Climate change and other anthropogenic disturbances are forcing many natural populations to adapt to new environmental pressures, but the role of selection in shaping genome evolution is not fully understood. What factors explain variability in how far and fast adaptation proceeds? Two fundamental challenges are identifying the molecular basis of adaptive phenotypic variation and elucidating the evolutionary processes acting on this variation. We would like to know which genes and, in particular, which alleles produce diversity, and how natural selection acts on this variation. In natural populations, putatively adaptive loci often have been identified using genome scans, which detect outlier loci with variation significantly different from neutral expectations. Yet, this approach has some limitations; for example, it cannot inform us about the mechanistic basis of selection, recombination can obscure signals of past selection, and it can be difficult to distinguish between patterns created by demographic versus selective forces. Experimental studies help clarify the genetics of adaptation by documenting the mechanisms and targets of selection that drive changes in allele frequency (the process) in ways that are not possible when investigating historical signatures of selection (the outcome). Here, I will describe some examples of my work with threespine stickleback fish and deer mice that use manipulative experiments to directly estimate how selection impacts the genome as populations adapt to new environments. The results shed light on the pace of adaptive evolution in nature and improve our understanding of the functional connections between genotype, phenotype, and fitness.