ITS gene tree of the 50 or so New Zealand Mollisia and Mollisia-like species for which there are cultures, comparing them with Joey Tanney (2016) Phialocephala specimens, Brian Douglas (2013, PhD thesis), and Genbank BLAST matches to accessions from type specimens. UNITE Species Hypothesis matches are noted. Morphology has barely been compared, but in the case of NZ Species 31 morphology does not support the ITS-based genetic match. Any matches need confirming with a more discriminatory gene; RPB1 has been used by Tanney and others. Generic limits remain poorly resolved.

Data in Geneious Dan Discos\28 Sept 2017\Mollisia

'Mollisia' in the sense discussed here includes most of the New Zealand specimens having a sexual fruiting body with a Dermateaceae morphology in the sense of Korf (excipulum of more or less globose cells, usually with dark walls) that have an ITS sequence available, in morphologically defined genera such as Mollisia, Pyrenopeziza, Niptera, and Tapesia. Also included are the (as yet unpublished) sequences from the Mollisia PhD thesis of Brian Douglas, the Phialocephala sequences from Joey Tanney (Mycologia, 2016), and sequences that represent type specimens from Genbank BLAST search results based on the New Zealand sequences.

New Zealand specimens match Phialocephala banmuru, P. nodosa, P. oblonga and C. dextrinospora. The other approximately 33 species appear to be distinct from all Genbank data.

Included in the phylogeny on the basis of genetic similarity are a range of Leotiomycetes with reduced ascomata (e.g. Loramyces), several genera based on asexual morphologies (e.g. Barrenia, Acephala, Fuscosclera and Phialocephala, in addition to the genus Vibrissea. Genetically robust generic limits amongst these fungi remain to be resolved.

Some specimens with a more or less Mollisia-like morphology are genetically distinct. For example, D1091, D818, D770, in UNITE Species Hypothesis SH021623.07FU and genetically close to fungi with an aquatic hyphomycete like morphology such as Helicodendron, Filosporella, Tricladium, etc.

Phialocephala s.l. is still currently polyphyletic, both by including distantly related species and by occurrence in numerous closely related clades intermixed with species named in other genera, some of which have nomenclatural priority (e.g. Cystodendron, Mollisia, Trimmatostroma). Based on ITS sequences Grünig et al. (2002) showed that Ph. fusca, Ph. humicola (= Ph. xalapensis) and Ph. virens are outside the main Phialocephala clade. ITS BLAST queries suggest the placement of Ph. fusca and Ph. humicola in the Chaetosphaeriaceae. Morphological and phylogenetic evidence also reveal that Ph. trigonospora is not congeneric with Ph. dimorphospora and most likely belongs to Verticicladiella (Grünig et al. 2009). Acephala, a genus with two described species belonging to the PAC, is congeneric with Phialocephala and differentiated only by the lack of observed sporulation in culture (Grünig and Sieber 2005), a taxonomic choice enabled by some interpretations of dual nomenclature but now unacceptable after recent changes to the Code. Although the core clade of Phialocephala s.s. clearly defined as the Phialocephala dimorphospora clade, the presence of Mollisia cinerea-like teleomorphs in this clade cast at least some doubt on its nomenclatural priority over Mollisia until this species and the genus are epitypified (an ongoing project; A. Gminder pers comm). The apparent phylogenetic affinity of the PAC and allied taxa to Vibrissea in most phylogenies is also a major taxonomic issue that requires resolution. is further evident that Phialocephala s.s. remains to be comprehensively circumscribed, awaiting reassignment of phylogenetically closely related and unrelated Phialocephala species, and the formal transfer of species currently congeneric with Phialocephala s.s. (e.g. in Acephala and Mollisia), to stable and monophyletic genus concepts.

If Ph. dimorphospora is indeed congeneric with M. cinerea, then nomenclatural decisions will have to consider the interests of users of these names and the independent taxonomic histories of these genera. A principle of the Code is priority of publication. Mollisia, described by Karsten in 1871, clearly has priority over Phialocephala (1961). Unfortunately Mollisia is not yet robustly circumscribed and the prevailing concept is broad, polyphyletic and paraphyletic (Crous et al. 2003, Grünig et al. 2009). A definitive nomenclatural conclusion requires at least a preliminary phylogenetic investigation of Mollisia. Based on Index Fungorum, 603 names have been applied to Mollisia. The number of accepted Mollisia species after excluding synonymized taxa and subspecific identifiers is 231, excluding species of other genera that are probably congeneric or that already appear to overlap phylogenetically, such as Belonopsis, Haglundia, Nimbomollisia, Pyrenopeziza and Tapesia. Only seven Mollisia species are represented in GenBank, including only one representing an ex-type strain, M. dextrinospora (better placed in Pyrenopeziza, B. Douglas unpubl).

[Phialocephala is polyphyletic but] most well-studied species belong in the P. fortinii sensu lato (s.l.)–Acephala applanata species complex. [Note that this is phylogentically distinct from P. dimorphospora, the type species of the genus]

The PAC comprises so-called dark septate root endophytes, which are ubiquitous in the Northern Hemisphere and form complex communities in the roots of conifers and ericaceous plants. Members of the PAC are apparently restricted to roots and corresponding apothecia have never been observed in nature. Other Phialocephala species are reported as foliar and branch endophytes that form apothecia on decomposing tissues.

Phialocephala and Mollisia are polyphyletic and the delineation of these two genera remains unclear; consequently, endophytes identified by ITS sequences are often arbitrarily designated as Phialocephala, Mollisia, or Acephala. While the type species of Phialocephala, P. dimorphospora, is designated by an ex-type strain and is phylogenetically well-defined, the precise identification of the type species of Mollisia, M. cinerea, is unclear and the holotype is lost, although efforts to epitypify M. cinerea are underway (A. Gminder, pers. comm.). Understanding the relationship between Phialocephala and Mollisia is crucial for defining generic boundaries within Mollisiaceae.