Schizosaccharomyces pombe (fission "yeast") has been classified in a taxonomic group termed 'archiascomycetes' that is believed to belong to an ancestral assembly of the ascomycetes. S.pombe is almost as easily cultured and manipulated as yeast, it is well characterized as to classical and molecular genetics, its nuclear genome has been sequenced, and it is an alternative fungal model system, comparable to that of the yeast, Saccharomyces cerevisiae.
In phylogenetic analysis using nuclear small subunit rRNAs (e.g., Nishida and Sugiyama, 1993), S. pombe branches before the divergence of budding yeasts and "filamentous" ascomycetes (such as Neurospora, Penicillium and Aspergillus), however with low bootstrap support, and by using the little sophisticated evolutionary models that were available at the time of publication. When applying maximum likelihood methods with among-site variation on similar datasets, results vary and the position of S. pombe in the tree is not supported by likelihood tests (e.g., Shimodaira, 2002). The view that S. pombe maps to a different part of the tree than expected is supported by phylogenetic analyses using mitochondrial sequence data , however, at this time point, also only with 'reasonably high' high bootstrap support, but not with ML tests. We currently add more species to our mitochondrial data set (e.g., Saitoella, Taphrina, Galiella, Peziza, and further basidiomyctes) in order to resolve the question if S. pombe branches at deeply within ascomycetes, and if the term 'archiascomyetes' indeed reflects a meaningful taxon (i.e., a monophyletic assemblage of species), with significant statistic support.
The universal translation code is used for all ubiquitous mitochondrial genes of S. pombe, which clearly distinguishes it from other ascomycetes that have one or more codon reassignments. The universal translation code is also used in mitochondria of several lower fungi, such as the zygomycetes (e.g. Rhizopus stolonifer and unpublished results) and certain lineages of the chytridiomycetes (e.g., Allomyces, belonging to the Blastocladiales; as well as Monoblepharella and Harpochytrium, belonging to the Monoblepharidales). The universal translation code in S. pombe can be explained as a primitive character which was inherited from its lower fungal ancestors.
In view of this special position of S. pombe within the ascomycetes, the common name "fission yeast" is misleading, because it has not more in common with budding yeasts (e.g. Saccharomyces, or Pichia) as have non-yeast ascomycetes (e.g., Neurospora or Penicillium ). Despite its use of a mitochondrial universal translation code, however, the tiny S. pombe mitochondrial genome rather reflects a very derived fungus.
On the basis of the combined phylogenetic data, it is quite impossible to defend the popular idea that S. pombe is significantly closer to animals (in a phylogenetic sense) than are Aspergillus, Neurospora or yeasts.
