One of the major aims in evolutionary enomics is to leverage comparative genomic data sets to understand the evolution of adaptively important traits. These comparisons may occur at multiple scales, but can be roughly classed into those that focus on differences between closely related species and those that aim to explain broad patterns across diverse groups of organisms. Perhaps the most significant contributions of genome comparisons thus far have been in highlighting broad evolutionary trends, such as identifying gene sets or pathways that have been adaptively important in the evolution of specific lineages, including our own. In contrast, the establishment of concrete links between genetic variation and specific traits remains rare, despite a handful of exciting early successes. We anticipate that the addition of more genome sequences will rapidly advance the field. In particular, we look forward to increasing integration between comparative genomic analyses and ecological and phenotypic data sets.

Key concepts:

• Comparisons between closely related species allow investigators to search for the genetic basis of recently evolved differences that distinguish those species.
  
• Comparisons across organisms that share a distant common ancestor allow investigators to search for the genetic basis of major shared differences that define these groups of related organisms.
  
• Genome comparisons often identify broad trends in trait evolution instead of specific genetic differences that influence a specific trait.
  
• Identification of specific genes that influence a specific trait requires not only genome-scale comparisons but also statistical filtering and experimental validation.
  
• Identification of regions of the genome that evolved under positive selection or that are functionally important is a useful method for narrowing down genome-wide differences to those that are most likely to have phenotypic effects.