Inference of selection from multiple species alignments

The selective pressure on a protein-coding gene can be measured by comparing silent (synonymous) and replacement (nonsynonymous) substitution rates. Higher replacement than silent rates provide unequivocal evidence for adaptive evolution driven by Darwinian selection. Previous employment of this criterion involved pairwise sequence comparison, averaging rates over time and sequences, resulting in virtually no power. Recent methods apply the criterion to particular lineages on a phylogeny or to individual sites in the gene and are much more powerful. Their application has led to detection of adaptive Darwinian selection in a number of genes and organisms.