In article <90luod$kkb$1 at mercury.hgmp.mrc.ac.uk>,
James McInerney <james.o.mcinerney at may.ie> wrote:
>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.
I believe such studies generally take this into account. They reckon up
how many sites *could* have a synonymous or nonsynonymous (S and N
from here on) substitution, and weight by how many such substitutions
could occur (a fourfold degenerate site contributes more possible
S substitutions than a twofold ones). So the actual statistic is the
ratio of "S mutations per S site" and "N mutations per N site". This is
often said as "ratio of S to N" but it's actually more complicated.
I think the original paper on this was by Masatoshi Nei.
Hope this helps,
Mary Kuhner mkkuhner at genetics.washington.edu