A recent paper in MBE presents evidence that the Taphrinomycota (containing S. pombe and Pneumocystis) are in fact a monophyletic group. This is considered an early branch in the Ascomycota with the Pezizomycotina (filamentous ascomycete fungi like Neurospora and Aspergillus) and Saccharomycotina (fungi mainly with yeast forms including Candida and Saccharomyces). The monophyly of Taphrinomyoctina fungi is something that has been fairly accepted but there are a few publications reporting conflicting evidence in some sets gene trees. This conflict is most likely due to Long Branch Attraction (LBA) and the Philippe lab has long worked on this problem of LBA working to develop tools like PhyloBayes that attempt to correct for LBA with a parameter rich model and using lots of data (like whole genomes). These authors are employing phylogenomics in the sense that multiple genes are used to reconstruct the phylogeny. This use is different from the J.Eisen/Sjölander sense which is to infer gene function from a phylogeny.
This paper presents evidence using proteins of 113 mitochondrial and nuclear genes and finds strong statistical support for this monophyly. They also note that it was necessary to remove fast evolving sites from a dataset of only mitochondrial genes in order to overcome LBA artifacts that lead to Saccharomyces and S. pombe sister relationship in previous analyses.
This paper also presents work using the Pneumocystis genome sequence helps resolve its placement and eventually understanding the evolution of this pathogen. In this tree the sister group to Pneumocystis is Schizosaccharomyces but both lineages have very long branches. The Saitoella lineage is basal in this paper which is different from what was found with a 4 gene (AFTOL) dataset (see Figure 2). Further work sampling more genes from these Taphrina lineages will likely help resolve the intra-clade relationships.
Y. Liu, J. W. Leigh, H. Brinkmann, M. T. Cushion, N. Rodriguez-Ezpeleta, H. Philippe, B. F. Lang (2008). Phylogenomic Analyses Support the Monophyly of Taphrinomycotina, including Schizosaccharomyces Fission Yeasts Molecular Biology and Evolution, 26 (1), 27-34 DOI: 10.1093/molbev/msn221