Statistical methods for detecting molecular adaptation

The past few years have seen the development of powerful statistical method s for detecting adaptive molecular evolution. These methods compare synonym ous and nonsynonymous substitution rates in protein-coding genes, and regar d a nonsynonymous rate elevated above the synonymous rate as evidence for d arwinian selection. Numerous cases of molecular adaptation are being identi fied in various systems from viruses to humans. Although previous analyses averaging rates over sites and time have little power, recent methods desig ned to detect positive selection at individual sites and lineages have been successful, Here, we summarize recent statistical methods for detecting mo lecular adaptation, and discuss their limitations and possible improvements .