  Many modified genetic codes are found in specific genomes in which one or
more codons have been reassigned to a different amino acid from that in the
canonical code. We present a model that unifies four possible mechanisms for
reassignment, based on the observation that reassignment involves a gain and a
loss. The loss could be the deletion or loss of function of a tRNA or release
factor. The gain could be the gain of a new type of tRNA for the reassigned
codon, or the gain of function of an existing tRNA due to a mutation or a base
modification. In the codon disappearance mechanism, the codon disappears from
the genome during the period of reassignment. In the other mechanisms, the
codon does not disappear. In the ambiguous intermediate mechanism, the gain
precedes the loss; in the unassigned codon mechanism, the loss precedes the
gain; and in the compensatory change mechanism, the loss and gain spread
through the population simultaneously. We present simulations of the gain-loss
model and demonstrate that all four mechanisms are possible. The frequencies of
the different mechanisms are influenced by selection strengths, number of
codons undergoing reassignment, directional mutation pressure and the
possibility of selection for reduced genome size.
