Title: Evolution of gene expression in yeast and Drosophila
Description: The wealth of genomic data and tools generated and developed in the last decade has offered unprecedented opportunities for our understanding of the ecological and evolutionary forces acting on genes on a genomic scale. Also, we can address how evolution shapes the functional architecture of genomes and how this architecture in turns impinges on the evolution of the genes that make up an organism. This thesis focuses on the evolution of gene expression in two model organisms, the wine yeast and the vinegar fly. In chapter one of this thesis, I review the recent literature on the budding yeast ecology and evolution to show that the integration of genetic and genomic data in an ecological perspective is now possible with model organisms and that this promises to be a fruitful approach for evolutionary biology in the years to come. In chapter two, using natural isolates of wine yeast grown along a gradient of stress conditions, I show that most genetic variation in gene expression is dependent of the growth conditions, a feature known as genotype-by-environment interaction, and that genes that are not essential for yeast survival and that have paralogs in the genome are particularly prone to show this genetic variation for transcriptional plasticity. In chapter three, using lines of yeast that have accumulated random, spontaneous mutations, I show that the sensitivity of genes to genetic perturbations, and thus their neutral rate of regulatory evolution, is influenced by particular features of genes regulatory sequences and the number of other genes in the genome that affect their expression. In chapter four, using two species of Drosophila and their F1 hybrid, I show that complex patterns of interaction between cis and trans regulatory divergence may explain a portion of the novel expression patterns observed in hybrids between species.

Finally, in chapter five, I investigate the polymorphism and divergence of gene expression in the phototransduction pathway of Drosophila melanogaster and Drosophila simulans and demonstrate that while the pathway shows global conservation, a gene involved in the fine tuning of visual sensitivity shows signs of expression divergence driven by natural selection.