As invasões biológicas tem alcançado ampla disseminação devido a ações antrópicas em todo o planeta. Drosophila suzukii (Matsumura, 1931) (Diptera: Drosophilidae), é uma espécie invasora global que vem promovendo grandes danos às culturas agrícolas. Nativa do Sudeste Asiático, D. suzukii recentemente (ano de 2013) invadiu e se dispersou pela América do Sul. Aqui, utilizamos uma abordagem filogeográfica baseada no fragmento do gene COI para explorar a dinâmica de invasão das populações de D. suzukii no Brasil. Identificamos cinco haplotipos e uma diversidade genética moderada nas populações brasileiras, que estão em expansão demográfica e espacial. A AMOVA indicou uma alta estrutura genética entre as populações, o que é parcialmente explicado pela sua origem morfoclimática e história de invasão. D. suzukii expandiu do sul para o sudeste do Brasil, auxiliado pelo transporte de frutas mediado por humanos de região para região. O compartilhamento de haplótipos entre as regiões brasileiras e outras regiões invadidas do mundo sugere um único evento de invasão de D. suzukii no Brasil, originário de áreas previamente invadidas (como América do Norte e Europa). A rápida dispersão geográfica e a grande variedade de frutas atacadas por D. suzukii requerem implementação imediata de estratégias de controle (legais e fitossanitárias) para gerenciar esta praga no Brasil. / Biological invasions have reached large parts of the globe, due to human actions across the planet. Drosophila suzukii (Matsumura, 1931) (Diptera: Drosophilidae) is a globally invasive species, always associated with enormous and costly damage to agricultural crops. Native to Southeast Asia, D. suzukii recently (i.e. 2013) invaded and is dispersing through South America. Here, we used a phylogeographic approach based on the COI gene fragment to explore the invasion dynamics of D. suzukii populations in Brazil. We identified five haplotypes and moderate genetic diversity in Brazilian populations, which are undergoing demographic and spatial expansion. The AMOVA indicated a high genetic structure among the populations, which is partially explained by their morphoclimatic origin and invasion history. D. suzukii expanded from southern to southeastern Brazil, aided by human-mediated transport of fruits from region to region. The sharing of haplotypes among Brazilian and other invaded regions of the world suggests a single invasion event of D. suzukii in Brazil, originating from previously invaded areas (e.g., North America and Europe). The rapid geographic dispersal and wide variety of fruits attacked by of D. suzukii require immediate implementation of control strategies (legal and phytosanitary) to manage this pest in Brazil.

As invasões biológicas tem alcançado ampla disseminação devido a ações antrópicas em todo o planeta. Drosophila suzukii (Matsumura, 1931) (Diptera: Drosophilidae), é uma espécie invasora global que vem promovendo grandes danos às culturas agrícolas. Nativa do Sudeste Asiático, D. suzukii recentemente (ano de 2013) invadiu e se dispersou pela América do Sul. Aqui, utilizamos uma abordagem filogeográfica baseada no fragmento do gene COI para explorar a dinâmica de invasão das populações de D. suzukii no Brasil. Identificamos cinco haplotipos e uma diversidade genética moderada nas populações brasileiras, que estão em expansão demográfica e espacial. A AMOVA indicou uma alta estrutura genética entre as populações, o que é parcialmente explicado pela sua origem morfoclimática e história de invasão. D. suzukii expandiu do sul para o sudeste do Brasil, auxiliado pelo transporte de frutas mediado por humanos de região para região. O compartilhamento de haplótipos entre as regiões brasileiras e outras regiões invadidas do mundo sugere um único evento de invasão de D. suzukii no Brasil, originário de áreas previamente invadidas (como América do Norte e Europa). A rápida dispersão geográfica e a grande variedade de frutas atacadas por D. suzukii requerem implementação imediata de estratégias de controle (legais e fitossanitárias) para gerenciar esta praga no Brasil. / Biological invasions have reached large parts of the globe, due to human actions across the planet. Drosophila suzukii (Matsumura, 1931) (Diptera: Drosophilidae) is a globally invasive species, always associated with enormous and costly damage to agricultural crops. Native to Southeast Asia, D. suzukii recently (i.e. 2013) invaded and is dispersing through South America. Here, we used a phylogeographic approach based on the COI gene fragment to explore the invasion dynamics of D. suzukii populations in Brazil. We identified five haplotypes and moderate genetic diversity in Brazilian populations, which are undergoing demographic and spatial expansion. The AMOVA indicated a high genetic structure among the populations, which is partially explained by their morphoclimatic origin and invasion history. D. suzukii expanded from southern to southeastern Brazil, aided by human-mediated transport of fruits from region to region. The sharing of haplotypes among Brazilian and other invaded regions of the world suggests a single invasion event of D. suzukii in Brazil, originating from previously invaded areas (e.g., North America and Europe). The rapid geographic dispersal and wide variety of fruits attacked by of D. suzukii require immediate implementation of control strategies (legal and phytosanitary) to manage this pest in Brazil.

La compréhension de l'émergence des maladies infectieuses végétales causées par les bactéries passe par l'identification des populations sources, des routes d'invasion et des voies de dissémination, ainsi que par l'estimation des paramètres biotiques et abiotiques associés. Xanthomonas citri pv. citri (Xcc) est l'agent pathogène responsable du chancre Asiatique des agrumes. La bactérie est distribuée dans plusieurs pays agrumicoles du monde et listée comme organisme de quarantaine par ceux où elle est absente. Nous avons abordé l'épidémiologie moléculaire de Xcc à deux échelles spatio-temporelles grâce à un schéma de 14 microsatellites (MLVA-14) et un schéma de 31 marqueurs minisatellites (MLVA-31). Le typage MLVA-14 s'est montré adapté au génotypage d'une bactérie monomorphe comme Xcc. Le typage MLVA-31 a permis de diviser le pathovar Xcc en quatre groupes génétiques distincts correspondant aux différences de gammes d'hôtes mise en évidence chez cette bactérie. Le pathotype A (souches à large gamme d'hôtes parmi les rutacées) est séparé en deux groupes génétiques, tandis que les pathotypes A* et Aw (souches à gamme d'hôtes restreinte au limettier Mexicain et quelques espèces proches) constituent chacun un groupe génétique. Alors que l'expansion géographique de Xcc depuis son aire d'origine dans la première moitié du XXème siècle a quasi exclusivement concerné un seul groupe génétique, trois des quatre groupes décrits ont contribué à l'émergence de Xcc en Afrique au cours de la dernière décennie. La bactérie est pré-adaptée et a été introduite avec son hôte depuis sa population d'origine, faisant de la barrière migratoire la seule étape à franchir pour rencontrer un succès d'invasion. L'objectif de cette thèse a été de décrire les différentes populations émergentes grâce à des approches d'épidémiologie moléculaire et inférentielles, et identifier les différentes origines, routes et acteurs de la dissémination. Nous avons dans un premier temps montré la coexistence de deux groupes génétiques distincts au Mali : DAPC1 qui est dispersé dans quatre provinces du pays et DAPC2 qui est resté cantonné à l'espace péri-urbain de Bamako. L'analyse de l'émergence de Xcc au Sénégal a révélé le succès invasif de DAPC2 dans un autre environnement. La structure des populations DAPC1 du Mali et DAPC2 du Sénégal suggèrent que les plants de pépinières constituent une voie de dissémination majeure dans ces pays. À l'opposé, DAPC2 de Bamako n'est pas détecté en pépinières au Mali et n'a pas montré de caractère invasif. L'existence d'une population « tête de pont » invasive de souches DAPC1 au Mali donnant lieu à une épidémie au Burkina Faso a été mise en évidence par une approche ABC (calcul Bayésien approché). Les populations DAPC2 du Mali et du Sénégal ne présentent pas de lien épidémiologique direct mais partagent des liens de parenté avec des souches présentes dans le sous-continent Indien. Dans un deuxième temps, l'analyse d'une population de souches appartenant au pathotype A* en Ethiopie nous a permis de procéder à des estimations de paramètres démographiques, tels que les tailles efficaces. Nous avons montré que l'approche inférentielle nous permettait d'éclairer l'histoire démographique de Xcc dans un cas d'émergence, et de mettre en avant une dynamique saisonnière accentuant probablement le déséquilibre mutation-dérive lié à la situation d'émergence. L'émergence de Xcc en Afrique est principalement associée aux activités humaines. Sa dissémination locale et globale peut alors être considérablement limitée par des mesures de gestion plus stricte au niveau des pépinières et des flux de commerces. / Several plant emerging infectious diseases are caused by bacteria. To improve our understanding of their emergence, a description of the emerging populations, the reconstruction of invasion routes and pathways, as well as the identification of involved biotic and abiotic parameters are fundamental. The bacterium Xanthomonas citri pv. citri (Xcc) is responsible for Asiatic citrus canker. It is present in many citrus producing countries and listed as a quarantine organism in canker-free countries.Two MLVA schemes were used for molecular epidemiological analyses of Xcc. The first one, MLVA-14, targeted 14 microsatellite markers, and is useful to describe the genetic diversity of this monomorphic bacterium. The second, MLVA-31, targeted 31 minisatellite markers, is suited to global epidemiology analyses. Based on MLVA-31 data, Xcc is divided in four genetic groups (referred to as DAPC clusters) corresponding to Xcc pathotype classification based on host range. Three pathotypes were described: pathotype A strains are able to infect most citrus species, while pathotypes A* and AW strains are naturally restricted to fewer host species.DAPC 1 is responsible for almost all cases of geographical expansion of Xcc over the first half of the 20th century, we show that three Xcc genetic clusters have emerged in Africa over the last decade. Xcc is pre-adapted to its host species. Invasive success of Xcc is then mostly conditioned by migration events. Our objectives were to describe these invasive populations using a molecular epidemiology approach and to assess the origin, routes and actors of this dissemination in Africa. Two genetic clusters were found in Mali: DAPC1 is present in four provinces while DAPC2 is restricted to the Bamako urban environment. In contrast, DAPC2 emerging populations in Senegal showed an invasive succes in an other environment. Populations structures of DAPC1 in Mali and DAPC2 in Senegal highlighted the role of nurseries in Xcc dissemination. On the contrary, DAPC2 strains in Bamako were not detected in Malian nurseries and showed a limited invasive success. Approximate Bayesian Computation highlighted an invasive bridgehead scenario between DAPC1 in Mali and Burkina Faso. DAPC2 populations in Mali and Senegal were not found epidemiologically related but were genetically related to strains previously reported from the Indian subcontinent.Demographic parameters inference, such as effective population sizes, were inferred from Ethiopian pathotype A* populations. The inference approach was useful to decipher the demographic history of this emerging population, and suggested seasonal fluctuations in population sizes over time.Emergence of Xcc in Africa was found strongly related to human activities. Therefore, the local and global dispersion could be limited by a better management of nurseries and trade.