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realistic amino acid subst. models

aroger at ac.dal.ca aroger at ac.dal.ca
Fri Jun 2 10:56:33 EST 1995

Des Higgins said:
> 1) why is reversibility suspect here (biologically)???  I would have guessed
> that the process could just as validly be treated as such (for almost
> all cases) with real proteins.  For individual cases where natural
> selection "drives" a substitution in one direction it will not hold
> but for neutral substitutions it will be perfectly valid (or am I being
> silly?).  By the looks of things, neutral changes are VERY common and
> possibly the great majority of changes are such.

I don't think that this argument is valid.  For instance if there is 
a bias towards mutation (say a bias to mutate from a pyrimidine
to a purine) and the change between two amino acids is neutral
9(say for the sake of argument that it is Asp and Glu). Then
over a period of time the accumulation of neutral mutations
in the third position will result in a bias of purines.  If you
look at a codon usage table, you can see that Glu has purines
in the third position and Asp has pyrimidines.  The accumlation
of purines in the third position of the GAN codons will thus
favour Glu over Asp.  Thus there could be a subsitution bias
towards Asp-->Glu and against Glu-->Asp...and this substitution
bias would be entirely the result of neutral changes.

Andrew Roger
aroger at ac.dal.ca

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