Xia Xuhua wrote:
>> Dear Colleagues,
>> Attached is a short (657 words) article of mine that I
> should appreciate your comments on. Thank you in advance.
>> Xuhua Xia
>...
> Therefore, a nonsynonymous
> substitution at the first or the third codon site is more
> nearly neutral and more likely fixed than a nonsynonymous
> substitution at the second codon site. This hypothesis
> ...
That was the first explanation that came to my mind
also. Leucine, isoleucine and valine all occur in the
codons with U in the second position.
I suspect the your explanation accounts for almost
all of the difference between observed and expected mutation
rates at the 3 codon sites. Other factors which might
influence the rate would be differences in transition/transversion
rates, differences in rates dinucleotide pairs (CpG mutates
frequently in mammals), and other biases. I suspect these
would be negligible in most genes, but could influence the
rates calculated from a few genes.
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