Archiascomycetes: detection of a major new lineage within the Ascomycota

For phylogenetic analysis of the higher fungi, we sequenced the nuclear small subunit rRNA (18S rRNA) gene fromTaphrina populina, the type species of the genusTaphrina, andProtomyces lactucae-debilis. The molecular phylogeny inferred from these 2 sequences and 75 sequences from the DNA data bank divided the Ascomycota into three major lineages: the hemiascomycetes, the euascomycetes, and the archiascomycetes, newly described herein. The former two lineages are monophyletic, whereas the archiascomycetes, which originated first and are comprised ofTaphrina, Protomyces, Saitoella, Schizosaccharomyces, andPneumocystis, may not be monophyletic. Among the archiascomycetes, theTaphrina/Protomyces branch is monophyletic. Confirmation of the archiascomycetes as a monophyletic taxonomic class will require comparison of additional genetically defined characters.This work was supported in part by grants 05454030 from the Ministry of Education, Science, and Culture of Japan (to J. S.) and 4369 from the Japan Society for the Promotion of Science Fellowship Programs (to H. N.).     

Relatedness, phylogeny, and evolution of the fungi

Recent advances in fungal systematics are reviewed in relation to our previous studies. The usefulness of the integrated analysis of genotypic (especially 18S rRNA gene sequence comparisons) and phenotypic (especially ultrastructural and chemotaxonomic data) characters has been emphasized for the major groups and selected taxa of the fungi, and the impact to fungal systematics and evolution is discussed. Our noteworthy studies and findings are: 1) polyphyly of the chytridiomycetes and zygomycetes, 2) phylogenetic origin of the entomophthoralean fungi includingBasidiobolus, 3) detection of a major new lineage “Archiascomycetes,” comprisingTaphrina, Protomyces andSaitoella, Schizosaccharomyces, andPneumocystis, within the Ascomycota, and its phylogenetic and evolutionary significance, 4) polyphyletic origins of species in the anamorphic genusGeosmithia, and 5) phylogenetic placement ofMixia osmundae, species correctly and incorrectly assigned to the genusTaphrina, and basidiomyceotus yeasts. The newest 18S rDNA sequence-based neighbor-joining trees of the Ascomycota are demonstrated. “Traditional studies of evolution have amply demonstrated that evolution at the phenotypic level is characterized by adaptation and opportunism, irregularity in pace, and inequality of rates among lineages. In contrast, studies of molecular evolution have revealed quite different features characterized by changes that are conservative in nature, random in pattern (independent of phenotypic characters), and quite regular in pace with equal rates among diverge [sic] lineages for a given protein”. (Kimura, M. 1983. The neutral theory of molecular evolution, pp. 308–309, Cambridge University Press, Cambridge.) Recipient of the 2nd Mycological Society of Japan's Excellent Achievement Award, 1998; the awarding lecture was given at the 42nd Annual Meeting of the Mycological Society of Japan, 16 May, 1998, Kyoto University, Kyoto. This review is based mainly on the publications intended for the Award.     

Evolutionary relationships of membrers of the generaTaphrina, Protomyces, Schizosaccharomyces, and related taxa within the archiascomycetes: Integrated analysis of genotypic and phenotypic characters

To study the phylogeny and evolution of archiascomycetes, we determined the full sequence of the nuclear 18S rRNA gene from 14Taphrina species and 2Protomyces species, and the partial sequence ofSchizosaccharomyces japonicus var.japonicus. The sequences were phylogenetically analyzed by the neighbor-joining, maximum parsimony, and maximum-likelihood methods. We also looked at their principal phenotypic characters and genotypic character. Relationships within the Ascomycota are concordant with the previously published phylogenies inferred from 18S rDNA sequence divergence and divide the archi-, hemi-and euascomycetes into distinct major lineages. All the trees show that, within the archiascomycete lineage, 11 of the 14Taphrina species and the 2Protomyces species are monophyletic. A core groups ofTaphrina andProtomyces is always monophyletic. The evidence from molecular and phenotypic characters such as cell wall sugar composition, ubiquinone, cell wall ultrastructure, and mode of conidium ontogeny, strongly suggests that ‘T’. californica CBS 374.39, ‘T’. maculans CBS 427.69 and ‘T’. farlowii CBS 376.39 should be excluded from the archiascomycete lineage. ‘Taphrina’ farlowii CBS 376.39 groups withCandida albicans in the Saccharomycetales, whereas ‘T’. californica CBS 374.39 and ‘T’. maculans CBS 427.69 have a basidiomycete affinity and group with Tremellalean members in the hymenomycete lineage.Schizosaccharomyces is monophyletic. The strictly anamorphic yeastSaitoella complicata groups with the apothecial ascomyceteNeolecta vitellina rather than theTaphrina/Protomyces branch.