I've asked around a bit and have not found an easy solution to this
problem. I've probably just overlooked it in the literature. I'm sure
somebody out there can answer this one very quickly.
If one suspects that a set of sequences that represent one monophyletic
clade are evolving at a different rate than a set that represent another
monophyletic clade, can this be tested in reference to some outgroup(s)? I
would like to test for a molecular clock (i.e. rate homogeneity) between
two clades in a maximum likelihood topology rather than two sequences. I
don't want to pick a representative of each clade as I might have
significant amount of rate variation within each of these clades.
I'm aware of how to do three-taxon tests with DNA distances (e.g.
with software like K2WuLi), but I would like to expand that to a larger
number or use some statistics from the tree itself. If one were to do all
the three-taxon comparisons, what would be the most statistically rigorous
way to combine those results? One could invoke a two rate model in Yang's
PAML, but it wasn't clear to me how to test for significance between an ML
two rate model tree and some other tree (e.g. all rates different or a
clocklike tree). Also, PAML does not support all DNA substitution models.
Although I am interested in the theoretical aspects of this problem,
I am not a programmer, and thus I would be very interested in any software
that might be able to conduct this test.