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Nelva, Pasqual Jean-Sébastien. "Exploration des réseaux d'interactions en écologie : de la structure vers la dynamique : signification des analyses des matrices de communauté en écologie des estuaires". Electronic Thesis or Diss., Bordeaux, 2014. http://www.theses.fr/2014BORD0114.
Pełny tekst źródłaNetworks are a key concept in ecology and a number of models and methods have been used. This PhD dissertation links two approaches, the community matrix and input-output analyses, which have been developed by separate streams of theory. It compares their assumptions with important features of estuarine systems. It explicitly analyses the links between the matrices and the significance of the mixed trophic impacts analysis. Matrices of storage and throughflow analyses are linked to Jacobian matrices of donor or recipient controlled compartment models. Unlike most of what can be seen in the litterature, here the mixed trophic impacts are interpreted as the effects of a compartment being present or absent. Using available data in the case of five European estuaries, qualitative and quantitative matrices are built in the aim of performing sensitivity analyses. First explorations reveal high levels of uncertainties, even in the sign of the predictions. Furthermore, this work examines in more details the possibilities to explore transient dynamics from the community matrix. This PhD dissertation emphasises important features which are necessary to consider when choosing such approaches
Nelva, Pasqual Jean-Sébastien. "Exploration des réseaux d'interactions en écologie : de la structure vers la dynamique : signification des analyses des matrices de communauté en écologie des estuaires". Thesis, Bordeaux, 2014. http://www.theses.fr/2014BORD0114/document.
Pełny tekst źródłaNetworks are a key concept in ecology and a number of models and methods have been used. This PhD dissertation links two approaches, the community matrix and input-output analyses, which have been developed by separate streams of theory. It compares their assumptions with important features of estuarine systems. It explicitly analyses the links between the matrices and the significance of the mixed trophic impacts analysis. Matrices of storage and throughflow analyses are linked to Jacobian matrices of donor or recipient controlled compartment models. Unlike most of what can be seen in the litterature, here the mixed trophic impacts are interpreted as the effects of a compartment being present or absent. Using available data in the case of five European estuaries, qualitative and quantitative matrices are built in the aim of performing sensitivity analyses. First explorations reveal high levels of uncertainties, even in the sign of the predictions. Furthermore, this work examines in more details the possibilities to explore transient dynamics from the community matrix. This PhD dissertation emphasises important features which are necessary to consider when choosing such approaches
Liautaud, Kevin. "Community stability and turnover in changing environments". Thesis, Toulouse 3, 2020. http://www.theses.fr/2020TOU30264.
Pełny tekst źródłaThe question whether communities should be viewed as superorganisms or loose collections of individual species has been the subject of a long-standing debate in ecology. Each view implies different spatial and temporal community patterns. When environment gradually changes in space or in time, the organismic view predicts that species turnover is discontinuous, while the individualistic view predicts gradual changes in species composition. The main objective of this thesis is to understand the theoretical conditions under which these various types of community response can occur. First, I study the role of interspecific competition can play in the emergence of various spatial community patterns. I investigate the theoretical conditions in competition under which smooth or discrete spatial patterns can emerge. Then, I study how interactions between species and their environment can lead to various community patterns in space. I notably show how ecological niche construction can lead to the emergence of abrupt changes in species composition and in the environment, and the role biodiversity plays therein. Finally, I focus on the role biodiversity can play against ecosystem collapse. In this section, I illustrate how diversity loss, through its effects on total biomass, can lead to ecosystem collapse
Génin, Alexandre. "Réseaux d'interactions écologiques, stabilité et résilience des écosystèmes". Thesis, Montpellier, 2018. http://www.theses.fr/2018MONTG031/document.
Pełny tekst źródłaEcological systems are not simple but composed of many different elements(species, for example) interacting with each other. These networks ofinteractions exhibit structural properties that determine ecological systems’ability to absorb and recover from perturbations. Mappinginteractions along with their changes in time and space is therefore key tounderstand and predict empirical communities' response to global changes.In this thesis, we used plant communities as model systems (i) to explore howspatial patterns may help identify feedbacks loops which make communities morefragile to upcoming changes and (ii) to map species interactions in empiricalcommunities and describe how they change along stress gradients and recover fromperturbations. To do so, we used two datasets documenting plant communities insubalpine meadows (USA) and Mediterranean grasslands (France).Our results show that feedback loops can be inferred to some extent from thespatial patterns of plant communities and hence help identify communities thatmay respond more abruptly to perturbations. Going to a more detailed level ofdescription, plant-plant interactions (as measured through spatial associations)were shown to respond strongly and consistently to stress but exhibited a weakresilience to disturbances.This work shows that plant-plant interactions -- which are linked to the response of the community to perturbations -- can be uncovered using spatial patterns. It paves the way towards a better understanding and a better anticipation capacity of how ecological communities might reorganize when subject to disturbances
Subrahmaniam, Jaishree. "Identification des bases génétiques de la coopération plante-plante chez la plante modèle Arabidopsis thaliana". Thesis, Toulouse 3, 2020. http://www.theses.fr/2020TOU30043.
Pełny tekst źródłaDespite the importance of plant-plant interactions in the functioning of both natural ecosystems and agro-ecosystems, studies on plant-plant interactions still have two major gaps to be addressed, that is (i) the genetics of natural variation of plant-plant interactions and (ii) the relative importance of positive interactions within plant species. After writing two reviews on the state-of- the-art related to these gaps, I decided to understand the adaptive genetic bases of intraspecific positive plant-plant interactions in Arabidopsis thaliana at two geographical scales. To do so, I adopted an interdisciplinary approach between quantitative genetics, ecology and genome-wide association mapping. Firstly, based on a field experiment designed to study natural variation of genotype-by-genotype interactions among 52 whole-genome sequenced natural populations from the Midi-Pyrénées region, I identified two different strategies of positive interactions, i.e. kin cooperation and overyielding. Natural variation of positive interactions among these populations were mainly associated with biotic ecological factors varying at a fine spatial scale, such as presence of commensal bacteria or Shannon index of plant communities in the native habitats. Importantly, QTLs associated with variation of positive interactions were significantly enriched in genomic signatures of local adaptation. Secondly, based on a greenhouse experiment using 195 whole-genome sequenced accessions collected in a local French population located in a highly diverse and competitive environment, we revealed the existence of certain genotypic combinations that were benefitting reciprocally to each other’s presence, resulting in a ‘super overyielding’ strategy. Importantly, genetic dissimilarity at the QTLs associated with this strategy was detected for such pairs, supporting the ‘compatibility genes’ hypothesis as underlying this ‘super overyielding’ strategy. Finally, at both geographical scales, we detected a predominance of metabolism related gene functions underlying natural variation of positive interactions, which might be explained by their putative roles in (i) recruitment of similar microbiota by kin to explain kin cooperation, and (ii) potential complementary metabolite cross-feeding to explain overyielding. The next step is undoubtedly cloning of the candidate genes to identify causal associations, thereby allowing to start getting a glimpse on the genetic and molecular landscape associated with positive interactions in A. thaliana
Ohlmann, Marc. "Vers une théorie spatiale des réseaux d'interaction en écologie : méthodes, concepts et applications Diversity indices for ecological networks : a unifying framework using Hill numbers Unveiling the food webs of tetrapods across Europe through the prism of the Eltonian niche A spatial theory of mutualistic metacommunities : assesment of metacommunity capacity (in prep) Mapping the imprint of biotic interactions on β-diversity Multi-trophic -diversity mediates the effect of environmental gradients on the turnover of multiple ecosystem functions Combining abundances from different markers for environmental DNA (in prep)". Thesis, Université Grenoble Alpes (ComUE), 2019. http://www.theses.fr/2019GREAV065.
Pełny tekst źródłaThis thesis focuses on the links between interaction networks, space and time. There is a paradigm shift in community ecology concerning the representation of a species community : from a collection of species towards species and their interactions, represented by an interaction network. We aim to build the bricks for a spatial network theory, by developing new methods, new models and applying it on ecological data. This manuscript contains four chapters. In a first chapter, we extend the diversity indices, built on Hill numbers, to network diversity indices. We define diversity indices across species aggregation levelsand show the interest of this method on a trophic network data set. In a second chapter, we develop a spatially explicit meta-community theory, with various kind of interactions. The theory contains a stochastic and a deterministic meta-community model. We then define the notion of meta-community persistence capacity. In a third chapter, we focus on network reconstruction from environmental DNA data along an environmental gradient.We show that the proposed method allows to evaluate the influence of environmental variables on community and infer a network in agreement with the literature on soil interactions. Finally, in a fourth chapter, we develop a method to combine environmental DNA data coming from different primers and show the efficiency of the method to better estimate plant abundances
Maghnia, Fatima-Zahra. "Décryptage des réseaux d'interactions plante-champignon pour une meilleure gestion des subéraies méditerranéennes". Thesis, Montpellier, 2017. http://www.theses.fr/2017MONTT073/document.
Pełny tekst źródłaThe Cork oak (Quercus suber) forests play an important role in terms of ecological services and socio-economic development for the Mediterranean populations. However, the cork oak forests, notably in the Southern Mediterranean basin are highly threatened by increasing human and climate pressures, which accelerates desertication. The conservation of this ecosytem is strongly dependent of our ability to predict the environmental changes induced by these pressures as well as to develop sustainable approach for their restoration. In this context, the identification of biological indicators of cork oak health and the intensification of plant-plant facilitation processes appears as promisising ecological strategies. Their success is however subjected to our understanding of plant-fungal interactions, notably with fungal mycorrhiza, key factors of forest ecosystem functionning. The current work aimed at deciphering plant-fungal networks, notably mycorrhizal networks with cork oak and its understory shrub vegetation in three Moroccan cork oak habitats (Maâmora, Benslimane, Chefchaoun) characterized by different degradation levels. The root-fungal diversity associated to cork oak and major components of its understory shrub vegetation (Cistus salviifolius, Cistus monpeliensis et Lavandula stoechas) has been analysed by combining traditional methods based on morphological identification, and new generation high- throughput DNA sequencing methods to characterize communities at the molecular level.The study represents the most extensive survey of soil fungal diversity, notably mycorrhizal diversity, in Moroccan cork oak ecosystems. Different fungal community structures were revealed, depending on habitat, plant host type, and degradation forest status. A wide range of fungal indicators of plant type × forest status has been identified, highlighting the importance of several ectomycorrhizal fungi (notably Cenococcum, Russula, Terfezia and Tomentella) as well as ericoid mycorrhizal fungi (Cladophialophora, Oidiodendron) and arbuscular mycorrhizal fungi (Rhizophagus, Redeckera, Racocetra, and Paraglomus). The current work provides an extensive database on the ecology of soil fungi related to the Moroccan cork oak forest, offers new insights into the potential of soil fungi for monitoring the health of the cork oak forest, and for the developement of efficient conservation programs of this ecosystem by taking into account the soil fungal communties associated. The use of proposed appoaches to a larger diversity of forest ecosystems are promising to better understand the biological fonctionning of forest ecosystem and their conservation in response to the worsening of worldwide human and climate pressures
Kamenova, Stefaniya. "Réseaux d'interactions, biodiversité et services éco-systémiques en milieu agricole : que nous apprennent les coléoptères carabiques ?" Thesis, Poitiers, 2013. http://www.theses.fr/2013POIT2319.
Pełny tekst źródłaBiological control is one of the main ecosystem services provided by biodiversity in agroecosystems. Communities of beneficial insects, hosted by agricultural areas exhibit high levels of species and functional diversity, and their biology and life history traits are well described today. These communities are therefore an excellent model for addressing issues of fundamental and applied interest about mechanisms at the origin of biodiversity and its impacts on the supply of ecosystem services. In this thesis, we develop an original combination of advanced molecular approaches and more traditional methods in order to elucidate trophic interaction network within the community of carabid beetles in agricultural areas. The carabid beetles can significantly contribute to the service of biological control, but their contribution and beneficial conditions are difficult to assess because of their opportunistic and plastic feeding behavior. A without a priori investigation of carabid diet at community level in a typical agricultural landscape reveals a resource partitioning between groups of species. Additional experimental studies in laboratory conditions indicate that interspecific competition could be the mechanism generating this partitioning. From a fundamental point of view, these results suggest a preponderance of deterministic processes (niche partitioning) compared to neutral processes (environmental stochasticity) to explain the coexistence of species. From an applied point of view, the importance of the resource in structuring carabid communities provides a potential lever of action for the development of efficient management strategies optimizing carabid function as crop auxiliaries
Auclair, Etienne. "Réseau bayésien dynamique étiqueté : cadre et apprentissage de structure pour application aux réseaux écologiques". Thesis, Toulouse 3, 2019. http://www.theses.fr/2019TOU30002.
Pełny tekst źródłaAn ecological network represents the interactions between living species within an ecosystem. The knowledge of the structure of such a network is an important challenge in the field of ecology.This task can be realized by inference methods : a set of methods that uses ecological observations data (species abundance, presence or absence of species...) in order to learn the interactions mathematically, by the exploitation of the effect of these interactions on the observed data.This thesis describes a case where the ecological data we dispose of are only data of presence/absence of species observed at different moments. The goal is to develop a method that exploits those kind of data in order to learn the interaction between these species. The main difficulty is that binary variables carry little information. Expert knowledge on the system is used to help learning the network's structure.We use the framework of dynamic Bayesian network : temporal presence/absence data are modeled as the realization of a set of dynamic random variables whose dependencies are described by an oriented graph. Such a model can be simplified using expert knowledge.This thesis describes a particular model of "labelled" dynamic Bayesian network. In this model, the graph is defined by a small number of different types of interactions that constitute a set of labels attributed to the edges of the graph.This model can describe several phenomena where an information or a perturbation can be propagated by contact (rumour, disease, forest fire....)This model describes the presence or absence probabilities of each species as a function of the number of interactions of each label this species is subject to. This model allows to describe every presence/absence probability of species using a small number of parameters independent from the network's structure. This is the framework used for the modeling of species dynamics within an ecological network : the information propagated is the presence or the absence of a species, knowing the interaction between the species of the network. Then, we describe the processes we use for learning the structure of a labelled dynamic Bayesian network using time series of binary variables. This 'Estimation-Restoration' algorithm alternates two steps : a phase of parameter estimation knowing the structure, and a phase of structure learning knowing the parameters. This last step can be complex. It is done by solving a integer linear programming problem. This allows to use efficient existing tools for solving those kind of problems. Moreover, we can easily add expert knowledge by the form of linear constraints. This process has been used on a particular case study :the observation of arthropods species trapped in experimental fields in the united kingdom. In order to highlight the differences between the different crops, different networks have been learnt. Finally, we compare the learnt network with others, learnt with different learning methods on the same data
Manincor, Natasha de. "Ecologie des plantes et des pollinisateurs dans les prairies calcaires le long d'un gradient latitudinal en France : diversité des espèces et structure des réseaux d'interaction plantes-pollinisateurs". Thesis, Lille 1, 2019. http://www.theses.fr/2019LIL1R024/document.
Pełny tekst źródłaIn the current context of biodiversity crisis and the associated risks of ecosystem service failure, plant-pollinator networks are among the most studied mutualistic networks. Without pollinators, many plants could not reproduce and set seed, and 70% of agricultural production directly depends on them. However, pollinating insects constitute some of the terrestrial taxa most affected by global changes. As such, understanding plant-pollinator networks is of particular relevance if we are to prevent catastrophic disruption of pollination interactions and associated ecosystem services. In plant-pollinator networks, species need to be present in the same site and at the same moment for interactions to occur. In France, plant and pollinator abundance, richness and presence differ along the latitudinal gradient, which correspond to natural variations in biodiversity, and these variations could potentially affect network structure. Moreover, interaction networks are often reported based on temporally aggregated data, but in truth pollination interactions are not static and vary in time, since different plant and pollinator species display different phenologies. Large datasets on plant-pollinator interactions which comprise the entire flowering season or multiple years and allow relevant comparisons among networks along environmental gradient are rare. Due to their complexity and variation among years, most studies of mutualistic networks have focused on predicting and comparing classic network metrics which are all influenced by network size, i.e. the number of plant and insect species. Furthermore, most of these networks are based on interactions observed in the field, and thus some existing links between species remain unobserved. As such, visit-based networks represent a subsample of possible interactions, which call for the development of new methodological approaches to better explore the ecological processes determining species interactions. The general aim of this study is to understand and help predict the effects of environmental changes on plant and pollinator communities by studying plant-pollinator associations along an environmental gradient. Here, I provide and analyse a new database made of geo-localized data characterizing plant-pollinator associations at the species level, spatial variation in community structure and trait assemblage, focusing on six different calcareous grasslands along a latitudinal gradient in France. I first compared the taxonomical diversity variation in space (between and within region) and time (along the season). Then, I used a new methodological approach to compare networks of different size and to study the consequences of environmental gradients on plant-pollinator interaction probability. To understand how much distorted is our vision of plant-pollinator networks sampled following classic methods, I built more complete interaction networks using the pollen found on insects. Finally, I studied the mechanism behind geographical variation of floral scents and among-populations differences linked to the variation in the pollinator community. Because of the complexity and variation of plant-pollinator interactions, our study highlighted the importance to consider the entire flowering season and insects flying period, using species-level identifications, to disentangle the ecological species' role and the network variations. The use of new methodological approach allowed us to make networks comparison along the environmental and diversity gradient avoiding data circularity. The high amount of data provided in this thesis permitted to make comparisons at different level, from the entire network to species-specific variation among-populations
Silva, Dayana Karla Melo da. "Mouvements-Réseau : technique, environnement et socialités à l'époque de l'Anthropocène". Thesis, Sorbonne Paris Cité, 2016. http://www.theses.fr/2016USPCB019/document.
Pełny tekst źródłaThis research reflects on the new forms of social mobilization that emerge in response to the advent of digital networks and the environmental crisis. We value two epistemological axes. The first based on the question of technology beyond the instrumentality and the second on the notion of ecosophy. Our empirical observation network is formed by the groups mobilized around the environmental theme relating to the more than three hundred canalized and buried rivers in the city of São Paulo, Brazil, henceforth visible through digital devices and architectures such as maps, audio guides, collaborative platforms, web sites and social networks. From the immersion in these networks, we try to expand our sociological view considering the social not as the field of exclusive human acting, but as consisting of different beings and modes of existence, including technical objects, natural elements and natural phenomena. In this sense, we propose in this research the concept of movements-network to give form to these new mobilizations and associations characterized by hybridity between the territory and urban, environmental and technical spaces, as well as the desire to dwell the Earth otherwise
Esta pesquisa se questiona sobre as novas formas de mobilização social que respondem ao surgimento das redes digitais e à crise ambiental. Privilegiamos duas linhas de compreensão epistemológica. A primeira baseada na questão da técnica para além da instrumentalidade e a segunda na noção de ecosofia. Nossa rede de observação empírica é formada pelos coletivos mobilizados em torno da temática ambiental que concerne aos mais de trezentos rios canalizados e enterrados na cidade de São Paulo, Brasil, doravante visíveis por meio de dispositivos e arquiteturas digitais, tais como mapas interativos, audioguias, plataformas colaborativas, sites e redes sociais. A partir da imersão nestas redes, tentamos expandir nossa visão sociológica compreensiva considerando o social não como o terreno de atuação exclusivo dos humanos, mas como composto por diferentes seres e modos de existência, incluindo os objetos técnicos e os elementos e fenômenos naturais. Neste sentido, propomos nesta pesquisa a noção de movimentos-rede a fim de dar uma forma a estas novas mobilizações e associações caracterizadas pelo hibridismo entre o território e os espaços urbano, ambiental e técnico, bem como pelo desejo de habitar a Terra diferentemente
Houssard, Patrick. "Variations des concentrations en mercure dans les réseaux trophiques marins de l'Océan Pacifique Sud : état des lieux, caractérisation des sources et relations avec la dynamique trophique et physique du milieu". Thesis, Nouvelle Calédonie, 2017. http://www.theses.fr/2017NCAL0001/document.
Pełny tekst źródłaMercury is a naturally distributed heavy metal which is characterized, under its organic form (monomethylmercury; MMHg), by its bioaccumulation in living organisms and its biomagnifications along food chains. Since the awareness of MMHg neurotoxicity, lots of research works have focused on understanding where and how MMHg is formed and transmited to marine food webs. Those questions are keys in order to anticipate how MMHg, in commercially fish species, will respond in a context of increasing mercury emissions and climate change.This work is part of this approach by studying total mercury spatial variations from muscle tissue of three tuna species: bigeye, albacore and yellowfin tuna, captured within the south Pacific Ocean. Every tuna species demonstrated a consistent and similar spatial trend, with higher total mercury concentrations in the southwest and lower concentrations in the western equatorial Pacific. This spatial trend seems to be in accordance with varying tuna diet linked to the thermal features of the water column. By combining archival tagging data and nitrogen stable isotope analysis, we showed that the deepening of bigeye tuna vertical habitat around New Caledonia might allow them to forage on deeper and MMHg enriched preys. Additionnaly, dissolved MMHg profiles in the southwest Pacific suggest higher methylation processes in the epipelagic zone leading, possibly, to higher MMHg bioavailability for marine food chains.This study highlighted the key role of tuna trophic ecology and particularly foraging depth in their MMHg exposure. Those features have to be considered in future studies evaluating food webs contamination at a spatial or temporal scale
Braga, Joăo. "Etude de la diversité spatiale des réseaux trophiques et ses implications pour la conservation". Thesis, Université Grenoble Alpes (ComUE), 2018. http://www.theses.fr/2018GREAV069.
Pełny tekst źródłaCo-occurring species share more than just physical space, they share also biotic interactions. Trophic interactions depict the flow of biomass from a prey species to its predator. Food webs, in their simplest form, are composed by producers, consumers and decomposers. Because of the nature of the interactions that food webs depict, their structure can be informative about the underlying processes responsible for the assembly of communities, the organization of biodiversity, the functioning of ecosystems and the services they provide to humans. Although the study of food webs across large spatial scales has been limited by data availability, a new generation of biogeography and food web ecology research is rising. In my PhD, I investigated the spatial diversity of food webs of European tetrapod species with the objective of merging biogeography, food web ecology and conservation biology. I started by combining two different sources of information, species distributions and an expert-based database of species interactions, to map the diversity of European food webs. This allowed me to uncover the spatial interactions between food web diversity, composition, environmental and land-use gradients. I found that the spatial diversity of food webs was highly linked with climatic conditions. Then, I used centrality indices to identify trophic keystone species. Losing central species in a food web can affect a community disproportionally, by disrupting its trophic structure and potentially causing other extinctions. Using three measures of centrality (degree, betweenness and eigenvector centralities), I investigated how these centrality indices correlated with the traits and phylogeny of European tetrapod species. I found that centrality was highly conserved through phylogeny, and active hunters of small prey were more likely to be central within a food web. Because centrality was restricted to few species, assessing the efficiency of current protected areas for these central species is crucial to persistence of European communities. Thus, I investigated the correlation between species extinction risk, centrality and also trophic level. On a positive note, I found weak to no links between extinction risk and species trophic features. I also performed a gap analysis to search for any links between species centrality, trophic level and their spatial protection, which showed that key species are generally well protected in Europe. My thesis brings together the three fields of biogeography, food web ecology, and conservation biology into one of the first comprehensive studies on the large-scale patterns of trophic structure and its drivers, and the dependencies between species trophic, functional and phylogenetic characteristics, finally providing an option to bring trophic information into conservation applications
Bles, Olivier. "Approche théorique et expérimentale du choix de source et de la gestion collective des ressources alimentaires chez la fourmi". Thesis, Strasbourg, 2019. http://www.theses.fr/2019STRAJ007/document.
Pełny tekst źródłaDuring my PhD I have developed theoretical (simulation) and experimental (tracking) tools to investigate the mechanisms underlying the collective food source choice as well as collective food management at the intranidal level in ants. A first part of my thesis reveals the influence of the physical (and in particular the angularity and the topography) properties of the trail to the food source on the ant behavior at the individual level and its resulting food source choice/exploitation at the collective level. The second part of my thesis is dedicated to the dynamics of the food flow entering the nest, its regulation and the food dissemination/accumulation processes at the intranidal level through trophallaxis (mouth-to-mouth fluid exchange). The networks of food distributions and exchanges were built for two ant species in various experimental conditions. Interestingly, all theses networks show several similar properties, such as a high degree of heterogeneity in the individual participation to the food exchange activity as well as a robustness facing environmental variabilities
Lievens, Eva J. P. "Biotic challenges for extremophiles : reproductive interference and parasite specialization in Artemia". Thesis, Montpellier, 2016. http://www.theses.fr/2016MONTT146/document.
Pełny tekst źródłaThe challenges posed by biotic factors – interactions with competitors, parasites, etc. – play a large role in the evolution of populations, but are generally difficult to study. In this work, we used the Artemia system in the hypersaline salterns of Aigues-Mortes, France, to study the character and evolution of several interspecific interactions. The system is eminently suited to such studies: it is simple, containing two Artemia species, three highly prevalent parasites (one helminth and two microsporidians), and various microbiota; and many of its interactions are newly-established, because one of the Artemia species is invasive. We studied two types of interactions. First, the presence and evolution of reproductive interference between the native and invasive Artemia species. We found that the invasive Artemia species, which is sexual, undergoes severe interference in sex allocation when in the presence of the native, asexual Artemia, but no interference in mate guarding. Second, the evolution of parasite specialization in two microsporidian parasites infecting the Artemia species. Using field data, experimental infections, and experimental evolution, we investigated the state, causes, and consequences of specialization in the microsporidians. Results consistently indicated that the microsporidians are specialized for one host species, despite being able to complete their life cycle in either host. This specialization appears to be imposed by the precise toolkits needed to exploit each host species; in the non-specialized hosts, these triggered suboptimal exploitation, maladaptive virulence, and immunopathology. Overall, these studies suggest that the biotic factors acting on Artemia impose strong selection pressures, to which they cannot always respond easily. The importance of biotic factors in a system which is otherwise dominated by extreme abiotic conditions underlines the importance of species interactions in shaping evolution
Lumbroso, Sarah. "Prospective et stratégies pour l’environnement : entre fabrique des futurs et situation de gestion, quelles prises pour l’action ?" Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLA001/document.
Pełny tekst źródłaFaced by challenges for the future such as that posed by the extent of ecological disruption (climate change, species extinction, pressure on water resource), the narratives regarding the future are ever multiplying, whether promising solutions via technology, models of a utopian society, or considering collapse as inevitable. Do said narratives play a part in the practical implementation of environmental management and are they supporting or restraining the action of those seeking to improve the state of ecosystems? This thesis addresses these issues by investigating the contribution of futures studies to the strategies of stakeholders acting for an effective management of environmental issues. Through eight case studies, the research work analyses how designers build futures studies so that they can provide opportunities for action to environmental actors (i.e. water agencies, protected areas managers, NGOs etc.). Futures studies influence the “manufacture of futures”, that is, the competition between various future depictions of sociotechnical systems which results in imposing or excluding certain pathways of change. By making visible, in the manufacture of futures, narratives which lend credibility to transformations of socioecological systems in favour of ecological issues, futures studies may empower environmental actors. Futures studies designers connect the results of their interventions with processes in environmental management situations. These connections can provide, not without difficulty, opportunities to influence power relationships, the negotiation of environmental management actions, and the internal processes of organisations involved. This thesis offers an analytical framework to support the strategic thinking of futures studies designers in the design and implementation of their interventions. Furthermore, it opens up new avenues on the strategic issues of producing narratives to support the transitions of sociotechnical systems
Ribeiro, Diogo. "Discovery of the role of protein-RNA interactions in protein multifunctionality and cellular complexity". Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0449/document.
Pełny tekst źródłaOver time, life has evolved to produce remarkably complex organisms. To cope with this complexity, organisms have evolved a plethora of regulatory mechanisms. For instance, thousands of long non-coding RNAs (lncRNAs) are transcribed by mammalian genomes, presumably expanding their regulatory capacity. An emerging concept is that lncRNAs can serve as protein scaffolds, bringing proteins in proximity, but the prevalence of this mechanism is yet to be demonstrated. In addition, for every messenger RNA encoding a protein, regulatory 3’ untranslated regions (3’UTRs) are also present. Recently, 3’UTRs were shown to form protein complexes during translation, affecting the function of the protein under synthesis. However, the extent and importance of these 3’UTR-protein complexes in cells remains to be assessed.This thesis aims to systematically discover and provide insights into two ill-known regulatory mechanisms involving the non-coding portion of the human transcriptome. Concretely, the assembly of protein complexes promoted by lncRNAs and 3’UTRs is investigated using large-scale datasets of protein-protein and protein-RNA interactions. This enabled to (i) predict hundreds of lncRNAs as possible scaffolding molecules for more than half of the known protein complexes, as well as (ii) infer more than a thousand distinct 3’UTR-protein complexes, including cases likely to post-translationally regulate moonlighting proteins, proteins that perform multiple unrelated functions. These results indicate that a high proportion of lncRNAs and 3’UTRs may be employed in regulating protein function, potentially playing a role both as regulators and as components of complexity
Jakuschkin, Boris. "Genetic architecture of the interactions between English oak (Quercus robur L.) and the microbial community of its phyllosphere". Thesis, Bordeaux, 2015. http://www.theses.fr/2015BORD0170/document.
Pełny tekst źródłaNumerous and various microorganisms inhabit inner and outer tissues of plant leaves, thephyllosphere. They influence many plant traits, biotic interactions, energy flux, host stresstolerance and ultimately the fitness of their hosts. Many plant quantitative traits wereshown to structure the phyllosphere microbial community. Hence quantitative trait loci(QTLs) linked to the structure of this community were expected. The main objective ofthis work was to search for genomic regions in oak (Quercus robur L.), whose effect extendsto the community level, influencing the phyllosphere microbiota. First, we studied thecomposition and the interaction network of oak phyllosphere microbiota with specific focuson Erysiphe alphitoides, a major biotrophic pathogen of oak. We showed that infection byE. alphitoides is accompanied by changes in the foliar fungal community composition butnot in the bacterial community composition. We highlighted likely interaction partners ofE. alphitoides and we showed that the complex microbial interaction network, in contrastto previous findings, was dominated by positive interactions. Next we performed QTLanalysis of microbial community descriptors in a full-sib mapping population of oak. Wefound 8 QTLs for microbial community traits: fungal and bacterial composition, fungaldiversity, and percentage of Erysiphe alphitoides reads. Three of these QTLs colocalizedwith a QTL for powdery mildew sensibility, suggesting for strong genetic determinism ofpowdery mildew resistance in Q. robur. Finally we present preliminary results of a geneticassociation study and discuss our findings within an evolutionary perspective
Laurent, Lisa. "Apports d’une approche écosystémique à l’étude de la dynamique des communautés végétales forestières : vers une prise en compte des interactions écologiques multiples". Thesis, Orléans, 2016. http://www.theses.fr/2016ORLE2050/document.
Pełny tekst źródłaOne of the main challenges to predict vegetation dynamics and plant community composition is to identify how biotic and abiotic factors modify the nature and magnitude of plant-plant interactions. The objective of my thesis is to highlight the leading role of multiple interactions (involving more than two biotic compartments) in forest understory dynamics and more specifically regeneration dynamics of target species such as sessile oak. The results emphasize the importance of: (i) effects of deer on response patterns of plant-plant interactions along resource gradients, (ii) indirect interactions, in particular indirect facilitation, (iii) demographic parameters in relation to species phenology, (iv) distinguishing among underlying mechanisms of multiple interactions thanks to environmental monitoring. Thus, my thesis supports the idea that management practices focusing on a single pressure, while ignoring others, are unable to conserve populations of target species because they don’t consider multiple interactions. This highlights the importance to use complementary management strategies to achieve sustainability in the context of global changes (climatic change and deer overabundance)
Quillien, Nolwenn. "Des écosystèmes naturellement stressés sous menace anthropique : réponses de la faune des plages de sable macrotidales aux marées vertes". Electronic Thesis or Diss., Brest, 2016. http://www.theses.fr/2016BRES0024.
Pełny tekst źródłaHighly dynamic systems, often considered as resilient systems, are characterised by abiotic and biotic processes under continuous and strong changes in space and time. Because of this variability, the detection of overlapping anthropogenic stress is challenging. Coastal areas harbour dynamic ecosystems in the for of open sandy beaches, which cover the vast majority of the world’s ice-free coastline. These ecosystems are currently threatened by increasing human-induced pressure, among which mass-development of opportunistic macroalgae (mainly composed of Chlorophyta, so called green tides), resulting from the eutrophication of coastal waters. The ecological impact of opportunistic macroalgal blooms (green tides, and blooms formed by other opportunistic taxa), has long been evaluated within sheltered and non-tidal ecosystems. Little is known, however, on how more dynamic ecosystems, such as open macrotidal sandy beaches, respond to such stress. This thesis assesses the effects of anthropogenic stress on the structure and the functioning of highly dynamic ecosystems using sandy beaches impacted by green tides as a study case. The thesis is based on four field studies, which analyse natural sandy sediment benthic community dynamics over several temporal (from month to multi-year) and spatial (from local to regional) scales. In this thesis, I report long-lasting responses of sandy beach benthic invertebrate communities to green tides, across thousands of kilometres and over seven years; and highlight more pronounced responses of zoobenthos living in exposed sandy beaches compared to semi-exposed sands. Within exposed sandy sediments, and across a vertical scale (from inshore to nearshore sandy habitats), I also demonstrate that the effects of the presence of algal mats on intertidal benthic invertebrate communities is more pronounced than that on subtidal benthic invertebrate assemblages, but also than on flatfish communities. Focussing on small-scale variations in the most affected faunal group (i.e. benthic invertebrates living at low shore), this thesis reveals a decrease in overall beta-diversity along a eutrophication-gradient manifested in the form of green tides, as well as the increasing importance of biological variables in explaining ecological variability of sandy beach macrobenthic assemblages along the same gradient. To illustrate the processes associated with the structural shifts observed where green tides occurred, I investigated the effects of high biomasses of opportunistic macroalgae (Ulva spp.) on the trophic structure and functioning of sandy beaches. This work reveals a progressive simplification of sandy beach food web structure and a modification of energy pathways over time, through direct and indirect effects of Ulva mats on several trophic levels. Through this thesis I demonstrate that highly dynamic systems respond differently (e.g. shift in δ13C, not in δ15N) and more subtly (e.g. no mass-mortality in benthos was found) to anthropogenic stress compared to what has been previously shown within more sheltered and non-tidal systems. Obtaining these results would not have been possible without the approach used through this work; I thus present a framework coupling field investigations with analytical approaches to describe shifts in highly variable ecosystems under human-induced stress