A introdução de espécies exóticas, resultando em processos de invasão biológica em ambientes naturais, é um dos efeitos humanos indiretos que atualmente mais ameaçam a biodiversidade global. Apesar das invasões biológicas causarem muitos impactos negativos, elas ainda são pouco estudadas nos ambientes tropicais megadiversos. A palmeira australiana Archontophoenix cunninghamiana, inicialmente introduzida para fins ornamentais, tornou-se invasora de fragmentos remanescentes de Mata Atlântica no estado de São Paulo. Foi sugerida como ação de manejo a substituição da A. cunninghamiana pela palmeira nativa Euterpe edulis. Assim, o objetivo geral deste estudo foi comparar os estágios demográficos inicias dessas duas espécies de palmeiras, visando subsidiar a substituição de A. cunninghamiana em fragmentos florestais invadidos. Realizamos experimentos no interior de um fragmento florestal urbano (Reserva Florestal do Instituto de Biociências, São Paulo/SP) impactado pela espécie invasora. No interior do fragmento, analisamos a chuva de sementes local (por meio de coletores distribuídos acima do solo), a longevidade das sementes (realizando um experimento de soterramento) e o estabelecimento de plântulas resultantes de semeadura direta de ambas as espécies. Em laboratório, testamos os efeitos diretos e indiretos da espécie invasora sobre a germinação de E. edulis, respectivamente por meio de experimentos de germinação conjunta e por meio da liberação de substâncias alelopáticas em soluções de lixiviados das folhas e frutos de A. cunninghamiana. A palmeira invasora não apresentou nenhum efeito sobre a germinação e formação de plântulas da E. edulis. Mesmo assim, a palmeira nativa apresentou desempenho inferior nesses estágios, devido às suas baixas taxas de germinação e de viabilidade resultando em poucas plântulas formadas, o que evidenciou um gargalo demográfico próprio da espécie. A composição da chuva de sementes indicou uma elevada pressão de propágulos da palmeira invasora sobre a comunidade nativa, já que mais de 30% das sementes zoocóricas encontradas pertenciam a A. cunninghamiana. O experimento de longevidade indicou que ambas as espécies apresentaram bancos de sementes transientes, o que é vantajoso no controle da espécie exótica, mas desvantajoso quando se deseja reintroduzir a palmeira nativa por meio de semeadura. No experimento de semeadura direta, a sobrevivência das plântulas de ambas as espécies também apontou um desempenho melhor de A.cunninghamiana. Portanto, nossos resultados demonstraram vantagens da palmeira invasora nos estágios demográficos inicias quando em o-ocorrência com a E. edulis, em condições florestais naturais. Por isso, recomendamos ações de manejo direcionadas majoritariamente aos indivíduos reprodutivos da A. cunninghamiana, já que eles produzem elevadas quantidades de sementes, que se estabelecem rapidamente. / The introduction of alien species in natural habitats resulting in processes of biological invasions is one of the indirect human actions which nowadays threaten global biodiversity. Although bioinvasions usually cause huge negative impacts in the native biota, they are still little studied in the megadiverse tropical environments. The Australian palm tree Archontophoenix cunninghamiana, initially introduced for ornamental purposes, became an invader in remnant patches of the Atlantic forest, in São Paulo state. The substitution of A. cunninghamiana by the native palm Euterpe edulis has been proposed as a management action. The main objective of this study was to compare the first demographic stages of these two palm species, aiming at subsidizing the substitution of A. cunninghamiana in invaded forest patches. We performed experiments inside an urban Atlantic forest patch (Reserva Florestal do Instituto de Biociências, São Paulo/SP) impacted by the invasive species. Inside the fragment we assessed local seed rain (through seed traps distributed above soil level), seed longevity (performing a burying experiment) and seedling establishment (resulting from direct seed sowing) of both species. At laboratory, we tested both direct and indirect effects of the invasive species over E. edulis germination through combined experiments - species were put to germinate together - and by testing for the release of allelopathic substances from A. cunninghamiana leaves and fruits on leachate solutions. The invasive palm did not show any effect on E. edulis germination and seedling formation. Even so, the native palm showed lower performance at these stages, due to low germination and viability rates, and consequently little seedling formation, evidencing a demographic bottleneck. The seed rain composition indicated high propagule pressure of the invasive palm over the forest community, since more than 30% of the zoochorous seeds belonged to A. cunninghamiana. The longevity experiment showed transient seed banks for both species, what is advantageous for controlling the alien species but not for reintroducing the native palm through seed sowing. In the seed sowing experiment, seedling survival of both species together pointed to a much better performance of A. cunninghamiana. In conclusion, our results showed advantages of the invasive palm in the initial phases when co-occuring with E. edulis in the forest conditions. We then recommend management actions directed primarily to A. cunninghamiana reproductive individuals, as they provide high amounts of seeds that quickly establish.

A introdução de espécies cresceu nos últimos séculos e muitas delas têm se tornado problema devido à alta capacidade de invasão, modificando ecossistemas naturais e ameaçando espécies nativas. O javali (Sus scrofa) tem demonstrado grande capacidade de invasão e de produção de danos à biodiversidade e agropecuária. No Brasil, a combinação de ambientes com grãos cultivados e remanescentes de vegetação silvestre parece oferecer aos javalis condições alimentares adequadas. Neste trabalho analisamos o conteúdo estomacal de javalis abatidos por controladores para caracterizar a composição de alimentos explorados em três ecorregiões brasileiras – os Campos Sulinos, as Florestas de Araucária e o Pantanal - e avaliar os possíveis riscos que a espécie pode representar para a produção agropecuária e a conservação da biodiversidade. Examinamos a existência de padrões de dieta em cada ecorregião e sua relação com atributos dos indivíduos, do ambiente e da caça através de métodos de ordenação. Visualizamos a distribuição de macronutrientes através da ferramenta gráfica Triângulo-Retângulo de Mistura. Partes aéreas de plantas frescas e raízes formaram a base da dieta nas três ecorregiões. Quando disponíveis, grãos cultivados nos Campos Sulinos e Florestas de Araucária e frutos e sementes silvestres no Pantanal parecem ser preferidos à forragem, o que pode ser explicado por possuírem alto valor energético. Raízes e invertebrados são importantes alimentos no Pantanal, principalmente no período de vazante. Além do registro do consumo de fauna nativa houve o consumo de ovinos. Nas três ecorregiões estudadas há grande variação na proporção em que itens são encontrados em cada estômago. Estes achados sugerem que as necessidades nutricionais são menos importantes ou de difícil ajuste nas condições limitantes dos ambientes silvestres. Nos Campos Sulinos o consumo de proteínas alcançou níveis ideais para crescimento e lactação quando comparado ao porco doméstico o que sugere melhores condições de expansão e abundância nessa região. De forma geral, a dieta de javalis nas ecorregiões estudadas sugere que os principais danos à biodiversidade estejam mais relacionados com a competição difusa por exploração de recursos e alterações nos hábitats e processos ecossistêmicos pela busca por recursos do que pela predação de espécies de interesse especial de conservação. / Introduction of species has grown in recent centuries and many have become a problem due to high invasiveness, modifying natural ecosystems and threatening native species. Wild boar (Sus scrofa) has demonstrated great capacity for invasion and production of damages to biodiversity and agriculture. In Brazil, the combination of environments with cultivated grains and remnants of wild vegetation seems to offer the wild boars adequate food conditions. In this study, we analyzed the stomach contents of wild boars slaughtered by controllers to characterize the composition of foods exploited in three Brazilian ecoregions characterized by mosaics of fields and forests – the South Brazilian Campos, the Araucaria Forests and Pantanal - and to evaluate the possible risks that the species can represent for agricultural production and conservation of biodiversity. We examined the existence of dietary patterns in each ecoregion and its relation with individuals' attributes, the environment and hunting through ordering methods. We visualize the macronutrient distribution through the right-angle misture triangle (RMT) tool. Aerial parts of fresh plants and roots formed the basis of diet in the three ecoregions. When available, grains grown in the South Brazilian Campos and Araucaria Forests and wild fruits and seeds in the Pantanal seem to be preferred to the forage, which can be explained by their high energy value. Roots and invertebrates are important food in the Pantanal, especially in the period of ebb. In addition to the consumption of native fauna, there was consumption of sheep. In the three ecoregions studied there is great variation in the proportion in which items are found in each stomach. These findings suggest that nutritional needs are less important or difficult to adjust under conditions that limit wild environments. In the Shouth Brazilian Campos the protein consumption reached optimal levels for growth and lactation when compared to the domestic pig, which suggests better conditions of expansion and abundance in this region. In general, the wild boar diet in the ecoregions studied suggests that the main damages to biodiversity are more related to the diffuse competition for resource exploitation and changes in habitats and ecosystem processes due to the search for resources than for the predation of species of special interest to conservation.

Esta tese examina as reações sociais ao processo de invasão biológica conduzido pelo javali asselvajado europeu (Sus scrofa) e seus cruzamentos com porcos domésticos, ou “javaporcos”, no Brasil Meridional desde um ponto de vista antropológico. Atualmente, esta espécie figura entre os cem piores organismos invasores do mundo conforme o painel sobre invasões biológicas da União Internacional para a Conservação da Natureza (IUCN, na sigla em inglês). Presente no Brasil desde o final da década de 1980, o javali tem provocado inúmeros danos ao meio ambiente e à produção agropecuária, o que levou o Ministério do Meio Ambiente a decretar sua nocividade e a autorizar sua captura e abate em todo território nacional, por tempo indeterminado. Na região onde a etnografia se concentrou, conhecida como Campanha gaúcha, os suínos asselvajados têm protagonizado ataques ao rebanho ovino, o que os alçou à condição de inimigos da pecuária local. Partindo deste conflito e das negociações estabelecidas entre agentes públicos, proprietários rurais e controladores voluntários, a tese rastreia as controvérsias hoje vigentes no país a respeito do Sus scrofa, bem como as escolhas técnicas efetuadas na região tendo em vista seu controle e manejo. Da mesma maneira, examina os impactos da presença do javali na Campanha gaúcha a partir das relações e analogias estabelecidas pelos agentes locais entre este e outros problemas que afetam o seu cotidiano, como: demais processos de invasão biológica que afetam o bioma Pampa, o declínio socioeconômico da pecuária sulina e o abigeato fronteiriço. Por fim, a tese também analisa os novos contextos de biossegurança produzidos no Brasil a partir da legalização do abate do animal, sob o prisma do conceito antropológico de sacrifício. No plano teórico, a tese se guia pelo conceito de feralidade, nela empregado para refletir sobre a resistência da espécie às tentativas humanas de domesticá-la. / This thesis examines the social reactions to the biological invasion process of European wild boar (Sus scrofa) and their breed with domestic pigs, known as "javaporcos", in southern Brazil from an anthropological perspective. Currently, this species is among the top one hundred worst invasive species in the world, according to the panel on biological invasions of the International Union for Conservation of Nature (IUCN). Present in Brazil since the late 1980s, the boar has caused countless damage to the environment and agricultural production, which led the Ministry of Environment to declare it a harmful animal and to allow its capture and slaughter throughout the country, indefinitely. In the region where the ethnography was focused, known as Campanha gaúcha, feral swine have attacked the sheep, which made them enemies of the local ranching community. From this conflict and the negotiations between government officials, landowners and volunteer controllers, the thesis traces the current controversy in the country regarding Sus scrofa, as well as the technical choices made in the region to control and manage it. Similarly, the thesis examines the impact of the presence of boars in the Campanha gaúcha region, based on the relationships and analogies established by local agents between this and other issues that affect their daily lives, such as other biological invasion process that affect the Pampa biome, the socio-economic decline of the southern livestock raising industry and livestock raiding at the borders. Finally, the thesis also analyzes new biosecurity contexts created in Brazil after the slaughter of the animal was authorized, from the perspective of the anthropological concept of sacrifice. Theoretically, the thesis is guided by the concept of ferality, thus used to reflect upon the resistance of the species to human attempts to domesticate it.

Spartina anglica est une espèce exotique hybride qui peuple les zones humides littorales. Elle s’est installée dans le Bassin d’Arcachon au cours des années 1980, envahissant fortement les prés salés et les platiers vaseux préalablement occupés par, respectivement, Spartina maritima et Zostera noltei. Face aux inquiétudes suscitées par cette installation, cette thèse vise à comprendre, par une approche pluridisciplinaire, les mécanismes d’invasion et ses conséquences sur le milieu physique et sur les espèces végétales natives. L’objectif de ce travail est d’étudier l’occupation de niche par S. anglica et ses interactions avec deux espèces intertidales natives : S. maritima et Z. noltei.L’analyse d’images aériennes et satellitales a montré que, 30 ans après l’invasion, dans une zone densément peuplée par la Spartine native, la zone haute des prés salés a peu changé : la Spartine anglaise a occupé des niches vides et n’a pas remplacé la végétation native. Une expérience de transplantation réciproque et de mesures de biomasses confirment ce résultat, en montrant que l’espèce native offre une résistance à la colonisation de l’espèce exotique. L’expansion de la Spartine anglaise vers les replats de marée de l’intérieur du Bassin serait ainsi liée à sa capacité à tolérer les perturbations physiques, à sa forte plasticité de croissance en milieu oxygéné et riche en nutriments et à son comportement auto-facilitateur. Sa forte capacité d’ingénieur d’écosystèmes semble être liée à son système racinaire très développé, qui améliore l’aération des sols fortement anoxiques.Les effets de la colonisation par l’espèce exotique des zones intertidales basses à subtidales sur la Zostère naine sont importants sur le long-terme (dizaines d’années). En tant qu’ingénieur d’écosystèmes, la Spartine exotique favorise l’élévation du sol par sédimentation, entrainant une dessiccation du sédiment, peu favorable à la Zostère. Des mesures physiques au sein de patchs de l’espèce exotique suggèrent que l’élévation du sédiment est toutefois lente, surtout liée à une allocation de biomasse spécifique aux racines ainsi qu’à des rhizomes qui permettent de résister à l’érosion.En termes de gestion et de conservation des prés salés du Bassin d’Arcachon, ces résultats indiquent l’importance de limiter les perturbations physiques et les apports nutritifs qui pourraient rompre la résistance à l’invasion de la Spartine native. Ils supportent aussi l’idée que la Spartine anglaise pourrait être un allié robuste face à l’élévation du niveau de la mer. / Spartina anglica is a hybrid exotic cordgrass that inhabits coastal salt marshes. This species arrived in the Bay of Arcachon in the 1980s and since has importantly colonized the salt marshes and tidal flats formerly only occupied by the native Spartina maritima and Zostera noltei, respectively. This work aims at understanding, with an interdisciplinary perspective, the invasion mechanisms of this exotic cordgrass and the outcoming changes of its introduction in the Bay, both to the physical environment and to the native vegetation. Different approaches were considered in order to assess the niche occupancy by the exotic Spartina and its interactions with the native intertidal species, Spartina maritima and Zostera noltei.The analysis of aerial and satellite images has shown that, in about 30 years after the invasion, within a zone densely populated by the native Spartina, the global high marsh zone did not suffer significant changes with the arrival of the invasive species. Spartina anglica did not replace the existent marsh vegetation, it occupied empty niches along the intertidal area instead. Additionally, experimental works of cross transplantation and biomass measurements have corroborated that the native Spartina maritima offers resistance to the colonization by the exotic Spartina. It was also shown that the invasive occupies the same intertidal niche along the elevation and anoxic gradient than the native. The successful extension of Spartina anglica into the mudflat towards the inner Bay was related to its likely ability to tolerate physical disturbances, its strong growth plasticity in nutrient- and oxygen- rich patches and its self-facilitator behaviour. This latter trait is related to its strong ecosystem-engineering ability due to its prominent root system and consequent ability to ameliorate the oxygenation of highly anoxic soils.The main effect of the exotic Spartina species on the seagrass is related to its stronger ecosystem-engineering ability, favouring bed accretion up to levels that are not favourable to Z. noltei through enhancement of desiccation stress. However, hydrodynamic and altimetry measurements have shown that the process of bed accretion is slow and, due to the cordgrass’ specific preferential biomass allocation to roots, its efficiency is more linked to its resistance to erosion rather than sediment trapping.The results of this study provide relevant information for the definition of appropriate action and conservation strategies of marsh zones in the Bay of Arcachon, and in particular the importance of limiting physical disturbance and nutrient pollution that could disrupt the biotic resistance of the native cord grass. They also suggest a potentially important role of the exotic species in facing increasing Sea Level Rise.

The purpose of this work was to describe the current status of benthic communities on the main stream of Elbe River and Ohře River and their tributaries affected and non-affected by biological invasions - especially by round goby (Neogobius melanostomus) and spiny - cheek crayfish (Faxonius limosus). Sampling for this research took place from April 2018 to August 2018, while morphiologic survey of waterbodies was done in November 2017. Two tributaries of the Elbe River (Milešovský brook and Ploučnice River) and one tributary of the Ohře River (Čepel) were selected for this research. Two 100 m long sections (lower stretch potentially affected by invaders and upper stretch as referential) were monitored at each tributary. At the same time a 100 m long main flow section was monitored near the mouth of the tributaries. The following parameters were monitored: morphology of the stream and basic physical and chemical parameters of water, zoobenthos community, crayfish occurrence, and fish community. The benthic communities of the upper streams were less affected by biological invasions. The biodiversity of the benthic communities in the upper sections was richer compared to the lower sections. The occurrence of the round goby seemed to be factor affecting benthic and fish communities at the sites concerned. It was an eudominant species in the Elbe section in Děčín and becoming dominant in the lower section of Ploučnice River.

Limportance des différentes sources de variation phénotypique que sont ladaptation, la plasticité phénotypique, les effets maternels environnementaux, le niveau de ploïdie et la dérive génétique, a été analysée pour différents traits dhistoire de vie, au sein de laire colonisée par une espèce végétale invasive. A cette fin, plusieurs expériences en jardins communs ont été installées, dont deux en transplantations réciproques. Les populations considérées étaient localisées en Belgique, en France, ainsi que dans laire dindigénat de lespèce. Senecio inaequidens DC. (Asteraceae), lespèce étudiée dans ce travail, est une plante dorigine africaine accidentellement introduite en Europe par le commerce lainier, vers la fin du 19ème siècle. Dans son aire dindigénat, elle présente deux niveaux de ploïdie, diploïde et tétraploïde. Seuls des plants tétraploïdes sont recensés en Europe. Lespèce présente un historique de colonisation particulier, bien documenté, qui en fait un modèle idéal pour les études évolutives. Les traits dhistoire de vie considérés ont été scindés en deux groupes. Les premiers concernaient la germination, la croissance et la reproduction sexuée. Les sources de variation phénotypique dans ces traits ont été principalement analysées en relation avec les variations climatiques dans laire dinvasion, le long de gradients daltitude, ainsi quen relation avec le niveau de ploïdie et laire dorigine (aire dindigénat vs aire dinvasion). Le deuxième groupe de traits considérés concernaient les capacités de dispersion de lespèce. Celles-ci ont été modélisées. La variabilité phénotypique dans ces traits a ensuite été analysée, parmi les populations françaises, en relation avec léloignement depuis le site de première introduction. Les résultats ont montré des différences entre les cytotypes de lespèce, principalement dans les capacités de survie hivernale. Le long des gradients daltitude, les populations de S. inaequidens présentaient des différenciations phénotypiques de type clinal, dans les traits de croissance. Ces différenciations étaient dorigine génétique, même si les effets maternels environnementaux sont apparus comme des sources non-négligeables de variation phénotypique dans les zones à climat rigoureux. Parmi les traits liés à la dispersion, le plume loading était le mieux corrélé aux capacités de dispersion par le vent. Des différenciations clinales ont été détectées dans les traits de dispersion, en jardin commun, mais nont pas été vérifiées en populations naturelles.

La formiga invasora Linepithema humile (Mayr), també coneguda com la formiga argentina, és una espècie present a la península Ibèrica. En aquesta tesi s'ha estudiat com afecta la presència d'aquesta espècie plaga a la comunitat de formigues autòctones y al procés de dispersió de llavors de plantes mediterrànies. L'estudi es va dur a terme en una àrea de sureda i brolla d'estepes i bruc boal situada al nord-est peninsular, prop de la línia de costa mediterrània. Un dels primers y més notables efectes de la invasió a les nostres àrees d'estudi és la dramàtica alteració de la comunitat de formigues, en forma de una reducció de la riquesa específica i de la homogeneïtat d'abundàncies. A més, a les zones envaïdes no hi queda cap espècie de formiga autòctona dispersant de llavors. A causa de la gran abundància d'obreres de la formiga argentina a les zones envaïdes, i del seu elevat ritme d'activitat, aquesta espècie efectua un intens rastreig del sòl, la qual cosa li permet localitzar els recursos en un temps menor que les formigues autòctones de les zones no envaïdes. No obstant, la obertura mandibular de la comunitat de formigues esdevé molt disminuïda a les zones envaïdes a causa de la desaparició de les espècies autòctones, la majoria d'elles de mida més grossa que la formiga argentina, la qual cosa podria limitar la capacitat de manipulació de l'entorn que té la comunitat de formigues a les zones envaïdes, i podria explicar la falta de reemplaçament d'alguns dels rols que duien a terme les espècies de formigues autòctones abans de la invasió.La formiga argentina es mostra atreta per les llavors de les nou espècies vegetals estudiades (dues euforbiàcies: Euphorbia biumbellata i E. characias; dues compostes: Cirsium vulgare i Galactites tomentosa; i cinc papilionàcies: Genista linifolia, G. monspessulana, G. triflora, Sarothamnus arboreus i Ulex parviflorus), arribant a transportar i fins i tot introduir al niu algunes llavors, però amb probabilitats inferiors a les realitzades per les formigues autòctones de les zones no envaïdes. No obstant, el seu comportament davant les nou espècies de llavors és variable, de manera que sembla que el seu efecte sobre la dispersió de llavors podria ser diferent per a cada espècie vegetal. L'alteració del procés de dispersió no sembla alterar l'èxit reproductiu d'una espècie concreta, Euphorbia characias, a les zones envaïdes; ni el seu reclutament, ni la distribució espacial, ni la supervivència de les plàntules són significativament diferents a les zones envaïdes que a les no envaïdes. La desaparició de les espècies de formigues granívores de les zones envaïdes pot afectar la dinàmica de les llavors de plantes no mirmecòcores. Així, les llavors de tres papilionàcies (Calicotome spinosa, Psoralea bituminosa i Spartium junceum) resulten amb un menor nivell de transports (i probablement menor depredació) a les zones envaïdes per la formiga argentina. / The invasive ant Linepithema humile (Mayr), known as the Argentine ant, is present in the Iberian peninsula. This thesis is focused on the effect of the presence of this pest ant over the native ant community and the seed dispersal process of Mediterranean plants. The study was carried out in a cork oak secondary forest situated in the north-eastern Iberian peninsula, near the Mediterranean coast.One of the first and most notorious effects of the invasion in our study areas is the dramatic alteration of the ant community, with a reduction of the ant species richness and the homogeneity of abundances. Moreover, any native seed dispersal ant remains at the invaded zones. Due to the higher abundance of Argentine ant workers in the invaded areas, and their higher "tempo" of activity, this species carries out an intense soil surface searching and can find resources in a lower time than native ants do in the non-invaded zones. However, the mandible gap of the ant community becomes highly reduced in the invaded zones due to the displacement of the native ant species, most of them bigger than the Argentine ant. This could limit the ability of ants in handling the environment in the invaded zones, and could explain the lack of replacement of some tasks carried out by the native ants before the invasion.The Argentine ant is attracted by the seeds of the nine studied plant species (two euforbiaceae: Euphorbia biumbellata and E. characias; two compositae: Cirsium vulgare and Galactites tomentosa; and five papilionaceae: Genista linifolia, G. monspessulana, G. triflora, Sarothamnus arboreus and Ulex parviflorus), transporting and even introducing some seeds to the nest, but with lower probabilities than the native ants in the non-invaded zones. However, its behavior in front of the nine seed species is variable, so the effect over the seed dispersal process could be different for each plant species. The alteration of the seed dispersal process appears not to affect the reproductive success of a single species, Euphorbia characias, in the invaded zones; neither recruitment, spatial distribution, nor survival of seedlings are significantly different between the invaded and the non-invaded zones. The disappearance of the native granivorous ant species from the invaded zones can affect the seed dynamics of non-myrmecochorous species. In this sense, seeds of three papilionaceae (Calicotome spinosa, Psoralea bituminosa and Spartium junceum) result with a lower level of transport (and probably lower predation) in zones invaded by the Argentine ant.

L’évolution des mises en liens en réponse aux changements globaux et à la globalisation contemporaine précipite le risque d’émergence infectieuse. Dans cette recherche, nous dressons une géographie des vulnérabilités territoriales face à l’émergence des risques zoonotiques. Notre cas d’étude est celui des dynamiques d’invasion d’un hôte commensal, le rat noir (Rattus rattus), dans les marges orientales du Sénégal, périphérie rurale ouest-africaine en mutation. Nous défendons l’idée que les sociétés façonnent des systèmes territoriaux inégalement vulnérables à la diffusion spatiale de l’hôte.Nous montrons que les espaces du Sénégal Oriental et leurs mises en liens se transforment sous l’action des multiples acteurs territoriaux. Les dynamiques d’invasion du rat noir reflètent ces évolutions. Pourtant, les facteurs spatiaux de diffusion des lieux, des foyers, et des chemins d’invasion sont inopérants pour expliquer les dynamiques spatio-temporelles de l’hôte. En outre, la distribution spatiale du rongeur apparaît en contradiction avec les modèles classiques de diffusion fondés sur la hiérarchie ou la distance spatiale des lieux. La diffusion de l’hôte s’inscrit dans des systèmes complexes et multiscalaires tissés dans la rencontre des espaces, des lieux, et des liens construits par les sociétés. Nous proposons une grille de lecture où les formes de la diffusion dans l’espace et le temps répondent des degrés de stabilité et d’instabilité de ces systèmes socio-spatiaux, façonnant ainsi des territoires inégalement vulnérables au risque d’émergence infectieuse. / The evolution of spatial relationships in the contemporary context of global changes and globalization promote disease emergence. In this study, we draw a geography of territorial vulnerabilities to the emergence of zoonotic risks. In southeastern Senegal, a changing rural periphery of West Africa, we address the issue of the spread of an invasive species and host of pathogens, the black rat (Rattus rattus). We argue that societies produce territorial systems that are unequally vulnerable to the spatial diffusion of the host.We evidence that the spaces of Southeastern Senegal and the spatial relationships among them are transformed under the action of multiple social actors. The spread of the black rat reflects these changes. Yet, the spatial characteristics of the invaded places (such as connectivity or centrality) as well as the spatial relationships among them are insufficient in understanding the spatial and temporal dynamics of the rodent invasion. Moreover, the spatial distribution of the black rat contradicts conventional models of hierarchical or contagious diffusion. The spatial diffusion of the host responds to spaces, places, and spatial links intimately woven by societies into complex and multiscale systems. We propose to understand the many forms of spatial diffusion as the response to the stability or instability of these socio-spatial systems, which then form territories unevenly vulnerable to the risk of disease emergence.

Pontoscolex corethrurus est le ver de terre le plus répandu dans les zones tropicales et sub-tropicales ; il est par conséquent très étudié en science du sol. Il est présent dans toutes sortes d’habitats, des sols pauvres de prairie aux sols riches de forêt primaire, et ses caractéristiques écologiques sont bien connues. Ses caractéristiques biologiques ont été moins étudiées. Peu de données sur la variation génétique au sein de cette morphoespèce sont disponibles à l’exception de la découverte en 2014 de deux lignées génétiquement différentes dans l’île São Miguel des Açores. De plus, son degré de ploïdie n’est pas connu et sa stratégie de reproduction n’est pas bien décrite. L’un des objectifs de cette thèse était de comprendre les mécanismes et les caractéristiques qui font de P. corethrurus un envahisseur efficace. Notre deuxième objectif était de rechercher des lignées cryptiques dans le monde entier et de décrire leurs relations phylogénétiques. Un troisième objectif était d’identifier quelle lignée était invasive et de caractériser la structure génétique de ses populations dans les aires native et d’introduction. Le dernier objectif était de tester si les différentes espèces du complexe avaient différents degrés de ploïdie, ce qui pourrait expliquer l’isolement reproducteur entre ces espèces. Une synthèse bibliographique de 265 études couvrant tous les aspects des connaissances sur P. corethrurus a montré que la stratégie – r et la plasticité de ce ver sont les caractéristiques clefs qui lui permettent d’envahir avec succès différents habitats. Afin d’étudier la diversité cryptique au sein de P. corethrurus à une échelle mondiale, j’ai examiné 792 spécimens collectés dans 25 pays et îles différents. Ces spécimens ont été analysés à l’aide de deux marqueurs mitochondriaux (COI et ADNr 16S), deux marqueurs nucléaires (internal transcribed spacers 2 et ADNr 28S) et une matrice de données de séquence multilocus obtenue à l’aide de la méthode AHE (Anchored Hybrid Enrichment). De plus, un total de 11 caractères morphologiques, internes comme externes, ont été étudiés dans toutes les lignées caractérisées génétiquement. Quatre espèces cryptiques (L1, L2, L3 et L4) ont été observées au sein du complexe d’espèces P. corethrurus. Elles ont été trouvées en sympatrie dans plusieurs localités et des analyses basées sur des marqueurs AFLP n’ont pas montré d’hybridation entre L1 et L3. La possibilité d’isolement reproducteur lié à des degrés de ploïdie différents a été évaluée à l’aide d’expérimentations de cytogénétique pour lesquelles plusieurs obstacles ont été rencontrés, à différentes étapes. Des résultats n’ont été obtenus que pour L4 (2n = 70). L’une des espèces du complexe, L1, était géographiquement répandue. Cette espèce correspondait aux spécimens topotypiques (échantillons provenant du jardin de Fritz Müller où P. corethrurus a été décrit en premier en 1856). Nous avons ciblé cette espèce invasive dans une étude de génétique des populations et de phylogéographie. En utilisant le gène COI et des marqueurs AFLP, nous avons révélé une faible diversité génétique dans la zone tropicale, probablement due à des évènements de colonisation récents et à une reproduction asexuelle. Cependant, la diversité génétique relativement élevée dans certaines populations, associée à un déséquilibre de liaison relativement faible, suggère aussi des évènements de reproduction sexuelle. A ce jour, c’est le premier travail réalisé à l’échelle mondiale sur la diversité génétique cryptique, la génétique des populations et la phylogéographie d’une espèce de vers de terre pérégrine dans la zone tropicale. J’ai produit la première revue complète des caractéristiques de P. corethrurus. De plus, son statut taxinomique a été clarifié ainsi que sa stratégie de reproduction qui est mixte (parthénogénèse et amphimixie). Ces informations seront utiles pour les expérimentations et les recherches futures sur les espèces du complexe P. corethrurus / Pontoscolex corethrurus is the most widespread earthworm species in the tropical and sub-tropical zones, it is hence one of the most studied earthworm in soil science. Ecological aspects of P. corethrurus, which is known to be present in a wide range of habitats from poor soils of pasture to rich soils of primary forest, were intensively investigated but biological aspects are less addressed. In particular, information on the genetic variation within the morphospecies is scarce except for the finding of two genetically differentiated lineages in São Miguel Island of Azores archipelago in 2014. Moreover, the ploidy degree of the morphospecies is not yet known and its reproduction strategy is not well understood. One of the objectives of this thesis was to understand the mechanisms and characteristics which make P. corethrurus a successful invader. Our second objective was to look for cryptic lineages in the whole world and to describe the phylogenetic relationships between them. A third objective was to identify which lineage was invasive and to characterize its population genetic structure in the native and the introduced ranges. The last objective was to test if the different species of the complex have different ploidy degrees (polyploid complex). This could eventually explain the reproductive isolation among these species. A bibliographic synthesis of 265 studies covering all subjects of knowledge on P. corethrurus showed that the r strategy and plasticity of this earthworm are the key characteristics which make it a successful invader in different habitats. In order to investigate the cryptic diversity within P. corethrurus in a world-wide scale, I examined 792 specimens collected from 25 different countries and islands. These specimens were analyzed using two mitochondrial (COI and 16S rDNA) and two nuclear (internal transcribed spacers 2 and 28S rDNA) markers and a large-scale multilocus sequence data matrix obtained using the Anchored Hybrid Enrichment (AHE) method. In addition, a total of 11 morphological characters, both internal and external, were investigated in all genetically characterized lineages. Four cryptic species (L1, L2, L3 and L4) were found within the P. corethrurus species complex, and four potentially new species within the genus Pontoscolex. The cryptic species were observed in sympatry at several localities, and analyses based on AFLP markers showed no hybridization among L1 and L3. The possibility of reproductive isolation among species of the complex because of different ploidy degrees was investigated by cytogenetic experimentations. Due to different obstacles encountered at different steps of the experimentations, results were just obtained for L4 (2n=70). One of the species belonging to the complex, L1, was particularly widespread per comparison with the others. This species corresponded to topotype specimens (samples from Fritz Müller’s garden where P. corethrurus was first described in 1856). Thus, we focused on this invasive species in a population genetics and phylogeography study. Using COI gene and AFLP markers, we revealed low genetic diversity through the tropical zone, probably due to recent colonization events and asexual reproduction type. Meanwhile, due to weak linkage disequilibrium and relatively high genetic diversity in some populations, sexual reproduction was suggested for L1.To date, this is the first study investigating at a world-wide scale, cryptic species diversity, population genetics and phylogeography of a peregrine earthworm species throughout tropical zone. I produced the first comprehensive review of all ecological and biological aspects of P. corethrurus. Moreover, the taxonomic status of P. corethrurus was clarified as well as its reproduction strategy which is mixed (parthenogenetic and sexual). All these findings represent potentially useful information for future experimentations and researches on species of P. corethrurus complex

Submitted by Socorro Pontes (socorrop@ufersa.edu.br) on 2017-05-18T15:15:57Z No. of bitstreams: 1 RogérioTVF_DISSERT.pdf: 779741 bytes, checksum: 9814a6c7549bf62e7bc2094c8b14cdb0 (MD5) / Made available in DSpace on 2017-05-18T15:15:57Z (GMT). No. of bitstreams: 1 RogérioTVF_DISSERT.pdf: 779741 bytes, checksum: 9814a6c7549bf62e7bc2094c8b14cdb0 (MD5) Previous issue date: 2013-12-19 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Here, we quantified the patterns of change in the similarity of the fish fauna of the Upper Paraná ecoregion, caused by the introduction of non-native species and anthropogenic factors, such as the construction of dams and the elimination of a biogeographic barrier. Additionally, we evaluated the importance of changes in rates of turnover and richness species in homogenization/differentiation dynamics. For the study, we mapped the spatial distribution of fish species through occurrence data georeferenced of Brazilian zoological museums. To evaluate temporal changes in the composition of the fish fauna, the data with the distribution of the species were divided into two periods: historical period composed entirely of native species, and the contemporary period, consisting of historical fauna plus non-native species. Changes in similarity patterns between fish assemblages were quantified using the Jaccard dissimilarity index to the historical and contemporary periods. To evaluate the influence of the non-native richness species, number of dam and distance to the Itaipu Dam on changes of similarity, we performed simple and partial Mantel tests. The results showed that the fish fauna has become more dissimilar over time, due to increases in turnover rates and addition of species. Furthermore, factors related to the heterogeneity of the basins and propagules pressure after removal of a biogeographical barrier has determined the patterns of changes in the similarity of the fish fauna / Nesse estudo foram quantificados os padrões de mudança na similaridade da fauna de peixes da ecoregião do alto Paraná, produzidas pela introdução de espécies não-nativas e de fatores antropogênicos, como a construção de barragens e a eliminação de uma barreira biogeográfica. Adicionalmente, foi avaliada a importância de mudanças nas taxas de turnover e de riqueza nas mudanças de similaridade das assembleias de peixes. Para realizar o estudo, a distribuição espacial de espécies de peixes de dez bacias de drenagem do alto Paraná foi mapeada através de dados de ocorrência geo-espacializados tombados em museus zoológicos de instituições brasileiras. Para avaliar as mudanças temporais na composição da fauna de peixes, os dados com as distribuição das espécies foi divido em dois períodos: período histórico, composto somente por espécies nativas, e período contemporâneo, composto por espécies nativas mais não-nativas. Os padrões de similaridade entre as assembleias de peixes para os períodos histórico e contemporâneo foram quantificados através do índice de dissimilaridade de Jaccard. As mudanças na similaridade entre assembleias foi calculada através da diferença entre as similaridades contemporâneas e históricas. Para avaliar os efeitos da riqueza de espécies não-nativas, número de barragens e área das bacias, e a distância das bacias até a barragem de Itaipu foram utilizados testes de Mantel simples e parciais. Os resultados demostraram que a fauna de peixes tem se tornado mais dissimilar ao longo do tempo, em função de aumentos nas taxas de turnover e de adição de espécies. Além disso, fatores relacionados à heterogeneidade das bacias e da pressão de propágulos após a eliminação de uma barreira biogeográfica tem determinado os padrões de mudanças na similaridade da fauna de peixes / 2017-05-18