Phylogenetic Analyses of the Fungi Based on Large rDNA Data Sets

Abstract

Two data sets of fungal small subunit (SSU) rDNA sequences, one from the Ribosomal Da- tabase Project (RDP) with 485 sequences, and the other from the rRNA WWW Server (RNA-S) with 785 sequences, have been analyzed to estimate group sup- port and to compare tree topologies resulting from independently aligned, large data sets of largely the same sequences. The analyses were conducted by us- ing a parsimony jackknifing computer program to search rapidly for supported groups in combination with branch swapping and random addition sequenc- es. The results show that gross topology is very simi- lar. The major differences were with the Ascomycetes, which were not recovered in the RDP tree, and with the Holobasidiomycetes, which were not recovered in the RNA-S tree. Both data sets identify and support many well known fungal groups such as the Gloma- les, Saccharomycetes, Dikaryomycetes, Basidiomy- cetes, Uredinomycetes, Ustilaginomycetes, Euasco- mycetes, Leotiomyceta, Sordariomycetes and the Chaetothyriomycetes. No support was found for some previously proposed groups, including the Chy- tridiomycetes, Taphrinomycotina, Pezizomycotina through Pezizales, Hymenomycetes, Tremellomyce- tes, Leotiomycetes and the Dothideomycetes. The analysis contradicted some other previously proposed groups, among them the Zygomycota, Zygomycetes, Lecanoromycetes and the Sordariomycetidae. Trans- version parsimony performed on the same data sets