Richard Zander bryo at COMMTECH.NET
Fri Dec 12 13:49:12 CST 1997

Ted Schultz wrote:
> >Richard Zander wrote:
> >Not as such. One might view, however, subclades that are identical in
> >all trees with posterior probabilities that add to .5 or to, say, .95,
> >as the equivalent (the first for more evidence for than against, the
> >second to maybe actually call it a good estimation). Perhaps this woul=
> >not work, what do you think?
> I think you could do this in the same way as has been suggested for
> bootstrap confidence tree "clouds" (see below).  However, I don't think=
> would be fair to calculate this by giving equal prior probability to al=
> possible trees.

You can give equal prior probability to all trees and get just a few
decent posterior probabilities.=20
Mau, B., M. A. Newton & B. Larget. 1997. Bayesian phylogenetic inference
via Markov chain Monte Carolo methods. Mol. Biol. Evol. 14: 717=96724.
got 250 trees with posterior probabilities adding to .95, and eliminated=20
10^40 trees. I think they used equal prior probabilities, at any rate,
the paper is dense.


> These approaches are unlikely to satisfy you, however, because the 95% =
> of bootstrap trees is still a small subset of all possible trees, and y=
> seem to want to calculate probability as a function of all possible tre=

No no. The curve of probability density as a function of all possible
gives only a few trees any decent posterior probability. Don't know how
they do this. A sufficiently advanced phylogenetic analytic method is
indistinguishable from magic--A.C.Clarke, paraphrased.

> A comment: There is probably a compromise between affording all possibl=
> trees equal a priori probability vs. affording a single (most
> parsimonious/most likely) tree all of the posterior probability.  For
> instance, every character implies a tree.  Trees implied by a single
> character are usually largely unresolved when lots of taxa are involved.
> If only the resolved parts of these trees are considered, we could come=
> with a set of resolved trees (including all possibilities in subtrees w=
> no character affords resolution, or in which characters conflict about
> topology) that is implied by all the characters considered individually.
> Add to this subset all possible trees that can be generated by the
> Archie/Faith permutation method (which probably includes the first set;=
> have to think about that) and all trees that have ever been proposed by=
> taxonomist, and you will have a subset of all possible trees where,
> arguably, the majority of prior probability should reside.  Now perform
> analyses and let the data suggest how the probability should be distrib=
> a posteriori.
> >Zander:
> >The frequentist statistical explanation is copasetic. So is the
> >Bayesian, but we must remember that we are assigning probabilities to
> >one event that happened in the past, one throw of the dice (worse, a
> >concatenated series of throws of the dice). So here we go with
> >statistical relevance again. An increase in probability does not
> >necessarily confer on a theory more evidence for than against. In
> >medicine, an increase in probability of disease is cause for concern b=
> >I for one would like to see *real good* confidence in a null, not just
> >an increase in probability. How is your confidence measured?
> >
> I will readily agree with you that there are too many papers using scan=
> (usually molecular) data to superficially "overturn" traditional system=
> groupings.  However, one series of studies that comes to mind in which =
> group of researchers has recovered largely congruent phylogenies from
> morphology and multiple genes is represented most recently by Fang et a=
> 1997.  Systematic Biology 46:269.  Regier, Mitter, Poole, and various g=
> students and postdocs have explored particular taxa and character syste=
> deeply.  This contrasts markedly with the more common approach of using
> whatever genes (primers) are available, producing a study, and moving o=
> and is much more likely to benefit phylogenetics in the long run.

Thanks for the fine review. I am illuminated but pleased in that we
agree on main points.


Richard H. Zander, Buffalo Museum of Science
1020 Humboldt Pkwy, Buffalo, NY 14211 USA bryo at

More information about the Taxacom mailing list