Genomic or detailed genetic data are now increasingly available for both model and non-model organisms, and this is allowing researchers to investigate the role that different forces play in shaping the evolution of species’ genomes. In this thesis I use large genetic and genomic datasets to attempt to quantify the action of natural selection and other forces on patterns of genetic polymorphism, differentiation and divergence in the natural world. These other forces include mutation, GC-biased gene conversion, genetic drift, and demography. Some of these forces act in the same direction in terms of their effect on the composition of genomes, and therefore the action of one may confound the detection of the action of others. To tell them apart, I often use a comparative method between different classes of sites, or between sites that differ in the extent to which they are subject to the relevant evolutionary pressures, as well as by using both polymorphism and divergence data. Where possible, I incorporate the effects of demography into these analyses. In the three main chapters that follow, I investigate 1) the forces that affect genetic differentiation between two populations of Drosophila melanogaster; 2) the forces underlying a naturally occurring colour polymorphism in the Australian finch Erythrura gouldiae; and 3) the forces which affect evolution at 4-fold degenerate sites in ancestral populations of D. melanogaster and D. simulans.