رسالة جامعية
Modelling the articulation of selective and neutral mechanisms in the evolution of protein-coding DNA sequences ; Modélisation de l’articulation des mécanismes sélectifs et neutres dans l’évolution des séquences d’ADN codant pour des protéines
| العنوان: | Modelling the articulation of selective and neutral mechanisms in the evolution of protein-coding DNA sequences ; Modélisation de l’articulation des mécanismes sélectifs et neutres dans l’évolution des séquences d’ADN codant pour des protéines |
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| المؤلفون: | Latrille, Thibault |
| المساهمون: | Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon, Nicolas Lartillot |
| المصدر: | https://theses.hal.science/tel-03405159Test ; Genomics [q-bio.GN]. Université de Lyon, 2020. English. ⟨NNT : 2020LYSE1228⟩. |
| بيانات النشر: | HAL CCSD |
| سنة النشر: | 2020 |
| المجموعة: | HAL Lyon 1 (University Claude Bernard Lyon 1) |
| مصطلحات موضوعية: | Phylogenetics, Effective population size, Mutation-selection, Codon models, Protein-coding DNA sequences, Non-synonymous substitutions, Substitution rate, Phylogénie, Taille efficace de population, Mutation-sélection, Modèles à codons, Séquences codantes, Substitutions non-synonymes, Taux de substitution, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] |
| الوصف: | Molecular evolution aims to characterize the mechanisms at work in the evolution of sequences, governed by a stochastic process whose main components are mutation, selection and genetic drift. In the long term, this stochastic process results in a history of substitution events along species trees, inducing complex patterns of molecular divergence between species. By analysing them, phylogenetic codon models aim at capturing the intrinsic parameters of evolution. In this context, this thesis has been focused on phylogenetic codon models, and on modelling the interplay between mutation, selection and drift shaping protein-coding DNA sequences. Because the composition of protein-coding DNA sequences does not reflect the underlying mutational process, but its filtering by selection at the level of amino acids, a careful modelling is necessary to tease apart mutation and selection. Therefore, I first developed a phylogenetic codon model of inference in which different rates of evolution give an accurate representation of how mutation and selection oppose each other at equilibrium. Between the opposing forces of mutation and selection, the balance is arbitrated by genetic drift, which in turn is modulated by effective population size. As a consequence, variation of effective population size along of a phylogeny can theoretically be inferred from the trails of substitutions along the lineages. I thus developed a second model of inference, reconstructing altogether site-specific fitness landscape, long-term trends in effective population size and in the changes in the mutation rate along the phylogeny. This Bayesian framework was tested against simulated data and then applied to empirical data. Estimates of the variation of effective population size corresponds to the expected direction of correlation with life-history traits or ecological variables. However, the magnitude of inferred variation is narrower than expected based on independent estimates. In order to understand this narrow variation in the estimated ... |
| نوع الوثيقة: | doctoral or postdoctoral thesis |
| اللغة: | English |
| العلاقة: | NNT: 2020LYSE1228; tel-03405159; https://theses.hal.science/tel-03405159Test; https://theses.hal.science/tel-03405159v2/documentTest; https://theses.hal.science/tel-03405159v2/file/TH2020LATRILLETHIBAULT.pdfTest |
| الإتاحة: | https://theses.hal.science/tel-03405159Test https://theses.hal.science/tel-03405159v2/documentTest https://theses.hal.science/tel-03405159v2/file/TH2020LATRILLETHIBAULT.pdfTest |
| حقوق: | info:eu-repo/semantics/OpenAccess |
| رقم الانضمام: | edsbas.8E584F73 |
| قاعدة البيانات: | BASE |
| الوصف غير متاح. |