Ulrich Melcher wrote:
> Here is my concern. If we have a tree whose statistics suggest
> that the star topology is not applicable, how can we be sure that the
> topology implying a line of descent is not due to limited sampling?
I don't think you *can* be sure: sensible people see trees as
estimates, not as revelations "written on stone tablets" (Yockey). But
one can do bootstrap, log-likelihood ratios, or other tests to see how
statistically *robust* one's tree is.
> Is it possible that there are only a limited
> number of regions of sequence space (corresponding to subtypes)
> compatible with a successful HIV-1? This would mean that the sequence
> space between subtypes consists of HIV-1's with poor "fitness". It
> would also mean that the subtypes were generated by rare events of a
> virus of one subtype jumping into another peak in sequence space.
Hmmm. Anybody else got an answer?
> Arguing against this are the observations of apparently successful
> recombinants between subtypes.
Ah, a Usenet poster who provides his own caveats. How refreshing. :)