Ribosomal DNA and resolution of branching order among the ascomycota: How many nucleotides are enough?

Molecular phylogenies for the fungi in the Ascomycota rely heavily on 18S r RNA gene sequences but this gene alone does not answer all questions about relationships, Particularly problematical are the relationships among the f irst ascomycetes to diverge, the Archiascomycetes, and the branching order among the basal filamentous ascomycetes, the Euascomycetes. Would more data resolve branching order? We used the jackknife and bootstrapping resamplin g approach that constitutes the "pattern of resolved nodes" method to addre ss the relationship between number of variable sites in a DNA sequence alig nment and support for taxonomic clusters, We graphed the effect of increasi ng sizes of subsamples of the 18S rRNA gene sequences on bootstrap support for nodes in the Ascomycota tree. Nodes responded differently to increasing data, Some nodes, those uniting the filamentous ascomycetes for example, w ould still have been well supported with only two thirds of the 18S rRNA ge ne. Other nodes, like the one uniting the Archiascomycetes as a monophyleti c group, would require about double the number of variable sites available in the 18S gene for 95% neighbor-joining bootstrap support, Of the several groups emerging at the base of the filamentous ascomycetes, the Pezizales r eceive the most support as the first to diverge. Our analysis suggests that we would also need almost three times as much sequence data as that provid ed by the 18S gene to confirm the basal position for the Pezizales and more than seven times as much data to resolve the next group to diverge. If mor e data from other genes show the same pattern, the lack of resolution for t he filamentous ascomycetes may indicate rapid radiation within this clade. (C) 2000 Academic Press.