Status of plant systematics

[Richard Zander]

Fear not that molecular systematics will render us classical
systematists obsolete. The problem is in computerized "reconstruction,"
which is all pretty much Bayesian. Check Farris' 1973 Dollo parsimony
paper for a curiously slanted discussion of probability that hides an
important fact: computerized phylogenetic analysis usually gives
improbable results.
  If you analyse a simple three-taxon cladogram, the shortest tree with
two taxa sharing one advanced character has a .67 posterior probability
of being right. This is better than random .33 but compared to the sum
of the other two hypotheses (possible trees), .33, its just fair. With
two characters, the probability of the shortest tree is .80, better.
With 4 terminal taxa, however, you have 9 hypotheses, and the likelihood
of the shortest tree must be far greater than with just 3 hypotheses to
be "probable." For trees with several terminal taxa, the posterior
probablility of the shortest tree is less than .5, and there is more
evidence against than for.
  Check also the marginalized probabilities of the few published papers
using Monte Carlo methods for maximum likelihood, sometimes disguised as
"frequency" or just not given at all. The likeliest tree for larger data
sets has a .10 chance of being correct. Even if the several likeliest
trees are similar to the likeliest, the sum of their probabilities is
very small. Example:
http://www.stat.wisc.edu/newton/papers/abstracts/tr96/a.html
  Phylogeneticists of any stripe are getting away with maybe one paper
in ten having a good chance of a correct result, and which paper that is
is unknown. (The intuited regularity assumptions of Bayesian analysis
are another problem which I won't even bring up...) Simplicity is useful
in other sciences where the "least wrong" answer(s) out of many can be
immediately checked for correctness, but we have no such tests in
systematics.
  This will be abundantly evident someday as maximum likelihood analyses
become more prevalent and posterior probabilities are published, and
then it's back to monography for systematists.

--

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