Sabine M. Huhndorf

A class-wide phylogenetic assessment of Dothideomycetes

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.

Fungi evolved right on track.

Dating of fungal divergences with molecular clocks thus far has yielded highly inconsistent results. The origin of fungi was estimated at between 660 million and up to 2.15 billion y ago, and the divergence of the two major lineages of higher fungi, Ascomycota and Basidiomycota, at between 390 million y and up to 1.5 billion y ago. Assuming that these inconsistencies stem from various causes, we reassessed the systematic placement of the most important fungal fossil, Paleopyrenomycites, and recalibrated internally unconstrained, published molecular clock trees by applying uniform calibration points. As a result the origin of fungi was re-estimated at between 760 million and 1.06 billion y ago and the origin of the Ascomycota at 500–650 million y ago. These dates are much more consistent than previous estimates, even if based on the same phylogenies and molecular clock trees, and they are also much better in line with the fossil record of fungi and plants and the ecological interdependence between filamentous fungi and land plants. Our results do not provide evidence to suggest the existence of ancient protolichens as an alternative to explain the ecology of early terrestrial fungi in the absence of land plants.

Myconet Volume 14. Part One. Outline of Ascomycota—2009. Part Two. Notes on Ascomycete Systematics. Nos. 4751–5113

Abstract Part One presents the current classification that includes all accepted genera and higher taxa above the generic level in the phylum Ascomycota. It is based on the changes listed in Myconet notes 4751–5113. In the current outline, three subphyla (Pezizomycotina, Saccharomycotina, Taphrinomycotina) are accepted. Taphrinomycotina includes four classes (Neolectomycetes, Pneumocystidomycetes, Schizosaccharomyces, Taphrinomycetes). Saccharomycotina consists of one class and Pezizomycotina includes eleven classes (Arthoniomycetes, Dothideomycetes, Eurotiomycetes, Geoglossomycetes, Laboulbeniomycetes, Lecanoromycetes, Leotiomycetes, Lichinomycetes, Orbiliomycetes, Pezizomycetes, Sordariomycetes). Part Two presents 363 notes on the taxonomy and nomenclature of ascomycetes (Ascomycota) at the generic and higher levels. Numerous changes in higher levels resulted from multi-authored phylogenetic papers resulting from the AFTOL and Deep Hyphae projects, especially a publication on a revised fungal classification spearheaded by David Hibbett in 2007 and a 2009 volume of Studies in Mycology edited by Conrad Schoch and others dedicated to the phylogeny of the Dothideomycetes. The new name Alectoria gowardii Lumbsch is proposed for Gowardia arctica P. Halonen, L. Myllys, S. Velmala & H. Hyvärinen (non Alectoria arctica Elenkin & Savicz).

Molecular systematics of the Sordariales: the order and the family Lasiosphaeriaceae redefined

The Sordariales is a taxonomically diverse group that has contained from seven to 14 families in recent years. The largest family is the Lasiosphaer-iaceae, which has contained between 33 and 53 genera, depending on the chosen classification. To determine the affinities and taxonomic placement of the Lasiosphaeriaceae and other families in the Sordariales, taxa representing every family in the Sordariales and most of the genera in the Lasiosphaeriaceae were targeted for phylogenetic analysis using partial sequences of the large-subunit (LSU) nrDNA. Based on molecular data, only genera within the families Chaetomiaceae, Lasiosphaeriaceae and Sordariaceae are retained within the redefined Sordariales. The order is a coherent group with morphologies that vary along well-defined lines, including large ascomata with large-celled membraneous or coriaceous walls and ascospores that show variation on a distinctive developmental theme, often with appendages or sheaths. The paraphyletic chaetomiaceous complex and the strongly supported Sordariaceae are nested among taxa traditionally placed in the Lasiosphaeriaceae. Analyses also indicate that 11 genera belong in the paraphyletic lasiosphaeriaceous complex. These taxa share a similar developmental pattern in their ascospore morphology that extends to the Sordariales as a whole. Based on these similarities in morphology, 13 additional genera are retained within the lasiosphaeriaceous complex and more than 35 genera have relationships in the order overall. Based on LSU data, 17 genera that have been assigned to the Lasiosphaeriaceae sensu lato are transferred to other families outside the Sordariales and 22 additional genera with differing morphologies subsequently are transferred out of the order. Two new orders, Coniochaetales and Chaetosphaeriales, are recognized for the families Coniochaetaceae and Chaetosphaeriaceae respectively. The Boliniaceae is accepted in the Boliniales, and the Nitschkiaceae is accepted in the Coronophorales. Annulatascaceae and Cephalothecaceae are placed in Sordariomycetidae inc. sed., and Batistiaceae is placed in the Euascomycetes inc. sed.

A molecular phylogenetic reappraisal of the Hysteriaceae, Mytilinidiaceae and Gloniaceae (Pleosporomycetidae, Dothideomycetes) with keys to world species

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 fungi, whether they relate to spore septation or the ascomata, in fact, represent symplesiomorphies, and most likely have arisen multiple times through convergent evolutionary processes in response to common selective pressures.

A natural classification of Lasiosphaeria based on nuclear LSU rDNA sequences

The current circumscription of Lasiosphaeria includes taxa with a wide variety of ascomatal walls, ascomatal wall vestitures, and ascospore morphologies and a broad range of putative anamorphs. Despite the complexity of morphological characters in the genus, species within Lasiosphaeria can be arranged into four groups based on ascospore morphology. Taxa which possessed ascospores in each of the four groups were used in phylogenetic analyses of partial nuclear large subunit (LSU) rDNA sequences to test the monophyly of the genus and determine relationships among its species. Lasiosphaeria was found to be highly polyphyletic in that species segregated into seven well-supported monophyletic clades dispersed among several orders. Three new genera, Echinosphaeria, Hilberina, and Immersiella, are erected for three of these clades while the genus Lasiosphaeris is reintroduced for a fourth clade. These data support Ruzenia as a previously established genus and the transfer of Lasiosphaeria raciborskii to Chaetosphaeria. The circumscription of Lasiosphaeria has been considerably narrowed to better reflect a natural classification. These taxonomic changes are additionally supported by a combination of morphological characters which are discussed in relation to the phylogenetic trees.

Using phylogenetic species recognition to delimit species boundaries within Lasiosphaeria

The genus Lasiosphaeria recently has been circumscribed more narrowly to include five mor-phospecies united by tomentose ascomata containing yellow centrum pigments. Species boundaries have not been established and phylogenetic relationships have not been clearly defined for these morphospecies. To delimit species boundaries and determine phylogenetic relationships among species, maximum parsimony, maximum likelihood and Bayesian analyses were conducted on sequence data from four nuclear genes, the ribosomal internal transcribed spacer (ITS) region, 28S large subunit (LSU) rDNA, β-tubulin and ribosomal polymerase II subunit 2 (RPB2). Representatives of L. glabrata, L. ovina, L. rugulosa and L. sorbina resolved as four highly supported monophyletic groups in almost all analyses and are recognized as well-defined species employing principles of genealogical concordance. These species delimitations are corroborated further by morphology. Representatives of L. lanuginosa were polyphyletic in almost all analyses. Although molecular analyses revealed that this morphospecies comprises several phylogenetic species, formal taxonomic recognition of these lineages is premature, so L. lanuginosa currently is treated as a morphological species complex. Complete species descriptions, including teleomorph, anamorph and culture characteristics, are given for L. glabrata, L. ovina, L. sorbina and the L. lanuginosa species complex along with detailed discussions of significant morphological characters used in recognizing species. These species are compared to five additional morphospecies that also may belong in the genus.

Two new genera in the Magnaporthaceae, a new addition to Ceratosphaeria and two new species of Lentomitella

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.

Parallel evolution of hysterothecial ascomata in ascolocularous fungi (Ascomycota, Fungi)

Abstract Ascoma morphologies have traditionally been used to classify filamentous ascomycete fungi. Phylogenies generated using DNA sequence data have since shown most of the previously identified groups not to be monophyletic. The relationships of hysterothecia‐bearing ascolocularous fungi have been unsettled for many years. Recent molecular studies have shown this group as currently circumscribed not to constitute natural groupings. This study targeted wide taxon sampling to assess the validity of the current classification in the group. A data set of 40 taxa was assembled including sequence data from nuclear large subunit rDNA and translation elongation factor 1 alpha for each taxon with 68 new sequences being generated for this study and aligned with 62 sequences obtained from GenBank. Parsimony, Bayesian and Maximum Likelihood analyses were performed on the data. Mytilinidiales was recovered as a strongly supported monophyletic clade, while a monophyletic Hysteriales was also recovered but with weak support. Gloniaceae (comprising the genus Glonium s. str. excluding Psiloglonium) was shown not to be monophyletic. This study established a monophyletic hysterothecial clade nested within Pleosporales, for which we proposed a new genus, Anteaglonium gen. nov. including two new species, A. globosum sp. nov. and A. latirostrum sp. nov. that are described. This relationship was strongly supported and most statistical analyses support the placement. The result of this study further indicates that the hysterothecial type of ascomata may have evolved several times within the ascolocularous fungi.

Molecular systematics of the Coronophorales and new species of Bertia, Lasiobertia and Nitschkia

The Nitschkiaceae has been placed in the Coronophorales or the Sordariales in recent years. Most recently it was accepted in the Coronophorales and placed in the Hypocreomycetidae based on sequence data from large subunit nrDNA. To confirm and corroborate the taxonomic placement and monophyly of the Coronophorales, additional taxa representing the diversity of the group were targeted for phylogenetic analysis using partial sequences of the large subunit nrDNA (LSU). Based on molecular data, the Coronophorales is found to be monophyletic and its placement in the Hypocreomycetidae is maintained. The order is a coherent group with morphologies that include superficial, often turbinate, often collabent ascomata that may or may not contain a quellkorper and asci that are often stipitate and at times polysporous. Three species with accepted Nitschkia names, together with Fracchiaea broomeiana and Acanthonitschkea argentinensis, comprise the paraphyletic nitschkiaceous complex. Two new families, Chaetosphaerellaceae and Scortechiniaceae fams nov., are described for the clades containing Chaetosphaerella and Crassochaeta and the taxa having a quellkorper (Euacanthe, Neofracchiaea and Scortechinia) respectively. The Bertiaceae is accepted for the clade containing Bertia species. Three new species are described: Bertia tropicalis, Lasiobertia portoricensis, and Nitschkia meniscoidea spp. nov.