On the evolution of redundancy in genetic codes

We simulate a deterministic population genetic model for the coevolution of genetic codes and protein-coding genes. We use very simple assumptions abo ut translation, mutation, and protein fitness to calculate mutation-selecti on equilibria of codon frequencies and fitness in a large asexual populatio n with a given genetic code. We then compute the fitnesses of altered,genet ic codes that compete to invade the population by translating its genes wit h higher fitness. Codes and genes coevolve in a succession of stages, alter nating between genetic equilibration and code invasion, from an initial who lly ambiguous coding state to a diversified frozen coding state. Our simula tions almost always resulted in partially redundant frozen genetic codes. A lso, the range of simulated physicochemical properties among encoded amino acids in frozen codes was always less than maximal. These results did not r equire the assumption of historical constraints on the number and type of a mino acids available to codes nor on the complexity of proteins, stereochem ical constraints on the translational apparatus, nor mechanistic constraint s on genetic code change. Both the extent and timing of amino-acid diversif ication in genetic codes were strongly affected by the message mutation rat e and strength of missense selection. Our results suggest that various omni present phenomena that distribute codons over sites with different selectiv e requirements-such as the persistence of nonsynonymous mutations at equili brium, the positive selection of the same codon in different types of sites , and translational ambiguity-predispose the evolution of redundancy and of reduced amino acid diversity in genetic codes.