Pervasive variation in the frequencies of synonymous codons across genes and genomes (codon usage bias) 1 suggests that selection may favour some synonymous codons over others. However, it has been recognized for sometime that this assumption may not always be correct. Synonymous mutations might be expected to have no detectable effect on fitness, as this class of mutation does not change the amino-acid sequence of the encoded protein.

These results provide unequivocal evidence that synonymous mutations can drive adaptive evolution and suggest that this class of mutation may be underappreciated as a cause of adaptation and evolutionary dynamics.

We show experimentally that these mutations increase fitness by an amount comparable to non-synonymous mutations and that the fitness increases stem from increased gene expression. Here we report the recovery of two beneficial synonymous single base pair changes that arose spontaneously and independently in an experimentally evolved population of Pseudomonas fluorescens. Synonymous mutations have been shown to impact gene expression, protein folding and fitness, however, direct evidence that they can be positively selected, and so contribute to adaptation, is lacking.

However, a growing body of evidence from both comparative and experimental studies suggests otherwise. Conventional wisdom holds that synonymous mutations, nucleotide changes that do not alter the encoded amino acid, have no detectable effect on phenotype or fitness.

Pervasive synonyms