Phylogenies and uncertainty

Wolfgang Wuster bss166 at BANGOR.AC.UK
Fri Jul 28 19:02:07 CDT 1995

On Fri, 28 Jul 1995, Steve Heydon wrote:

> >I also agree that there is a vast difference between 10% completely correct
> >trees and 10% correct nodes of a tree.  Kim et al. 1993. Evolution 47:
> >471-486. have shown that in their simulations about 55% of the nodes are
> >correct.  As I have tried to indicate in a previous message, even if we know
> >that a certain percent of the tree or nodes of the tree are, on average,
> >correct, we don't know which ones they are.  Such a tree is close to useless,
> >in my opinion.
> >
> >-Warren Lamboy
> Perhaps this only means that we have a statistical problem of a slightly
> different nature. Certainly a node defined by one apomorphic character is
> less likely to be "real" than a node defined by three or more characters.
> For all its problems, techniques like Bootstrapping do provide such
> information. Other statistical techniques comparing phylogenies of the same
> group derived with different kinds of data sets would also provide
> information on the amount of support for different nodes. Perhaps what we
> need is actually more phylogenies.

We can also analyse all data with a number of different phylogenetic
algorithms, to determine to what extent the various nodes on a tree are
assumption-dependent. This may reduce the resolution of the method, but
will allow us to concentrate on those nodes which are actually well
corroborated, independent of methodology. A shift of emphasis from maximum
resolution to identifying robust, well-corroborated nodes would appear to
be in order. Nothing seems more futile than endless disputes between
adherents of one particular phylogenetic algorithm and another, or the
desperate attempts by some to wittle down 1000 equally parsimonious trees
to 1 by various methods of weighting etc. These are the pratices which
will be really badly affected by the lack of resolving power of current
phylogenetic algorithms.

Wolfgang Wuster
School of Biological Sciences, University of Wales, Bangor, UK
e-mail: bss166 at

Thought for the day: If you see a light at the end of the tunnel,
it is probably a train coming your way.

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