During a time of habitat loss, climate change and loss of biodiversity, efficient analytical tools are vital for population monitoring. This thesis concerns the modelling of butterflies, whose populations are undergoing various changes in abundance, range, phenology and voltinism. In particular, three-quarters of UK butterfly species have shown declines in their distribution, abundance, or both over a ten-year period. As the most comprehensively monitored insect taxon, known to respond rapidly and sensitively to change, butterflies are particularly valuable, but devising methods that can be fitted to large data sets is challenging and they can be computer intensive. We use occupancy models to formulate occupancy maps and novel regional indices, which will allow for improved reporting of changes in butterfly distributions. The remainder of the thesis focuses on models for count data. We show that the popular N-mixture model can sometimes produce infinite estimates of abundance and describe the equivalence of multivariate Poisson and negative-binomial models. We then present a variety of approaches for modelling butterfly abundance, where complicating features are the seasonal nature of the counts and variation among species. A generalised abundance index is very efficient compared to generalised additive models, which are currently used for annual reporting, and new parametric descriptions of seasonal variation produce novel and meaningful parameters relating to phenology and survival. We develop dynamic models which explicitly model dependence between broods and years. These new models will improve our understanding of the complex processes and drivers underlying changes in butterfly populations.

No description available.

La Corse abrite une grande diversité de zones humides soumises à des pressions et menaces d’origine anthropique qui n’ont cessé de croître et de se diversifier au cours de ces dernières décennies. La conservation de ces milieux à forte valeur patrimoniale et du peuplement d’odonates original qui s’y développe, représente aujourd’hui d’importants enjeux environnementaux et sociétaux afin de préserver les services écologiques essentiels rendus par ces éléments clefs des écosystèmes aquatiques et terrestres. Le projet de recherche appliquée développé dans le cadre de cette thèse s’est attaché à améliorer les connaissances disponibles sur les libellules de Corse, afin de proposer des mesures de conservation et de gestion concrètes en faveur de ce groupe et de ses principaux habitats naturels sur l’île. Dans cet objectif, la première partie de ces travaux s’est employée à combler les principales lacunes de connaissance identifiées par les études antérieures sur la situation des espèces, notamment en intensifiant l’effort de prospection consenti à l’échelle régionale. Les particularités, la répartition, les exigences et habitats écologiques de nombreuses libellules se développant en Corse ont pu être décrits avec précision. Les informations disponibles sur certains taxons à forte valeur patrimoniale ont particulièrement augmenté comme l’illustre la définition très complète de la situation éco-biogéographique de Chalcolestes parvidens. La deuxième partie de ces travaux s’est attachée à évaluer et comparer l’efficacité des principales méthodes d’échantillonnage couramment utilisées pour l’étude des populations d’odonates. Dans ce cadre, les nombreuses informations récoltées sur l’organisation spatiale et la dynamique des populations étudiées ont notamment été employées afin de proposer aux principaux gestionnaires d’espaces naturels de l’île (Conseils départementaux, PNRC, Communes…) des méthodes adaptées pour l’évaluation et le monitoring des espèces à fort enjeu de conservation, dont l’emblématique et menacé Lestes macrostigma.La troisième partie de ces travaux est consacrée au développement d’outils pour le suivi de la qualité des principaux habitats d’odonates. Elle a permis d’aboutir à l’élaboration d’un tout nouvel indice biologique adapté à l’évaluation de l’état écologique des rivières de Corse : « Odonata Community Index – Corsica » (OCIC). Cet outil innovant, basé sur l’étude du peuplement caractéristique des libellules des cours d’eau, s’est montré particulièrement performant lors de sa confrontation aux autres indices biologiques actuellement utilisés sur l’île. L’indice OCIC et le groupe des odonates apparaissent aujourd’hui clairement comme des solutions alternatives prometteuses, en vue d’améliorer l’efficacité du système d’évaluation de la qualité écologique des rivières de Corse, compte tenu des failles de représentativité mises en évidence par les expérimentations réalisées.La dernière partie de cette thèse, basée sur des évaluations patrimoniales et écologiques du peuplement insulaire d’odonates réalisées à l’aide des informations produites, se conclue par le développement de nouveaux dispositifs régionaux de conservation en lien avec les services de l’Etat : un Plan Régional d’Actions, une liste rouge d’espèces menacées ainsi qu’une liste actualisée d’espèces déterminantes pour les Zones Naturelles d’Intérêt Ecologique Faunistique et Floristique. Ces dispositifs permettront d’améliorer l’état de conservation des libellules de Corse et des principales zones humides qui les abritent.Au final, ces travaux de thèse qui ont permis de plus de tripler les données disponibles jusqu’alors sur les libellules de Corse, fourniront un nouveau cadre de développement pour l’odonatologie insulaire. / Corsica is home to a great diversity of wetland subject to anthropogenic pressures and threats which have continued to grow and diversify in recent decades. The conservation of these environments with high heritage value and of the original Odonata community that develops in it, today represents significant environmental and societal challenges in order to preserve essential ecological services provided by these key elements of aquatic and terrestrial ecosystems. The applied research project developed as part of this thesis is focused on improving the knowledge available on the corsican dragonfly’s community, to propose concrete conservation and management measures for this group and its main insular natural habitats.In this objective, the first part of this work has sought to fill principal knowledge gaps identified by previous studies on the situation of listed species, including by greatly intensifying exploration effort at the regional level. The special features, distribution, habitat requirements and ecological of many dragonflies growing in Corsica have been described with great precision. The information available on some taxa with high heritage value increased as illustrated by the comprehensive definition of eco-bio-geographical situation of Chalcolestes parvidens.The second part of this work has sought to evaluate and compare the effectiveness of the main sampling methods commonly used for the study of dragonfly’s populations. In this context, the informations collected on the spatial organization and dynamics of the populations studied were especially used to propose appropriate methods for evaluation and monitoring the species to high conservation issue to main managers of natural areas of the island (County Councils, PNRC, municipalities ...), including the emblematic and threatened Lestes macrostigma.The third part of this work is devoted to the development of tools for monitoring the quality of the main Odonata habitats. It lead to the development of a new biological index adapted to assess the ecological status of corsican rivers: "Odonata Community Index - Corsica '(OCIC). This innovative tool, based on the study of characteristics of Odonata community of watercourses, was particularly effective during its confrontation with other biological indicators currently used on the island. The OCIC index today appear clearly as an alternative solution to improve the efficiency of the ecological quality assessment system of the Corsican rivers, given the representativeness vulnerabilities which have been highlighted by the tests performed.The final part of this thesis, based on heritage and environmental assessments of the insular dragonfly’s community made with all the information produced, ended with the development and the proposal of several regional conservation devices whose implementation is encouraged by the state services: a first regional actions plan, a first red list of threatened species and an updated list of species determinative for natural areas of ecological, flora and fauna interest. These important features are intended to contribute to improve the overall state of conservation of Corsican dragonflies and main wetlands that support them. They should enable the implementation of truly operational management actions and ensure better consideration of the main regional conservation and valuation issues identified.In the end, the thesis work that increased more than triple the previously available data on dragonflies of Corsica, will provide a new framework to developpe the isular odonatology.

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The insecticide resistance mechanisms present in the aphids Myzus persicae and Aphis gossypii have been characterised and sensitive biochemical assays have been developed to monitor their presence in individual aphids. It was found that enhanced esterase activity is present in both aphid species, and that this enhanced activity results from the presence of larger amounts of the same enzyme rather than the presence of a more efficient enzyme. In Myzus persicae this mechanism alone is sufficient to confer high levels of insecticide resistance. In Aphis gossypii, it appears that the presence of insensitive acetylcholinesterase (AChE) is necessary for measurable levels of resistance to occur. During the course of this work, insensitive AChE was detected in Myzus persicae for the first time. This additional resistance mechanism, when combined with the enhanced esterase activity, was found to confer extremely high levels of tolerance against specific insecticides. This additional mechanism is rare in the UK at present but the use of sensitive assays to monitor its existence is of increasing importance. When the AChE mechanism becomes more prevalent in the UK, as it almost certainly will, new strategies for aphid control will be needed. Further examples of insensitive AChE conferring insensitivity not only to carbamates, but also to organophosphates, have also been detected in Aphis gossypii. The inter-relationships of the two mechanisms in this species have been resolved and new monitoring methods made available.

Les termites ont un rôle clé dans le fonctionnement de l’écosystème forêt en particulier celui du recyclage de la litière en matière organique. Cependant, quelques espèces de termites sont des xylophages spécialisés dans la dégradation du bois des forêts, mais sont considérés comme des nuisibles dans les zones anthropisées.En France, le problème « termites » lié aux constructions n’a été traité que dans les années 90. La loi n°99-471, votée le 8 juin 1999 définit les modalités de mise en oeuvre d´une politique de lutte dans laquelle sont engagés tous les acteurs: l´Etat, les collectivités locales, les professionnels ainsi que les propriétaires d´immeubles. La Guyane-française est située dans la carte établie par le FCBA des départements de France où l’arrêté est effectif. Toutefois, ce département d’outre-mer reste aujourd’hui avec beaucoup de lacunes en termes de connaissances sur ses termites.On connaît de façon exhaustive le nombre et les différentes espèces de termites xylophages et on sait également quelles sont les principales familles qui sont présentes dans les bâtiments. Mais on ne sait pas dire quelles sont les espèces de termites qui s’intéressent à nos bois d’œuvres.L’objectif de cette étude est d’identifier les genres et espèces de termites qui s’attaquent à trois essences de bois de durabilité faible ou moyenne (Gonfolo, Simarouba et Yayamadou) et de comprendre comment ces attaques se produisent, en contexte forestier, en lien avec des variables du milieu, et l’effet de la saison de mise en contact.Le Yayamadou est une espèce très appétante pour les termites de Guyane, à condition de disposer de tas de bois d’un volume suffisant (> 500cm3), c’est l’espèce qui présente la plus grande diversité de termites actifs. 18 espèces de termites ont été trouvées sur les tas de bois, mais 10 seulement avec une fréquence dépassant le %. Une description détaillée et une clé d’identification sont proposées pour ces espèces.La diversité des termites est plus importante dans les milieux forestiers naturels. Les résultats montrent, qu’Heterotermes tenuis est l’espèce la plus fréquente quel que soit le milieu. Il y a une spécificité attractive de certaines espèces de termites pour telle essence plutôt que telle autre.Enfin, la saisonnalité, correspondant au moment où l’on installe les échantillons de bois en forêt, joue un rôle dans l’apparition de termites sur telle ou telle essence de bois. Il existe dans chaque milieu des espèces qui peuvent potentiellement s’attaquer au bois des habitations / The termites have a role key in the functioning of the ecosystem forest in particular the one of the recycling of the litter in organic matter. Nevertheless, some termites species are specialized in the degradation of the wood of the forests, but are considered plagues in humans place.In France, the problem « termites » linked by the buildings was treated only in the 90’s. The law n°99-471, voted by the 8 June 1999 defines the methods of implement of politics to fights in which are engaged all the actors: the government, the local groups, the professionals as well as the owners of buildings. The French Guiana-is in the map established by the FCBA that departments of France where the law is effective. Nevertheless, this “outre-mer” department remains today with a lot of gaps in terms of knowledge on its termites. We know in a manner exhaustive the number and the different types of xylophagous termites and we know too which are the principal families that are present in the buildings. But we don’t know to say which are the types of termites that are very interested in our lumber.The objective of this study is to identify the genera and termites species that attack themselves to three sorts of wood of weak or average durability (Gonfolo, Simarouba et Yayamadou) and to understand how these attacks produce themselves, in forest context, in link with variables of the environment, and the effect of the season of placement in contact.The Yayamadou is a Wood specie that atracts a lot of termites in French Guiana, to condition to have access to pile of wood of a sufficient volume (> 500cm3), it is the type that presents the biggest diversity of active termites. 18 species of termites were found on the wood piles, but 10 only with a frequency surpassing the 80%. A detailed description and an identification key are proposed for these species. The diversity of the termites is more important in the natural forest environments. The results show, that Heterotermes tenure is the type the does more frequent whatever the environment. There is an attractive specificity of some types of termites for such wood species rather than such other.Finally, the seasonality, corresponding the moment when we installs the wood samples in forest, plays a role in the appearance of termites on such or such wood species. There are in every environment of the types that potentially can attack the wood of the buildings.

Les arbovirus (virus transmis par des arthropodes) sont à l'origine de maladies humaines telles que la dengue, le chikungunya ou encore le Zika. Le moustique Aedes aegypti, est le vecteur majeur de ces trois arbovirus. La faible efficacité des méthodes de contrôle des populations de moustiques, principalement réalisées au moyen d'insecticides chimiques ouvre un champ de développement de nouvelles approches en lutte antivectorielle. Le moustique, hôte vecteur, contrôle la réplication virale en limitant les réponses immunitaires antivirales. La machinerie RNA interférence (RNAi) est la voie jouant un rôle majeur dans l'immunité antivirale chez le moustique. Alors que le rôle des deux voies, siRNA (" small interfering RNA ") et piRNA (" piwi-interfering RNA "), est de mieux en mieux compris dans les réactions antivirales du vecteur, peu de connaissances sont disponibles à ce jour en ce qui concernent les interactions entre la voie miRNA (" micro RNA ") et les arbovirus. Ainsi, nous proposons une analyse détaillée des mécanismes par lesquels les miARN tentent de réguler la réplication virale chez le moustique. Dans la première partie de la thèse, nous avons effectué une analyse génomique pour identifier les miRNAs pouvant interagir chez Ae. aegypti avec divers lignées/génotypes des virus chikungunya (CHIKV), de dengue (DENV) et de Zika. Avec l'aide d'outils de prédiction faisant appel à divers algorithmes, plusieurs sites de liaison de miARN avec différents lignées/génotypes de chaque arbovirus ont été identifiés. Nous avons ensuite sélectionné les miARN pouvant cibler plus d'un arbovirus et nécessitant un faible seuil d'énergie lors de la formation des complexes entre l'ARNm. / Mosquito-borne arboviruses cause some of the world’s most devastating diseases and are responsible for recent dengue, chikungunya and Zika pandemics. The yellow-fever mosquito. Aedes aegypti, plays an important role in the transmission of all three viruses. The ineffectiveness of chemical control methods targeting Ae. aegypti makes urgent the need for novel vector-based approaches for controlling these diseases. Mosquitoes control arbovirus replication by triggering immune responses. RNAi machinery is the most significant pathway playing a role on antiviral immunity. Although the role of exogenous siRNA and piRNA pathways in mosquito antiviral immunity is increasingly better understood, there is still little knowledge regarding interactions between the mosquito cellular miRNA pathway and arboviruses. Thus further analysis of mechanisms by which miRNAs may regulate arbovirus replication in mosquitoes is pivotal. In the first part of the thesis, we carried out genomic analysis to identify Ae. aegypti miRNAs that potentially interact with various lineages and genotypes of chikungunya (CHIKV), dengue (DENV) and Zika viruses. By using prediction tools with distinct algorithms, several miRNA binding sites were commonly found within different genotypes/and or lineages of each arbovirus. We further analyzed the miRNAs that could target more than one arbovirus and required a low energy threshold to form miRNA-vRNA (viral RNA) complexes and predicted potential RNA structures using RNAhybrid software. Thus, we predicted miRNA candidates that might participate in regulating arboviral replication in Ae. aegypti. In the second part of the thesis, we developed a miRNA-based approach that results in a dual resistance phenotype in mosquitoes to dengue serotype 3 (DENV-3) and chikungunya (CHIKV) viruses for stopping arboviruses spreading within urban cycles. The target viruses are from two distinct arboviral families and the antiviral mechanism is designed to function through the endogenous miRNA pathway in infected mosquitoes. Ten artificial antiviral 4 miRNAs capable of targeting ~97% of all published strains were designed based on derived consensus sequences of CHIKV and DENV-3. The antiviral miRNA constructs were placed under control of either an Aedes PolyUbiquitin (PUb) or Carboxypeptidase A (AeCPA) gene promoter triggering respectively expression ubiquitously in the transgenic mosquitoes or more locally in the midgut epithelial cells following a blood meal. Challenge experiments using viruses added in blood meals showed subsequent reductions in viral transmission efficiency in the saliva of transgenic mosquitoes as a result of lowered infection rate and dissemination efficiency. Several components of mosquito fitness, including larval development time, larval/pupal mortality, adult lifespan, sex ratio, and male mating competitiveness, were examined: transgenic mosquitoes with the PUb promoter showed minor fitness costs at all developing stages whereas those based on AeCPA exhibited a high fitness cost. Further development of these strains with gene editing tools could make them candidates for releases in population replacement strategies for sustainable control of multiple arbovirus diseases.

In the light of increasing pesticides resistance in agricultural pests and in insect vectors of human diseases, leading to the rise in occurrence of mosquito-borne diseases, new, efficient and environmentally friendly methods of pest control are needed. Sterile Insect Technique (SIT), relying on mass releases of radiation sterilised males to reduce reproductive potential of target pest populations, although not new, offers an alternative to the use of pesticides and is an environmentally non-polluting method of insect control. Many insect species, however, are not very amenable to classical SIT, due to detrimental side-effects of radiation treatment. We propose a new method, a genetically engineered modification of classical SIT, replacing radiation with genetically induced sterility. Based on conditional expression of male-germline targeted nucleases which introduce double strand breaks into the male germline DNA to render males sterile, this method emulates SIT mechanism, at the same time eliminating radiation and associated detrimental side-effects. Different variants of such a system were investigated in this project, eventually leading to the creation of functional conditional male-sterility systems in two model organisms – the Yellow fever mosquito, Aedes aegypti and the Mediterranean fruit fly, Ceratitis capitata. Both systems utilise chimeric nuclease composed of protamine and FokI cleavage domain fusion. The sperm-specificity and the conditionality of the sterile phenotype have been achieved through the use of tetracycline repressible expression system driven by the β2-tubulin promoter in Ceratitis capitata and by the Topi promoter in Aedes aegypti.

Individuals engage in competitive and cooperative interactions with conspecifics. Furthermore, within any population of interacting individuals there are typically consistent differences among-individuals in behavioural traits. Understanding the importance of both these types of individual-specific behaviours allows us to understand why populations are structured as they are, why individuals show apparently limited behavioural flexibility, and how these elements link to population-level properties. I used extensive video camera monitoring of a population of wild field crickets (Gryllus campestris) to study the interactions and behaviours of uniquely identified individuals. I studied the shyness, activity and exploration of individuals of this population across contexts: from young to old and between captivity and the wild. This allowed me to confirm that individuals were relatively consistent across their adult lifetimes for all three traits, but only consistent between captivity and the wild for activity and exploration. I then found that high activity levels were positively related to high mating rates and short lifespans. Crucially, lifetime mating success was not related to activity level, indicating that the trade-off between lifespan and mating success was sufficient to allow variation in activity level to persist across generations. I also found that cricket social network structure is stable across generations despite the complete turnover of individuals every year. This social network structure influences sexual selection, with some male crickets heavily involved in networks of both pre- and post-copulatory competition, yet males are unable to use pre-copulatory competition to avoid post-copulatory competition. Additionally, positive assortment by mating rate between males and females may reduce the fitness of males with high mating rates, as they face stronger sperm competition. Finally, I used actor-based models to determine the factors predicting cricket social network structure and to test and reject the social-niche hypothesis for the maintenance of among-individual variation in behaviour. I also demonstrated that little else is needed in a stochastically changing network aside from positive assortment by mating rate to simulate a population with a similar skew in mating success to the one observed in the real cricket population. These results give insights into the importance of trade-offs and stochasticity in maintaining the extensive variation in the natural world.

Termites are important ecosystem engineers in tropical and sub-tropical terrestrial regions where they influence ecosystem processes by altering the physical and chemical structure of the habitat. Termites affect nutrient availability by decomposition and comminution (shredding) of organic matter and act as agents of bioturbation as they re-work substrates during the construction of nests, tunnels and runways. At present we have a relatively good understanding of termite diversity patterns in the tropics through the extensive use of the standardised transect sampling protocol by Eggleton et al. (1995). These diversity data suggest that there is a functional difference in termite assemblage structure, and potentially in termite abundance and biomass, among comparable habitats across continents. However due to the lack of comparable abundance and biomass data from South America this has not previously been confirmed. In this thesis I, therefore, collected extensive data on termite taxonomic and functional assemblage structure in a South American site in Peru. The data were used to compare termite abundance and biomass from two comparable sites in Africa (Cameroon) and south east Asia (Malaysia) in order to gain better understanding of the role termites play in ecosystem processes. I found that there was an intercontinental difference in the abundance and biomass of termite feeding-groups mainly due to the dominance of soil-feeding termites in Cameroon and the absence of fungus-growing termites from Peru. The impact of certain lineages on the intercontinental differences suggests that the differences may be due to biogeographical evolution. Moreover, Eggleton et al. (1998) show that larger-bodied soil-feeding termites in Cameroon process more energy per unit area than predicted by their body size. Due to the need for an examination of the allometric relationships in termite assemblages outside Africa and the development of a more sophisticated feeding-group classification I explore the findings in Eggleton et al. (1998) further using population density - body mass relationships in three termite feeding-groups among the three continental sites in Cameroon, Peru and Malaysia. I found that large-bodied soil-feeding termites in Cameroon and large-bodied wood-feeding termites in Peru had higher population densities than expected by their body masses. As the population density - body mass relationship is inverse to that of the energy - body mass relationship the results suggest that the two feeding-groups also use more energy than expected by their body masses. Further, we have a relatively good understanding of the role termites play as ecosystem engineers e.g. in nutrient cycling and distribution, however, compared with our understanding of wood and litter decomposition in tropical forests quantitative data on the impact of termites in soil processes is poorly understood. In this thesis I conducted, to our knowledge, the first in situ soil macrofauna exclusion experiment using translocated soil in Peru to examine the impact of termites on soil C and N loss. I found that termites promote soil C and N loss which may be linked to the increase in microbial activity due to the passage of soil through the termite gut as well as the affect termites have on bioturbation and nutrient distribution. To conclude, in this thesis I present the first intercontinental comparison of abundance and biomass as well as the first in situ soil macrofauna exclusion experiment to date. The link between termite ecology, biogeography and evolution is discussed as well as the contribution of this thesis to the field of termite ecology.