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Ka/Ks ratio - selection on "silence"

Donald Forsdyke forsdyke at post.queensu.ca
Sat Oct 19 08:37:52 EST 2002


James says: "We have seen this case and we just handle it by saying that
positive
selection has been very strong - just non-synonymous changes and no time for
observations of silent changes."

     Actually, the system may be telling you something more Michael. There
is a powerful "genome phenotype" which acts on so-called silent sites. One
explanation of zero synonymous changes is, as James says, not time for
mutations to occur (e.g. a recent population bottle-neck). Another
explanation is that there has been selection against silent changes. For
more, in the context of the genome of a malaria parasite, please see:
http://post.queensu.ca/~forsdyke/pfalcip01.htm

Donald Forsdyke, Department of Biochemistry, Queen's University, Canada


"Michael Steiper" <steiper at fas.harvard.edu> wrote in message
news:aoi30d$niv$1 at mercury.hgmp.mrc.ac.uk...
> Hi-
>
> I am trying to detect positive natural selection in a group of sequences
> using Ka/Ks comparisons.  The problem is that my number of Ks is zero in
> one of my branches.  With this zero in the denominator, I get undefined
> answers and strange results using the PAML program.
>
> Has anyone seen a case like this?  It seems like someone must have
> encountered this before, and I'd like to see how it was handled.  Any
> other ideas might be helpful, too.
>
> THanks,
>
> Michael Steiper
>
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