Integrating phylogenetic analysis and classification in fungi

Abstract

The central goal of taxonomic mycology is to create classifications that communicate understanding of fungal phylogeny. To insure that taxonomy reflects up-to-date phylogenetic hypotheses, there must be efficient mechanisms for translating phylogenetic trees into classifications. The current taxonomic system, which is based on the hierarchy of Linnaean ranks and the International Code of Botanical Nomenclature, is unsatisfactory for this purpose. One problem with the current taxonomic system is that a large number of ranks are necessary to classify complex phylogenetic trees. Rank proliferation creates a tension between the desire to name clades and the need to keep the number of ranks manageable. In addition, ranked classifications are quite sensitive to minor changes in tree topology, and are therefore unstable. The instability of ranked tree-based classifications encourages systematists to defer naming strongly supported clades if their internal structure or higher-level relationships are not well resolved. Thus, the current taxonomic system impedes progress toward a phylogenetic classification of fungi. As an alternative to the current taxonomic system, de Queiroz and Gauthier developed a system of “phylogenetic taxonomy,” which explicitly defines taxon names as designating clades, and which does not use taxonomic ranks. Eliminating the concept of rank promotes nomenclatural stability because the names of taxa are not sensitive to changes in their position in the tree relative to other taxa. As published fungal phylogenies grow in size and number, the problems of rank proliferation and nomenclatural instability caused by the current taxonomic system will become more severe. Serious consideration should be given to replacing the Code with a rankless system based on phylogenetic taxonomy. Although at this time there is no alternative to the Code, it is likely that detailed proposals for rankless codes of nomenclature will be developed in the next few years.