COMMENTS ON THE PHYLOCODE
Richard H. Zander
Buffalo Museum of Science
1020 Humboldt Pkwy
Buffalo, NY 14211
July 19, 2001
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Note: The first Smithsonian Botanical Symposium "Linnaean Taxonomy in the 21st Century" was held on 30-31 March 2001 in Washington, D.C. at the National Museum of Natural History. A primary feature was consideration by speakers of the proposed PhyloCode as a substitute for the Linnaean system of nomenclature presently embodied in the nomenclatural codes of zoology and botany. The PhyloCode is based entirely on modern methods of analysis of evolutionary relationships, and is supposedly therefore better. Short invited comments on the subject by non-speaking participants in the symposium were posted on the Smithsonian Web site and also printed in The Plant Press, a publication of the Smithsonian Dept. of Systematic Biology. The following is reprinted from The Plant Press to make it more available to interested biologists:

Richard H. Zander
Buffalo Museum of Science

The two terminating branches and one basal free branch attached to any internal cladogram branch can be arranged in three ways giving ((AB)C) or ((AC)B) or ((BC)A). There is commonly support (shared traits) for one or both of the two arrangements alternative to the optimal. If the conflicting units of support (steps) are equal evidence of shared relationships, then the best assurance (without additional information on branch reliability) that parsimony analysis can give us is that there is a little better than 33% probability that the optimum branch represents the correct arrangement, not the two closest alternatives. Bootstrapping and decay index are not direct measures of branch support.

The null hypothesis in cladistics is a bush. Any shortest resolved tree is best evidence of relationship. But best for what use? Consider: Flip a coin 100 times to see if it is (phylogenetically) loaded. Cladistic philosophy: 50 heads and 50 tails means the null cannot be falsified, and we cannot hypothesize the coin is loaded. But, for instance, 54 heads and 46 tails is taken as evidence of loading for the head side up, being the "best explanation." Statistically, however, one could do a non-parametric test with the null being "equiprobable and randomly distributed" (54 or more heads would only occur randomly 24% of the time, and the null cannot be rejected at, say, the .95 confidence level), therefore there is no evidence of loading that one would act on. We are left with the unimpressive probabilistic proportion 54/100 for the chance of loading on heads. Only recently have statistical tests (other than subsampling) been introduced for gauging the reliability of individual branch arrangements.

While many obvious or "uncontested" phylogenies are supported by parsimony analysis, a PhyloCode implies additional resolution and reliability. Over the past 30 years, however, published resolved branch arrangements that are less than acceptably probable or which are not distinguishable from a random distribution have not been identified as such though doubtless common. An additional problem exists with molecular studies - differential lineage sorting of genes may produce well supported gene trees that are different from the species tree. One needs a minimum (by exact binary calculation) of three identical gene trees (with no contrary trees) for probabilistic reconstruction of the species tree, five if introgression is suspected (in ms.). Thus, identifiable probabilistic reconstructions of absolute branch orders are still in the future, and a PhyloCode based on past cladistic studies is not an acceptable alternative to standard nomenclature. For more discussion, see "Deconstructing Reconstruction" and various reprints.

Originally published as: Richard H. Zander. 2001. Invited comments, First Smithsonian Botanical Symposium. Plant Press 4(2): 15.