An investigation of mushroom phylogeny using the largest subunit of RNA polymerase II gene sequences (RPB1) was conducted in comparison with nuclear ribosomal large subunit RNA gene sequences (nLSU) for the same set of taxa in the genus Inocybe (Agaricales, Basidiomycota). The two data sets, though not significantly incongruent, exhibit conflict among the placement of two taxa that exhibit long branches in the nLSU data set. In contrast, RPB1 terminal branch lengths are rather uniform. Bootstrap support is increased for clades in RPB1. Combined data sets increase the degree of confidence for several relationships. Overall, nLSU data do not yield a robust phylogeny when independently assessed by RPB1 sequences. This multigene study indicates that Inocybe is a monophyletic group composed of at least four distinct lineages-subgenus Mallocybe, section Cervicolores, section Rimosae, and subgenus Inocybe sensu Kühner, Kuyper, non Singer. Within subgenus Inocybe, two additional lineages, one composed of species with smooth basidiospores (clade I) and a second characterized by nodulose-spored species (clade II), are recovered by RPB1 and combined data. The nLSU data recover only clade I. The genera Astrosporina and Inocybella cannot be recognized phylogenetically. "Supersections" Cortinatae and Marginatae are not monophyletic groups.

Using RPB1 sequences to improve phylogenetic inference among mushrooms (Inocybe, Agaricales)