I have a question about selection on genes in HIV (but probably anywhere).
In some HIV genes there is often a great excess of replacement substitutions
over silent substitutions. In the past we would say that this meant that
there was a positive selection event involved. However, if there is no
selective difference between substitutions that occur in synonymous and
non-synonymous sites then we would see about three times as many
substitutions that are replacement than silent.
Am I correct?
This would mean that the number of replacement changes could be about three
times as many as the silent substitutions in a gene that is not under any
selective pressure, either negative or positive.
The rates would be the same, but the absolute number of replacements would
be mostly replacement.
Does this mean that the value of 1, which is the arbitrary value chosen to
distinguish between positive and negative selection for Ka:Ks ratio
estimates might not be such a good cutoff point?
Does anybody have some thoughts on this?
Dr. James O. McInerney,
Department of Biology,
National University of Ireland,
+353 1 708 3860
+353 1 708 3845