We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.

The classification of Pleosporales has posed major challenges due to the lack of clear understanding of the importance of the morphological characters used to distinguish between different groups in the order. This has resulted in varied taxonomic treatments of many families in the group including Melanommataceae and Lophiostomataceae. In this study we employ two nuclear DNA gene markers, nuclear ribosomal large subunit DNA and translation elongation factor 1-alpha in order to examine the molecular phylogenetics of Pleosporales with strong emphasis on the families Melanommataceae and Lophiostomataceae. Phylogenetic analyses recovered Melanommataceae, Lophiostomataceae, Hypsostromataceae, and a few others as strongly supported clades within the Pleosporales. Melanommataceae as currently circumscribed was found to be polyphyletic. The genera Byssosphaeria, Melanomma, and Pseudotrichia were recovered within the family, while others such as Ostropella and Xenolophium nested outside in a weakly supported group along with Platystomum compressum and Pseudotrichia guatopoensis that may correspond to the family Platystomaceae. The genus Byssosphaeria was recovered as a strongly supported group within the Melanommataceae while Melanomma was weakly supported with unclear relationships among the species. The genera Herpotrichia and Bertiella were also found to belong in the Melanommataceae. Lophiostomataceae occurs as a strongly supported group but its concept is here expanded to include a new genus Misturatosphaeria that bears morphology traditionally not known to occur in the family. The strongly supported clade of Misturatosphaeria contains nine species that have gregarious, papillate ascomata with lighter coloured apices and plugged ostioles and that vary in ascospore morphology from 1- to 3-septate to muriform. Along with a strongly supported Lophiostoma clade, also within the family are Thyridaria macrostomoides based on new sequences from Kenyan collections and Massariosphaeria triseptata, M. grandispora, Westerdykella cylindrica and Preussia terricola based on GenBank sequences. The family Hypsostromataceae was recovered as a strongly supported monophyletic group nested within the Pleosporales.

A reappraisal of the phylogenetic integrity of bitunicate ascomycete fungi belonging to or previously affiliated with the Hysteriaceae, Mytilinidiaceae, Gloniaceae and Patellariaceae is presented, based on an analysis of 121 isolates and four nuclear genes, the ribosomal large and small subunits, transcription elongation factor 1 and the second largest RNA polymerase II subunit. A geographically diverse and high density taxon sampling strategy was employed, including multiple isolates/species from the following genera: Anteaglonium (6/4), Encephalographa (1/1), Farlowiella (3/1), Gloniopsis (8/4), Glonium (4/2), Hysterium (12/5), Hysterobrevium (14/3), Hysterographium (2/1), Hysteropatella (2/2), Lophium (4/2), Mytilinidion (13/10), Oedohysterium (5/3), Ostreichnion (2/2), Patellaria (1/1), Psiloglonium (11/3), Quasiconcha (1/1), Rhytidhysteron (8/3), and 24 outgroup taxa. Sequence data indicate that although the Hysteriales are closely related to the Pleosporales, sufficient branch support exists for their separation into separate orders within the Pleosporomycetidae. The Mytilinidiales are more distantly related within the subclass and show a close association with the Gloniaceae. Although there are examples of concordance between morphological and molecular data, these are few. Molecular data instead support the premise of a large number of convergent evolutionary lineages, which do not correspond to previously held assumptions of synapomorphy relating to spore morphology. Thus, within the Hysteriaceae, the genera Gloniopsis, Glonium, Hysterium and Hysterographium are highly polyphyletic. This necessitated the transfer of two species of Hysterium to Oedohysterium gen. nov. (Od. insidens comb. nov. and Od. sinense comb. nov.), the description of a new species, Hysterium barrianum sp. nov., and the transfer of two species of Gloniopsis to Hysterobrevium gen. nov. (Hb. smilacis comb. nov. and Hb. constrictum comb. nov.). While Hysterographium, with the type Hg. fraxini, is removed from the Hysteriaceae, some of its species remain within the family, transferred here to Oedohysterium (Od. pulchrum comb. nov.), Hysterobrevium (Hb. mori comb. nov.) and Gloniopsis (Gp. subrugosa comb. nov.); the latter genus, in addition to the type, Gp. praelonga, with two new species, Gp. arciformis sp. nov. and Gp. kenyensis sp. nov. The genus Glonium is now divided into Anteaglonium (Pleosporales), Glonium (Gloniaceae), and Psiloglonium (Hysteriaceae). The hysterothecium has evolved convergently no less than five times within the Pleosporomycetidae (e.g., Anteaglonium, Farlowiella, Glonium, Hysterographium and the Hysteriaceae). Similarly, thin-walled mytilinidioid (e.g., Ostreichnion) and patellarioid (e.g., Rhytidhysteron) genera, previously in the Mytilinidiaceae and Patellariaceae, respectively, transferred here to the Hysteriaceae, have also evolved at least twice within the subclass. As such, character states traditionally considered to represent synapomorphies among these f...

Ceratosphaerella is described as a new genus for C. castillensis and C. rhizomorpha. The genus is related to Ophioceras but distinguished by ascomata with a basal stroma and shorter, fusiform ascospores. Muraeriata is described for M. collapsa and M. africana, two species that are distinguished by having a vacuolate middle ascomal wall layer. The ascospores resemble those of Ceratosphaerella and ascospores in both genera are morphologically similar to those of Ceratosphaeria lampadophora. Both new genera are placed in the Magnaporthaceae based on LSU and SSU data. A species previously identified as Ophioceras tenuisporum was re-examined, found to fit the description of Pseudohalonectria phialidica and is transferred to Ceratosphaeria based on LSU data. Lentomitella tropica and L. pallibrunnea are described for two species that have long-necked ascomata with pale brown, ellipsoid ascospores and large ascal rings. Sequence data from the LSU places them in a clade with hyaline-spored Lentomitella crinigera and L. cirrhosa.