Meloidogyne graminicola est un nématode à galle du genre Meloidogyne spp. (RKN) qui est prépondérant dans les rizières d’Asie du Sud-Est et qui provoque des pertes significatives chez le riz. Malgré son impact négatif sur le rendement, les moyens de control et les méthodes d’identification de cette espèce sont encore limités. Dans cette étude, nous avons évalué l'incidence et la prévalence des RKN dans les rizières du Cambodge, du Laos et du Vietnam grâce à des marqueurs moléculaires développés dans cette étude. Nous avons de plus évalué, sur une séquence de deux ans, les effets de l'Agriculture de conservation (CA) sur la présence et la dynamique des nématodes parasites des racines (RPN) du riz, en relations avec le rendement et la qualité du sol, dans un champ d’expérimentation sableux de bas fond au Cambodge. Nous avons parallèlement évalué la susceptibilité à M. graminicola de 13 plantes adventices couramment utilisées en CA, ainsi que celle de trois variétés de riz, et identifié des plantes réservoir poussant dans les rizières Cambodgiennes. Dans une autre partie, nous avons validé des marqueurs intraspécifiques pour M. graminicola et étudié sa diversité génétique en Asie du Sud-Est. Par des approches de génomique comparative nous avons discuté des relations évolutives qu’il y aurait pu potentiellement y avoir entre M. graminicola et les espèces génétiquement proches. / The rice Root-knot nematode (RKN), Meloidogyne graminicola, reduces significantly rice yield in Southeast (SE) Asia and is prevalent in rice fields in this region. Despite its negative impact on yields, suitable methods of controls and current molecular markers used for M. graminicola identification are still limited. In this study, we evaluated the current occurrence of RKN in rice fields of Cambodia, Laos and Vietnam, and identified those RKN species using molecular markers developed in this study. We then evaluated, during two years sequences, the effects of the Conservation agriculture (CA) on the occurrence and dynamics of root-parasitic nematodes (RPN) of rice, in relation with yields and soil nutrients, in a lowland-sandy field in Cambodia. Host response to M. graminicola of 13 selected cover crops commonly used in CA, of three rice cultivars as well as rice weeds as reservoirs for M. graminicola, were evaluated. Furthermore, we validated intraspecific markers for M. graminicola, studied its genetic diversity in SE Asia, and discussed the potential evolutionary relations of Meloidogyne species using comparative genomics approaches.

Os extratos de média polaridade de sete indivíduos de Piper solmsianum coletados em diferentes localidades foram analisados por cromatografia líquida de alta eficiência para se verificar diferenças quantitativas na concentração relativa de apiol, dilapiol, miristicina, grandisina, elemicina, isoelemicina e lignana tetraidrofurânica rel- (7R, 8R, 7\'R, 8\'R)-3,4,3\',4\'-dimetilenodioxi-5,5\'-dimetoxi-7,7\'-epoxilignana. Todos os perfis cromatográficos consistiam de apenas dois, três ou quatro picos majoritários. O(s) composto(s) majoritário(s) era(m) distinto(s) de planta para planta, e em um dos espécimes o pico predominante não era nenhum dos sete metabólitos secundários avaliados. Estudaram-se as variações diárias e anuais em três espécimes de uma população selvagem de P. solmsianum localizada na Reserva da CUASO, em São Paulo. A grandisina apresentou teores máximos no início da noite e teores mínimos no início da manhã. Apiol/dilapiol apresentou variação circadianas evidentes apenas em dois indivíduos, sendo que em um deles o teor máximo ocorreu por volta das oito horas da noite, e no outro, o teor máximo ocorreu por volta das cinco horas da manhã. A variação sazonal mostrou pequena amplitude de oscilação. Em dois espécimes o máximo teor de apiol/dilapiol e grandisina ocorreu no verão. No terceiro espécime não se observou variação periódica anual. / The crude extracts of seven individuals of Piper solmsianum collected in different places were analyzed by high efficiency liquid chromatography (HPLC) in order to determine changes in the relative content of apiol, dillapiol, myristicin, grandisin, elemicin, isoelemicin, and tetrahydrofuran lignan rel-(7R,8R,7R,8R)-3,4,3,4- dimethylenedioxy-5,5-dimethoxy-7,7-epoxylignan. All chromatographic profiles consisted of two, three or four major peaks with significant qualitative and quantitative differences. Major components were different from plant to plant and in one specimen an component different from the seven metabolites observed in most cases. The leaf extracts from three wild specimens of P. solmsianum collected at CUASO Reserve, showed annual and diurnal variations in apiol/dillapiol and grandisin relative concentrations. Three plants presented circadian variation with maximum content of grandisin late afternoon, and minimum content in the dawn. Apiol/dillapiol displayed clear circadian variation in two individuals, but without synchrony between phases. The maximum content was observed and in a second specimen around 8 p.m., and in the another specimen, the maximum content occur was observed at 5 a.m. The seasonal variation showed small amplitude of oscillation and in two individuals the maxima contents of apiol/dillapiol and grandisin were observed in summer

L'objectif de cette thèse a été de caractériser les patrons spatiaux de diversité inter- et intraspécifique au sein des réseaux dendritiques, d'expliciter les processus évolutifs et écologiques qui les sous-tendent, et d'isoler les possibles covariations spatiales et interactions existant entre ces différentes facettes de biodiversité. Pour cela, j'ai tout d'abord développé de nouvelles méthodes statistiques permettant l'analyse, par des modèles causaux, de données sous la forme de matrices de distances, afin de pouvoir analyser plusieurs facettes de biodiversité dans un unique cadre statistique au niveau alpha et bêta. J'ai par la suite étudié de manière intégrative les patrons de diversité interspécifique et intraspécifique génétique d'une part, et intraspécifique génétique et intraspécifique phénotypique d'autre part, au sein du bassin versant Garonne- Dordogne. Enfin, j'ai utilisé un modèle de dynamique éco-évolutive afin d'étudier l'impact de la structure et des gradients environnementaux caractérisant les réseaux dendritiques sur l'adaptation locale au sein de ces réseaux. / The aim of this thesis was to characterized the spatial patterns of inter- and intraspecific diversity within riverine networks, to better understand the ecological and evolutionary processes underlying them and to explore how the different facets of biodiversity interact with one another. First, I developed novel statistical approaches allowing the application of causal modeling to data in the form of pairwise matrices, thus allowing the study within integrative frameworks of several biodiversity facets at the alpha and beta levels. I then studied integratively the patterns of interspecific and intraspecific genetic diversity and of intraspecific genetic and intraspecific phenotypic diversity within the Garonne-Dordogne river basin. Finally, I used an eco-evolutionary metapopulation dynamics model to assess the impacts of the structure and environmental gradients that characterize riverine networks on local adaptation.

Phlebotomine sand flies (Diptera, Psychodidae) are small blood sucking insects which are only proven vectors of neglected tropical disease called leishmaniasis. Sand flies of the genus Phlebotomus act as vectors in the Old World and those of genus Lutzomyia are vectors in the New World. However, not all of them are capable of transmitting the disease. It is therefore crutial to conclusively determinate the species and have up-to-date knowledge of their natural occurence. Routine identification based on morphological characters is challenging due to intraspecific variability of these or their possible damage during the capture and preparation. In adition, correct assessment of distinctive cahracters, especially for females, is difficult and requires certain expertise. Thus, approaches of molecular taxonomy have been recently increasingly used for sand flies species determination. This thesis presents usage of DNA sequencing and MALDI-TOF protein profiling for routine determination of sand flies caught in southeastern Europe and adjacent regions, where we have lack of information of present sand flies species. Another part of this thesis focus on closer examination of relations between selected closely related species within species complexes. Key words: Phlebotomus, molacular identification, DNA...

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Plants are threatened by global change, increasing variability in weather patterns, and associated abiotic stress. Consequently, there is an urgent need to enhance our ability to predict plant community dynamics, shifts in species distributions, and physiological responses to environmental challenges. By building a fundamental understanding of plant stress tolerance, it may be possibly to protect the ecological services, economic industries, and communities that depend on plants. Dehydration tolerance (DhT) is an important mechanism of water stress tolerance with promising translational applications. Here, I take advantage natural variation in DhT to gain a deeper insight into this complex trait. In addition, I address questions related to the causes and consequences of sexual dimorphisms in DhT. Understanding sexual dimorphisms in stress tolerance is critical because these dimorphisms can drive spatial segregation of the sexes, biased sex ratios, and may ultimately reduce sexual reproduction and population persistence. This work takes an integrated approach, addressing DhT on multiple scales from ecology, to physiology, to genomics in the tropical liverwort Marchantia inflexa. Initially, I tested for correlations between DhT and environmental dryness, sex differences in DhT, and genetic vs. plastic contributions to DhT variability. I found that patterns of variation in DhT are associated with environmental variability, including complex sexual dimorphisms, and derive from a combination of plasticity and genetic differences in DhT. Subsequently, I leveraged the variability in DhT to identify candidate DhT enhancing genes. In M. inflexa intraspecific differences in DhT are impacted by baseline variability among plants, as well as unique gene expression responses initiated during drying. In parallel, I assembled a draft genome assembly for M. inflexa, which was employed to investigate questions of sex chromosome evolution and sexual dimorphism in DhT. Finally, the bacteriome of M. inflexa was characterized and found to be extremely diverse and variable. Collectively, this work adds to a growing understanding of DhT and highlights the importance of sampling approaches that seek to comprehensively describe variability in DhT. I detected complex patterns of variability in DhT among populations and the sexes of M. inflexa, which were used to gain insight into the genetic intricacies of DhT.

The study of speciation is key to understanding the origins of biodiversity. Model organisms, with a host of genetic and molecular tools, are crucial to dissecting the genetics of speciation. Crosses between the recently-discovered Caenorhabditis sp. 9 and the well-known C. briggsae produce fertile F1 hybrid females, opening the door to genetic studies of speciation for the first time within the genus. I crossed eight different isogenic strains of C. briggsae reciprocally with six inbred lines of C. sp. 9 to investigate: Haldane’s rule, systematic asymmetries in hybrid viability, and whether genetic variation for hybrid viability segregates within each species. Results of these crosses confirm Haldane’s rule and demonstrate strong asymmetric parent-of-origin effects. Furthermore, I observed genotype-dependent differences in the number of F1 hybrid progeny. This provides evidence for genetic variation for hybrid viability within both species, allowing insights into the genetic forces driving the evolution of incompatibility loci.

The study of speciation is key to understanding the origins of biodiversity. Model organisms, with a host of genetic and molecular tools, are crucial to dissecting the genetics of speciation. Crosses between the recently-discovered Caenorhabditis sp. 9 and the well-known C. briggsae produce fertile F1 hybrid females, opening the door to genetic studies of speciation for the first time within the genus. I crossed eight different isogenic strains of C. briggsae reciprocally with six inbred lines of C. sp. 9 to investigate: Haldane’s rule, systematic asymmetries in hybrid viability, and whether genetic variation for hybrid viability segregates within each species. Results of these crosses confirm Haldane’s rule and demonstrate strong asymmetric parent-of-origin effects. Furthermore, I observed genotype-dependent differences in the number of F1 hybrid progeny. This provides evidence for genetic variation for hybrid viability within both species, allowing insights into the genetic forces driving the evolution of incompatibility loci.

Cannibalism is a seemingly aberrant interaction, appearing counter to the fitness of individuals. Yet cannibalism is not overly uncommon, and naturally occurs among aquatic organisms, including larval amphibians. In temporary wetlands larval amphibians are in a race to complete metamorphosis before their aquatic habitat disappears. When intraspecific competition intensifies, eating conspecifics may represent a beneficial if not necessary strategy. The research presented within this thesis aims to characterize factors that influence cannibalism within populations of larval amphibians. Wood frog tadpoles (Lithobates sylvaticus) were used to test potential benefits of cannibalism as a diet, determine if dietary quality and nutritional stress influence cannibalism, and investigate the roles of competition and chemical cues in influencing cannibalism. Larval long-toed salamanders (Ambystoma macrodactylum), and ringed salamanders (A. annulatum) were used to investigate a functional link between trophic polymorphism and cannibalism in natural populations. Results suggest that perceived increases in competition may stimulate some individuals to become less risk averse, and more aggressive, which may in turn facilitate cannibalistic behaviour. Cannibalism itself provided only conditional benefits to larval wood frogs, rather than the optimal growth that would be expected from an ideal diet. However, this may have been the result of individual variation in response to the diet and/or conspecific cues as opposed to a nutritional deficit. In conditions where tadpoles could perceive increased competition they altered their behaviour and morphology in ways that may improve their foraging success and potentially promote cannibalism. Finally, a functional link appears to exist between head morphology and cannibalism in natural wetlands. However, the appearance of this morphology appears related to conditions that may facilitate increased population densities through rapid pond drying.

Abstract The negative impact of invasive plant species on biodiversity and ecosystem functions, such as productivity and nutrient cycling has been deemed a global epidemic. To address this worldwide concern, information is needed on how the invasion process happens and how to control an existing invasion. The main aim of the research presented in this thesis was to develop a better understanding of the interacting role different mechanisms play in facilitating invasion and then link this understanding to the design of more effective control strategies. This aim is significant because traditional weed control strategies are not working. The estimated cost of controlling weeds in Australia is $1.4 billion per year in agricultural landscapes. Despite this substantial investment, invasive weed species are estimated to continue to cost the agricultural industry $2.2 billion per year in loss of yield. Current control strategies tend to focus on killing or removing an invasive plant species directly with the application of herbicides and/or mechanical removal. These strategies have proven ineffectual because the plant communities that assemble after management often remain dominated by the same invader or another. In this thesis, I use a combination of empirical and modelling techniques to investigate how disturbance regimes and competitive interactions between invasive plants and native plants can be manipulated to improve the efficacy of restoration efforts. To do this, I use the model scenario of the invasion of Eragrostis curvula (African lovegrass), an invasive grass species introduced into Australia in the early 1900s from South Africa. This species has now spread into every Australian state and territory (chapter 2). I specifically focus on two mechanisms: (1) disturbance, i.e. cattle grazing, and (2) competitive interactions. In chapter 3, I examine connections between dominance and competitive differences among African lovegrass and several functionally similar native grass species in a pasture community. To test the displacement hypothesis, I used a glasshouse competition trial to investigate interactions between African lovegrass and two non-persisting native grass species (Themeda australis and Bothriochloa decipiens) with manipulations of resources, neighbour density, and establishment order. To test the partitioning hypothesis, I compared in situ water use patterns among African lovegrass and two coexisting native grass species (Aristida calycina and Aristida personata) based on the assumption that water is the most limiting resource in this system. The key finding of this chapter is that competition can have important, but contingent, impacts on dominance. Competitive differences appear to partially contribute to abundance patterns after establishment, but may be relatively unimportant during the establishment phase where disturbance appears more critical. In chapter 4, I provide evidence that the identification of mechanisms that led to an invasion, while crucial for the development of effective preventative measures and understanding the invasion process, may not be necessary for the design of more effective control strategies. To examine the effects of different control strategies on African lovegrass and the resultant community, I established a large factorial field-trial with a split-plot design. I manipulated grazing, soil nutrient levels and the presence of the invader. The most common control strategy (removing the causal disturbance and killing the invasive grass), based implicitly on traditional equilibrium models, was not an effective option for restoring a desirable native community. Instead, this strategy led to the dominance of a secondary invader. The most effective control strategy was based on alternative stable states models and involved maintaining grazing, and increasing the palatability of the invader with fertilizers. The key finding of this chapter is that novel approaches for control, which consider the dynamics of the invader-dominated system, are needed. In chapter 5, I investigate the benefits of explicitly incorporating actions that manipulate disturbance (natural or imposed) into control efforts. To do this, I first developed a process model that described the dynamics of an invader whose establishment is preferentially favoured by disturbance. I then couched this model in a decision theory framework, a stochastic dynamic program, and applied a case-study of another invasive plant species, Mimosa pigra (a perennial legume shrub and pan-tropical weed). The key finding of this chapter is that strategies should not only focus on existing invader-dominated sites, but should also protect sites occupied by native species from disturbances that facilitate invasion. The research discussed in this thesis makes three key contributions to a better understanding of the invasion process and the design of more effective control strategies: 1) the search for one key mechanism is not sufficient because multiple mechanisms can interact or shift in importance to facilitate different stages of invasion, 2) a novel approach is needed to restore a more desirable native community because the dynamics of the invader-dominated system can differ from the historical native community, and 3) control efforts should be broadened in focus to include protection of the integrity of native communities from disturbances that facilitate invasion.