comprendre comment évoluent des quantités agrégées, propose d’étudier la dynamique de la population à une échelle plus fine, celle de l’individu. Après un premier chapitre introductif en langue française, détaillant les motivations et les principales contributions, nous proposons d’abord dans le Chapitre 2 la description du cadre général de la modélisation dynamique aléatoire de populations structurées en caractéristiques et en âges, sur la base de Bensusan et al. (2010–2015), ainsi que plusieurs exemples motivés par les applications démographiques et actuarielles. Nous détaillons la construction mathématique de tels processus ainsi que le lien avec les équations déterministes classiques en démographie. Nous discutons également l’impact de l’hétérogénéité sur l’exemple d’un effet cohorte, ainsi que le rôle de l’environnement aléatoire. Les deux chapitres suivants mettent en avant l’importance de la pyramide des âges. Le modèle de population général issu du Chapitre 2 est décliné dans le Chapitre 3 pour étudier des processus de Hawkes avec immigrants généraux, pour lesquels nous exploitons le concept de pyramide des âges. Dans cette étude théorique, basée sur Boumezoued (2015b), nous établissons de nouveaux résultats sur leur distribution pour une classe de fonctions qui généralisent le cas exponentiel étudié jusqu’ici. Dans le Chapitre 4, qui reprend Arnold et al. (2015), nous analysons l’impact de changements dans la mortalité par causes de décès sur la dynamique de la pyramide des âges, et en particulier sur le ratio de dépendance qui est un indicateur crucial du vieillissement de la population. En incluant le jeu des naissances dans la dynamique, ce travail de simulations, basé sur les données de l’OMS, permet de compléter la littérature existante sur les causes de décès qui se focalise traditionnellement sur des indicateurs de mortalité. Les deux derniers chapitres étudient plus particulièrement l’hétérogénéité des populations. Le Chapitre 5, basé sur Boumezoued et al. (2015), propose de mesurer l’hétérogénéité de la mortalité dans les données de l’Échantillon Démographique Permanent de l’INSEE. Dans le cadre de cette contribution d’adaptation de méthodes statistiques et de sa mise en oeuvre sur données réelles, nous proposons une méthode d’estimation paramétrique par maximum de vraisemblance pour les modèles multi-états qui prend en compte à la fois la censure par intervalle, caractéristique des données longitudinales issues du recensement, et également le retour dans les états intermédiaires. Enfin, le Chapitre 6, tiré de Boumezoued (2015a), reprend le modèle général du Chapitre 2 dans lequel les individus peuvent donner naissance, changer de caractéristiques et décéder. La contribution de cette partie théorique est d’étudier le comportement de la population lorsque les caractéristiques individuelles changent fréquemment. Nous établissons un thèorème limite en grande population pour le processus de pyramide des âges, dont le comportement est alors décrit par des taux de naissance et mort agrégés sur la structure stable en terme de caractéristiques. / This thesis focuses on population dynamics models and their applications, on one hand to demography and actuarial science, and on the other hand to Hawkes processes. This work explores through several viewpoints how population structures evolve over time, both in terms of ages and characteristics. In five chapters, we develop a common philosophy which studies the population at the scale of the individual in order to better understand the behavior of aggregate quantities. The first chapter introduces the motivations and details the main contributions in French. In Chapter 2, based on Bensusan et al. (2010–2015), we survey the modeling of characteristic and age-structured populations and their dynamics, as well as several examples motivated by demographic issues. We detail the mathematical construction of such population processes, as well as their link with well known deterministic equations in demography. We illustrate the simulation algorithm on an example of cohort effect, and we also discuss the role of the random environment. The two following chapters emphasize on the importance of the age pyramid. Chapter 3 uses a particular form of the general model introduced in Chapter 2 in order to study Hawkes processes with general immigrants. In this theoretical part based on Boumezoued (2015b) we use the concept of age pyramid to derive new distribution properties for a class of fertility functions which generalize the popular exponential case. Chapter 4 is based on Arnold et al. (2015) and analyses the impact of cause-of- death mortality changes on the population age pyramid, and in particular on the dependency ratio which is crucial to measure population ageing. By including birth patterns, this numerical work based on WHO data gives additional insights compared to the existing literature on causes of death focusing only on mortality indicators. The last two chapters focus on population heterogeneity. The aim of Chapter 5, based on Boumezoued et al. (2015), is to measure mortality heterogeneity on French longitudinal data called Échantillon Démographique Permanent. In this work, inspired by recent advances in the statistical literature, we develop a parametric maximum likelihood method for multi-state models which takes into account both interval censoring and reversible transitions. Finally, Chapter 6, based on Boumezoued (2015a), considers the general model introduced in Chapter 2 in which individuals can give birth, change their characteristics and die. The contribution of this theoretical work is the analysis of the population behavior when individual characteristics change very often. We establish a large population limit theorem for the age pyramid process, whose dynamics is described at the limit by birth and death rates which are averaged over the stable population composition.

L'isolement géographique est une menace élevée pour le maintien des populations sur le long terme. Il est donc primordial de comprendre selon quel degré la viabilité des populations est affectée par leur isolement, notamment en vue de définir des priorités en terme de conservation. Eryngium viviparum J.Gay (Apiaceae) est une des espèces végétales les plus menacées d'Europe avec une distribution ibéro-armoricaine très fragmentée. En France, son statut de conservation est devenu particulièrement critique avec la disparition de la presque totalité de ses populations au cours des années 1980, à l'exception d'une seule, suite à la destruction de son habitat par les activités humaines. Cette unique population fait depuis plusieurs années l'objet d'une conservation et d'une gestion attentives au sein d'une réserve protégée. Malgré ces actions, l'isolement de cette population soulève des interrogations quant à sa viabilité sur le long terme. Dans ce cadre, et à travers une approche multidisciplinaire, la thèse propose un renforcement des connaissances sur les caractéristiques écologiques et biologiques d'E. viviparum, et plus particulièrement concernant sa dernière population française. Elle s'articule selon trois axes principaux : (1) L'étude de l'amplitude écologique de l'espèce, puis la caractérisation de ses préférences écologiques à fine échelle au sein de la dernière population française (2) L'évaluation de la viabilité de la population isolée d'après ses paramètres démographiques, son niveau de diversité génétique et son degré de différenciation avec d'autres populations. (3) L'expérimentation des modalités de réintroduction en France. Les résultats apportés par ce travail contribueront à définir les prochaines priorités en matière de gestion et de conservation pour assurer le maintien d'E. viviparum sur le long terme en France. Le cas d' E. viviparum fournit un bon modèle d'étude pour évaluer l'effet de l'isolement sur la dynamique d'une population isolée et pour appliquer une conservation adaptée à cette problématique. / The geographical isolation is an important threat for the long term preservation of populations. It is crucial to understand how the viability of populations is affected in such context, in particular to define conservation priorities. Eryngium viviparum J.Gay (Apiaceae) is one of the most endangered plant in Europe, with a fragmented distribution between the NW of the Iberian peninsula and Brittany. ln France, the species is maintained only on a single locality, after the destruction of its habitat by human activities during 1980s. Despite a conservation program and an attentive management within a protected area, the strong isolation experimented by this population bring up questions about its long-term viability. In this context, through a multidisciplinary approach, this thesis aims to improve the biological and ecological knowledge of E. viviparum, and more particularly within its last French population. This thesis is organized according three main axes : (1) The study of large-scale E. viviparum ecological amplitude, and the characterization of its fine scale ecological preferences within the last french population. (2) The viability evaluation of the isolated population according to its demographic modalities, and to its genetic structure in comparison with Iberian populations. (3) The experiment of its reintroduction modalities in France.The results of this study will contribute to define the long-term conservation priorities of E. viviparum in France. Finally, the case of E. viviparum is a good model to study the effect of the isolation on an isolated population dynamic, and to apply adapted conservation for species in a similar context.

1. The success of invasive species is often thought to be due to release from natural enemies. This hypothesis relies on the assumption that species are regulated by top-down forces in their native range and implies that species are likely to be regulated by bottom-up forces in the invasive range. Neither of these assumptions has been consistently supported with insects, a group which include many highly destructive invasive pest species. 2. Winter moth (Operophtera brumata) is an invasive defoliator in North America that appears to be regulated by mortality in the larval stage in its invasive range. To assess whether regulation in the invasive range is caused by top-down or bottom-up forces, we sought to identify the main causes of larval mortality. 3. To measure the importance of different sources of winter moth larval mortality, we used observational and manipulative field studies to measure dispersal, predation, parasitism, disease. We measured the response of larval dispersal in the field to multiple aspects of foliar quality, including total phenolics, pH 10 oxidized phenolics, trichome density, total nitrogen, total carbon, and carbon-nitrogen ration. We also used manipulative laboratory studies to measure the presence of cannibalism and dispersal. 4. Tree-level declines in density were driven by density-dependent larval dispersal of early instars with very little mortality caused by other factors. Later instar larvae dispersed at increased rates from previously damaged vs. undamaged foliage, and field larval dispersal rates were related to proportion of oxidative phenolics in 2015, suggesting that larval dispersal may have been mediated by an induced decline in foliar quality. 5. We conclude that winter moth population densities are regulated in New England by density-dependent larval dispersal possibly mediated by phenolic oxidative capacity. The suggested role of host plant quality in mediating dispersal means that winter moth population densities in New England appear to be regulated by bottom up forces, aligning with the assumptions of the natural enemy release hypothesis. This is the first study known to the authors presenting data showing a negative effect on insect herbivore performance from pH 10 oxidized phenolics.

South African southern right whales (SRWs; Eubalaena australis) have been studied intensively since 1969, and annual aerial surveys between 1971 and 2006 indicate a predominant 6.9% annual population growth rate – a conservation success story after the species’ legal protection from commercial whaling in 1935. However, the prevalence of South African SRW unaccompanied adults (non-calving adults) and cow-calf pairs dropped sharply after 2009 and 2015, respectively. Additionally, the calving interval of many female South African SRWs has shifted from a three-year cycle to a four- or five-year cycle, since 2010, suggesting calving failure. This has resulted in a decrease in the population growth rate from 6.9% between 1971 and 2006, to 6.5% in 2017. SRWs are capital breeders that meet migratory and reproductive costs through seasonal energy intake, leading to strong links between their calving and foraging success. The anomalous trends in the South African SRW population have therefore raised concern about the ecological status of its broad feeding range in the Southern Ocean and ultimately about its continued population recovery. This necessitated investigation firstly into the influence of large-scale global climate drivers, Antarctic winter sea-ice extent and summer ocean productivity on the calving output of the South African SRW population. Auto-regressive integrated moving average models revealed significant model performance improvement through the inclusion of the Oceanic Niño Index (a key measure of El Niño events), the Antarctic Oscillation (the leading mode of atmospheric variability in the Southern Ocean) and chlorophyll a concentrations. The findings indicate that the South African SRW calving output appears closely influenced by not only the species’ life cycle, but also by foraging ground productivity and global climate. Secondly, the foraging strategies of South African SRWs during the 1990s (i.e. a period of high calving rates) and the late 2010s (i.e. a period of low calving rates), were assessed, through the analyses of stable carbon (δ13C) and nitrogen (δ15N) isotope values in SRW skin biopsy samples (n = 122). Results show that South African SRWs underwent a dramatic northward shift in foraging location, as well as a diversification in foraging strategy, between the 1990s and 2010s. Bayesian mixing models suggest that during the 1990s, the population foraged on prey with isotopic values similar to krill from around South Georgia. By contrast, in the 2010s, it is inferred that the population foraged on prey with isotopic values consistent with prey found in the waters of the Subtropical Convergence, Polar Front, and Marion Island. This shift could represent a new strategy to cope with changes in the availability of preferred prey or changes in habitat productivity. However, the co-occurring reproductive declines show that altering foraging strategies may not be sufficient to successfully adapt to a changing ocean. Overall, the results of this dissertation advocate that South African SRWs have recently been affected by environmental change at their foraging grounds, in turn affecting their reproductive success. Their predictive coastal presence and the existing long-term monitoring suggest that the species should be regarded as an indicator species – illustrative of climate change impacts in Southern Ocean ecosystems. / Dissertation (MSc ((Zoology))--University of Pretoria, 2020. / Zoology and Entomology / MSc (Zoology) / Restricted