Phylogenetic analyses of the fungi based on large rDNA data sets

Two data sets of fungal small subunit (SSU) rDNA sequences, one from the Ribosomal Database Project (RDP) with 485 sequences, and the other from the rRNA WWW Server (RNA-S) with 785 sequences, have been analyzed to estimate group support and to compare tree topologies resulting from independently aligned, large data sets of largely the same sequences. The analyses were conducted by using a parsimony jackknifing computer program to search rapidly for supported groups in combination with branch swapping and random addition sequences. The results show that gross topology is very similar. 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 Glomales, Saccharomycetes, Dikaryomycetes, Basidiomycetes, Uredinomycetes, Ustilaginomycetes, Euascomycetes, Leotiomyceta, Sordariomycetes and the Chaetothyriomycetes. No support was found for some previously proposed groups, including the Chytridiomycetes, Taphrinomycotina, Pezizomycotina through Pezizales, Hymenomycetes, Tremellomycetes, Leotiomycetes and the Dothideomycetes. The analysis contradicted some other previously proposed groups, among them the Zygomycota, Zygomycetes, Lecanoromycetes and the Sordariomycetidae. Transversion parsimony performed on the same data sets resulted in extremely poor resolution in both trees and evidently transitional mutations are important contributors to the structure of the trees.