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Détection de l’évolution convergente à l’échelle génomique : développement de méthodes et étude des adaptations indépendantes à la vie en milieu aride chez les rongeurs

Abstract : Phenotypic convergence, the independent acquisition of similar characters by different species,is widespread in nature and has been extensively studied. But this evolutionary process is not well understood. For example, many researchers seek to understand whether there are convergent genetic bases underlying these phenotypic convergences.Some convergent substitutions correlated with a convergent phenotype have been described in the literature, but there are few studies at the genome scale. This can be explained by two methodological problems : 1 / On the one hand, the difficulty of creating multi-species datasets for comparative analyses. 2 / On the other hand, the lack of dedicated methods to detect convergence at the genomic scale.During my thesis, I proposed solutions to these two challenges. As a first step, I created a program (CAARS) to automate the assembly of datasets composed of orthologous families from RNA-Seq data. Then I created a tool (PCOC) to study convergent substitutions within coding sequences, based on the identification of amino acid profile changes rather than strict amino acid changes. These tools have been developed for the sake of reproducibility and ease of use. I then studied the ability of different methods, including PCOC, to detect convergent substitutions in the presence of confounding factors. Finally, I applied these methods to a biological case where I sought to characterize the genomic bases of adaptation to arid environments in rodents.
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Carine Rey. Détection de l’évolution convergente à l’échelle génomique : développement de méthodes et étude des adaptations indépendantes à la vie en milieu aride chez les rongeurs. Bio-informatique [q-bio.QM]. Université de Lyon, 2019. Français. ⟨NNT : 2019LYSEN060⟩. ⟨tel-02476370⟩

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