clade level molecular clock test?

Javier Quinteiro bnjquint at usc.es
Tue Jun 5 03:56:06 EST 2001

Hi, PHYLTEST: A program for phylogenetic hypothesis testing, S.Kumar 2.0
(1996), is useful to conduct the relative rate test between selected clades.

Chris Conroy wrote:

> Hello,
>      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.
> Thanks,
> Chris
> ---

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