Automated Phylogenetic Taxonomy: An Example in the Homobasidiomycetes (Mushroom-Forming Fungi)

Abstract

Systematists confront a truly formidable task, which is to construct a comprehensive, phylogenetically accurate classification for all of life. Progress toward this goal has accelerated in recent years through analyses of DNA and protein sequences. The dramatic growth of molecular phylogenetics prompts us to ask whether established taxonomic practices are equipped to deal with the rapidly accumulating data. Here, we consider the current status of phylogenetics and classification in the homobasidiomycetes (mushroom-forming fungi), which includes roughly 17,000 described species (Kirk et al., 2001). We find that the available data are not being integrated, and that there is a significant gap between current taxonomy and understanding of phylogenetic relationships. To close this gap, we suggest that there is a need for new approaches that use the tools of bioinformatics to automate the process of phylogenetic analysis and classification, and we describe a prototype software package that we have developed for this purpose. The tools that we have created are applied to homobasidiomycetes, but can be adapted for use in any group of organisms.