Re: Mutation equiprobability

If I understand you correctly, you are talking about reversible models
of sequence evolution in which the "forward" and "backward" mutations
occur at equal rates. There is no biological justification for this
simplifying assumption.

The assumption is made solely to make the mathematics easier to
calculate. Mutation rates are often inferred by fitting the model of
sequence evolution to a phylogenetic tree. If the root of the tree is
unknown then we do not know the direction (forwards or backwards) of
mutations along some branch of the tree. Assuming that such mutations
occur at equal rates reduces the computational burden of fitting the
model to a branch, since the directionality of that branch is
considered unimportant.

There are methods using hidden markov models rather than likelihood
models that abandon the reversibility assumption, as you suggest is
appropriate. However for estimating large phylogenetic trees the
reversibility assumption is useful in speeding up the calculations.
The forward and backward mutation rates often do not vary all that
much, so the assumption of reversibility may often be "good enough".

I'm not really sure what you mean by "backward evolution". If you are
suggesting that different forward and backwards rates of substitution
may result in a tendency for some nucleotides to predominate over
others in the genome, then in current models that possibility is taken
into account by inferring the equilibrium base frequencies for the
sequence in question.

Mick

On Aug 3, 5:02 pm, vent.du....@xxxxxxxxx wrote:
I have a question for the biochemists/geneticians:

As far as I know, it is assumed that the probablity p(A->B) of a
mutation from A to B is equal to its reverse p(B->A).
Is there any proof for such a statement. From a thermodynamical point
of view one expects the probability to be Boltzmann like:

p(A->B)= Cte* exp (-Eab/kT)

Where Eab is the energy gap between A and B

A direct consequence of the equiprobablilty is that the evolution is
only due to the selection process and in theory reversing the external
conditions should reverse the selection rules and leads to a backward
evolution. The geological data provide ample evidences of swings in
the climate but no evidence (or very few though I do not know any
example) of species experiencing a backward evolution.

Does anyone know why mutations are not considered like a chemical
reaction and why one does not use a Bolztmann probability ?



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