L'évolution moléculaire, basée sur l'étude des données de séquençage, s'est imposée comme une approche majeure pour l'étude de l'Histoire des organismes vivants (notamment à travers les arbres phylogénétiques). Ses méthodes classiques reposent sur un découpage des génomes en entités supposées indépendantes : les gènes. Or, les gènes n'évoluent pas indépendamment : au sein de l'histoire des espèces qui le portent, l'histoire d'un gène s'inscrit. En outre, leur position le long des chromosomes fait qu'ils partagent des événements de mutations structurales (duplications, pertes de fragments chromosomiques) avec les gènes proches. Enfin, leur potentielle fonction biologique les amène à être influencés par (et à influencer en retour) l'évolution d'autres gènes. Je montre que ne pas prendre en compte ces relations d'inter-dépendances évolutives (de coévolution) lors de l'inférence d'arbres de gènes résulte en une suresti mation des différences entre les arbres des différents gènes ainsi qu'entre les arbres des gènes et l'arbre des espèces. Des modèles permettent déjà d'intégrer la coévolution des gènes avec les espèces à la reconstruction des arbres de gènes. Par ailleurs, on connaît des modèles décrivant l'évolution des relations entre gènes, néanmoins sans intégrer ces informations à la reconstruction des arbres de gènes. Je reprends ces avancées et les combine au sein d'une méthode qui modifie les arbres de gènes selon un critère qui prend en compte les séquences ainsi que des relations de coévolution avec les espèces et d'autres gènes. Cette méthode, appliquée à des mammifères et des champignons, permet de produire des histoires de gènes cohérentes entre elles / Molecular evolution, based on the study of sequencing data, established itself as a fundamental approach in the study of the history of living organisms (noticeably through the inference of phylogenetic trees). Classical molecular evolution methods rely on the decomposition of genomes into entities that are supposed independent: genes. However we know that genes do not evolve independently: their potential biological function lead them to be influenced by (and influence) the evolution of other genes. Moreover, their position along chromosomes imply that they share events of structural mutations (duplication, loss of a chromosome fragment) with neighbouring genes. Similarly, a gene individual history inscribes itself in the history of the species that bears it. I show that not taking into account this inter-dependency relationships (co- evolutionary relationships) during the inference of gene trees results in an overesti- mation of the differences between gene trees as well as between gene tree and species tree. Modelling efforts these last year have allowed the integration of gene and species co-evolution information to the reconstruction of gene trees. Besides, researchers have proposed models describing the evolution of the relationships linking genes, but without integration of this information in the tree building process. My works aim to combine these advances in a method that modify gene trees according to a criterion that integrates sequence information and information coming from co-evolution relationships. This method, applied to mammals and fungi, leads to gene histories that are more congruent (simpler adjacency histories, longer events of loss or transfer, ...)

No description available.

<p>  </p> <p>Predators and parasites are critical, interconnected members of the community and have the potential to influence host populations. Predators, in particular, can have direct and indirect impacts on disease dynamics. By removing hosts and their parasites, predators alter both host and parasite populations and ultimately shape disease transmission. Our ability to accurately predict disease dynamics requires understanding the ecological effects of predation on prey and host densities and its role in the coevolution of host resistance and parasite virulence. While the impact of predators on disease dynamics has received considerable attention, research has focused on selective predation on infected prey. There is, however, substantial evidence that some predators avoid infected prey, preferentially attacking uninfected individuals. Such different strategies of prey selectivity by predators modulate host-parasite interactions, changing the fitness payoffs both for hosts and their parasites. I use empirical results and theoretical predictions as a framework to discuss the mechanisms by which predation for infected versus uninfected individuals can affect disease dynamics. First, by integrating hypotheses from behavioral ecology and disease ecology, I outlined novel perspectives that complement the prevailing view of selective predation of infected individuals (Chapter 1). Then, exploring short-term ecological outcomes and long-term host-parasite coevolution, I investigated patterns of <em>Daphnia dentifera</em> host population densities and host susceptibility over several generations under different types of predation pressure, including selective predation on infected and uninfected individuals (Chapter 2). Finally, building on the results of this research, I developed a high school project-based lesson plan that facilitates the instruction of the nature of science, implementing on-going ecological research in activities to improve student learning based on a constructivist approach to learning (Chapter 3). Together this research highlights the differential ecological and evolutionary outcomes of host-parasite interactions under varying community contexts.</p>

The interaction between pollinators and flowers affects the fitness of both pollinators and flowering plants, which can result in the co-evolution of pollinator and floral traits. Some pollination systems contain flower-dwelling ambush predators that attack visiting pollinators. This interaction could result in co-evolution of predator and pollinator traits as is typical in predator-prey systems. The presence of these predators could also have indirect negative fitness effects on flowering plants by killing or deterring pollinators. This raises the possibility that predator and floral traits also co-evolve. Furthermore, it is possible that this system is best described as a three-species game where predator, pollinator, and floral traits all co-evolve. The ultimate goal of my thesis is to explore this possibility. This is achieved in Chapter 5, which consists of a game theory model of the co-evolution of floral colour with predator and pollinator behavioural strategies. This model is novel, both within the pollination context described here and within a wider context. Furthermore this model is the first to propose that the evolution of floral colour might be affected by the presence of flower-dwelling ambush predators. This is particularly significant given that there has been little discussion about what floral traits might be adaptations to the presence of these predators. A secondary goal of this thesis is to explore how pollinators detect and respond to the presence of flower-dwelling ambush predators as an important subcomponent of predator-pollinator-flower co-evolutionary dynamic. Chapter 2 demonstrates that bumblebees avoid evidence of past predation events, and Chapter 3 demonstrates that the honeybee recruitment dance is affected by exposure to cues of predation risk in a way that should reduce the colony's exposure to predators. Chapter 4 is a model that suggests novel factors that might affect how a population of pollinators distributes itself between predator-free and predator-containing flowers. / Thesis / Doctor of Philosophy (PhD)

No description available.

Software Product Lines (SPLs) are a successful approach to software reuse in the large. Even though tools exist to create SPLs, their evolution is widely unexplored. Evolving an SPL manually is tedious and error-prone as it is hard to avoid unintended side-effects that may harm the consistency of the SPL. In this thesis, the conceptual basis of a system for the evolution of model-based SPLs is presented, which maintains consistency of models and feature mapping. As basis, a novel classification is introduced that distinguishes evolutions by their potential to harm the mapping of an SPL. Furthermore, multiple remapping operators are presented that can remedy the negative side-effects of an evolution. A set of evolutions is complemented with appropriate remapping operations for the use in SPLs. Finally, an implementation of the evolution system in the SPL tool FeatureMapper is provided to demonstrate the capabilities of the presented approach when co-evolving models and feature mapping of an SPL.

Software Product Lines (SPLs) are a successful approach to software reuse in the large. Even though tools exist to create SPLs, their evolution is widely unexplored. Evolving an SPL manually is tedious and error-prone as it is hard to avoid unintended side-effects that may harm the consistency of the SPL. In this thesis, the conceptual basis of a system for the evolution of model-based SPLs is presented, which maintains consistency of models and feature mapping. As basis, a novel classification is introduced that distinguishes evolutions by their potential to harm the mapping of an SPL. Furthermore, multiple remapping operators are presented that can remedy the negative side-effects of an evolution. A set of evolutions is complemented with appropriate remapping operations for the use in SPLs. Finally, an implementation of the evolution system in the SPL tool FeatureMapper is provided to demonstrate the capabilities of the presented approach when co-evolving models and feature mapping of an SPL.:1 Introduction 1.1 Motivation for Evolving Software Product Lines 1.2 Outline of the Thesis 2 Background and Scope 2.1 Concepts and Terminology 2.1.1 Software Product Lines 2.1.2 Model-Driven Software Development 2.1.3 FeatureMapper 2.2 Scope 2.3 Related Work 3 Evolution of Software Product Lines 3.1 Evolutions 3.1.1 Evolutions in the Problem Space 3.1.2 Evolutions in the Solution Space 3.2 Classification Systems for Evolutions 3.2.1 Classification by Behavior Preservation 3.2.2 Classification Systems in the Literature 3.2.3 Classification by Semantical Extent of Model Changes 3.3 Remapping Operations 3.3.1 Remapping in the Problem Space 3.3.2 Remapping in the Solution Space 3.4 Classification and Remapping of Evolutions 3.4.1 Classification and Remapping of Problem Space Evolutions 3.4.2 Classification and Remapping of Solution Space Evolutions 4 A Framework for Evolutions in FeatureMapper 4.1 Relevant Technology 4.1.1 Refactory 4.1.2 EMFText 4.2 Implementation 4.2.1 Implementation of the Evolutions System 4.2.2 Implementation of the Remapping System 4.2.3 Implementation of the User Interface System 4.2.4 Implementation of the Test Suite 4.3 Possibilities for Extension 4.3.1 Adding New Evolutions 4.3.2 Adapting Existing Evolutions 5 Example Project 5.1 Initial Situation in 2001 5.2 First Revision in 2006 5.2.1 Removing the Cassette Player 5.2.2 Adding an MP3 CD Player 5.2.3 Adding a Personal Navigation Device 5.2.4 Changing the Implementation of the UI Builder 5.2.5 Summary of the Changes of the First Revision in 2006 5.3 Second Revision in 2011 5.3.1 Creating a Multi-Format CD Player 5.3.2 Enhancing Voice Recognition to Control the Audio Player 5.3.3 Restructuring Personal Navigation Maps 5.3.4 Changing the Implementation of the CD Player 5.3.5 Summary of the Changes of the Second Revision in 2011 5.4 Conclusion of the Example Project 6 Conclusion 6.1 Summarized Findings 6.2 Limitations and Drawbacks 6.3 Possibilities for Future Work 6.4 Theoretical and Practical Contributions A Object Remapping Specification (*.orspec) A.1 Object Remapping Specification Model A.2 Object Remapping Specification Syntax B DocBooklet (*.docbooklet) B.1 DocBooklet Model B.2 DocBooklet Syntax C NavMap (*.navmap) C.1 NavMap Model C.2 NavMap Syntax List of Figures List of Tables List of Listings Bibliography

Thesis (PhD)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Tuberculosis (TB) disease results in approximately 2 million deaths annually and is the leading cause of death due to a single infectious agent. Previous studies have indicated that host genetics play an important role in the development of TB. This together with pathogen and environmental factors intensifies the complexity of this disease. The Major Histocompatibility Complex (MHC) and Leukocyte Receptor Complex (LRC) comprise several genes which are known to be important modulators of the host immune response. The human leukocyte antigen (HLA) class-I genes of the MHC are involved in the presentation of pathogenic antigens on the surfaces of infected cells, while the killer cell immunoglobulin-like receptors (KIRs) of the LRC are involved in the recognition of self and non-self cells. Natural Killer (NK) cells through their KIRs are thus able to kill non-self cells through recognition of the class-I molecules expressed. Additionally, HLAs and KIRs are extremely polymorphic and differ markedly across populations of different ethnicities. Here we studied these genes and their polymorphisms in the South African Coloured (SAC) population to determine their involvement in susceptibility to TB, susceptibility to disease caused by specific Mycobacterium tuberculosis subtypes, and understanding their ancestral contribution to the SAC with regards to the development of TB. We showed that the KIR3DS1 gene and KIR genotypes with five or more activating KIRs, and the presence of 3DS1, protected against the development of active TB in the SAC population. Several HLA class-I alleles were identified as susceptibility factors for TB disease. With regards to genes of the MHC and LRC, several loci were found to alter susceptibility to TB in the SAC population, including MDC1, BTNL2, HLA-DOA, HLA-DOB, C6orf10, TAP2, LILRA5, NCR1, NLRP7 and the intergenic regions between HLA-C/WASF5P and LAIR1/TTYH1. We showed that the Beijing strain occurred more frequently in individuals with multiple disease episodes, with the HLA-B27 allele lowering the odds of having an additional episode. Associations were identified for specific HLA types and disease caused by the Beijing, Latin America-Mediterranean (LAM), Low-Copy Clade (LCC), and Quebec strains. HLA types were associated with disease caused by strains from the Euro-American or East Asian lineages, and the frequencies of these alleles in their sympatric human populations identified potential co-evolutionary events between host and pathogen. Finally, we showed that the SAC population is the most diverse SA population with regards to HLA alleles and KIR genotypes, as would be expected given the admixture of the SAC. Based on the HLA allele class-I profiles across SA populations, we noted that the Ag85BESAT- 6, Ag85B-TB10.4 and Mtb72f vaccines currently undergoing clinical trials would have low efficacy across most SA populations. We showed that the MHC and LRC regions in SAC healthy controls are predominantly of European ancestry, and that SAC TB cases are more closely related to Khoisan and black SA population groups. Our work highlights the importance of investigating both host and pathogen genetics when studying TB disease development and that understanding the genetic ancestral contributions to the SAC population can contribute to the identification of true and novel TB causing variants. / AFRIKAANSE OPSOMMING: Tuberkulose (TB) is jaarliks verantwoordelik vir ongeveer 2 miljoen sterftes en is die hoofoorsaak van dood as gevolg van „n aansteeklike siekte. Vorige navorsingstudies het aangedui dat die genetiese samestelling van die gasheer „n beduidende rol speel in die ontwikkeling van TB. Die kompleksiteit van hierdie siekte word vererger deur die betrokkenheid van die gasheer genoom sowel as bakteriële en omgewings faktore. Die Major Histocompatibility Complex (MHC) en Leukocyte Receptor Complex (LRC) bestaan uit verskeie gene wat die gasheer immuunrespons verstel. Die human leukocyte antigen (HLA) klas I gene van die MHC is betrokke by die aanbieding van patogeniese antigene op die oppervlak van geïnfekteerde selle, terwyl die killer cell immunoglobulin-like receptors (KIRs), geleë in die LRC, betrokke is by die herkenning van eie en vreemde selle. NK selle, deur middel van hul KIRs, kan dus vreemde selle uitwis aangesien hulle die uitgedrukte klas I molekules kan herken. Beide HLA en KIRs is hoogs polimorfies en verskil beduidend tussen etniese groepe. In hierdie studie is die bogenoemde gene en hul polimorfismes in die Suid Afrikaanse Kleurling bevolking (SAC) ondersoek om vas te stel tot watter mate dit genetiese vatbaarheid vir TB, asook vatbaarheid vir TB wat deur spesifieke Mycobacterium tuberculosis subtipes veroorsaak word, beïnvloed. Daar is ook gepoog om te verstaan hoe die voorouerlike bydrae van hierdie gene die SAC met betrekking tot TB vatbaarheid affekteer. Die resultate van die studie het aangedui dat die KIR3DS1 geen en KIR genotipes met vyf of meer aktiewe KIRs en die teenwoordigheid van 3DS1, die SAC bevolking beskerm teen die ontwikkeling van aktiewe TB. Verskeie HLA klas I allele is geïdentifiseer as vatbaarheidsfaktore vir TB. Talle lokusse van die MHC en LRC gene is ook as vatbaarheidsfaktore vir TB in die SAC bevolking geïdentifiseer, insluitende MDC1, BTNL2, HLA-DOA, HLA-DOB, C6orf10, TAP2, LILRA5, NCR1, NLRP7 en die intergeniese areas tussen HLA-C/WASF5P en LAIR1/TTYH1. Die studie het aangedui dat die Beijing stam meer voorkom in individue wat verskeie kere TB gehad het en dat die HLA-B27 alleel die kanse om „n verdere episode te hê, verlaag het. Assosiasies is geïdentifiseer tussen spesifieke HLA tipes en siekte veroorsaak deur die Beijing, LAM, LCC, en Quebec TB stamme. HLA tipes was geassosieer met siekte veroorsaak deur TB stamme van Euro-Amerikaanse en Oos-Asiëse afkoms. Die frekwensies van hierdie allele, in hul ooreenstemmende mensbevolkings, dui op „n potensïele koevolusionêre gebeurtenis tussen die gasheer en patogeen. Die studie het ook vasgestel dat die SAC populasie die mees diverse SA bevolking is met betrekking tot die HLA allele en KIR genotipes, soos verwag sou word gegewe die gemengde genetiese herkoms van die SAC. Gebaseer op die HLA allele klas I profiel van verskillende SA bevolkings merk ons op dat die Ag85B-ESAT-6, Ag85B-TB10.4 en Mtb72f vaksiene, wat huidiglik kliniese toetsing ondergaan, nie so effektief in die meeste SA bevolkings sal wees nie. Die studie het ook bewys dat die MHC en LRC streke in gesonde SAC kontroles, grootliks afkomstig was van „n Europese nalatenskap en dat die SAC TB gevalle meer verwant is aan die Khoisan en swart SA bevolkings. Hierdie studie beklemtoon die noodsaaklikheid om beide gasheer en patogeen genetika te bestudeer wanneer die ontwikkeling van TB ondersoek word en dat die verstaan van die genetiese voorouerlike bydrae van die SAC bevolking kan bydra tot die identifisering van ware en nuwe TB-veroorsakende variante.

Ces travaux de recherche portent sur l'aide à l'exploration de bases de données.La particularité de l'approche proposée repose sur un principe de co-évolution de l'utilisateur et d'une interface intelligente. Cette dernière devant permettre d'apporter une aide à la compréhension du domaine représenté par les données. Pour cela, une métaphore de musée virtuel vivant a été adoptée. Ce musée évolue de façon incrémentale au fil des interactions de l'utilisateur. Il incarne non seulement les données mais également des informations sémantiques explicitées par un modèle de connaissances spécifique au domaine exploré.A travers l'organisation topologique et l'évolution incrémentale, le musée personnalise en ligne le parcours de l'utilisateur. L'approche est assurée par trois mécanismes principaux : l'évaluation du profil de l'utilisateur modélisé par une pondération dynamique d'informations sémantiques, l'utilisation de ce profil dynamique pour établir une recommandation ainsi que l'incarnation des données dans le musée.L'approche est appliquée au domaine du patrimoine dans le cadre du projet ANTIMOINE, financé par l'Agence Nationale de la Recherche (ANR). La généricité de cette dernière a été démontrée à travers son application à une base de données de publications mais également à travers l'utilisation de types d'interfaces variés (site web, réalité virtuelle).Des expérimentations ont permis de valider l'hypothèse que notre système s'adapte aux évolutions des comportements de l'utilisateur et qu'il est capable, en retour, d'influencer ce dernier. Elles ont également permis de comparer une interface 2D avec une interface 3D en termes de qualité de perception, de guidage, de préférence et d'efficacité. / This thesis focus on a proposition that helps humans during the exploration of database. The particularity of this proposition relies on a co-evolution principle between the user and an intelligent interface. It provides a support to the understanding of the domain represented by the data. A metaphor of living virtual museum is adopted. This museum evolves incrementally according to the user's interactions. It incarnates both the data and the semantic information which are expressed by a knowledge model specific to the domain of the data. Through the topological organization and the incremental evolution, the museum personalizes online the user's exploration. The approach is insured by three main mechanisms: the evaluation of the user profile modelled by a dynamical weighting of the semantic information, the use of this dynamic profile to establish a recommendation as well as the incarnation of the data in the living museum. The approach has been applied to the heritage domain as part of the ANTIMOINE project, funded by the National Research Agency (ANR). The genericity of the latter has been demonstrated through its application to a database of publications but also using various types of interfaces (website, virtual reality).Experiments have validated the hypothesis that our system adapts itself to the user behavior and that it is able, in turn, to influence him.They also showed the comparison between a 2D interface and a 3D interface in terms of quality of perception, guidance, preference and efficiency.

The Loricariinae belong to the Neotropical mailed catfish family Loricariidae, the mostspeciose catfish family in the world, and are united by a long and flattened caudal peduncle and the absence of an adipose fin. Despite numerous works conducted on this group, no phylogeny is presently available. Prior to conduct evolutionary studies, an exhaustive and robust phylogeny was reconstructed using mitochondrial and nuclear data. Then, this phylogeny was used in multivariate and multi-table analyses to reveal the main evolutionary trends of the subfamily. The resulting phylogeny indicated that the Harttiini tribe, as classically defined, formed a paraphyletic assemblage and was restricted to three genera, and within the Loricariini tribe, two sister subtribes were distinguished, Farlowellina and Loricariina, both displaying complex evolutionary patterns. In addition several new taxa were highlighted and described. Subsequently using this phylogeny as exploratory tool, we demonstrated: (1) using co-inertia analysis that the diagnostic features provided to define the different genera were phylogenetically dependent; (2) using multiple co-inertia analysis that the underlying evolutionary forces shaping their diversification included intraphenotypic (morphology and genetics) and extraphenotypic (ecology and distribution) components; (3) using the RLQ analysis that co-dispersion events occurred between co-distributed species responsible for the current fish distribution; and (4) using the multi-scale pattern analysis that the co-evolution in traits related to the mouth characteristics was linked to reproductive functions responsible for a tertiary evolution of this organ.