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.