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Plant pathogens often adapt to plant genetic resistance so characterization of the architecture under-lying such an adaptation is required to understand the adaptive potential of pathogen populations. Erosion of banana quantitative resistance to a major leaf disease caused by polygenic adaptation of the causal agent, the fungus Pseudocercospora fijiensis, was recently identified in the northern Caribbean region. Genome scan and quantitative genetics approaches were combined to investigate the adaptive architecture underlying this adaptation. Thirty-two genomic regions showing host se-lection footprints were identified by pool sequencing of isolates collected from seven plantation pairs of two cultivars with different levels of quantitative resistance. Individual sequencing and phenotyping of isolates from one pair revealed significant and variable levels of correlation be-tween haplotypes in 17 of these regions with a quantitative trait of pathogenicity (the diseased leaf area). The multilocus pattern of haplotypes detected in the 17 regions was found to be highly varia-ble across all the population pairs studied. These results suggest complex adaptive architecture un-derlying plant pathogen adaptation to quantitative resistance with a polygenic basis, redundancy, and a low level of parallel evolution between pathogen populations. Candidate genes involved in quantitative pathogenicity and host adaptation of P. fijiensis were highlighted in genomic regions combining annotation analysis with available biological data.

International audience; Plant pathogens often adapt to plant genetic resistance so characterization of the architecture underlying such an adaptation is required to understand the adaptive potential of pathogen populations. Erosion of banana quantitative resistance to a major leaf disease caused by polygenic adaptation of the causal agent, the fungus Pseudocercospora fijiensis, was recently identified in the northern Caribbean region. Genome scan and quantitative genetics approaches were combined to investigate the adaptive architecture underlying this adaptation. Thirty-two genomic regions showing host selection footprints were identified by pool sequencing of isolates collected from seven plantation pairs of two cultivars with different levels of quantitative resistance. Individual sequencing and phenotyping of isolates from one pair revealed significant and variable levels of correlation between haplotypes in 17 of these regions with a quantitative trait of pathogenicity (the diseased leaf area). The multilocus pattern of haplotypes detected in the 17 regions was found to be highly variable across all the population pairs studied. These results suggest complex adaptive architecture underlying plant pathogen adaptation to quantitative resistance with a polygenic basis, redundancy, and a low level of parallel evolution between pathogen populations. Candidate genes involved in quantitative pathogenicity and host adaptation of P. fijiensis were identified in genomic regions by combining annotation analysis with available biological data.

International audience; Understanding the mechanisms involved in pathogen adaptation to quantitative resistance in plants has a key role to play in establishing durable strategies for resistance deployment, especially in perennial crops. The erosion of quantitative resistance has been recently suspected in Cuba and the Dominican Republic for a major fungal pathogen of such a crop: Pseudocercospora fijiensis, causing black leaf streak disease on banana. This study set out to test whether such erosion has resulted from an adaptation of P. fijiensis populations, and to determine whether or not the adaptation is local. Almost 600 P. fijiensis isolates from Cuba and the Dominican Republic were sampled using a paired-population sampling design on resistant and susceptible banana varieties. A low genetic structure of the P. fijiensis populations was detected in each country using 16 microsatellite markers. Cross-inoculation experiments using isolates from susceptible and resistant cultivars were carried out, measuring a quantitative trait (the diseased leaf area) related to pathogen fitness on three varieties. A further analysis based on those data suggested the existence of a local pattern of adaptation to resistant cultivars in both of the study countries, due to the existence of specific (or genotype by genotype) host-pathogen interactions. However, neither cost nor benefit effects for adapted populations were found on the widely used "Cavendish" banana group. These results highlight the need to study specific host-pathogen interactions and pathogen adaptation on a wide range of quantitative resistance phenotypes in banana, in order to develop durable strategies for resistance deployment.

Black Leaf Streak Disease (BLSD) is the most severe foliar disease of banana and plantain. BLSD is caused by Pseudocercospora fijiensis, an ascomycete fungus which produces wind-borne spores responsible for its spatial dispersal. In order to evaluate the BLSD long-distance dispersal and to better understand the effect of environmental factors on its invasive spatial spread, a spatio-temporal study was set up during the recent BLSD invasion in the Martinique island (FWI). Disease detection was carried out from September2010 to May 2012 and sampling squares were defined from a regular spatial grid built over the island. In this paper, we consider a stochastic model of spatio-temporal propagation of BLSD in an heterogeneous landscape and we present mathematical and computational results for this continuous-time model. Statistical inference of parameters is carried out from presence-absence data using a Bayesian framework based on a data augmentation method with respect to square first colonization times. Parameter posterior distribution calculations made possible the evaluation of the BLSD long-distance dispersal and land-cover influence on the disease propagation. Our results enabled the re-enactment of the invasion.

Mycosphaerella fijiensis Morelet (anamorph Pseudocercospora fijiensis Morelet), the causal agent of black Sigatoka disease of banana, is considered to be the greatest economical threat for export-banana cultivation throughout the world because most cultivars are highly susceptible. The disease has a worldwide distribution throughout the humid tropical regions, but was still absent in some Caribbean islands hitherto. In Martinique Island, an intensive survey has been conducted by the plant protection service and the Fédération Régionale de Défense Contre les Organismes Nuisibles (FREDON) since April 2008 to detect as early as possible any outbreak of infection by M. fijiensis. In September 2010, typical symptoms of black Sigatoka were observed in a plantain crop located in Ducos Municipality (14°35.702′N, 60°58.221′W) in the west-central area of the island. Typical early symptoms were 1- to 4-mm long brown streaks on the abaxial leaf surface. The presence of the disease was further confirmed by the in situ observation of microscopic features of the anamorphic form of the pathogen (3). Typical pale brown, straight or slightly geniculate conidiophores were observed occurring singly or in little groups without any stroma, with a thickened wall at the conidial scars. Conidia were hyaline to pale olive, straight or slightly curved, with one to eight septa, and a conspicuous scar at the basal cell. The diagnosis was confirmed by real-time PCR targeting M. fijiensis-specific regions within the β-tubulin gene (1). Positive results were consistently obtained with DNA extracted from infected banana tissue samples, and the identity of the amplicon was confirmed by sequencing (Accession No. HQ412771) and comparison with reference sequences deposited on GenBank. After this first finding, the survey was intensified and black Sigatoka symptoms were also observed in several other locations on the island, affecting a large range of susceptible cultivars (Grande Naine, French, and Figue Sucrée), and in plantations, backyards, and private gardens. The presence of the fungus in the samples was confirmed by PCR analysis of DNA extracted from symptomatic leaves with a M. fijiensis-specific ITS-based primer pair (2). The pathogen may have been introduced into Martinique by ascospores, from islands where black Sigatoka is present, that were blown by continuous southerly winds over a 2-week period in August 2010 that was immediately followed by heavy rains that favor disease development. To our knowledge, this is the first report of M. fijiensis on Martinique Island, showing that the disease is still spreading northward in this region of the Caribbean. References: (1) M. Arzanlou et al. Phytopathology 97:1112, 2007. (2) J. Henderson et al. Page 59 in: Mycosphaerella Leaf Spot Disease of Bananas: Present Status and Outlook. L. Jacome et al., eds. International Network for the Improvement of Banana and Plantain (INIBAP), Montpellier, France. 2003. (3) M. F. Zapater et al. Fruits 63:389, 2008.

International audience; Black leaf streak disease, or black Sigatoka, is caused by the fungus Pseudocercospora fijiensis, and has been identified as a major constraint to global production of banana and plantain. We fitted a climatic niche model (CLIMEX) for P. fijiensis to gain an understanding of the patterns of climate suitability, and hence hazard from this disease. We then calibrated the climate suitability patterns against the results of an expert elicitation of disease pressure patterns. We found a moderately strong non-linear relationship between modelled climate suitability for P. degrees fijiensis and the expert ratings for disease pressure. The strength of the relationship provides a cross-validation between the CLIMEX model and the expert elicitation process. The bulk of global banana production experiences high potential threat from P. fijiensis, and the higher yielding areas for banana and plantain production are at greatest threat. By explicitly considering the role of irrigation we have been able to identify how strategic irrigation could be used to support banana production in areas that are at low risk from P. fijiensis.

International audience; Among the emerging fungal diseases threatening food security, the Pseudocercospora fijiensis fungus causing black leaf streak disease of banana is one of the most marked examples of a recent worldwide pandemic on a major crop. We assessed how this pathogen spread throughout the latest invaded region, i.e. Central America and the Caribbean. We retraced its population history combining detailed monitoring information on disease outbreaks and population genetic analyses based on large-scale sampling of P. fijiensis isolates from 121 locations throughout the region. The results first suggested that sexual reproduction was not lost during the P. fijiensis expansion, even in the insular Caribbean context, and a high level of genotypic diversity was maintained in all the populations studied. The population genetic structure of P. fijiensis and historical data showed that two disease waves swept northward and southward in all banana-producing countries in the study area from an initial entry point in Honduras, probably mainly through gradual stepwise spore dispersal. Serial founder events accompanying the northern and southern waves led to the establishment of two different genetic groups. A different population structure was detected on the latest invaded islands (Martinique, Dominica and Guadeloupe), revealing multiple introductions and admixture events that may have been partly due to human activities. The results of this study highlight the need to step up surveillance to limit the spread of other known emerging diseases of banana spread mainly by humans, but also to curb gene flow between established pathogen populations which could increase their evolutionary potential.

Black leaf streak disease (BLSD), caused by the fungal pathogen Mycosphaerella fijiensis, is considered as the most destructive foliar disease of banana. To advance our knowledge of the dynamics of the disease at plant scale as well as of the components of varietal resistance, we designed, calibrated and evaluated a mechanistic model to simulate the disease on a banana plant. The model runs in discrete time at plant scale and describes plant growth and pathogen dynamics under optimal epidemiological conditions. The model is divided into two modules: a deterministic plant sub-model that simulates the simplified architecture and growth of the banana, and a pathogen sub-model that simulates the detailed life cycle of the pathogen including infection, lesion growth, asexual and sexual sporulation, and the dispersal of spores on the plant. The three most influential epidemiological parameters identified by sensitivity analysis of the model (lesion growth rate, infection efficiency, and incubation period) were estimated in a Bayesian framework using Markov chain Monte Carlo methods and acquired data on the dynamics of leaf lesions under natural conditions. The posterior densities provided precise knowledge on pathogen life history traits. The evaluation of the model using an independent data set confirmed the good quality of the predictions. Simulations allowed us to evaluate the impact of host resistance components, auto-infection at plant scale, and of the leaf emergence rate, which is linked with cropping practices, on the severity of BLSD. This foliar disease simulation model will help design new methods of controlling BLSD. (Resume d'auteur)

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During Iron Ages, the Rhône valley was at the junction between the Celtic northern and central world and the Mediterranean one. In this way, it constitutes a circulation area, subject to different cultural influences. The archaeological faunas’ analysis from our corpus offer an opportunity to approach particularities of breeding, hunting and protohistoric people’s consumption. In short, it permits to reflect on protohistoric people and animals relationships. Through zooarchaeology, the Rhône valley appears as an area totally included in the whole Gallic world. In this way, during the first Iron Age, eating and breeding habits show a division, on our region, between influences from the north alpine region and the celtic Mediterranean region. During the second Iron Age, customs implying animals and products linked with them indicate evolutions, among which a pork increase in diet. Those modifications correspond to those we notice elsewhere in Gaul. Moreover, they are probably linked with a society reorganisation. Domestic species’ morphology and its evolution also are more or less similar to those appearing elsewhere in Gaul between the 8th and the 1st centuries BC. We could say the same about hunting habits, which present a low decline. The Greek and Italic cultures’ influence, in term of diet, seem to be anecdotic, evolutions appearing more linked with people and society’s organisation and demography. The Rhône valley diet appears as fully integrated into Celtic diet cultures and presents evolutions less linked with environmental transformations than with social and economic changes.; Durant les âges du Fer, la vallée du Rhône se trouve à la jonction entre le monde celtique du nord et du centre de l’Europe et le monde méditerranéen. Elle constitue donc un espace de circulation soumis à différentes influences culturelles. L’étude des faunes archéologiques issues des sites de la région permet donc d’approcher les spécificités de l’élevage, de la chasse et de la consommation carnée des populations protohistoriques, en un mot, de la relation entre elles et les populations animales. Par le prisme de l’archéozoologie, la vallée du Rhône apparaît comme un espace parfaitement intégré au reste de la Gaule. Ainsi, au premier âge du Fer, les pratiques alimentaires et d’élevage montrent une partition de la région entre l’influence des mondes nord-alpin et celtique méditerranéen. Au second, les pratiques impliquant des animaux et des produits d’origine animale présentent des évolutions, parmi lesquelles une augmentation plus ou moins forte de la part des porcs dans l’alimentation. Ces changements correspondent à ceux qui s’observent dans l’ensemble de la Gaule et qui sont sans doute en lien avec une réorganisation de la société. La morphologie des espèces domestiques et son évolution, de même que la pratique de la chasse, sont également plus ou moins similaires à celles du reste de la Gaule, du VIIIe au Ier siècle av. J.-C. L’influence des cultures grecque et italique, en matière alimentaire, semble être anecdotique, du point de vue des produits d’origine animale, les évolutions semblant davantage liées à l’organisation et à la démographie des populations. L’alimentation rhodanienne nous offre donc l’image d’une région pleinement intégrée aux cultures alimentaires celtiques et présente des évolutions moins liées à celles de l’environnement qu’à des problématiques sociales et économiques.

In agricultural production systems, the use of varietal resistance is an ecological alternative to the application of phytosanitary products in the control of plant pathogens. However, several examples of breakdown or erosion of varietal resistance due to adaptation in populations of pathogens have been reported. A recent case is the erosion of quantitative resistance in bananas by the fungus Pseudocercospora fijiensis, the causative agent of Black Leaf Streak Disease. The objectives of this thesis aimed to highlight an adaptation of P. fijiensis populations to quantitative resistance with in vitro inoculations, to identify the underlying adaptive architecture and to find out if adapted genotypes were introduced in other countries, in particular in the French West Indies. Cross inoculations of detached leaves of resistant and sensible varieties of banana, suggest the existence of local adaptation to quantitative resistance in populations of P. fijiensis from Cuba and the Dominican Republic. Population genomics and quantitative genetics analyses identified 25 genomic regions potentially involved in adaptation to these resistances. These results suggest a complex adaptive architecture involving a polygenic basis, functional redundancy and low level of convergence between the populations studied. Annotation of genes detected in genomic regions and biological data support the hypothesis that some of them may play a role in pathogenicity. Finally, a genetic analysis of populations in the Latin America - Caribbean region made it possible to propose the hypothesis of an introduction in Guadeloupe of genotypes pre-adapted to resistance from Cuba, which could explain the high levels of disease observed in resistant varieties. This study provides first elements and a methodology to understand the adaptation of fungi to quantitative resistance.; Dans les systèmes de production agricole, l'utilisation de résistances variétales représente une alternative écologique aux produits phytosanitaires pour lutter contre les agents pathogènes de plantes. Cependant, il existe de nombreux exemples de contournement ou d'érosion de résistances variétales dues à l'adaptation des populations d'agents pathogènes. Un exemple récent est celui de l'érosion de résistances quantitatives du bananier par le champignon Pseudocercospora fijiensis, agent responsable de la Maladie des Raies Noires (MRN). Pour mieux comprendre ces érosions, les travaux de cette thèse avaient pour objectif de mettre en évidence une adaptation des populations de P. fijiensis à des résistances quantitatives, d'identifier l'architecture adaptative sous-jacente et de rechercher si des génotypes adaptés ont pu être diffusés en particulier dans les Antilles Françaises. L'existence d'une adaptation locale à des résistances quantitatives a été démontrée chez des populations P. fijiensis de Cuba et de République Dominicaine grâce à des inoculations in vitro. Des analyses de génomique des populations et de génétique quantitative ont permis d'identifier 25 régions génomiques potentiellement impliqués dans l'adaptation à ces résistances. Ces résultats suggèrent une architecture adaptative complexe impliquant une base génétique polygénique, de la redondance fonctionnelle et peu de convergence entres les populations étudiées. L'annotation des gènes détectés dans les régions génomiques et des données biologiques confortent l'hypothèse que certains d'entre eux puissent jouer un rôle dans la pathogénicité. Enfin, une analyse de génétique des populations de la régions Amérique Latine - Caraïbes a permis de proposer l'hypothèse d'une introduction en Guadeloupe de génotypes pré-adaptés à des résistances depuis Cuba qui pourraient expliquer les forts niveaux de maladie observés récemment sur des géniteurs résistants. Cette étude apporte des premiers éléments et une méthodologie pour comprendre l'adaptation des champignons aux résistances quantitatives.

Engineering school; Currently, the most sustainable and environmentally acceptable lever for controlling diseases is genetic resistance, through the use of resistant varieties. The objective of this study is to identify which spatial arrangements can efficiently control black Sigatoka by modelling. To do this, the approach consisted of: i) parameterising a generic demo-genetic model (landsepi) to black sigatoka, and ii) comparing different resistance deployment strategies in real landscapes. Statistical analyses of the simulated scenarios show that random mixtures within a plot are more effective than mosaic of fields, regardless of the type of landscape and the type of spore considered. The proportion of resistant varietydeployed is the most influent factor on the level of disease severity in the landscape. These results should be confirmed on smaller landscapes and finer parameterisation of the model to better take into account the infectious cycle of Pseudocercospora fijiensis.; Actuellement, le levier le plus durable et acceptable pour l’environnement pour lutter contre les maladies est la résistance génétique, par l’utilisation de variétés résistantes. L’objectif de cette étude est d’identifier les agencements spatiaux permettant de contrôler efficacement la cercosporiose noire par modélisation. Pour cela, la démarche a consisté : i) à paramétrer un modèle démo-génétique générique (landsepi) au cas de la cercosporiose noire et ii) à comparer différentes stratégies de déploiement de variétés résistantes dans des paysages réels. L’analyse statistique des scénarios simulés montre que les mélanges aléatoires au sein d’une parcelle sont plus efficaces que les mosaïques parcellaires, quels quesoit le type de paysage et le type de spore considérés. La proportion de variété résistante déployée est le facteur le plus impactant sur le niveau de sévérité de la maladie dans le paysage. Ces résultats devront être confirmés sur des paysages moins grands et un calibrage plus fin du modèle pour mieux prendre en compte le cycle infectieux de Pseudocercospora fijiensis.

Diadems, in classical Antiquity, are usually discovered in funerary sites from the Greek Mediterranean world or under Greek influence. They are made from various materials, precious or not, gold is mainly represented. We have established a catalogue making an inventory of a great number of diadems made of precious metal, dated between 9th-4th century BC. The corpus is based on several research areas: technological, iconographic, typological, bibliographic, graphic and archaeological. The use of macro photography, a method of observation recently developed to understand the stages of manufacture of antique jewellery, helped to define the design of the structures and the items of the jewels, to emphasize the type of solder used and to identify different series of diadems, linked to a workshop or a common matrix. This approach, combined with the confrontation of archaeological contexts of the diadems of the corpus, as well as an iconographic analysis, highlighted the various functions of the diadems during this period, and pointed out, in some cases, the social and cultural background of the holders., Les diadèmes, dans l’Antiquité grecque, sont des bijoux essentiellement mis au jour dans des ensembles funéraires du monde méditerranéen grec ou sous influence grecque. Ils sont confectionnés à partir de divers matériaux, précieux ou non, l’or étant majoritairement représenté. Nous avons établi un catalogue recensant la quasi-majorité des diadèmes en matériaux précieux datés entre le IXe siècle et le IVe siècle avant J.-C. Le corpus s’appuie sur plusieurs champs de recherche : technologique, iconographique, typologique, bibliographique, graphique et archéologique. L’emploi de la macrophotographie, technique d’observation récemment développée pour comprendre les étapes de fabrication des bijoux anciens, a permis de définir la conception des structures et éléments des bijoux, de mettre en évidence le type de soudure utilisé et d’identifier différentes séries de diadèmes, liées à un atelier ou à une matrice commune. Cette démarche, associée à la confrontation des contextes archéologiques dont sont issus les exemplaires du corpus, ainsi qu’à une analyse iconographique, a mis en évidence les différentes fonctions prêtées aux diadèmes durant cette période, et a souligné, dans certains cas, l’appartenance sociale et culturelle des porteurs.

Le déroulement des banquets gréco-romains, les mets proposés et les rites socioculturels accompagnant l'acte de partage de nourriture sont désormais relativement bien connus des chercheurs. En revanche, peu d'intérêt a été porté aux banquets et aux pratiques alimentaires des populations locales qui entrent peu à peu dans l’orbite de Rome, notamment celles qui sont araméophones. Pratiquent-elles le même art du banquet ? Ont-elles subi les influences des élites gréco-romaines ou, au contraire, certaines pratiques gréco-romaines ont-elles été modifiées par la présence araméenne ?

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