Coevolution within and between genes.

Interacting biological systems do not evolve independently, as exemplified many times at the cellular, organismal and ecosystem levels. Biological molecules interact tightly, and should therefore coevolve as well. Here we review the literature about molecular coevolution, between residues within RNAs or proteins, and between proteins. A panel of methodological and bioinformatic approaches have been developed to address this issue, yielding contrasting results: a strong coevolutionary signal is detected in RNA stems, whereas proteins show only moderate, uneasy to interpret departure from the independence hypothesis. The reasons for this discrepancy are discussed.