Molecular taxonomy: on way out?

[A.P. Jason de Koning]

> Why bother expurging the data matrix from non-informative
> characters when the algorithm doesn't take them into account?
>

I agree that throwing out data here is unnecessary, and in general
can be biasing.

An unmentioned issue to consider with respect to probabilistic
analyses (of molecular or phenotypic characters): the inclusion of
characters with phylogenetically non-informative character state
distributions can be beneficial because they may contribute
information to the estimation of model parameters (such as relative
rates of character state transformation), which can have an
"indirect" effect on the selection of an optimal topology (though
perhaps rarely, and not strongly).  Why?  Because the effect on
relative rate estimates by 'non-informative' characters can alter the
relative probabilities of trees for other 'informative' characters!
For a very large dataset, inclusion of such characters could matter
for any given phylogeny problem...certainly it matters in molecular
evolutionary analyses where phylogeny is not the desired endpoint.

Cheers,
- Jason