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In recent years, understanding of fungal phylogeny has been dramatically improved through the use of molecular characters in phylogenetic analyses. To effectively communicate this new knowledge, a system of rules or conventions should be adopted by which classifications become dependent functions of phylogenetic hypotheses. A variety of mechanisms have been proposed for translating phylogenetic trees into classifications. The Linnaean ranked hierarchy has been criticized as inadequate for phylogenetic classification. Maintaining the Linnaean system and requiring sister clades to have equal ranks results in a proliferation of trivial ranks. The 'sequencing convention' reduces the number of ranks needed, but requires that users of classifications understand the convention. Integrating ranked classifications for disparate lineages may be problematic. Rankless classification systems, such as the 'Phylogenetic Taxonomy' of de Queiroz and Gauthier, are better suited to representing phylogeny than the Linnaean hierarchy. Rankless systems also preclude the misinterpretation of ranks as biologically meaningful categories. Finally, we will examine the actual practices of fungal systematists as evidenced in current literature. Our preliminary survey indicates that there is a persistent dichotomy between phylogenetic studies and classification in fungi.

The order Arthoniales includes c. 1200 species which are classified in c. 60 genera. We present an investigation of phylogenetic relationships within the Arthoniales focussing on the Arthoniaceae. Studies on a broad range of arthonioid taxa show that character state delimitation is a non-trivial problem because intermediate traits are common in the Arthoniales. This will be demonstrated with characters used for description of ascomatal anatomy. Implications of phylogenetic analyses for the classification within the Arthoniales are pointed out. The relationships to other ascomycetous orders are discussed.

The Phylogenetic Mycology Group (PMG) at Umea University, Sweden, continuously updates a classification of orders and higher taxa of Ascomycota. The classification is based on molecular as well as other criteria and is published on the Internet (http://www.ekbot.umu.se/pmg/outline.html). Three subphyla are recognized, Taphrinomycotina, Saccharomycotina, and Pezizomycotina. Taphrinomycotina is divided into three classes, Neolectomycetes, Schizosaccharomycetes, and Taphrinomycetes. The single class in Saccharomycotina is Saccharomycetes. Pezizomycotina has two superclasses, Pezizomyceta with the single class Pezizomycetes, and Leotiomyceta with five classes, Dothideomycetes ('bitunicate pyrenomycetes', etc.), Eurotiomycetes ('plectascalean ascomycetes'), Lecanoromycetes (majority of lichens), Leotiomycetes ('inoperculate discomycetes', etc.), and Sordariomycetes ('unitunicate pyrenomycetes'). The bases for this provisional classification will be discussed, especially the information from SSU rDNA data.