Malaria is the main cause of approximately one million deaths every year that mostly affect children in south of Sub-Saharan Africa. The Anopheles gambiae complex consists of seven morphologically indistinguishable sibling species. However, their behavior, ecological adaptations, vectorial capacity, and geographical distribution differ. Studying the phylogenetic relationships among the members of the complex is crucial to understanding the genomic changes that underlie evolving traits. These evolutionary changes can be related to the gain or loss of human blood choice or to other epidemiologically important traits. In order to understand the phylogenetic relationships and evolutionary history of the members of the An. gambiae complex, breakpoints of the 2Ro and 2Rp inversions in An. merus and their homologous sequence in the outgroup species were analyzed using fluorescent in situ hybridization (FISH), library screening, whole-genome mate-paired sequencing and bioinformatics analysis. Molecular phylogenies of breakpoint genes were constructed afterwards. In addition, multigene phylogenetic analyses of African malaria vectors were performed. Our findings revised the chromosomal phylogeny, and demonstrated the ancestry of 2Ro, 2R+p and 2La arrangements.  Our new chromosomal phylogeny strongly suggests that vectorial capacity evolved repeatedly in members of the An. gambiae complex, and the most important vector of malaria in the world, An. gambiae, is more closely related to ancestral species than was previously thought. Our molecular phylogeny data were in agreement with chromosomal phylogeny, indicating that the position of the genetic markers with respect to chromosomal inversion is important for interpretation of the  phylogenetic trees. Multigene phylogenetic analysis revealed that a malaria mosquito from humid savannah and degraded rainforest areas, An. nili, belongs to the basal clade and is more distantly related to other major African malaria vectors than was assumed previously. Finally, for the first time a physical map of 12 microsatellite markers for the Asian malaria vector An. stephensi was developed. Knowledge about the chromosomal position of microsatellites was shown to be important for a proper estimation of population genetic parameters. In conclusion, our study improved understanding of genetics and evolution of some of the major malaria vectors in Africa and Asia. / Ph. D.

Le plateado ou dorado - Brachyplatystoma rousseauxii (Pimelodidae, Siluriformes) est un grand poisson-chat Amazonien d’intérêt commercial, qui présente un des cycles de vie les plus surprenants et énigmatiques, avec la plus grande migration connue en eaux douces, entre l’estuaire de l'Amazone et les têtes de fleuves en Amazonie occidentale. Le but de ce travail était de déterminer, au niveau moléculaire, la position phylogénétique du plateado dans la famille Pimelodidae ainsi que sa structure génétique dans le Haut Madera (Villa Bella–VB, Cachuella Esperanza–CE, Puerto Maldonado–PM, Rurrenabaque–RU, Puerto Villarroel–PV) et ouest de l'Amazonie (Iquitos–IQ) bassins (Bolivie et Pérou). Les relations phylogénétiques ont été définies par une analyse du maximum de vraisemblance (ML) des séquences nucléotidiques de deux gènes mitochondriaux (Région de Contrôle–RC, ~ 900 pb, 32 taxons; Cytochrome Oxydase 1-CO1, ~ 650 pb, 61 taxons), et d’un gène nucléaire (F-reticulon4–RTN4, ~ 1700 pb, 38 taxons). La structure génétique des populations a été évaluée par le polymorphisme de longueur de neuf microsatellites (284 inds) et par les variations de séquence de la RC (461 inds + 45 en provenance du Brésil, disponibles dans GenBank). Les variations de fréquences des microsatellites ont été utilisées pour identifier les unités panmictiques (clusters) les plus probables dans l'ensemble des données, à travers une approche bayésienne (BAPS), après avoir démontré une déviation significative à l'équilibre de Hardy-Weinberg (HWE) quand l’ensemble des données étaient analysé comme faisant partie d’une seule unité.L’analyse phylogénétique concaténée (ML) a montré que la famille Pimelodidae était un groupe monophylétique. Les résultats les plus notables de la phylogénie sont la monophylie peu soutenue (77%) de la tribu Brachyplatystomatini et la non-monophylie des Brachyplatystoma. Seul le sous-genre Malacobagrus (B. rousseauxii + (B. filamentosum + B. capapretum)), défini morphologiquement, s’est avéré monophylétique. Ces résultats suggèrent que le genre Brachyplatystoma pourrait contenir Platynematichthys ou pourrait être limité au sous-genre Malacobagrus.L'analyse des microsatellites sur l'ensemble des échantillons (ouest Amazone + haut Madera) a montré un écart significatif á la panmixia, ainsi que sur l'ensemble des échantillons du haut Madera. A la lumière de ces résultats, l’approche bayésienne a été développée, montrant qu'au moins trois clusters (1, 2, 3) sont présents dans les bassins du haut Madera et de l'ouest de l'Amazone, avec des répartitions qui se chevauchent partiellement. En parallèle á l'identification des clusters, il a été mis en évidence une différence significative au sein de B. rousseauxii entre l’ouest de l'Amazonie et le haut Madera bassin.L'analyse généalogique (ML) des séquences de la RC a montré une topologie en peigne, sans groupe d'haplotypes montrant une histoire commune. En revanche, l'analyse des fréquences haplotypiques a révélé l’existence de 4 haplogroupes, liés à la géographie. Un haplogroupe a été identifié le long de l'axe principal de l’Amazonas-Solimões (Belem-Brésil et Iquitos-Pérou) et 3 autres dans le haut Madera (VB; CE+MD; RU+PV), organisés selon une tendance aval - amont. Ainsi, nous observons d’un coté 3 populations (clusters) avec une distribution géographique partiellement chevauchante, et de l’autre quatre haplogroupes positionnés selon une logique géographique. Le scenario le plus probable implique un comportement de homing des individus du cluster 1 (homing à l’échelle des grands sous-bassins), qui préfèrent ou tendent à retourner dans le sous-bassin du Madera. Les 3 populations coexisteraient alors dans le haut Madera en se reproduisant à des périodes (phénologie) ou à des endroits différents (ségrégation spatiale). Enfin, les résultats sont discutés à la lumière des résultats précédemment publiés dans le bassin de l'Amazone et des menaces qui pèsent sur l'espèce dans le bassin du Madera. / The Plateado or Dorado - Brachyplatystoma rousseauxii (Pimelodidae, Siluriformes) is a commercial migratory catfish species with one of the most surprising and enigmatic life histories in the Amazon basin, involving the largest migration known for a freshwater species, between the estuary and the head waters in the Andean piedmont. The aim of the present work was to determine the molecular phylogenetic position of the Plateado in the Pimelodidae family and its population genetic structure in the Upper Madera (Villa Bella – VB, Cachuella Esperanza – CE, Puerto Maldonado – PM, Rurrenabaque – RU, Puerto Villarroel - PV) and Western Amazon (Iquitos - IQ) basins (Bolivia and Peru). The phylogenetic relationships were defined through a Maximum Likelihood (ML) analysis of nucleotide sequences of two mitochondrial (Control Region – CR, ~ 900 pb, 32 taxa; Cytochrome Oxidase 1 – CO1, ~ 650 bp, 61 taxa), and a nuclear fragment (F-reticulon4 - RTN4, ~1700 bp, 38 taxa). The population genetic structure was evaluated through the length polymorphism of nine microsatellites (284 inds) and CR sequence variations (461 inds + 45 from Brazil available in GenBank). Microsatellites frequencies variations were used to identify through a Bayesian approach (BAPS) the most probable panmictic units (clusters) in the whole data, after previous demonstration of a deviation to Hardy-Weinberg Equilibrium (HWE). The ML phylogenetic concatenated analysis showed the Pimelodidae family as a monophyletic group, with the genera Phractocephalus and Leiarius as basal lineages. The most notable results in the phylogeny were the not well-supported monophyly (77%) of the tribe Brachyplatystomatini and the non-monophyly of Brachyplatystoma. Only the morfologically defined subgenus Malacobagrus (B. rousseauxii + (B. filamentosum + B. capapretum)) was recovered as monophyletic. These results suggest that Brachyplatystoma could contain Platynematichthys or be restricted to the subgenus Malacobagrus, and the other species be related to distinct (earliest) genera, in agreement with another study carried out in parallel with other markers.Microsatellite analysis of the whole data (Western Amazon + Upper Madera) showed a significant departure of the HWE expectations, as well as the analysis of the whole data from the Upper Madera region. In the light of these results, the Bayesian approach has been implemented, showing that at least three clusters (1, 2, 3) are present in the Upper Madera and Western Amazon basins with partial overlapping distribution.To the margin of the cluster identification, it was evident the significant difference between Western Amazon (Iquitos region) and the Upper Madera basin.The genealogical analysis (ML) of the CR sequences showed a generalized comb-like topology without group of haplotypes with common ancestry. On the other hand, CR frequency analysis showed the conformation of four haplogroups associated to geography. One haplogroup was identified along the main axis of the Amazonas-Solimões, from Belem (Brazil) to Iquitos (Peru), and three other haplogroups were observed in the Upper Madera basin (VB; CE+PM; RU+PV), positioned in a downstream - upstream pattern.Hence, we observed on the one hand three genetic populations (clusters), distributed in partially overlapping geographical areas, and on the other hand four haplogroups, positioned according to a geographical pattern. The most probable scenario involves a homing behavior of individuals from cluster 1 (homing at the scale of large watersheds), which prefer or tend to return to the Madera basin, with the three populations coexisting within the upper Madera because they reproduce at different moments (phenology) or different places (spatial segregation). Finally, the results are discussed in the light of previous results in the Amazon basin and the threats to the species in the Madera basin (p.e. fragmentation by dams, overfishing, climate variability, among other).

La leishmaniose à Leishmania infantum est une zoonose transmise de mammifère à mammifère par la piqûre d'un insecte vecteur, le phlébotome femelle. S'il est classiquement décrit la leishmaniose viscérale avec la triade classique fièvre, pâleur et splénomégalie, de nombreuses formes cliniques peuvent être associées à ce parasite. Le portage asymptomatique est la forme la plus fréquente et la plus répandue dans l'Ancien Monde ou le Nouveau Monde. Entre la leishmaniose viscérale et le portage asymptomatique, plusieurs formes cliniques sont présentes. Ainsi certains sujets vont exprimer la leishmaniose sous forme d'adénopathies isolées. Ces formes sont intermédiaires entre une expression pauci symptomatique et une leishmaniose viscérale larvée. Alors que L. infantum n'est pas classiquement retrouvé dans des formes muqueuses, des cas ont été récemment décrits. Ces formes muqueuses isolées ne sont pas rares puisque sur les 3 CHU Marseille, Montpellier et Nice, entre 1997 et 2009, 10 cas de leishmaniose muqueuse à L. infantum ont été diagnostiquées principalement chez des sujets immunodéprimés. Il est important de faire le diagnostic de ces formes cliniques particulières puisqu'elles ont pour diagnostic différentiel des néoplasies (lymphome pour la première et néoplasie de la sphère ORL pour la seconde). Afin d'appréhender le rôle du parasite dans l'expression clinique, il a été réalisé le typage par les microsatellites de neuf souches isolées de sujets porteurs asymptomatiques. Il s'avère que ces neuf souches sont très peu polymorphes et que sept d'entre elles possèdent un génotype unique. / Leishmaniasis due to Leishmania infantum is a zoonotic disease transmitted from mammal to mammal through the bite of an insect vector the sandfly female. Beside the classical triad of visceral leishmaniasis symptoms: fever, pallor and splenomegaly, many clinical forms could be associated with this parasite infection. Asymptomatic carriage of L. infantum is the most common and the most widespread in the Old World and New World. Many other clinical forms are present and some subjects will develop only isolated lymphadenopathy. These forms are intermediate between pauci symptomatic and visceral leishmaniasis forms. Whereas L. infantum is not typically associated with mucosal forms, several cases have been described. Indeed, in the 3 academic hospitals of Marseille, Montpellier and Nice from 1997 to 2009, 10 cases were revealed mainly in immunocompromised patients. To understand the role of parasite in clinical expression, nine strains isolated from asymptomatic carriers were genotyped using microsatellite. The nine strains have few polymorphisms and seven of them are identical with a unique genotype. In addition, those strains are very different from strains of HIV-positive subjects. If the strains genetic appears to have a role in the clinical expression of the disease, the environment in which individuals live in endemic areas is associated with an excess of risk to develop visceral leishmaniasis. While in Marseille, cases of visceral leishmaniasis occur in an urban environment, they take place in Nice in a rural environment, as it is classically described. To investigate differences between parasite strains form Nice and Marseille studies with microsatellites are ongoing.

Les phlébotomes sont des insectes hématophages appartenant à la famille des Psychodidae et à la sous-famille des Phlebotominae. Cet insecte diptère, jaunâtre, relativement petit (2 à 3 mm) compte environ 800 espèces. 70 de ces espèces ont été identifiées comme vecteurs potentiels dont une quarantaine sont des vecteurs prouvés. Ils peuvent transmettre différents pathogènes dont les principaux sont les leishmanies et les phlébovirus. Ce travail de thèse est focalisé sur les phlébotomes vecteurs de la leishmaniose. Les leishmanioses sont des maladies parasitaires causées par un protozoaire du genre Leishmania. Elles touchent un large panel d’hôtes vertébrés, dont l’homme et le chien. Elles sont toujours un problème de santé publique majeur dans de nombreux pays et sont actuellement en expansion. Bien que cette maladie soit largement étudiée, nous avons encore beaucoup apprendre sur son vecteur : le phlébotome. Par exemple, l’organisation des populations dans les écosystèmes et les paramètres qui les structurent, sont à l’heure actuelle très peu étudiés. Il est pourtant primordial de bien connaitre la biologie des différents acteurs d’un cycle parasitaire pour mieux comprendre la transmission du pathogène, évaluer les risques et enfin être capable de lutter efficacement contre la maladie. Dans ce contexte, le but de cette thèse est d’étudier l’écologie et la structure des populations de phlébotomes dans un foyer connu de leishmaniose et l’impact des facteurs biotiques et abiotiques sur leur organisation. Pour atteindre cet objectif, nous avons réalisé une collecte de phlébotomes le long d’un transect de 14km localisé dans la région de Montpellier, présentant une diversité altitudinale, climatique et environnementale. Les populations de phlébotomes ont été caractérisées d’un point de vue taxonomique, spatio-temporel, génétique (microsatellites), et morphométrique (géométrie morphométrie). Les résultats génétiques, morphométriques et de distribution des espèces ont été ensuite confrontés à des paramètres climatiques (température, humidité) ou environnementaux (altitude, versant, station, microhabitat).Durant ce travail, 4 espèces ont été capturées : Phlebotomus ariasi (93,23%), P. perniciosus (0,48%), P. mascittii (0,11%) et S. minuta (6,18%). Elles ont une activité saisonnière de Mai à Octobre avec un pic d’abondance en Juillet-Août quand les températures moyennes sont optimales pour les phlébotomes (20-30°C). Bien que l'environnement ait été considérablement transformé dans notre zone d'étude en 30 ans, l'abondance des phlébotomes ne semble pas avoir changé de façon significative, soulignant leur capacité d'adaptation aux modifications de l'écosystème à court et long terme. La présence et l’abondance des deux espèces prédominantes (P. ariasi et S. minuta) sont significativement influencées par l’altitude, la température, l’humidité relative, le versant ainsi que l’orientation des murs. Les analyses génétiques montrent que la diversité est conservée à toutes les échelles d’études et qu’il existe une structuration des phlébotomes en micropopulations. Les données de géométrie morphométrie révèlent un dimorphisme sexuel bien connu chez les insectes mais également une structuration phénotypique en fonction des facteurs environnementaux ou temporels (mois, versant, altitude et station). Ces deux types d’approches permettent grâce à leur complémentarité d’apporter des informations sur l’écologie et l’organisation des populations de phlébotomes et de discuter des conséquences sur la transmission de la leishmaniose. / Sandflies are hematophagous insects belonging to the family Psychodidae and the subfamily phlebotominae. This diptera, yellowish, relatively small (2-3 mm) has about 800 species. 70 of these species have been identified as potential vectors of which forty are proven ones. They can transmit different pathogens; the main ones are Leishmania and phlebovirus.This thesis focused on sandflies, vectors of leishmaniasis. Leishmaniases are parasitic diseases caused by protozoa of the genus Leishmania. They affect a wide range of vertebrate hosts, including humans and dogs. They are still a major problem of public health in many countries and are currently in expansion. Although this disease is widely studied, we still have a lot to learn about its vector: the sandfly. For example, the organization of populations in ecosystems and the parameters which structure them are very little studied up to now. It is therefore essential to know the biology of the different actors of a parasite cycle to better understand the transmission of pathogens, to assess risks of transmission, and finally to be able to effectively fight against the disease.In this context, the aim of this thesis is to study the ecology and the structuring of sandfly populations in a known endemic area of leishmaniasis and the impact of biotic and abiotic factors on their organization. To reach this objective, we performed captures of sandflies along a 14km transect located in the Montpellier region which presents an altitudinal, climate and environmental diversity. Sandfly populations have been characterized by taxonomic, spatio-temporal, genetic (microsatellites) and morphometric (geometry morphometry) approaches. The genetic, morphometric and species distribution results were then confronted with climatic (temperature, relative humidity) or environmental parameters (altitude, slope, station, microhabitat).During this work, four species were captured: Phlebotomus ariasi (93.23%), P. perniciosus (0.48%), P. mascittii (0.11%) and S. minuta (6.18%). They have a seasonal activity from May to October with an abundance peak in July-August when average temperatures are optimal for sandflies (20-30°C). Although the environment has been considerably transformed in our study area in 30 years, the abundance of sandflies does not seem to have changed significantly, highlighting their ability to adapt to ecosystem modifications in short and long-term. The presence and abundance of the two predominant species (P. ariasi and S. minuta) are significantly influenced by altitude, temperature, relative humidity, slope and wall orientation.The genetic analyses show that diversity is maintained at all scales of study and that sandflies are organized in micropopulations. The morphometric geometry data reveal a sexual dimorphism, well known in insects but also a phenotypic structuring correlated to environmental or temporal factors (month, slope, altitude and station).Both of these approaches, because of their complementarity, help provide information on the ecology and organization of sandfly populations and to discuss about the consequences in terms of leishmaniasis transmission.

Chez les insectes sociaux, les reproductrices doivent faire face à un dilemme entre coûts et bénéfices de la reproduction asexuée et sexuée. Récemment, il a été montré que les reines termites pouvaient résoudre ce dilemme en optant pour l’utilisation alternée de la reproduction asexuée et sexuée, en produisant des femelles secondaires néoténiques par parthénogenèse, et les ouvriers, soldats et futurs essaimants par reproduction sexuée. Cette stratégie, appelée AQS pour « Asexual Queen Succession », a été décrite chez trois termites souterrains xylophages de la famille des Rhinotermitidae. Deux espèces humivores appartenant à la famille des Termitidae et particulièrement abondantes en forêt néotropicale, Embiratermes neotenicus et Silvestritermes minutus (Syntermitinae), semblaient être des nouvelles candidates pour cette stratégie, car elles présentaient des nids menées par de nombreuses femelles néoténiques. Pour confirmer cette hypothèse et déterminer l’origine génétique de ces femelles, des castes stériles et des futurs essaimants, nous avons développé une banque de microsatellites spécifiques pour E. neotenicus et S. minutus, et génotypé une dizaine de colonies du site de Petit Saut en Guyane, pour chaque espèce. Nous avons confirmé que les castes stériles et les imagos étai ent issus pour la très grande majorité de reproduction sexuée, alors que les femelles néoténiques étaient issues de parthénogenèse avec fusion centrale, un mécanisme différent de celui décrit chez les Rhinotermitidae. La reconstruction détaillée du cycle de vie de S. minutus nous a permis de conclure que l’AQS, au-delà des bénéfices communs à toutes les espèces i.e. la succession de plusieurs générations de reproductrices sans dilution de la participation génétique de la reine fondatrice, l’augmentation du potentiel reproductif de la colonie et la prévention de la consanguinité chez les castes stériles et les imagos, permettait à cette espèce d’investir dans un seul évènement massif d’essaimage pendant un cycle de vie très court. D’autre part, nous avons réalisé une analyse de structuration génétique des colonies et des populations d’E. neotenicus et de S. minutus dans le but de comprendre les conséquences de la dispersion, des modalités d’appariement et de la participation des différents reproducteurs sur la consanguinité des colonies et la potentialité de colonisation de ces espèces. Pour environ 40 colonies de chaque espèce, nous avons montré que les reproducteurs fondateurs étaient très majoritairement non apparentés, et une absence de viscosité à une échelle locale (1 à 11 km), suggérant une dispersion importante des essaimants. De plus, seule une très faible structuration génétique a pu être détectée sur l’ensemble du site d’échantillonnage, indiquant des flux de gènes peu contraints / In social insects, reproductive females have to face a dilemma between costs and advantages of asexual and sexual reproduction. Recently, termite queens were shown to be able to solve this dilemma by using alternatively asexual and sexual reproduction, with the production of secondary neotenic females by parthenogenesis, and workers, soldiers and future alate reproductives by sexual reproduction. This strategy, called AQS for Asexual Queen Succession, was described in three subterranean xylophagous termites of the Rhinotermitidae family. Two soil-feeding species belonging to the Termitidae family, and particularly abundant in Neotropical forest, Embiratermes neotenicus and Silvestritermes minutus (Syntermitinae), seemed to be new candidates for this strategy since they showed colonies headed by numerous neotenic females. In order to confirm this hypothesis and determine the genetic origin of these females, of sterile castes and future imagoes, we developed specific microsatellite libraries for E. neotenicus and S. minutus, and genotyped about ten colonies for each species, on the site of Petit Saut in French Guiana. We confirmed that sterile castes and imagoes were mostly produced by sexual reproduction, while neotenic females were produced by parthenogenesis with central fusion, a mechanism different from that described in Rhinotermitidae species. The detailed reconstruction of S. minutus life cycle allowed us to conclude that AQS, in addition to advantages common to all species i.e. succession of queen generations with undiluted genetic input of the foundress, multiplication of reproductive potential of the colony and prevention of inbreeding in sterile castes and dispersers, would allow this species to optimize a single dispersal event within a very short life cycle. Otherwise, we realized an analysis of colony and population genetic structuration of both species in order to understand consequences of dispersion, mating strategies and parental allocation on inbreeding and colonization abilities of both species. For about 40 colonies of each species, we showed that most of founding reproductives were not related, and absence of genetic viscosity at a local scale (1 to 11 km) suggesting long dispersal flights of alates. Furthermore, only a weak genetic structuration was detected, indicating unfettered gene flows on the sampling site

L’aire de distribution des espèces est conditionnée à la fois par des facteurs biotiques et abiotiques et ses frontières dépendent généralement des limites physiologiques de l’espèce. Ainsi, en bordure d’aire de répartition, les populations se caractérisent par une diversité génétique moindre ainsi qu’une forte différentiation génétique et leur existence dépend d’un équilibre fragile entre événements de colonisation et d’extinction.Depuis les années 1970, l’augmentation et l’accélération des pressions anthropiques exercées sur les écosystèmes bouleversent ces équilibres et des modifications de l’aire de répartition sont observées chez certaines espèces dont le bivalve Macoma balthica, espèce clé des écosystèmes littoraux en Europe, dont la limite sud de répartition s’est décalée vers le nord-est au cours des quarante dernières années.Afin d’évaluer les capacités adaptatives de M. balthica et dans un but de conservation, deux approches complémentaires ont été menées dans des environnements contrastés qui ont permis de mettre en évidence des signes d’adaptation locale.D’une part, l’étude du génome neutre à l’aide des outils méthodologiques et concepts de la génétique des populations a permis d’inférer l’histoire démographique de l’espèce avec une attention particulière portée sur une baie en limite d’aire de répartition (Baie de Marennes Oléron, France) et sur une baie soumise à de fortes pressions physico-chimiques (Baie de Gdansk, Pologne). Nous avons mis en évidence notamment :(i) un polymorphisme significatif dans les populations en limite d’aire en opposition avec les attendus théoriques(ii) des ruptures au flux de gènes dans le golfe de Gascogne soumis au réchauffement des eaux de surface mais aussi le long d’un gradient environnemental dans la baie de Gdansk. D’autre part, l’étude moléculaire de la sélection a été menée par la méthode de pyroséquençage sur le transcriptome d’individus prélevés en milieux contrastés. Cette étude a permis de mettre en évidence des tendances d’expression différentielle de gènes de réponse générale au stress selon le milieu considéré. / Species distribution is conditioned by biotic and abiotic factors and its borders depend generally on physiological limits of species. At the edge of their distribution, populations are characterized by a less genetic diversity as well as a strong genetic differentiation and their existence depends on a fragile balance between colonization and extinction.Since the 1970s, the increase and the acceleration of the anthropological pressures exercised on ecosystems upset this balance. As a consequence, modifications of many species distributions are observed. As an example, the south end of the distribution of the bivalve Macoma balthica, a key species of the european littoral ecosystems has moved towards the northeast during the last forty years.In order to conserve this species, we need to estimate the adaptive capacities of M. balthica. Two complementary approaches were undertaken in contrasting environments. The neutral genome was studied using population genetics methods to the demographic history of the species with a particular attention at the edge of its distribution (Bay of Marennes Oléron, France) and in a bay subjected to strong physico-chemical pressures (Bay of Gdansk, Poland). We brought to light in particular:1) A significant polymorphism in the populations at the edge of the distribution in contrast to theoretical predictions.2) A geneflow rupture correlated with high sea surface temperature (in the Bay of Biscay) and also along an environmental gradient ( derived from multiple parameters) in the bay of Gdansk.The molecular study of natural selection was conducted by the method of pyroséquençage using transcriptome from individuals at specific locations. This study allowed us to bring to light tendencies of differential gene expression implicated in the general response to stress.

Freshwater streams in the developed world are becoming increasingly dominated by treated wastewater. Continually discharged into most surface waters, these effluents contain a suite of bioactive man-made chemicals, including steroid and non-steroid oestrogens, which have been found to feminise male fish, skew sex ratios, and cause reproductive failure. However, the consequences of reproductive disruption remain poorly explored at the population level. This thesis was initiated to evaluate how oestrogenic contaminants might influence the population ecology of a common cyprinid, the roach (Rutilus rutilus). An investigation encompassing population structure, multigenerational exposure and the role of additional drivers of fish population dynamics was undertaken to contextualise the effects of oestrogenic effluents on wild fish populations. Population genetic analysis of UK roach found they exhibit moderately high levels of genetic diversity and significant intra-river genetic structure. Genetically differentiated local subpopulations indicate little interbreeding and limited gene flow, consistent with a typical metapopulation that has not been homogenised by restocking. Similarly, my thesis demonstrates no significant relationship between effluent exposure and Ne (effective population size) or genetic diversity of roach populations, albeit a 65% reduction in Ne is possible at highly polluted sites. River stretches contaminated with high levels of effluent can support breeding populations, which recruit successfully with minimal immigration from less contaminated sites. Multigenerational effects of effluent exposure on roach were also evaluated experimentally using reproductive success from breeding adults over three generations. Lifelong exposure to 100% treated effluent resulted in feminised phenotypes (ovarian cavities and intersex condition) in males but no observable effect on females. Additionally, despite gonadal disruption in males and effluent exposure of their mothers, I found no detrimental effect on their ability to compete with control fish. Instead, reproductive success was primarily determined by body size. A novel approach considering additional fish population drivers suggests that genetic diversity and species diversity decline in parallel with an increasing presence of disturbed land, when combined with geographical isolation. In conclusion, group assemblage and genetic structure of fish populations appears multi-causal and cannot be disaggregated, such that a single environmental characteristic can be shown to drive patterns of population success.

Microsatellites are short (1-6bp long) highly polymorphic tandem repeats, found in all genomes analyzed so far. Popular genetic markers for many applications including population genetics, pedigree analysis, genetic mapping and linkage analysis, some microsatellites also can cause a variety of human neurodegenerative diseases and may act as agents of adaptive evolution through the regulation of gene expression. As a consequence of these diverse uses and functions, the mutational and evolutionary dynamics of microsatellite sequences have gained much attention in recent years. Mostly, the focus of studies investigating microsatellite evolution has been to develop more refined evolutionary models for estimating parameters such as genetic distance or linkage disequilibrium. However, there is an incentive in using our understanding of the evolutionary processes that affect these sequences to examine the functional implications of microsatellite evolution. What has emerged from nearly two decades of study are highly complex mutational dynamics, with mutation rates varying across species, loci and alleles, and a multitude of potential influences on these rates, most of which are not yet fully understood. The increasing availability of whole genome sequences has immensely extended the scope for studying microsatellite evolution. For example, where once it was common to examine single loci, it is now possible to examine microsatellites using genome wide approaches. In the first part of my dissertation I discuss approaches and issues associated with detecting microsatellites in genomic data. In Chapter 2 I undertook a meta-analysis of studies investigating the distribution of microsatellites in yeast and showed that studies comparing the distribution of microsatellites in genomic data can be fraught due to the application of different definitions for microsatellites by different investigators. In particular, I found that variation in how investigators choose the repeat unit size of a microsatellite, handle imperfections in the array and especially the choice of minimum array length used, leads to a large divergence in results and can distort the conclusions drawn from such studies, particularly where inter-specific comparisons are being made. In a review of the currently available suite of bioinformatics tools (Chapter 3), I further showed that this bias extends beyond a solely theoretical controversy into a methodological issue because most software tools not only incorporate different definitions for the key parameters used to define microsatellites, but also employ different strategies to search and filter for microsatellites in genomic data. In this chapter I provide an overview of the available tools and a practical guide to help other researchers choose the appropriate tool for their research purpose. In the second part of my thesis, I use the analytical framework developed from the previous chapters to explore the biological significance of microsatellites exploiting the well annotated genome of the model organism Saccharomyces cerevisiae (baker’s yeast). Several studies in different organisms have indicated spatial associations between microsatellites and individual genomic features, such as transposable elements, recombinational hotspots, GC-content or local substitution rate. In Chapter 4, I summarized these studies and tested some of the underlying hypotheses on microsatellite distribution in the yeast genome using Generalized Linear Models (GLM) and wavelet transformation. I found that microsatellite type and distribution within the genome is strongly governed by local sequence composition and negative selection in coding regions, and that microsatellite frequency is inversely correlated with SNP density reflecting the stabilizing effect point mutations have on microsatellites. Microsatellites may also be markers for recent genome modifications, due to their depletion in regions nearby LTR transposons, and elements of potential structural importance, since I found associations with features such as meiotic double strand breaks, regulatory sites and nucleosomes. Microsatellites are subject to local genomic influences, particularly on small (1-2kb) scales. Although, these local scale influences might not be as dominant as other factors on a genome-wide scale they are certainly of importance with respect to individual loci. Analysis of locus conservation across 40 related yeast strains (Chapter 5) showed no bias in the type of microsatellites conserved, only a negative influence of coding sequences, which supports again the idea that microsatellites evolve neutrally. Polymorphism was rare, and despite a positive correlation with array length, there was no relationship with either genomic fraction or repeat size. However, the analysis also revealed a non-random distribution of microsatellites in genes of functionally distinct groups. For example, conserved microsatellites (similar to general microsatellites in yeast) are mostly found in genes associated with the regulation of biological and cellular processes. Polymorphic loci show further an association with the organization and biogenesis of cellular components, morphogenesis, development of anatomical structures and pheromone response, which, is absent for monomorphic loci. Whether this distribution is an indication of functionality or simply neutral mutation (e.g. genetic hitch-hiking) is debatable since most conserved microsatellites, particularly variable loci, are located within genes that show low selective constraints. Overall, microsatellites appear as neutrally evolving sequences, but owing to the sheer number of loci within a single genome, individual loci may well acquire some functionality. More work is definitely needed in this area, particularly experimental studies, such as reporter-gene expression assays, to confirm phenotypic effects.

Recent observed changes in bird distributions provide an unprecedented opportunity to gain a deeper understanding of the processes that influence species' persistence. By modelling presence-absence data from the North American Breeding Bird Survey, we found evidence that the breeding range of the western burrowing owl has contracted at its northern, western, and eastern boundaries since 1967. We suggest that the species' breeding distribution is also expanding southwards to former wintering grounds into northern Mexico, facilitated by the appearance of new breeding habitat created by irrigated agriculture in the arid areas of southwestern United States and northwestern Mexico. This dissertation explores the hypothesis that burrowing owls from northern migratory populations have become resident breeders in areas of northwestern Mexico that were formerly used only by migratory owls during winter, contributing to both population declines near the northern extent of the species' breeding range and population increases in the southern half of the species' range. We used novel DNA microsatellite markers to test patterns of gene flow predicted by this migration-mediated range-shift hypothesis. We genotyped 1,560 owls from 36 study locations in Canada, Mexico, and the United States. Analyses of molecular variance provided evidence that burrowing owl populations in both northwestern Mexico and Canada are genetically different from the rest of the populations in the breeding range, lending some support to the migration-mediated range-shift hypothesis. We found evidence of subtle genetic differentiation associated with subtropical irrigated agricultural areas in southern Sonora and Sinaloa, demonstrating that land use can produce location-specific population dynamics leading to genetic structure even in the absence of dispersal barriers. We also used stable isotopes 2/H, 13/C, and 15/N in feathers to test philopatry and breeding dispersal patterns predicted by this migration-mediated range-shift hypothesis. Burrowing owl populations near the northern edge of the species' breeding range had a high proportion of immigrants compared to interior populations, while other populations had high levels of philopatry. Stable isotopes also provided evidence of breeding dispersal events from Canadian populations to northwestern Mexico in support of the migration-mediated range-shift hypothesis, but similar isotope signatures in nestling feathers between these two regions prevent stronger inferences.

Anolis carolinensis has been a model organism for ecology and evolutionary biology since the seventies, yet there are still understudied aspects of their ecology. A five-year study has provided microsatellite genotypes to be used in building a pedigree and assess relatedness, enabling us to evaluate the spatial distribution of an urban population of A. carolinensis. Results indicate no correlation between a male’s size and the distance others keep from it; however, males belonging in the heavyweight morph are dictating the spatial distribution in this population. In addition, juvenile dispersal of male offspring and partial philopatry of female offspring are key in this dynamic, where a single heavyweight male will actively defend a small area that contains multiple females, some of which are be daughters, and multiple unrelated males, most likely sneaker males.