The aim of the PopPhyl project is to characterize the population genetic environment of many representative plant and animal species, in order to elucidate which biological and ecological factors determine molecular evolutionary processes - we want to know why genomes evolve the way they evolve. We will establish predictions about the influence of ecological (population size, varying environment) and genetical (mating systems, life cycle, mutation rate) variables on comparative genomic patterns thanks to improved molecular evolutionary theory relying on Fisher's geometric model. Predictions will be checked empirically by collecting extensive data sets of within-species and between-species genomic diversity in a large number of well-chosen taxa, with monitored life history traits. Massive gene sequences will be obtained from the extraction and analysis of abundant mRNA's, ensuring comparability between even distant taxa. These data will allow us to assess, and compare across species, the population genetic parameters relevant to molecular evolution: effective population size, mutation rate, strength of positive and negative selection. The main focus of the project is on the influence of population size, mating systems and life-span on molecular evolutionary rates. Are abundant species genetically more diverse? Do they adapt more efficiently? Is self-fertilization the evolutionary dead-end it is said to be? Why are fast-evolving proteomes fast: higher mutation rate, or prominent adaptive evolution ? PopPhyl is an ambitious, long-term multi-disciplinary project lying at the boundary of phylogenetics and population genetics, and requiring intensive theoretical and bioinformatic developments. We want to explore a new dimension of evolutionary biology by making population genetics comparative, and by injecting species ecology into genomic analyses.