Subcellular structure and biochemical characters in fungal phylogeny

To clarify the past and potential roles of ultrastructural and biochemical characters in understanding fungal phylogeny and to make these data available for a wider range of fungal studies, we review the history of their study, especially since the mid-twentieth century. Recent molecular phylogenetic studies have revealed major gaps in the structural and biochemical data for Fungi as well as the incompleteness of studies within well-known taxonomic groups. We also consider the efforts to make the limited data on subcellular and biochemical characters available in the Structural and Biochemical Database. This database is a compilation of subcellular and biochemical information from the literature in a standardized format to permit precise data comparisons, identify phylogenetically informative characters, and provide character state coding and illustrations of character states; data are linked to voucher information for each taxon. The data are exportable in NEXUS format, which permits phylogenetic tree and ancestral character state reconstructions. Methods for incorporating structural and biochemical data into phylogenetic and other analyses are discussed, as is the role of the Fungal Subcellular Ontology in promoting data retrieval for use in related cellular, genetic, and ecological studies. Methods for obtaining subcellular data for Fungi are described to provide guidance for the evaluation of existing data and to assist in future data acquisition.