Molecular evolution and phylogenetic analysis among higher fungi

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Using a phylogeny from molecules (mainly 18S rRNA gene sequences) and morphology, we drew the modern phylogenetic pictures in the major higher fungal taxa. The principal results are as follows. 1.We detected the major new lineage "Archiascomycetes", which we proposed, within the Ascomycota based on the 18S rRNA sequences. This lineage diverged first among the ascomycetes, prior to the divergence of the himiascomycetes and euascomycetes. 2.To date almost all mycologists have believed that Mixia osmundae is a member of the ascomycetes, related to the Protomycetales and Taphrinales. An analysis from both molecule (18S rRNA) and morphology (sporangium) indicated that this fungus is assigned to the simple septate basidio-mycetes. 3.We found a common group I intron sequence between a plant-parasitic fungus Proto-myces inouyei, and its host, Youngia japonica. It strongly suggests that the group I intron had been transferred from the host plant to the parasitic fungus in the course of evolution. 4.Phylogenetically three major lineages among basidiomycetes have been detected. A good correlation between 18S rRNA gene, septal Pore types, and cell wall chemistry was found in basidiomycetous yeasts. 5.The ascomycetes and basidiomycetes are monophyletic, whereas the chytridiomycetes and zygomycetes are polyphyletic. Our analysis suggests loss of flagella on several lineages and great divergence among the chytrids. 6.Using KL1C/KL1, a parallel logic programming language, we developed programs Contour/1 and Transverse/3 to calculate maximum likehood values of arbitary molecular phylogenetic trees.