Physical activity is an essential component of the life history for most animals, and it also promotes both physical and mental health. Activity is a complex trait, affected by both genetics and numerous environmental factors, and the result of both motivation and physical ability. To elucidate the evolution of physical activity, the High Runner selection experiment was begun with 4 lines of mice bred for high voluntary wheel running (HR lines) and 4 non-selected control (C) lines. Although the HR lines evolved to run ~3 times as much as C lines daily, and numerous physiological and morphological differences have been documented, little is known about the genetic factors that differentiate HR and C lines. The first chapter utilizes whole-genome sequence data from 79 individuals from the 8 lines at generation 61 to identify signatures of selection. Three analytical methods agreed in identifying 13 genomic regions. These regions included genes associated with reward pathways and neural development, limb development, and other intuitive functions for wheel running. The second chapter uses the same genomic data and performs similar analyses, except dropping one line at a time. This identifies several new selection signatures and highlights how the replicate HR lines have responded to selection via "multiple solutions." The greatest change comes from dropping line HR3, which became fixed for a gene of major effect (i.e., the mini-muscle allele) that substantially alters the genetic background. The third chapter analyzes generation 22 allele frequencies obtained from sequencing pooled samples of approximately 10 males and 10 females from each line. Analyses identified not only many more selection signatures than at generation 61, but also very different genomic regions, with many of the strongest signatures in one generation being only weakly supported in the other. Simulations demonstrated that a hypothetical physiological constraint on wheel running reduces the power to detect selection and increases the likelihood of detectable signatures changing as selection limits are reached and passed. Each chapter identifies candidate genes for wheel-running behavior, related to both motivation and ability. Overall, these results enhance our understanding of the genetics and evolution of complex traits.