Au sein de la famille des Cyprinidés (Téleostéens), Parachondrostoma toxostoma (le toxostome) et Chondrostoma nasus (le hotu) sont deux espèces (respectivement endémique et invasive) qui se rencontrent dans le sud de la France, formant deux zones hybrides distinctes : la zone de la Durance (un milieu fortement fragmenté) et la zone de l'Ardèche (un milieu non fragmenté). La présence de ces deux zones hybrides nous a donné l'opportunité de caractériser les parts respectives de la sélection exogène (l'environnement) et endogène (compatibilité génomique) permettant d'expliquer les patterns d'hybridation entre les deux espèces. Les travaux présentés dans le cadre de cette thèse illustrent parfaitement la complexité des phénomènes d'hybridation, chaque situation étant fortement dépendante du contexte d'étude et ce à l'échelle même de la station. Nous avons montré dans certaines stations que l'espèce endémique résiste à l'introgression de son génome par l'espèce invasive, dans d'autres cas nous avons des scénarios plus complexe d'admixture qui évoluent au cours du temps. Le potentiel évolutif engendré par les phénomènes d'hybridation est cependant indéniable et nous préconisons de prendre en compte ces processus d'hybridation dans les programmes de gestions et de conservation de la biodiversité. / In the Cyprinidae family (Teleostei), Parachondrostoma toxostoma (the sofie) and Chondrostoma nasus (the nase) are respectively endemic and invasive species which are found in sympatry in the south of France. They form two distinct hybrid zones: the Durance River (a highly fragmented environment) and the Ardèche basin (an unfragmented area). The existence of these two different zones allow us to characterize the respective contributions of exogenous selection (environmental factors) and endogenous selection (genomic compatibility) to explain hybridization patterns between the two species.This PhD thesis highlights the complexity of hybridization phenomena. Each situation is highly dependent of the study context. We showed the resistance of the genome of the endemic species to introgression by the genome of the invasive species in some stations. In other cases, we demonstrated more complex scenarios of admixture that evolve over time. The evolutionary potential generated by hybridization is undeniable, and we recommend to take the hybridization process into account in management programs and conservation of biodiversity.

Made available in DSpace on 2014-06-11T19:30:58Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-05-06Bitstream added on 2014-06-13T19:40:38Z : No. of bitstreams: 1 vieira_dcm_dr_rcla.pdf: 661675 bytes, checksum: 027c5de7e016fd68cc667e08fc20b57d (MD5) / As espécies invasoras são reconhecidas como um dos mais importantes e difíceis fatores que influenciam a conservação dos ecossistemas nativos. Na restauração de ambientes degradados, estas espécies podem afetar profundamente a trajetória do recobrimento vegetal pelas espécies nativas e, conseqüentemente, a composição do ecossistema. Um fator importante para o sucesso de algumas espécies vegetais invasoras é a plasticidade fenotípica, dandolhes grande capacidade de aclimatação em diversas condições ambientais. O conhecimento dos fatores ambientais e das características da planta que contribuem para o sucesso das espécies invasoras é de grande importância para predizer a habilidade de invasão e para esforços de manejo. Neste contexto, o objetivo principal deste estudo foi conhecer algumas características fisiológicas e ecológicas de Clausena excavata Burm. f., uma espécie de árvore exótica reconhecida como invasora em algumas regiões no mundo, no intuito de compreender o sucesso da espécie como invasora e contribuir com informações relevantes para possíveis tentativas de controle. Primeiramente, foram avaliados os efeitos da luz e da temperatura em sua germinação (condição controlada) e o efeito da luz na emergência de suas plântulas (condição natural, a pleno sol e sob a copa das árvores). As sementes germinaram tanto na presença como na ausência de luz, nas temperaturas de 20 a 35°C, sem diferença entre a porcentagem de sementes germinadas nas diferentes temperaturas. Sementes mantidas a 20°C, em ambas as condições de luz, germinaram mais lentamente em relação às demais temperaturas. Independente da temperatura, na presença de luz as sementes apresentaram uma germinação muito mais sincronizada do que aquelas mantidas no escuro. Tais resultados mostraram que as sementes de C. excavata são fotoblásticas neutra. Em campo, a emergência... / The invasive species are recognized one of more important and difficult factors that prejudice the conservation of native ecosystems. In the restoration of degraded environment, these species can to affect profoundly the trajectory of recovery by native species and, therefore, the ecosystems composition. An important factor to the success of invasive species is their phenotypic plasticity, which gives them a great ability to adjust in several environmental conditions. The knowledge of environmental factors and plant characteristics that contribute to the success of invasive species is very important to predict the invasion capacity and to manage efforts. In this context, the main objective of this study was to know some physiological and ecological characteristics of Clausena excavata Burm. f., a nonnative tree species recognized as invasive somewhere of the world, with intention to understand the success of this species as invasive and to contribute with relevant informations for a possible management. At first, were evaluated the effects of light and temperature on their seeds germination (controlled condition) and the effect of light on seedling emergence (natural condition, at full sun and shade). The seeds germinated in presence and absence of light, from 20 to 35°C, without difference among the germination percentage at different temperatures. Seeds maintained in 20°C, at both light conditions, germinated slowly than others temperatures. Independent of temperature, in light the seeds showed a germination more synchronized than the seeds kept in darkness. Those results showed that C. excavata have neuter photoblasics seeds. On the field, the emergence occurred at both environments, but at full sun all seeds produced a seedling. The seedling emergence occurred with same rate and synchronization index on two tested conditions. Thereafter, the seedlings were observed with purpose... (Complete abstract click electronic access below)

Les rats introduits (Rattus spp.) sont des espèces invasives majeures menaçant la biodiversité sur la plupart des îles de laPlanète. Deux espèces, le rat noir (R. rattus) et le rat du Pacifique (R. exulans) vivent en sympatrie au sein des forêts deNouvelle-Calédonie, où la question de la faisabilité et de l' intérêt de leur contrôle (i.e. limitation locale de leur 'abondance)pour la conservation de la biodiversité native est posée. En raison d'un manque de cadre conceptuel des projets de contrôle,nous avons d'abord réalisé une synthèse et une analyse des opérations de contrôle de rats invasifs dans les milieux naturelsdes îles du monde. Puis, nous avons cherché à caractériser et à comprendre la dynamique des populations de ces deux espècesde rats sympatriques ainsi que leurs interactions avec la biodiversité native en forêt dense humide du massif du Mont Panié.Des opérations de piégeage létal et de capture-marquage-recapture ont montré que les rats noirs étaient plus abondants que lesrats du Pacifique. Les analyses de leur régime alimentaire ont révélé que les deux espèces ont à la fois des proies communeset des proies qui leur sont propres impliquant un renforcement ainsi qu'un élargissement de leurs impacts sur la biodiversiténative. Les rats consomment une grande majorité de fruits et de graines, d'invertébrés et de Squamates mais les oiseaux, quijustifient souvent la mise en place de projets de gestion de rats, ne semblent pas ici être une de leur proie préférentielle. Depotentiels effets positifs des rats sur la dispersion des graines ont également été mis en évidence au travers d'une comparaisondu potentiel germinatif de graines après passage par leur tractus digestif et celui de frugivores natifs. Enfin, nous avons puproposer des stratégies de piégeage létal afin de contrôler efficacement les populations de rats invasifs. Une meilleurecompréhension des impacts des rats en situation de sympatrie ainsi qu' une meilleure connaissance du lien entre densité de ratset intensité des effets sur la biodiversité permettraient d'optimiser les stratégies de contrôle de rats invasifs lorsquel'éradication n'est pas envisageable. / Introduced rats (Rattus spp.) are one of the major invasive species threatening native biodiversity on islands worldwide. Twospecies, the black rat (R. rattus) and the Pacifie rat (R. exulans) are sympatric in New Caledonian rainforests, where questionsasto the feasibility and the utility of their control (i.e. local limitation of their abundance) for the conservation of nativebiodiversity remain unanswered. ln response to the lack of a conceptual framework for control projects, we fi rst conducted areview of invasive rat control operations in island natural areas worldwide. Then we sought to characterize and understand thepopulation dynamics of these two sympa tric rat species and the ir interactions with native biodiversity in the rainforest of MontPanié mountain. Lethaltrapping operations and capture-mark-recapture showed that black rats were more abundant thanPacifie rats. Diet analysis revealed that the two species consume both shared and unshared prey likely resulting in astrengthening and a broadening oftheir impacts on native biodiversity, relative to the impact that each species would haveal one. Rats consume a large quantity of fruits and seeds, invertebrates, and Squamates. However, birds, which often justify theimplementation of rat management projects, do not appear here to be one of the ir preferred prey, either as adults or throughnest predation. A potential positive rat impact on seed dispersal was a Iso highlighted through a comparison of seedgermination after seeds had passed through rat versus native frugivore digestive tracts. Finally, we propose lethal trappingstrategies to efficiently control invasive rat populations. A better understanding ofboth rat impacts in sympatric situations,and the link between rat density and the intensity of their effects on biodiversity would allow optimizing rat control strategieswhen eradication is not feas ible.

O Parque Nacional da Serra do Cipó tem passado por um importante desafio de manejo que é a definição sobre o uso de animais de montaria por parte dos visitantes. Recentemente, o Governo Brasileiro lançou um documento intitulado Diretrizes para visitação em unidades de conservação o qual dita algumas normas para essa atividade de uso público. No entanto, há questões relevantes de incoerências deste com o Sistema Nacional de Unidades de Conservação. A presença dos animais numa unidade de conservação pode causar diversos impactos ambientais, entre eles, a entrada e dispersão de espécies exóticas causando contaminação biológica em área protegida. Os cavalos e muares utilizados pelos visitantes podem ser veículo de entrada dessas espécies exóticas, seja por meio dos pelos, das patas e também das fezes. Esta investigação teve por objetivo investigar se há relação entre o uso de animais de montaria e a contaminação biológica de gramíneas exóticas pelas fezes dos animais no Parque Nacional da Serra do Cipó. Para tanto foram selecionadas duas trilhas do Parque, a do Capão dos Palmitos e a trilha da Farofa, sendo que as mesmas apresentam diferenças relevantes em termos de relevo e de histórico de uso. Com base no trabalho de Campbell e Gibson (2001) definiu-se o método. Em cada uma das trilhas procedeu-se a coleta de fezes eqüinas e de amostras de solo em dois períodos do ano (outono e verão). As amostras foram distribuídas em dois experimentos de germinação, um instalado in situ e outro no Laboratório de Biologia Reprodutiva e Genética de Espécies Arbóreas da ESALQ / USP. Outro experimento, também realizado in situ, verificou a presença de espécies de gramíneas exóticas e de plantas nativas nas áreas de abrangência das duas trilhas. Foram definidos quatro pontos para as amostragens tendo como referência o centro das trilhas, são eles: centro, borda, transição e interior. As análises estatísticas foram realizadas com uso do programa SAS versão 9.3.1. Os resultados mostraram que há maior presença de gramíneas exóticas na trilha da Farofa em relação à trilha do Capão. Na trilha da Farofa houve diferença significativa entre o ponto do centro com os demais. Na trilha do Capão não houve diferença entre os pontos avaliados. As espécies nativas foram encontradas com maior frequência na trilha do Capão. Houve diferença do ponto centro para os demais nas duas trilhas avaliadas. Os resultados obtidos pelas amostras de solos que estavam no experimento controlado em laboratório revelaram que não há diferença na germinação de sementes entre as trilhas. As amostras de fezes, no entanto, mostraram diferença entre as trilhas, sendo que há maior germinação de sementes na trilha da Farofa. Tanto para as amostras de fezes como para as de solo, houve grande diferença para a germinação entre os períodos de outono e de verão. Não houve nenhuma germinação no experimento instalado in situ. / Serra do Cipó National Park has undergone a major management challenge that is the definition of the use of horse riding by the visitors. Recently, the Brazilian Government launched a document entitled Diretrizes para visitação em unidades de conservação (Guidelines for visitation in protected areas) which dictates certain rules for recreation ecology activities. However, there are relevant issues that are incoherent with the Brazilian law for protected areas called the Sistema Nacional de Unidades de Conservação (National System of Conservation Areas). The presence of domestic animals in protected areas can cause several environmental impacts, including the entry of alien species causing biological contamination. The horses used by visitors can be a vehicle of entry of alien species, either through the hair, the legs and also the dung. This research aimed to investigate whether there is a relation between the use of horses and biological contamination of exotic grasses by horses\' dung in the Serra do Cipó National Park. Therefore, we selected two trails of the park which present significant differences in terms of topography and land use history: the Capão dos Palmitos trail and the Farofa trail. The method was defined based on the work of Campbell and Gibson (2001). From each of the tracks were collected equine dung and soil samples in two seasons (autumn and summer). The samples were divided into two experiments, one installed in situ and another at the Laboratory of Reproductive Biology and Genetics of Tree Species of ESALQ / USP. Another experiment, also conducted in situ, verified the presence of exotic grasses and native plants in areas served by the two trails. Four points, which had as reference the center of the trails, were defined for sampling: center, edge, transition and interior. Statistical analysis was performed using SAS software, version 9.3.1. The results showed that there has been an increase in the amount of exotic grasses in the trail of Farofa when compared with the path of Capão. On the trail of Farofa significant difference was found among the center point and the others. On the trail of Capão no difference among the points was assessed. The native species were found more frequently on the trail of the Capão. There was a statistical difference between the center points on both trails. The results obtained from soil samples that were in the controlled experiment in the laboratory revealed that there is no difference in germination between the trails. Dung samples, however, showed differences between the tracks, and there is a greater germination in the trail of Farofa. A significant difference in germination between the periods of autumn and summer was found both in the dung samples and in the soil samples. There was no germination in the experiment installed

Introduced populations of Eichhornia crassipes (Pontederiaceae) possess extremely low levels of genetic diversity due to severe bottleneck events and clonal reproduction. While populations elsewhere have been well studied, North American populations of E. crassipes remain understudied. We used Amplified Fragment Length Polymorphism markers to assess genetic diversity and population structure in North American E. crassipes populations. Patterns of diversity over the past fifty years were analyzed using herbarium specimens. Furthermore, we sampled populations across the Gulf Coast of the United States throughout a year to determine contemporary genetic diversity and assess potential seasonal effects. Genetic diversity was found to be scant in the United States without population structure, agreeing with previous studies from other regions. Genetic diversity has remained consistently low over the past fifty years despite significant changes in selection pressure. However, evidence for and against population structure between seasons was found and the consequences of this are discussed.

La fourmi d'Argentine (Linepithema humile) est une des espèces invasives parmi les plus nuisibles au monde. Dans le cadre des invasions biologiques, les résistances biotiques sont souvent les dernières barrières des écosystèmes. Une hypothèse, jamais testé in natura, de résistance de la part d'une fourmi du genre Tapinoma face à L. humile a été émise. Pour le démontrer, nous avons choisi d'expérimenter en laboratoire et in natura. Nos terrains d'études privilégiés ont été, outres des sites du littoral méditerranéen français, 4 îles situées en face du littoral envahi par la fourmi d'Argentine. Parmi celles-ci, deux contiennent à la fois la fourmi d'Argentine et des espèces du genre Tapinoma. L'identification difficile des espèces du genre Tapinoma étant sujette à une controverse scientifique, nous avons dû différencier de façon certaine cinq d'entre elles, par leurs morphologies et leurs signatures chimiques. En Provence, trois espèces ont été observées : T. erraticum, T. madeirense et T. nigerrimum. Sur l'île de Ratonneau, un suivi sur 2 ans de la vitesse d'invasion de L. humile en milieu naturel, avec ou sans T. nigerrimum, met en évidence une vitesse d'invasion très faible, voire un recul dans la zone à T. nigerrimum. Les colonies de T. nigerrimum de l'île de Ratonneau semblent faire obstacle à la progression de l'invasion. Des études comportementales préliminaires, conduites en laboratoire, entre fragments de nids de T. nigerrimum et L. humile nous avaient permis de confirmer les capacités de T. nigerrimum à résister face à l'invasive. Ainsi, les ouvrières T. nigerrimum défendent mieux leurs territoires, allant jusqu'à accaparer celui des L. humile. / The Argentine ant (Linepithema humile) is one of the world's worst invasive species. We used various analyses to determine its invasion pattern on the Provence coast, confirming the presence of a second supercolony. Chemical and behavioral analyses of worker interactions on the supercolony border identified a peaceful border zone. When biological invasion occurs, biotic resistance is often ecosystems' last defense. Could a dominant ant from Tapinoma genus resist L. humile invasion? To demonstrate this possibility, we conducted both laboratory and in natura experiements. Besides the invaded Mediterranean coast, we selected four nearby islands, two of which were found to contain both L. humile and Tapinoma spp. Identification of Mediterranean Tapinoma being controversial, we used both morphological and chemical analyses to ensure reliable discrimination. On the coast, we found T. erraticum, T. madeirense and T. nigerrimum. In natura, on Ratonneau Island, two-year field monitoring showed a slow rate of Argentine ant invasion and even retreat, faced with T. nigerrimum. T. nigerrimum colonies seem to block L. humile invasion. Laboratory behavioral studies between nests of T. nigerrimum and L. humile confirm T. nigerrimum's ability to stand up to Argentine ants: T. nigerrimum workers protect and defend their territories better, even taking over Argentine ant nests.

Adaptive radiation – the proliferation of species from a single ancestor and diversification into many ecologically different forms – has long been heralded as an important process in the generation of phenotypic diversity. However, the early stages of adaptive radiation are notoriously elusive to observe and study. In this dissertation, I capitalize on communities of introduced non-native Anolis lizards as analogues of early stage adaptive radiations. In Chapter II, I begin by reviewing the concept of “ecological opportunity” – a classic hypothesis put forward as a potential key to understanding when and how adaptive radiation occurs. In Chapter III, I investigate the mechanisms which allow for coexistence and community assembly among ecologically-similar species. To do this I investigate range dynamics and assembly patterns of introduced anoles on the oceanic island of Bermuda. I discover that interspecific partitioning of the structural environment facilitates species coexistence, however the order of species assembly was an important predictor of final community composition. In Chapter IV, I then investigate how interspecific interactions between coexisting species may drive phenotypic divergence. This is the process of character displacement, which has been widely hypothesized to be an important mechanism driving phenotypic divergence in adaptive radiations. To do this I investigate sympatric and allopatric populations of introduced Cuban brown anoles (Anolis sagrei) and Puerto Rican crested anoles (A. cristatellus) in Miami FL, USA. I identify morphological shifts in sympatry, driven by divergence in habitat use and decreases in abundance. This study provides evidence of how selection on both ecologically and sexually-important traits can both drive phenotypic divergence during character displacement. Finally, in Chapter V, after taking advantage of non-native species as model eco-evolutionary systems in previous chapters, I investigate the potentially harmful effects that their presence may have on vulnerable native biodiversity. To do this I investigate the conservation risk posed by newly-discovered populations of A. sagrei on Bermuda to Critically Endangered endemic Bermuda skinks (Plestiodon longirostris). Through a detailed analysis of habitat use, diet, population size, and morphology of A. sagrei on Bermuda, we conclude it likely poses a high conservation threat to P. longirostris through interspecific competition.

Invasive species represent a major concern; they can result in serious ecological and economic losses and are recognised as one of the most serious threats to global species diversity. Plant invasions are of particular concern in New Zealand, which has high proportions of both naturalised and endemic plant species. In this thesis I focussed on the invasive plant Hieracium lepidulum, an exotic weed introduced from Europe to New Zealand prior to 1941. It is invasive in a variety of habitats in the South Island, where it has steadily increased in distribution and abundance over the last 50 years, and is thought to have detrimental impacts on native plant communities. I investigated factors influencing its invasion success and tested for impacts on native plant communities, making extensive use of existing plots into which H. lepidulum was experimentally introduced in 2003. I examined how community richness, turnover, resource availability and propagule pressure of the invader interacted to determine the invasion success of H. lepidulum. Results differed markedly above and below treeline. Above treeline, plots with higher richness and turnover were more invaded; below treeline, plots with higher available light were more invaded. In both habitats, these findings were modified by the influence of propagule pressure; at low propagule pressure, site characteristics were non-significant in explaining invasion success, while at higher propagule pressure these effects became significant. To test for impacts resulting in altered community composition and structure, I looked for changes in community richness, diversity and evenness subsequent to H. lepidulum introduction. As impacts may be more apparent at fine spatial scales, I made measurements at a 5 x 5 cm cell scale in addition to the established 30 x 30 cm plot scale. Plot species richness increased from 2003 to 2009 and a component of this increase was associated with H. lepidulum density. Other relationships between the plant community and H. lepidulum were generally non-significant. Results showed that H. lepidulum has had no negative effects on community richness, evenness or diversity. Despite being able to opportunistically colonise grassland sites with high turnover, and forest sites subject to canopy disturbance, dependant on propagule pressure, it appears H. lepidulum has not impacted community composition or structure.

Human-mediated introductions of non-indigenous species now threaten to homogenize the biota of the Globe, causing huge economic and ecological damage. This thesis studies the ecological role of 3 invasive planktonic crustaceans, the omnivorous copepod Acartia tonsa (western Atlantic and Indo-Pacific) and the predatory cladocerans, Cercopagis pengoi (Ponto-Caspian) and Bythotrephes longimanus (Eurasian). B. longimanus invaded the North American Great Lakes in 1982, C. pengoi the Baltic in 1992 and the Great Lakes in 1999, while A. tonsa has an extensive invasion history that includes the Baltic. We review current knowledge on feeding biology of the predatory cladocerans. A study of stable C and N isotope ratios indicated mesozooplankton as the main food source of C. pengoi in the northern Baltic Sea proper, with young C. pengoi also eating microzooplankton, such as rotifers. Young-of-the-year herring did eat C. pengoi and herring trophic position shifted from 2.6 before the invasion to 3.4 after, indicating that C. pengoi had been “sandwiched” into the modified food web between mesozooplankton and fish. Salinity tolerance experiments on Acartia tonsa and co-occurring Acartia clausi showed the formers euryhaline character and high grazing potential. Energy partitioning between ingestion, production and respiration was rather constant over the tested salinity range of 2 to 33, with small differences in gross growth efficiency and cost of growth, but maximum ingestion at 10-20. Egg hatching in A. tonsa was only reduced at the lowest salinity. Extreme changes in salinity were needed to cause significant mortality of A. tonsa in the field, but its feeding activity could be severely reduced by salinity changes likely to occur in estuaries. A study of a hypertrophic estuary showed that A. tonsa can sustain a population despite very high mortality rates, caused by predation, high pH and low oxygen, helping explain the success of A. tonsa as an invader of estuaries.

Aquatic sediments are, by surface, the largest habitat on Earth. A wide diversity of organisms inhabit these sediments and by their actions they have a large influence on and also mediate many ecosystem processes. Several of these processes, such as decomposition and remineralisation of organic matter are important on a global scale and are essential to sustain life on Earth. The main aim of this thesis was to use an experimental ecosystem ecology approach in order to study some of these ecosystem processes in marine sediments and how they are linked to biodiversity. Paper I and II found that an increased species richness of sediment deposit feeders increases the processing of organic matter from phytoplankton settled on the sea-floor, and that species-rich communities have a more efficient resource utilization of deposited organic matter. The results in paper IV and V also suggest that there is a link between microbial diversity in sediments and the degradation of organic contaminants. Paper V also shows that antibiotic pollution is a potential threat to natural microbial diversity and microbially mediated ecosystem services. The introduction of invasive species to ecosystems is another major threat to biodiversity and was studied in Paper II and III, by investigating the ecology of Marenzelleria arctia, a polychaete worm recently introduced in the Baltic Sea. Paper II suggests that M. arctia mainly utilize food resources not used by native deposit feeders, thus potentially increasing the benthic production in the Baltic Sea by increasing resource use efficiency. Paper III, however, show that M. arctia is protected from predation by the native benthic invertebrate predators, due to its ability to burrow deep in the sediment, suggesting that predation on M. arctia by higher trophic levels is restricted, thereby limiting trophic transfer. In conclusion, this thesis gives some examples of the importance of marine biodiversity for the generation of a few key ecosystem processes, such as organic matter processing and the degradation of harmful contaminants. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript. Paper 4: In press.