Simulation of the evolution of codon usage in cpDNA

The codon usage of the Angiosperm psbA gene is atypical for flowering
plant chloroplast genes but similar to the codon usage observed in highly
expressed plastid genes from some other Plantae, particularly
Chlorobionta, lineages. The pattern of codon bias in these genes is
suggestive of selection for a set of translationally optimal codons but
the degree of bias towards these optimal codons is much weaker in the
flowering plant psbA gene than in high expression plastid genes from
lineages such as certain green algal groups. Two scenarios have been
proposed to explain these observations. One is that the flowering plant
psbA gene is currently under weak selective constraints for translation
efficiency, the other is that there are no current selective constraints
and we are observing the remnants of an ancestral codon adaptation that is
decaying under mutational pressure. We test these two models using
simulations studies that incorporate the context-dependent mutational
properties of plant chloroplast DNA. We first reconstruct ancestral
sequences and then simulate their evolution in the absence of selection on
codon usage by using mutation dynamics estimated from intergenic regions.
The results show that psbA has a significantly higher level of codon
adaptation than expected while other chloroplast genes are within the
range predicted by the simulations. These results suggest that there have
been selective constraints on the codon usage of the flowering plant psbA
gene during Angiosperm evolution.