Through a glass, clearly: Experimental evolution as a window on adaptive genome evolution

This chapter explores recent examples where experimental evolution, empowered by genomic technologies and increasingly informed by systems biology, has fundamentally advanced our understanding of adaptive evolution. It focuses on genomically enabled insights into the following issues: how prevalent adaptive parallelism is; what the relative contributions of structural versus regulatory mutations are to the adaptive process; whether trade offs inevitably result from pleiotropy; how and why loss of function occurs under strong selection; and how much and how often adaptations arise from large-scale structural changes, such as gene duplications, deletions, and translocations. The chapter also offers perspective on how whole-genome sequencing and bioinformatics have been and can be fruitfully applied in the context of experimental evolution.