Gobiidae is one of the largest families of teleost fishes with nearly 2000 species currently recognized. They have a worldwide distribution with exception of Arctic and Antarctic areas, inhabiting marine, brackish and freshwaters. Mostly, they are small-sized and live inconspicuously on the bottom. Their phylogeny has been studied only partially. In Europe, three independent lineages of gobies exist (Gobius-, Aphia- and Pomatoschistus-lineage), most of the species of these lineages are marine. In this work, I performed a multilocus study of the Gobius-lineage encompassing the majority of the species. Mitochondrial (cytochrome b and cytochrome c oxidase I) as well as nuclear (rhodopsin and recombination activating gene) markers were used. 480 individuals of 30 species were analyzed in the laboratory and sequences of further 25 - 32 species were downloaded from the Genbank and added to a dataset of each marker according to availability. Mitochondrial markers were more informative than the nuclear ones. The usefulness of cytochrome c oxidase I for studying phylogenetic relationships of gobies was compared with cytochrome b. Cytochrome c oxidase I showed to be useful for identification of the species, but has some limitations in resolving deeper phylogenetic relationships in gobies. Cytochrome b showed...

La génétique des populations est l’étude de l’évolution des fréquences alléliques au sein d’une population et de l’influence des pressions évolutives sur ces fréquences. Au sein de cette discipline, des modèles de population et des mesures génétiques sont développés pour pouvoir expliquer et prédire les données génétiques. Toutefois, au fur et à mesure des avancées technologiques, de nouveaux types de données sont disponibles, et il devient primordial de développer de nouveaux modèles et de nouvelles mesures pour pouvoir expliquer ces nouvelles données génétiques, plus denses et plus riches en marqueurs génétiques grâce à l’avènement de techniques comme la Next Generation Sequencing. Pour ce faire, nous proposons dans cette thèse de développer de nouvelles mesures avec une approche dite multilocus, qui considère le génome comme un tout plutôt que comme un agglomérat de locus indépendants. Dans un premier temps, nous avons tenté de construire une base théorique de l’approche multilocus en génétique des populations. Ensuite, nous avons illustré une telle approche à travers l’étude de l’identité par descendance, des graphes de recombinaison ancestraux et des autocorrélogrammes dans les modèles de génétique des populations. À travers ces différentes études de cas, nous avons tenté d’identifier les principaux enjeux et questions que soulève la génétique des populations multilocus. / Population genetics is the study of the evolution of allelic frequencies within a population and the influence of evolutionary pressures on these frequencies. Within this field, one could develop population models and measures to explain and predict genetic data. However, as technologie evolves new types of data are available, and it becomes essential to develop new models and new measures to reflect these new genetic marker data, increasingly richer and denser thanks to the advent of new techniques such as the Next Generation Sequencing. To this end, we propose in this thesis to develop new measures with the so-called multilocus approach, which considers the genome as a whole rather than an agglomerate of independent loci. We have first tried to build a theoretical basis for the multilocus approach in population genetics. Then, we have illustrated this multilocus approach with the case studies of identity by descent, ancestral recombination graphs and autocorrelograms in population genetics models. Through these different studies, we tried to identify the main issues and questions that the multilocus population genetics raises.