In article <ednah-0911951913500001 at johnh.hip.berkeley.edu>,
ednah at mws4.biol.berkeley.edu (Huelsenbeck) wrote:
> It sounds as if you want to test whether estimates from different data
> partitions (e.g., genes) are significantly different (more different than
> would be expected by stochastic variation). There are a couple of tests
> available that might prove acceptable.
No, this is not what I wish to test. The question is whether
or not a collection of sequences all BELONG to the same gene
tree; it is not whether or not different genes give the same tree.
This collection of sequences produce proteins that all have the
same function, but the sequence similarities of some of them
to the others are very low; there are conserved residues that
are present in some, but not all of the sequences.
Another way to put it is that I would like to know if this
collection of sequences is monophyletic on the grand tree of
all gene trees, or if it is para/polyphyletic with the intervening
sequences being of different function. While this is
fundamentally a phylogenetic question (presuming such a
grand tree of all gene trees exists), it is a horrendous one
to answer in that the sequences are so divergent that
one can't do a normal phylogenetic analysis on them - there's
just nothing to get a hold of.
So has anyone written about possible methods of coping with
such problems? (Obviously some of the general
literature on phylogenetic inference has some applicable stuff,
but I want to know if anyone has anyone has talked about this
specific problem, even if they have done so without presenting
it fully as a phylogenetics problem.)
David R. Maddison
Department of Entomology
University of Arizona
Tucson, AZ 85721
beetle at ag.arizona.edubeetle at ag.arizona.edu