As formigas cortadeiras (Hymenoptera-Formicidae) estão distribuídas desde o sul dos Estados Unidos até a Argentina. São herbívoros comuns de florestas que coletam material vegetal para cultivar um fungo mutualista específico. São conhecidas pelo seu papel ecológico na aeração do solo, na infiltração da água e na ciclagem de nutrientes. Atividades humanas, como o desmatamento e a agricultura, afetam o ambiente, alterando também o comportamento das saúvas, que acabam atacando os espécimes cultivados. Devido aos prejuízos causados à agricultura, novos inseticidas específicos são necessários. Muitos trabalhos têm sido desenvolvidos usando metabólitos secundários para essa finalidade. Este trabalho tem como objetivo avaliar o efeito da cafeína na mortalidade de Atta sexdens rubropilosa (Forel, 1908) e no crescimento in vitro de seu fungo mutualístico Leucoagaricus gongylophorus (Möller) Singer (Leucocoprineae: Agaricaceae), obtidos de sauveiros mantidos em laboratório. Foram utilizadas quatro concentrações de cafeína, 0,01%, 0,05%, 0,10% e 0,50%. Mortalidade das formigas foi avaliada pelo ensaio de ingestão, acrescentando a cafeína a dietas artificiais sólidas. A cafeína foi incorporada ao meio de cultura para medir a sua influência no crescimento in vitro. Independente das concentrações de cafeína, esse metabólito parece atuar como repelente para a saúvas. A respeito do fungo, quanto maior a concentração de cafeína, menor o crescimento in vitro. Inibição do crescimento foi observada em 0,10% e 0,50% e morte do fungo foi observada em algumas amostras Em conclusão, os resultados sugerem que a cafeína pode ser usada como fungicida, sendo adicionada a iscas que serão coletadas pelas formigas e carregada aos ninhos, causando a redução do fungo e/ou a morte e consequentemente, a morte das formigas. / The leaf-cutting ants (Hymenoptera-Formicidae) are found from south of United States to Argentina. They are common florest herbivorous which collect plant material to feed a specific mutualist fungus. These insects are known by their ecological role at soil aeration, water permeation and nutrient cycling. Human activities, like deforestation and agriculture, affect the environment, affecting the behavior of leaf-cutting ants, which start to attack the crops. Due to crops lost, new specific pesticides are needed. Several researches have been developed using secondary metabolites for this purpose. The present work aimed to evaluate the effect of caffeine at Atta sexdens rubropilosa (Forel, 1908) mortality, and at in vitro growth of the mutualist fungus Leucoagaricus gongylophorus (Möller) Singer (Leucocoprineae: Agaricaceae), collected from laboratory nests. Four caffeine concentrations were tested: 0.01%, 0.05%, 0.10% and 0.50%. Ant\'s mortality was evaluated by ingestion assay, adding caffeine to artificial diets. Caffeine was added to culture medium, to measure its influence on in vitro fungus growth. Despite caffeine concentrations, this compound seems to act as repellent to ants. Concerning to the fungus, the higher the caffeine concentration, the lower the in vitro fungus growth. Growth inhibition was observed at both 0.10% and 0.50% concentrations and death of fungus was observed in some samples. In conclusion, the results suggest that caffeine could be used as fungicide, being added to baits which could be collected by ants and carried to the nests, causing fungus reduction and/or death and consequently, the death of the nests.

As formigas cortadeiras (Hymenoptera-Formicidae) estão distribuídas desde o sul dos Estados Unidos até a Argentina. São herbívoros comuns de florestas que coletam material vegetal para cultivar um fungo mutualista específico. São conhecidas pelo seu papel ecológico na aeração do solo, na infiltração da água e na ciclagem de nutrientes. Atividades humanas, como o desmatamento e a agricultura, afetam o ambiente, alterando também o comportamento das saúvas, que acabam atacando os espécimes cultivados. Devido aos prejuízos causados à agricultura, novos inseticidas específicos são necessários. Muitos trabalhos têm sido desenvolvidos usando metabólitos secundários para essa finalidade. Este trabalho tem como objetivo avaliar o efeito da cafeína na mortalidade de Atta sexdens rubropilosa (Forel, 1908) e no crescimento in vitro de seu fungo mutualístico Leucoagaricus gongylophorus (Möller) Singer (Leucocoprineae: Agaricaceae), obtidos de sauveiros mantidos em laboratório. Foram utilizadas quatro concentrações de cafeína, 0,01%, 0,05%, 0,10% e 0,50%. Mortalidade das formigas foi avaliada pelo ensaio de ingestão, acrescentando a cafeína a dietas artificiais sólidas. A cafeína foi incorporada ao meio de cultura para medir a sua influência no crescimento in vitro. Independente das concentrações de cafeína, esse metabólito parece atuar como repelente para a saúvas. A respeito do fungo, quanto maior a concentração de cafeína, menor o crescimento in vitro. Inibição do crescimento foi observada em 0,10% e 0,50% e morte do fungo foi observada em algumas amostras Em conclusão, os resultados sugerem que a cafeína pode ser usada como fungicida, sendo adicionada a iscas que serão coletadas pelas formigas e carregada aos ninhos, causando a redução do fungo e/ou a morte e consequentemente, a morte das formigas. / The leaf-cutting ants (Hymenoptera-Formicidae) are found from south of United States to Argentina. They are common florest herbivorous which collect plant material to feed a specific mutualist fungus. These insects are known by their ecological role at soil aeration, water permeation and nutrient cycling. Human activities, like deforestation and agriculture, affect the environment, affecting the behavior of leaf-cutting ants, which start to attack the crops. Due to crops lost, new specific pesticides are needed. Several researches have been developed using secondary metabolites for this purpose. The present work aimed to evaluate the effect of caffeine at Atta sexdens rubropilosa (Forel, 1908) mortality, and at in vitro growth of the mutualist fungus Leucoagaricus gongylophorus (Möller) Singer (Leucocoprineae: Agaricaceae), collected from laboratory nests. Four caffeine concentrations were tested: 0.01%, 0.05%, 0.10% and 0.50%. Ant\'s mortality was evaluated by ingestion assay, adding caffeine to artificial diets. Caffeine was added to culture medium, to measure its influence on in vitro fungus growth. Despite caffeine concentrations, this compound seems to act as repellent to ants. Concerning to the fungus, the higher the caffeine concentration, the lower the in vitro fungus growth. Growth inhibition was observed at both 0.10% and 0.50% concentrations and death of fungus was observed in some samples. In conclusion, the results suggest that caffeine could be used as fungicide, being added to baits which could be collected by ants and carried to the nests, causing fungus reduction and/or death and consequently, the death of the nests.

No description available.

Much research debates whether properties of ecological networks such as nestedness and connectance stabilise biological communities while ignoring key behavioural aspects of organisms within these networks. Here, we computationally assess how adaptive foraging (AF) behaviour interacts with network architecture to determine the stability of plant-pollinator networks. We find that AF reverses negative effects of nestedness and positive effects of connectance on the stability of the networks by partitioning the niches among species within guilds. This behaviour enables generalist pollinators to preferentially forage on the most specialised of their plant partners which increases the pollination services to specialist plants and cedes the resources of generalist plants to specialist pollinators. We corroborate these behavioural preferences with intensive field observations of bee foraging. Our results show that incorporating key organismal behaviours with well-known biological mechanisms such as consumer-resource interactions into the analysis of ecological networks may greatly improve our understanding of complex ecosystems.

Insetos como formigas cortadeiras, cupins e alguns besouros têm sido descritos como agricultores de fungos mutualistas. No entanto, apenas recentemente esse fenômeno foi descrito em abelhas. O objetivo desse trabalho foi estudar os micro-­organismos associados à abelha sem ferrão Scaptotrigona depilis, a primeira abelha agricultora descrita. Foram isolados 149 micro-­organismos a partir de diferentes materiais coletados da colônia, e destes, 28% apresentaram atividade antimicrobiana frente a patógenos humanos. Os micro-­organismos Bacillus sp. SDLI1, Candida sp. SDCP2, Zygosaccharomyces sp. SDBC30G1 e Monascus ruber SDCP1, isolados do favo de cria de S. depilis, foram selecionados para estudo químico e biológico. Foi demonstrado que o fungo-­alimento de S. depilis é Zygosaccharomyces sp., que produz grande quantidade de adipossomos. Os lipídeos e esteroides estocados nessas organelas citoplasmáticas podem ajudar na nutrição larval, uma vez que Zygosaccharomyces sp. é requerido para o desenvolvimento das larvas de S. depilis. Em culturas in vitro de ovos dessa abelha, verificou-­se que ergosterol depempenha papel semelhante ao de Zygosaccharomyces sp. para a metamorfose de S. depilis, indicando que esse mutualista serve como fonte de esteroides para as larvas. Verificou-­se que compostos voláteis produzidos por Candida sp. SDCP2 estimulam o crescimento de Zygosaccharomyces sp. SDBC30G1. Análises revelaram que os compostos voláteis majoritários produzidos por Candida sp. SDCP2 foram etanol (C1) e álcool isoamílico (C2), e essas substâncias também foram encontradas nas células de cria dessa abelha. Já o fungo M. ruber SDCP1 produz lovastatina (M6), um produto natural reconhecido pela inibição da enzima HMG-­CoA redutase, essencial para biossíntese de esteroides, e M6 pode modular o desenvolvimento de Zygosaccharomyces sp. SDBC30G1. Candida sp. SDCP2 estimula a produção de monascinol (M2) e monascina (M3) pelo fungo M. ruber SDCP1 em co-­cultura. Monascina (M3) é ativa frente Candida sp. SDCP2, podendo controlar o crescimento dessa levedura, sendo a produção de M3 aumentada em 57 vezes após sete dias de cocultivo. A investigação química de Bacillus sp. SDLI1 revelou que essa bactéria produz sete surfactinas (B1-­B7) e bacillomicina D (B8), que apresentam atividade antifúngica. O cromossomo circular de Bacillus sp. SDLI1 possui oito clursters biossintéticos para a produção de diferentes classes de antimicrobianos. Bacillus sp. SDLI1 também produz o fago SDLI1-­1, ativo contra Paenibacillus larvae, patógeno causador da cria pútrida americana em Apis mellifera. Cultivos de larvas in vitro revelaram que S. depilis apresenta resistência contra os entomopatógenos Beauveria bassiana e Metarhizium anisopliae, sendo que Bacillus sp. SDLI1 pode desempenhar um papel protetivo para as larvas de S. depilis contra o patógeno P. larvae. Os resultados sugerem que o ambiente encontrado nas colônias de S. depilis favorece o desenvolvimento de uma microbiota especializada. Esses micro-­ organismos interagem e beneficiam a abelha hospedeira, estabelecendo relações de simbiose que devem ser preservadas para a sobrevivência desse polinizador / Some ants, termites and beetles have established mutualistic relationship with fungi that they culture for food. However, just recently a fungus agricultural behavior has been described for bees. The main goal of this study was to investigate the microbiota associated with the stingless bee Scaptotrigona depilis, the first fungus-­ farming bee described. Different materials from S. depilis colony were used to isolate 149 microbial strains, and among these microorganisms, 28% showed antimicrobial activity against human pathogens. The microorganisms Bacillus sp. SDLI1, Candida sp. SDCP2, Zygosaccharomyces sp. SDBC30G1 and Monascus ruber SDCP1, isolated from brood cells of S. depilis, were selected for further studies. Using different approaches, it was confirmed that Zygosaccharomyces sp. SDBC30G1 is the fungus required for S. depilis larval development. This fungus accumulates cytoplasmic lipid droplets that can be a source of sterols and lipids to the larvae. Using in vitro eggs culturing, it was verified that ergosterol, the major sterol produced by Zygosaccharomyces sp. SDBC30G1, can stimulates larval metamorphosis, confirming this yeast as an important sterol source. Co-­cultures provided information about Candida sp. SDCP2 volatile organic compounds (VOCs) production, which stimulates Zygosaccharomyces sp. SDBC30G1 growth. The majoritarian VOCs produced by Candida sp. SDCP2 were ethanol (C1) and isoamyl alcohol (C2), which were also detected in S. depilis brood cells. The fungus M. ruber SDCP1 produces lovastatin (M6), an inhibitor of HMG-­CoA reductase, which can modulate Zygosaccharomyces sp. SDBC30G1 pellicle formation and lipids accumulation. Candida sp. SDCP2 stimulates the production of monascinol (M2) and monascin (M3) by M. ruber SDCP1 in co-­culture. Monascin (M3) is active against Candida sp. SDCP2 and can control the growth of this yeast, once M3 biosynthesis increased ~ 57 folds after seven days of co-­culturing. Bacillus sp. SDLI1 produces seven surfactins (B1-­B7) and bacillomycin D (B8) that presented antifungal activity against pathogenic fungi. This bacterium had its whole-­genome sequenced and the circular chromosome harbors biosynthetic gene clusters to produce eight classes of antimicrobial compounds. The phage SDLI1-­1, which presented activity against Paenibacillus larvae, a pathogen causative of American Foulbrood Disease, was also produced by Bacillus sp. SDLI1. S. depilis larvae were resistant against Beauveria bassiana and Metarhizium anisopliae infections, and Bacillus sp. SDLI1 was capable to increase larval survival during in vitro culturing with P. larvae. The results suggest that the environmental conditions found in S. depilis colonies favor the development of a specialized microbiota. These microorganisms interact and produce beneficial factors to its host. These stablished symbiotic relationships contribute with the homeostasis inside the colony and they must be preserved to safeguard S. depilis survival

Hydrolytic enzymes degrade macromolecules into smaller components. These enzymes are important in fungal nutrition and have been implicated in the pathogenicity and virulence of pathogenic fungi towards their hosts. However, it is unknown if hydrolytic enzymes play important roles in mutualistic symbioses. In this study, the function of two different classes of hydrolytic enzymes was examined in the mutualistic symbiosis between the fungal endophyte Epichloë festucae and perennial ryegrass (Lolium perenne cv. Nui). Nine members of a gene family encoding subtilisin-like proteases were identified in E. festucae. The prt2, prt3 and prt5 genes encode putative extracellular proteins belonging to the proteinase K subfamily 1, and prt1 and prt6 encode putative extracellular proteins belonging proteinase K subfamily 2. The prt7 and prt8 genes encoded pyrolysin-like enzymes from subfamilies 1 and 2. The prt4 gene encodes a putative vacuolar protease, while the kex2 gene encodes a putative proprotein convertase. Expression analysis showed that the prt1, prt3, prt5, prt4 and kex2 genes, but not the prt2 gene, were expressed in culture. The prt1 and prt3 genes appeared to be up-regulated in planta compared to culture. The function of prt1 and prt2 in the symbiotum between E. festucae and perennial ryegrass was characterised by expressing these genes under the control of the Aspergillus nidulans gpdA or the E. festucae F11 ltmM promoters. No major differences in hyphal or plant morphology were observed between symbioses containing wild type E. festucae or endophyte strains containing the prt1 or prt2 transgenes. The gcnl gene, which encodes a β-1,6-glucanase, was identified immediately downstream of the prt2 gene. The function of the gcnl gene was characterised by gene replacement and testing the phenotype during growth in culture and in planta. E. festucae ∆gcnl strains grew normally on glucose-containing media. On media containing the β-1,6-glucan pustulan, ∆gcnl strains did not form aerial hyphae or hydrolyse pustulan, which the wild type strain did. This phenotype was partially complemented by growth of the ∆gcnl mutant in close proximity to wild type strains, and fully complemented by insertion of the gcnl gene. This suggests that the gcnl gene encodes the major β-1,6-glucanase activity of E. festucae.

Lors de cette thèse, nous avons présenté trois principaux types d'analyses du métabolisme, dont la plupart impliquaient la symbiose : dialogue métabolique entre un trypanosomatide et son symbiote, analyses comparatives de réseaux métaboliques et exploration de données métabolomiques. Tous ont été essentiellement basés sur des données de génomique où les capacités métaboliques ont été prédites à partir des gènes annotés de l'organisme cible, et ont été affinées avec d'autres types de données en fonction de l'objectif et de la portée de chaque analyse. Le dialogue métabolique entre un trypanosomatide et son symbiote a été explorée avec des objectifs fonctionnels et évolutifs qui comprenaient une analyse des voies de synthèse des acides aminés essentiels et des vitamines telles que ces voies sont classiquement définies, une exploration de réseaux complets métaboliques et une recherche de potentiels transferts horizontaux de gènes des bactéries vers les trypanosomatides. Les analyses comparatives effectuées ont mis l'accent sur les capacités métaboliques communes de bactéries appartenant à différents groupes de vie, et nous avons proposé une méthode pour établir automatiquement les activités métaboliques communes ou spécifiques à chaque groupe. Nous avons appliqué notre méthode d'énumération d'histoires métaboliques à la réponse de la levure à une exposition au cadmium comme une validation de cette approche sur une réaction au stress bien étudiée. Nous avons montré que la méthode a bien capté la connaissance que nous avons de cette réponse en plus de permettre de nouvelles interprétations des données métabolomiques mappées sur le réseau métabolique complet de la levure / In this thesis, we presented three main types of analyses of metabolism, most of which involved symbiosis: metabolic dialogue between a trypanosomatid and its symbiont, comparative analyses of metabolic networks and exploration of metabolomics data. All of them were essentially based on genomics data where metabolic capabilities were predicted from the annotated genes of the target organism, and were further refined with other types of data depending on the aim and scope of each investigation. The metabolic dialogue between a trypanosomatid and its symbiont was explored with functional and evolutionary goals which included analysing the classically defined pathways for the synthesis of essential amino acids and vitamins, exploring the genome-scale metabolic networks and searching for potential horizontal gene transfers from bacteria to the trypanosomatids. The comparative analyses performed focused on the common metabolic capabilities of different lifestyle groups of bacteria and we proposed a method to automatically establish the common and the group-specific activities. The application of our method on metabolic stories enumeration to the yeast response to cadmium exposure was a validation of this approach on a well-studied biological response to stress. We showed that the method captured well the underlying knowledge as it extracted stories allowing for further interpretations of the metabolomics data mapped into the genome-scale metabolic model of yeast

The fig–fig wasp interaction is a classic example of obligate mutualism and coevolution. It is also a nursery pollination mutualism and supports a diversity of exploiter/parasite/non-pollinating fig wasp species. Mutualists and exploiters comprise the fig wasp community. All the wasp community members are obligately dependent on the fig syconium (a globular closed structure comprising of hundreds to thousands of uniovulate florets) for completing their life cycle. The fig florets can be sessile (without a stalk) or pedicellate (stalked) and can support a community comprising 3–30 wasp species. Fig wasps can access the floral resources for oviposition directly by entering into the syconium (internal oviposition) or by penetration of the syconium surface (external oviposition). Most studies on the fig–fig wasp interaction have investigated the stability of the interaction, pollination biology, pollen dispersal, co-evolution or the effect of exploiters on this mutualism. However, studies dealing with community ecology and species coexistence mechanisms in these communities are rare. Factors contributing to coexistence of mutualists and exploiters in a fig wasp community were studied using a reasonably speciose fig wasp community associated with Ficus racemosa in south India. The wasp community of Ficus racemosa comprises a single species of pollinator and six species of exploiters; together they represent three genera of fig wasp species. The community members show differences in their feeding habit; they could be 1) gallers (feed on floral tissue after pollination and/or after inducing abnormal tissue development of the floret that is also called the gall), 2) inquilines (feed on gall tissue but cannot induce galling; survive by feeding on gall tissue and starving the host larva to death), or 3) parasitoids (lay eggs in or on developing offspring of a galler or inquiline species; develop by feeding on host tissue). Resource partitioning across temporal and spatial axes on this fig wasp community have been quantified. Ovipositor traits of each community member were also investigated since variation in ovipositor traits might facilitate resource partitioning. Finally, the role of life-history traits in species coexistence in this community was also explored. Temporal resource partitioning among members of the fig wasp community was studied (1) across the resource phenology, i.e. over the development phases of the fig syconium, and (2) on a diel scale. The seven members of the wasp community were found to partition their oviposition periods across fig syconium development phenology; some species used very young syconia (soft and smaller in size) for oviposition whereas others used mature (hard and bigger in size) syconia for oviposition. The first species to colonise the syconia were gallers and these were followed by parasitoids in a definite oviposition sequence. Pollinators arrived concurrently with an exploiter galler species and had the shortest oviposition window in terms of days. Although fig wasps are known to be largely diurnal, night oviposition in several fig wasp species was documented for the first time. Wasp species showed a peak in their activity period across the diel cycle and phenology. This is probably the first study to simultaneously investigate temporal partitioning across the syconium phenology as well as the diel scale in a fig wasp community. Partitioning of syconium space was investigated by quantifying the quality (type of floret—sessile or pedicellate) of floral resources. The number of individuals of each species developing in a syconium was quantified along with host accessibility during oviposition by each wasp species. The association between community members developing within a syconium was also tested. The differential occupancy of florets by each species based on their distance from the base of the syconium was evaluated. For the first time the relative distribution of males and females of the entire fig wasp community was quantified. The wasp community members used similar types of florets for oviposition. Seeds were found mostly in sessile florets and wasps were present in large numbers in pedicellate florets. Except for one wasp species, all others occurred uniformly within the syconium with respect to the distance from the base of the syconium. Species distribution models revealed higher prediction ability for the location of mutualists (seed and pollinator) within the syconium compared to exploiters. Within a syconium, all species pairs exhibited positive associations indicating either an absence of or low competitive exclusion. Some florets were modified by their gall occupants such that they were longer in length indicating the possibility of creation of an enemy-free zone by the gall occupant. Yet, most florets were accessible to ovipositing wasps based on ovipositor lengths and flexibility. The probability of finding a male decreased with increase in floret length when all wasp species were grouped together; however, this trend did not hold true when males and females of species were tested individually. Based on these results, the fig wasps of F. racemosa could be grouped into—(1) Early-arriving galler species which used immature florets, inducing large galls that protruded into the cavity, and with fewer individuals per syconium, (2) Galler species arriving concurrently with the pollinator, inducing galls that were morphologically indistinguishable from those of the pollinator, and with many individuals developing per fig syconium, and (3) Parasitoids and/or inquilines of the galler species, with variable abundance per syconium. Thus, these results show that the wasp species do not clearly partition floral resources between syconia and within syconium but they can modify their oviposition sites and also differ in the proportion of florets within a syconium used for oviposition. Oviposition sites of the fig wasps can be reached only by using their ovipositor. The resources for oviposition are hidden and hence might require tools for resource location and utilisation. The frequency and diversity of sensilla on the ovipositor, as well as ovipositor structure (morphology and sclerotisation of the tip) was documented for the entire wasp community. The internally-ovipositing pollinator had the simplest ovipositor, negligible sclerotisation and only one type of sensillum on its ovipositor; the externally ovipositing exploiter species had teeth on their ovipositors, sclerotisation and various types of ovipositor sensilla. Ovipositor sclerotisation and lateness of arrival for oviposition in syconium development were positively correlated. Ovipositor teeth height increased from gallers to parasitoids. Presence of different types of sensilla was noted which included mechano- and chemosensilla, as well as combined mechano-chemosensilla. Chemosensilla were most concentrated at ovipositor tips while mechanoreceptors were more widely distributed. Ovipositor traits of one putative parasitoid/inquiline species differed from those of its syntopic galler congeners and clustered with those of parasitoids within a different wasp subfamily. Thus ovipositor tools show lability based on adaptive necessity, and are not constrained by phylogeny. Life-history traits such as fecundity, pre-adult and adult lifespan were studied for each wasp member of the community. Trade-offs in life-history traits were also investigated. Interspecific variation in life-history traits was observed. Gallers were pro-ovigenic (all eggs were mature upon adult emergence) whereas parasitoids were synovigenic (eggs matured progressively during adult lifespan). Initial egg load was correlated with body size for some species, and there was a trade-off between egg number and egg size across all species. Although all species completed their development and left the syconium concurrently, they differed in their adult and preadult lifespans. Providing sucrose solutions increased parasitoid lifespan but had no effect on the longevity of some galler species. While feeding regimes and body size affected longevity in most species, an interaction effect between these variables was detected for only one species. Life-history traits of wasp species exhibited a continuum in relation to their arrival sequence at syconia for oviposition during syconium development, and therefore reflected their ecology. The largest number of eggs, smallest egg sizes, and shortest longevities were characteristic of the earliest-arriving galling wasps at the smallest, immature syconia; the converse characterised the later-arriving parasitoids at the larger, already exploited syconia. Thus life-history is an important correlate of community resource partitioning and can be used to understand community structure. The comparative approach revealed constraints and flexibility in trait evolution. This is probably the first comprehensive study of life-history traits in a fig wasp community.

Les communautés écologiques présentent une diversité importante d'organismes et d'interactions. Comprendre le fonctionnement de ces différents types d'interactions constitue l'un des enjeux majeurs de l'écologie des communautés. Cependant, une large majorité des travaux s'intéressant à ces questions s'est focalisée sur les différents types d'interactions séparément. Cette thèse cherche à comprendre comment le couplage entre différents types d'interactions affecte la dynamique des communautés naturelles. Au travers d'une approche théorique, des modèles simples de communautés comprenant deux types d'interactions sont construits. Ces communautés sont constituées de trois espèces : une espèce basale, plante, interagissant avec un antagoniste, herbivore et un mutualiste, pollinisateur. Nous décrivons comment l'effet indirect entre interactions antagonistes et mutualistes affecte les dynamiques écologiques et évolutives des communautés face à une perturbation. Nous montrons que la relation entre pollinisateurs et herbivores à des conséquences importantes pour le maintien éco-Évolutif de la communauté et pour sa stabilité. Nous étudions ensuite la dynamique évolutive de traits particuliers, qui sont impliqués dans chaque type d'interactions. Certains traits attractifs ou de défense des plantes, affectent à la fois les interactions avec les pollinisateurs et les herbivores. Nous montrons comment les pressions de sélection opposées dues à la pollinisation et à l'herbivorie modifient l'évolution de ces traits et peuvent amener à la diversification des plantes. / Ecological communities involve an amazing diversity of organisms and interactions. Understanding how this diversity of interaction types (competition, mutualism or predation) affects the ecological and evolutionary dynamics of natural systems is an important challenge of community ecology. However, a large majority of works in community ecology theory considers interaction types separately. This thesis focus on the interplay between antagonism and mutualism. With a theoretical approach, small community models, including antagonistic and mutualistic interactions are built. These communities contain three species : one basal species (a plant) with an antagonist (herbivore) and a mutualistic species (pollinator). First, we study how the indirect effect between the two interaction types affects the ecological and evolutionary dynamics of communities in the currency of a disturbance. Second, we study the evolutionary dynamics of special traits, that are involved in each interaction type. Attractive traits or defensive traits of plants affect both interaction with pollinators and herbivores. We depict how the opposite selective pressures due to pollination and herbivory modify the evolution of these traits and show that they can lead to evolutionary diversification of plants. Following this diversification, the coevolutionary emergence of complex interaction networks is studied.

abstract: Complex dynamical systems are the kind of systems with many interacting components that usually have nonlinear dynamics. Those systems exist in a wide range of disciplines, such as physical, biological, and social fields. Those systems, due to a large amount of interacting components, tend to possess very high dimensionality. Additionally, due to the intrinsic nonlinear dynamics, they have tremendous rich system behavior, such as bifurcation, synchronization, chaos, solitons. To develop methods to predict and control those systems has always been a challenge and an active research area. My research mainly concentrates on predicting and controlling tipping points (saddle-node bifurcation) in complex ecological systems, comparing linear and nonlinear control methods in complex dynamical systems. Moreover, I use advanced artificial neural networks to predict chaotic spatiotemporal dynamical systems. Complex networked systems can exhibit a tipping point (a “point of no return”) at which a total collapse occurs. Using complex mutualistic networks in ecology as a prototype class of systems, I carry out a dimension reduction process to arrive at an effective two-dimensional (2D) system with the two dynamical variables corresponding to the average pollinator and plant abundances, respectively. I demonstrate that, using 59 empirical mutualistic networks extracted from real data, our 2D model can accurately predict the occurrence of a tipping point even in the presence of stochastic disturbances. I also develop an ecologically feasible strategy to manage/control the tipping point by maintaining the abundance of a particular pollinator species at a constant level, which essentially removes the hysteresis associated with tipping points. Besides, I also find that the nodal importance ranking for nonlinear and linear control exhibits opposite trends: for the former, large degree nodes are more important but for the latter, the importance scale is tilted towards the small-degree nodes, suggesting strongly irrelevance of linear controllability to these systems. Focusing on a class of recurrent neural networks - reservoir computing systems that have recently been exploited for model-free prediction of nonlinear dynamical systems, I uncover a surprising phenomenon: the emergence of an interval in the spectral radius of the neural network in which the prediction error is minimized. / Dissertation/Thesis / Doctoral Dissertation Electrical Engineering 2020