The taxonomy of the model filamentous fungus Podospora anserina.

The filamentous fungus Podospora anserina has been used as a model organism for more than 100 years and has proved to be an invaluable resource in numerous areas of research. Throughout this period, P. anserina has been embroiled in a number of taxonomic controversies regarding the proper name under which it should be called. The most recent taxonomic treatment proposed to change the name of this important species to Triangularia anserina. The results of past name changes of this species indicate that the broader research community is unlikely to accept this change, which will lead to nomenclatural instability and confusion in literature. Here, we review the phylogeny of the species closely related to P. anserina and provide evidence that currently available marker information is insufficient to resolve the relationships amongst many of the lineages. We argue that it is not only premature to propose a new name for P. anserina based on current data, but also that every effort should be made to retain P. anserina as the current name to ensure stability and to minimise confusion in scientific literature. Therefore, we synonymise Triangularia with Podospora and suggest that either the type species of Podospora be moved to P. anserina from P. fimiseda or that all species within the Podosporaceae be placed in the genus Podospora.

IMA Genome - F13: Draft genome sequences of Ambrosiella cleistominuta, Cercospora brassicicola, C. citrullina, Physcia stellaris, and Teratosphaeria pseudoeucalypti.

Draft genomes of the fungal species Ambrosiella cleistominuta, Cercospora brassicicola, C. citrullina, Physcia stellaris, and Teratosphaeria pseudoeucalypti are presented. Physcia stellaris is an important lichen forming fungus and Ambrosiella cleistominuta is an ambrosia beetle symbiont. Cercospora brassicicola and C. citrullina are agriculturally relevant plant pathogens that cause leaf-spots in brassicaceous vegetables and cucurbits respectively. Teratosphaeria pseudoeucalypti causes severe leaf blight and defoliation of Eucalyptus trees. These genomes provide a valuable resource for understanding the molecular processes in these economically important fungi.

Re-Evaluation of the Order Sordariales: Delimitation of Lasiosphaeriaceae s. str., and Introduction of the New Families Diplogelasinosporaceae, Naviculisporaceae, and Schizotheciaceae.

The order Sordariales includes the polyphyletic family Lasiosphaeriaceae, which comprises approximately 30 genera characterized by its paraphysate ascomata, asci with apical apparati, and mostly two-celled ascospores, which have a dark apical cell and a hyaline lower cell, frequently ornamented with mucilaginous appendages[...].

Phylogenetic relationships of five uncommon species of Lasiosphaeria and three new species in the Helminthosphaeriaceae (Sordariomycetes).

In an ongoing effort to monograph the genus Lasiosphaeria, it is desirable to obtain estimates of the phylogenetic relationships for five uncommon species, L. coacta, L. munkii, L. punctata, L. sphagnorum and L. stuppea. Three additional species previously placed in Lasiosphaeria, Echinosphaeria canescens, Hilberina caudata and Ruzenia spermoides, also were included in this study as well as three undescribed species. These species were believed to have relations elsewhere based on various ambiguous morphological characters, so an independent dataset from one or more genes was used to resolve their phylogenetic affinities. Sequences from the nuclear ribosomal 28S large subunit (LSU) and ß-tubulin genes were generated for these taxa. Maximum likelihood and Bayesian analyses indicated these taxa form a well supported monophyletic group with members of the Helminthosphaeriaceae and therefore, should be transferred out of Lasiosphaeria. Except for Helminthosphaeria gibberosa, Hilberina elegans, Ruzenia spermoides and Synaptospora plumbea, all taxa within this clade possess ascomata with distinct thick-walled setae. Based on a combination of morphological and molecular data, Helminthosphaeria tomaculum, Helminthosphaeria triseptata and Hilberina robusta are described as new and four new combinations are proposed: Helminthosphaeria ludens, Hel. stuppea, Hilberina punctata and H. sphagnorum. Ten new combinations are proposed based on morphological data: Echinosphaeria heterostoma, Helminthosphaeria flavocompta, Hel. gibberosa, Hel. heterotricha, Hilberina breviseta, H. elegans, H. foliicola, H. meznaensis, H. moseri and H. rhynchospora. Lasiosphaeria coacta is placed in synonymy with Hel. ludens and the previous transfer of Hilberina munkii is accepted. Synaptospora plumbea was found to belong in the family. Illustrations are provided for most Helminthosphaeriaceae taxa seen in this study.

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi.

Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

A new species and new records of Cercophora from Argentina.

Three species of Cercophora were found during a survey of the biodiversity of microfungi in northwest Argentina. Cercophora argentina possesses a unique combination of morphological characters and is described as a new species, while C. costaricensis and C. solaris are reported as new records for Argentina. Other species of Cercophora known from this region include C. natalita and C. coprogena, which is fully illustrated for the first time and determined herein to be a synonym of C. californica. All other species are described and illustrated.

The amsterdam declaration on fungal nomenclature.

The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19-20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). The purpose of the symposium was to address the issue of whether or how the current system of naming pleomorphic fungi should be maintained or changed now that molecular data are routinely available. The issue is urgent as mycologists currently follow different practices, and no consensus was achieved by a Special Committee appointed in 2005 by the International Botanical Congress to advise on the problem. The Declaration recognizes the need for an orderly transitition to a single-name nomenclatural system for all fungi, and to provide mechanisms to protect names that otherwise then become endangered. That is, meaning that priority should be given to the first described name, except where that is a younger name in general use when the first author to select a name of a pleomorphic monophyletic genus is to be followed, and suggests controversial cases are referred to a body, such as the ICTF, which will report to the Committee for Fungi. If appropriate, the ICTF could be mandated to promote the implementation of the Declaration. In addition, but not forming part of the Declaration, are reports of discussions held during the symposium on the governance of the nomenclature of fungi, and the naming of fungi known only from an environmental nucleic acid sequence in particular. Possible amendments to the Draft BioCode (2011) to allow for the needs of mycologists are suggested for further consideration, and a possible example of how a fungus only known from the environment might be described is presented.

Multigene phylogeny of the Coronophorales: morphology and new species in the order.

The phylogenetic relationships within Coronophorales have been debated because of uncertainty over the taxonomic usefulness of characteristics such as quellkörper, number of ascospores per ascus, presence of ascospore appendages, presence of subiculum and ascomatal vestiture. The phylogenetic relationships are examined with DNA sequence data from three nuclear genes targeting 69 taxa and 130 new sequences representing collections from Africa and the Americas. Analyses recovered monophyletic Bertiaceae, Chaetosphaerellaceae and Scortechiniaceae and a paraphyletic Nitschkiaceae. A single collection of Coronophora gregaria is included and Coronophoraceae is accepted. Bertiaceae is expanded to include Gaillardiella, and Thaxteria is synonymized with Bertia with a new combination, B. didyma. Three new species of Bertia are described: B. ngongensis from Kenya, B. orbis from Kenya and Costa Rica and B. triseptata from Ecuador and Puerto Rico. Bertia gigantospora is transferred from Nitschkia. Scortechiniaceae is confirmed for the quellkörper-bearing taxa including monotypic Biciliospora, Coronophorella, Neofracchiaea, Scortechiniella and Scortechiniellopsis. Tympanopsis is reinstated for T. confertula and T. uniseriata, while Scortechinia is more narrowly circumscribed to include S. acanthostroma and the new species, S. diminuspora from Ecuador. Cryptosphaerella is accepted in Scortechiniaceae including six new species from Kenya and Costa Rica, C. celata, C. costaricensis, C. cylindriformis, C. elliptica, C. globosa and C. malindensis. Spinulosphaeria is accepted in Coronophorales with uncertain family placement. The number of ascospores in the ascus is not phylogenetically useful in distinguishing genera within the order. The quellkörper continues to be an important character in defining the Scortechiniaceae, while taxa within the group show a mixture of morphological characteristics of varying phylogenetic importance. The presence of smooth versus spinulose subiculum aids in separating Tympanopsis and Scortechinia, and erumpent ascomata distinguish Cryptosphaerella species. Taxa within the Bertiaceae vary along the lines of robust, tuberculate, collapsing ascomata and large, hyaline to pigmented, septate ascospores.

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.

Amplistroma gen. nov. and its relation to Wallrothiella, two genera with globose ascospores and acrodontium-like anamorphs.

Amplistroma is described as a new genus for A. carolinianum, A. diminutisporum, A. guianense, A. hallingii, A. ravum, A. tartareum and A. xylarioides. Species of Amplistroma are distinguished by large stromata of textura intricata with polystichous ascomata and long necks that are either erumpent from the stromatal surface or form bumps or protuberances. The type collection of Ceratostoma sphaerospermum was examined and found to be synonymous with Wallrothiella congregata. The distribution of W. congregata is expanded by collections from Costa Rica, the eastern United States and Puerto Rico. Wallrothiella congregata has ascomata that are long-necked and develop individually or are gregarious on the substrate but do not form large stromata. Amplistroma and Wallrothiella are distinguished by small asci with eight, minute, globose ascospores. An acrodontium-like anamorph occurs in both genera. Phylogenetic analyses of 28S large-subunit rDNA sequences group these taxa in a well supported clade distinct from known orders within the Sordariomycetidae but showing unsupported relationships with the Chaetosphaeriales and the Magnaporthaceae. Family Amplistromataceae is described for this clade and placed within the Sordariomycetidae incertae sedis.

A re-evaluation of genus Chaetomidium based on molecular and morphological characters.

Chaetomidium, a genus in the Chaetomiaceae, comprises 12 species that produce similar cleistothecial ascomata with a membranous, mostly pilose, peridium. Approximately six species of this genus produce some type of modified peridium composed of cephalothecoid plates that previous authors have hypothesized to be a homologous character within the genus. To better understand the phylogenetic affiliations of Chaetomidium and distribution of the cephalothecoid peridium within this genus we performed phylogenetic analyses with LSU, beta-tubulin and rpb2 sequence data. The results of these analyses showed that Chaetomidium is polyphyletic and should be restricted to its type, C. fimeti, and C. subfimeti. The remaining cephalothecoid and non-cephalothecoid species were scattered throughout the Chaetomiaceae and Lasiosphaeriaceae. The cephalothecoid species of Chaetomidium were distributed in three unrelated clades, suggesting that the morphological similarity amo'ng these particular species resulted from convergence instead of ancestry.

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.

Whatever happened to the pyrenomycetes and loculoascomycetes?

An overview of current phylogenetic studies employing molecular data to test previously formulated hypotheses of relationships of loculoascomycetes and pyrenomycetes is given, concentrating on three topics: (1) circumscription and classification of loculoascomycetes, (2) a new classification of Sordariales, and (3) the phylogenetic occurrence of lichenized pyrenomycetes. With regard to these three examples, our review indicates: (1) In traditional taxonomy ascomycetes were classified according to their ascoma-types, with the class Pyrenomycetes including all taxa having perithecia. Later, the development of ascomata and the type of ascus were employed for higher-level classification, and consequently, Loculoascomycetes was separated from Pyrenomycetes. However, molecular studies show that even these revised classifications were too coarse. The Loculoascomycetes fall into two distinct and not closely related groups, which are placed in two clades: Chaetothyriomycetidae and Dothideomycetes. (2) Ascospore morphology has been widely used in taxonomy of ascomycetes, and Sordariales is a prominent example of this. Molecular data suggest that ascomatal wall morphology is a better predictor of phylogenetic relationships in these fungi. Further, the molecular data helped to redefine the circumscription of Sordariales. (3) The majority of non-lichenized pyrenomycetes form a monophyletic group: Sordariomycetes. However, the lichenized pyrenomycetes are highly polyphyletic. Pyrenocarpous lichen-forming fungi occur in several lineages each in Dothideomycetes, Chaetothyriomycetidae, and Lecanoromycetes, whereas no lichenized forms are currently known in the classical pyrenomycetous Sordariomycetes.

Cercophora rubrotuberculata sp. nov., a new pyrenomycete from the Great Smoky Mountains National Park.

An interesting wood-inhabiting pyrenomycete was discovered while collecting for the All Taxa Biodiversity Inventory currently being conducted in the Great Smoky Mountains National Park. This species is unique in possessing superficial ascomata with reddish tubercles and ascospores that develop an apical swollen brown cell and a long, basal hyaline cell. Because these ascospore characters fit the traditional morphological circumscription of Cercophora, this species is described as a new species within this genus.

A higher-level phylogenetic classification of the Fungi.

A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecanoromycetidae, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae. The most dramatic shifts in the classification relative to previous works concern the groups that have traditionally been included in the Chytridiomycota and Zygomycota. The Chytridiomycota is retained in a restricted sense, with Blastocladiomycota and Neocallimastigomycota representing segregate phyla of flagellated Fungi. Taxa traditionally placed in Zygomycota are distributed among Glomeromycota and several subphyla incertae sedis, including Mucoromycotina, Entomophthoromycotina, Kickxellomycotina, and Zoopagomycotina. Microsporidia are included in the Fungi, but no further subdivision of the group is proposed. Several genera of 'basal' Fungi of uncertain position are not placed in any higher taxa, including Basidiobolus, Caulochytrium, Olpidium, and Rozella.

Systematics of the genus Chaetosphaeria and its allied genera: morphological and phylogenetic diversity in north temperate and neotropical taxa.

Chaetosphaeria is a common saprobic pyrenomycete genus with simple, homogeneous teleomorphs and complex, diverse anamorphs. As currently circumscribed in the literature, the genus encompasses 30 species distributed in four 'natural groups', and includes morphological entities in 11 anamorphic genera. Species frequently have been defined primarily based on characters of the anamorphs resulting in species with almost indistinguishable teleomorphs. This study aimed to assess the value and significance of morphological characters in resolving phylogenetic relationships in Chaetosphaeria and its allied genera. Phylogenetic relationships of 42 taxa, representing 29 species distributed in Chaetosphaeria and five related genera, were estimated with partial sequences of the nuclear LSU rDNA and beta-tubulin genes. Sequences were analyzed with maximum parsimony, maximum likelihood and Bayesian methods. Phylogenetic analyses of these two genes combined revealed two major lineages. The Chaetosphaeria lineage includes 21 species possessing both typical and new sexual and asexual morphologies. The lineage contains a strongly supported monophyletic clade of 13 species and eight paraphyletic taxa; the latter includes C. innumera, the type species of the genus. The second major lineage includes groupings concordant with the morphological circumscriptions of the genera Melanochaeta, Melanopsammella, Striatosphaeria, Zignoëlla and the new genus Tainosphaeria.

An overview of the systematics of the Sordariomycetes based on a four-gene phylogeny.

The Sordariomycetes is one of the largest classes in the Ascomycota, and the majority of its species are characterized by perithecial ascomata and inoperculate unitunicate asci. It includes more than 600 genera with over 3000 species and represents a wide range of ecologies including pathogens and endophytes of plants, animal pathogens and mycoparasites. To test and refine the classification of the Sordariomycetes sensu Eriksson (2006), the phylogenetic relationship among 106 taxa from 12 orders out of 16 in the Sordariomycetes was investigated based on four nuclear loci (nSSU and nLSU rDNA, TEF and RPB2), using three species of the Leotiomycetes as outgroups. Three subclasses (i.e. Hypocreomycetidae, Sordariomycetidae and Xylariomycetidae) currently recognized in the classification are well supported with the placement of the Lulworthiales in either a basal group of the Sordariomycetes or a sister group of the Hypocreomycetidae. Except for the Microascales, our results recognize most of the orders as monophyletic groups. Melanospora species form a clade outside of the Hypocreales and are recognized as a distinct order in the Hypocreomycetidae. Glomerellaceae is excluded from the Phyllachorales and placed in Hypocreomycetidae incertae sedis. In the Sordariomycetidae, the Sordariales is a strongly supported clade and occurs within a well supported clade containing the Boliniales and Chaetosphaeriales. Aspects of morphology, ecology and evolution are discussed.

Multi-gene phylogenies indicate ascomal wall morphology is a better predictor of phylogenetic relationships than ascospore morphology in the Sordariales (Ascomycota, Fungi).

Ascospore characters have commonly been used for distinguishing ascomycete taxa, while ascomal wall characters have received little attention. Although taxa in the Sordariales possess a wide range of variation in their ascomal walls and ascospores, genera have traditionally been delimited based on differences in their ascospore morphology. Phylogenetic relationships of multiple representatives from each of several genera representing the range in ascomal wall and ascospore morphologies in the Sordariales were estimated using partial nuclear DNA sequences from the 28S ribosomal large subunit (LSU), beta-tubulin, and ribosomal polymerase II subunit 2 (RPB2) genes. These genes also were compared for their utility in predicting phylogenetic relationships in this group of fungi. Maximum parsimony and Bayesian analyses conducted on separate and combined data sets indicate that ascospore morphology is extremely homoplastic and not useful for delimiting genera. Genera represented by more than one species were paraphyletic or polyphyletic in nearly all analyses; 17 species of Cercophora segregated into at least nine different clades, while six species of Podospora occurred in five clades in the LSU tree. However, taxa with similar ascomal wall morphologies clustered in five well-supported clades suggesting that ascomal wall morphology is a better indicator of generic relationships in certain clades in the Sordariales. The RPB2 gene possessed over twice the number of parsimony-informative characters than either the LSU or beta-tubulin gene and consequently, provided the most support for the greatest number of clades.

Performance of four ribosomal DNA regions to infer higher-level phylogenetic relationships of inoperculate euascomycetes (Leotiomyceta).

The inoperculate euascomycetes are filamentous fungi that form saprobic, parasitic, and symbiotic associations with a wide variety of animals, plants, cyanobacteria, and other fungi. The higher-level relationships of this economically important group have been unsettled for over 100 years. A data set of 55 species was assembled including sequence data from nuclear and mitochondrial small and large subunit rDNAs for each taxon; 83 new sequences were obtained for this study. Parsimony and Bayesian analyses were performed using the four-region data set and all 14 possible subpartitions of the data. The mitochondrial LSU rDNA was used for the first time in a higher-level phylogenetic study of ascomycetes and its use in concatenated analyses is supported. The classes that were recognized in Leotiomyceta (=inoperculate euascomycetes) in a classification by Eriksson and Winka [Myconet 1 (1997) 1] are strongly supported as monophyletic. The following classes formed strongly supported sister-groups: Arthoniomycetes and Dothideomycetes, Chaetothyriomycetes and Eurotiomycetes, and Leotiomycetes and Sordariomycetes. Nevertheless, the backbone of the euascomycete phylogeny remains poorly resolved. Bayesian posterior probabilities were always higher than maximum parsimony bootstrap values, but converged with an increase in gene partitions analyzed in concatenated analyses. Comparison of five recent higher-level phylogenetic studies in ascomycetes demonstrates a high degree of uncertainty in the relationships between classes.