Coding flexibility being greatest in the third position, if the first two
positions are fixed by high pressures on the conventional phenotype then
only the third position can respond to pressures on the genome phenotype
(stem-loop potential, GC%, purine-loading, etc.). In the case of R-loading,
for example, if the conserved codon is YYR, then the third position R will
be conserved. If there is more flexibility in the first two positions (e.g.
RYN, YRN, RRN), then the third position can also be more flexible (e.g. RYY,
"Thorsten Burmester" <burmeste at mail.Uni-Mainz.de> wrote in message
news:9j786i$2ea$1 at mercury.hgmp.mrc.ac.uk...
>> Does anybody know why the synonymous and non-synonymous substition rates
> are correlated in many genes? I.e., in highly conserved genes one may
> find that both Ka and Ks are strongly reduced when compared to a less
> conserved paralogous gene.