Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit

The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits

We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.

A novel phylogenetic group withinThozetella(Chaetosphaeriaceae): a new taxon based on morphology and DNA sequence analyses

A new species, Thozetella pinicola , was isolated from leaf litter of Pinus elliottii Engelm. in Hong Kong. This taxon is described and compared with existing species in the genus. It occurs on the substrate as creamy white sporodochia and has short black conidiophores. Morphological characters are typical of Thozetella and it most closely resembles Thozetella falcata , Thozetella gigantea and Thozetella nivea , but may be distinguished by its distinct microawns and different conidial size. To gain further taxonomic insight into the phylogenetic relationships of our new taxon and its allies, we sequenced and analysed 6 different regions of 3 genes (ribosomal DNA and protein coding genes: RNA polymerase II largest subunit (RBP2) and β-tubulin). Resulting phylogenies are compared with existing morphological information. Molecular data support the relationship between Thozetella species and the Chaetosphaeriaceae (Chaetosphaeriales, Sordariomycetes). In addition, we recovered a new phylogenetic lineage (or group) within the existing phylogenetic framework of Thozetella as previously proposed. In particular, there is a close association between T. pinicola and T. nivea, which is strongly supported. The affinities of these 2 newly sequenced taxa are discussed in light of morphological and molecular characters.

Molecular systematics of the cotton root rot pathogen, Phymatotrichopsis omnivora

Cotton root rot is an important soilborne disease of cotton and numerous dicot plants in the south-western United States and Mexico. The causal organism, Phymatotrichopsis omnivora (= Phymatotrichum omnivorum), is known only as an asexual, holoanamorphic (mitosporic) fungus, and produces conidia resembling those of Botrytis. Although the corticoid basidiomycetes Phanerochaete omnivora (Polyporales) and Sistotrema brinkmannii (Cantharellales; both Agaricomycetes) have been suggested as teleomorphs of Phymatotrichopsis omnivora, phylogenetic analyses of nuclear small- and large-subunit ribosomal DNA and subunit 2 of RNA polymerase II from multiple isolates indicate that it is neither a basidiomycete nor closely related to other species of Botrytis (Sclerotiniaceae, Leotiomycetes). Phymatotrichopsis omnivora is a member of the family Rhizinaceae, Pezizales (Ascomycota: Pezizomycetes) allied to Psilopezia and Rhizina.

Penicillium parvulum and Penicillium georgiense, sp. nov., isolated from the conidial heads of Aspergillus species

Two new Penicillium species were isolated from peanut-field soils in Georgia. The species were noted particularly because they sporulated on the conidial heads of Aspergillus species. Phenotypic descriptions were prepared with standard media. LSU-rDNA sequences were determined for the new species and compared to existing homologous sequences from Penicillium species with parsimony analysis. The monoverticillate species, P. parvulum, was related most closely to E. cinnamopurpureum, while the furcate species, P. georgiense, appeared in the tree near P. thiersii. Because P. parvulum was closely related to E. cinnamopurpureum additional loci were sequenced (beta-tubulin and calmodulin) for these and some other closely related species to establish the status of the species through genealogical concordance. Some proposed synonymies from prior studies were examined and resolved.

Reconsideration of Protocrea (Hypocreales, Hypocreaceae)

The genus Protocrea is redefined, based on holotype and fresh specimens of its type species P. farinosa, using morphology of teleomorph and anamorph and phylogenetic analyses of rpb2 sequences. Data based on currently available specimens suggest the existence of three well defined and three still unnamed species. Apart from the type, P. farinosa, none of the species originally included are accepted in the genus. Species of Protocrea are characterized by perithecia formed in or on a subiculum, bicellular ascospores that disarticulate at the septum while still in the ascus and by anamorphs belonging to Gliocladium sensu stricto. For Hypocrea farinosa sensu auct. the new species H. decipiens is introduced. Hypocrea pallida is recognized as a species of Protocrea. It is closely related to P. farinosa, morphologically, phylogenetically and by habit. Protocrea illinoënsis is described here as the sister taxon of P. farinosa found in the USA. All species are polyporicolous, with the principal hosts Skeletocutis nivea for P. farinosa and P. illinoënsis, and species of Oligoporus/Tyromyces for P. pallida. In addition to hosts the main differences among these species are a stronger (orange) pigmentation of perithecia and subiculum in P. pallida and a violaceous KOH reaction in P. pallida and P. illinoënsis. P. farinosa is known only from Europe with certainty and P. illinoënsis only from the USA, while P. pallida is probably cosmopolitan. Putative synonymy of some similar species is discussed.

Didymella pisi sp. nov., the teleomorph of Ascochyta pisi

The anamorphic pycnidial fungus Ascochyta pisi is one member of a species complex that causes Ascochyta blight of pea, a potentially devastating disease. The teleomorphic state of this fungus was induced under laboratory conditions. Using morphological and molecular characters, we placed the teleomorph within the genus Didymella as D. pisi and describe a heterothallic mating system using a PCR-based mating type assay and in vitro crosses. We compare D. pisi with other Didymella spp. with which it might be confused.

Multi-locus phylogeny of Pleosporales: a taxonomic, ecological and evolutionary re-evaluation

Five loci, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, are used for analysing 129 pleosporalean taxa representing 59 genera and 15 families in the current classification of Pleosporales. The suborder Pleosporineae is emended to include four families, viz.Didymellaceae, Leptosphaeriaceae, Phaeosphaeriaceae and Pleosporaceae. In addition, two new families are introduced, i.e. Amniculicolaceae and Lentitheciaceae. Pleomassariaceae is treated as a synonym of Melanommataceae, and new circumscriptions of Lophiostomataceaes. str., Massarinaceae and Lophiotrema are proposed. Familial positions of Entodesmium and Setomelanomma in Phaeosphaeriaceae, Neophaeosphaeria in Leptosphaeriaceae, Leptosphaerulina, Macroventuria and Platychora in Didymellaceae, Pleomassaria in Melanommataceae and Bimuria, Didymocrea, Karstenula and Paraphaeosphaeria in Montagnulaceae are clarified. Both ecological and morphological characters show varying degrees of phylogenetic significance. Pleosporales is most likely derived from a saprobic ancestor with fissitunicate asci containing conspicuous ocular chambers and apical rings. Nutritional shifts in Pleosporales likely occured from saprotrophic to hemibiotrophic or biotrophic.

Molecular systematics of the marine Dothideomycetes

Phylogenetic analyses of four nuclear genes, namely the large and small subunits of the nuclear ribosomal RNA, transcription elongation factor 1-alpha and the second largest RNA polymerase II subunit, established that the ecological group of marine bitunicate ascomycetes has representatives in the orders Capnodiales, Hysteriales, Jahnulales, Mytilinidiales, Patellariales and Pleosporales. Most of the fungi sequenced were intertidal mangrove taxa and belong to members of 12 families in the Pleosporales: Aigialaceae, Didymellaceae,Leptosphaeriaceae, Lenthitheciaceae, Lophiostomataceae, Massarinaceae,Montagnulaceae, Morosphaeriaceae, Phaeosphaeriaceae, Pleosporaceae, Testudinaceae and Trematosphaeriaceae. Two new families are described: Aigialaceae and Morosphaeriaceae, and three new genera proposed: Halomassarina, Morosphaeria and Rimora. Few marine species are reported from the Dothideomycetidae (e.g. Mycosphaerellaceae, Capnodiales), a group poorly studied at the molecular level. New marine lineages include the Testudinaceae and Manglicolaguatemalensis in the Jahnulales. Significantly, most marine Dothideomycetes are intertidal tropical species with only a few from temperate regions on salt marsh plants (Spartina species and Juncus roemerianus), and rarely totally submerged (e.g. Halotthia posidoniae and Pontoporeia biturbinata on the seagrasses Posidonia oceanica and Cymodocea nodosum). Specific attention is given to the adaptation of the Dothideomycetes to the marine milieu, new lineages of marine fungi and their host specificity.

European species of Hypocrea Part I. The green-spored species

At present 75 species of Hypocrea have been identified in temperate Europe. Nineteen green-spored species and their Trichoderma asexual states are here described in detail. Extensive searches for Hypocrea teleomorphs in 14 European countries, with emphasis on Central Europe, yielded more than 620 specimens within five years. The morphology of fresh and dry stromata was studied. In addition, available types of species described from Europe were examined. Cultures were prepared from ascospores and used to study the morphology of cultures and anamorphs, to determine growth rates, and to extract DNA that was used for amplification and sequencing of three genetic markers. ITS was used for identification, while RNA polymerase II subunit b (rpb2) and translation elongation factor 1 alpha (tef1) were analyzed for phylogenetic reconstruction of the genus.SEVERAL UNEXPECTED FINDINGS RESULTED FROM THIS PROJECT: 1) The previous view that only a small number of Trichoderma species form a teleomorph is erroneous. 2) All expectations concerning the number of species in Europe are by far exceeded. Seventy-five species of Hypocrea, two species of Protocrea, and Arachnocrea stipata, are herein identified in temperate Europe, based on the ITS identification routine using fresh material, on species described earlier without molecular data and on species recently described but not collected during this project. 3) Current data suggest that the biodiversity of Hypocrea / Trichoderma above soil exceeds the number of species isolated from soil. 4) The number of Trichoderma species forming hyaline conidia has been considered a small fraction. In Europe, 26 species of those forming teleomorphs produce hyaline conidia, while 42 green-conidial species are known. Three of the detected Hypocrea species do not form an anamorph in culture, while the anamorph is unknown in four species, because they have never been cultured.This work is a preliminary account of Hypocrea and their Trichoderma anamorphs in Europe. Of the hyaline-spored species, H. minutispora is by far the most common species in Europe, while of the green-spored species this is H. strictipilosa.General ecology of Hypocrea is discussed. Specific associations, either with host fungi or trees have been found, but the majority of species seems to be necrotrophic on diverse fungi on wood and bark.The taxonomy of the genus will be treated in two parts. In this first part 19 species of Hypocrea with green ascospores, including six new teleomorph and five new anamorph species, are described in detail. All green-spored species belong to previously recognised clades, except H. spinulosa, which forms the new Spinulosa Clade with two additional new species, and H. fomiticola, which belongs to the Semiorbis Clade and forms effuse to large subpulvinate stromata on Fomes fomentarius, a trait new for species with green ascospores. Anamorph names are established prospectively in order to provide a basis for possible policy alterations towards their use for holomorphs.

Phylogenetic relationships of Polyporus and morphologically allied genera

Polyporus accommodates morphologically heterogeneous species and is divided into six infrageneric groups based on macromorphological characters. On the other hand allied genera have macro- and microscopic characters similar to those of Polyporus. The phylogenetic relationships of Polyporus and allied genera were established from sequences of RNA polymerase II second largest subunit (RPB2), nuclear ribosomal large subunit (nucLSU) and mitochondrial ATPase subunit 6 (ATP6). The molecular phylogenetic trees confirmed that Polyporus is a polyphyletic genus and recognized six major clades (1-6) containing species of Polyporus and several allied genera. Among the clades one contained three infrageneric groups of Polyporus and two allied genera, Datronia and Pseudofavolus while one other contained group Polyporellus and Lentinus. Five of the six major clades contained species belonging to a single infrageneric group, Favolus, Melanopus, Polyporellus or Polyporus. This suggests that morphological characters used to define these groups have phylogenetic significance and reveals the need for a taxonomic revision of Polyporus and its allied genera.

Advances in the phylogenesis of Agaricales and its higher ranks and strategies for establishing phylogenetic hypotheses

We present an overview of previous research results on the molecular phylogenetic analyses in Agaricales and its higher ranks (Agaricomycetes/Agaricomycotina/Basidiomycota) along with the most recent treatments of taxonomic systems in these taxa. Establishing phylogenetic hypotheses using DNA sequences, from which an understanding of the natural evolutionary relationships amongst clades may be derived, requires a robust dataset. It has been recognized that single-gene phylogenies may not truly represent organismal phylogenies, but the concordant phylogenetic genealogies from multiple-gene datasets can resolve this problem. The genes commonly used in mushroom phylogenetic research are summarized.

Multi-gene phylogeny and morphotaxonomy of Amniculicola lignicola: a novel freshwater fungus from France and its relationships to the Pleosporales

A collection of submerged wood samples in the Pyrénées, France, led to the discovery of a new freshwater Dothideomycetes genus. Amniculicola lignicola gen sp. nov, is described and illustrated. In addition, rDNA and RPB2 gene sequences are analysed phylogenetically to investigate its ordinal and familial placement. Morphologically, Amniculicola resembles species of Ostropella and Xenolophium in having subglobose ascomata with prominent lips surrounding a slit-like ostiole. However, it is readily distinguished from Ostropella and Xenolophium by ascus shape and in having a short pedicle and thin peridium. Phylogenetic analyses based on 28S rDNA sequences also indicated that A. lignicola and O. albocincta (type species of Ostropella) are phylogenetically distinct. Morphological characters indicate that Amniculicola belongs in the Pleosporales and this is supported by molecular data. Sequences analyses from three loci suggest that it is closely related to anamorphic fungi, such as Anguillospora longissima, Spirosphaera cupreorufescens, and Repetophragma ontariense; however, its affinities with known Dothideomycetes and its familial placement are still unresolved.

Multilocus sequence identification of Penicillium species in cork bark during plank preparation for the manufacture of stoppers

Despite several studies reporting Penicillium as one of the most frequent fungal genera in cork planks, the isolates were rarely identified to species level. We conducted a detailed study to identify Penicillium species from the field to the factory environment prior to and after boiling the cork planks. A total of 84 samples were analyzed. Of the 486 Penicillium isolates phenotypically identified, 32 representative or unusual strains were selected for identification by multilocus DNA sequence type. Cork proved to be a rich source of Penicillium biodiversity. A total of 30 taxa were recognized from cork including rarely seen species and 6 phylogenetically unique groups. Spores of some species lodged deep in cork can survive the boiling process. P. glabrum, P. glandicola and P. toxicarium, species with high CFU numbers in the field, are still frequently present in cork after boiling. Other species are killed by the boiling treatment and replaced by Penicillium species originating from the factory environment. Species known to contribute to cork taint were isolated at all stages. Good manufacturing practices are necessary at all stages in the preparation of cork planks to minimize the load of Penicillium species that produce cork taint.

Phylogenetic placement and taxonomic review of the genus Cryptosporella and its synonyms Ophiovalsa and Winterella (Gnomoniaceae, Diaporthales)

The type species of Cryptosporella, C. hypodermia, and Ophiovalsa, O. suffusa, as well as closely related species were studied using morphological, cultural, and DNA sequence characteristics. DNA sequence data from three different loci (ITS, LSU, and RPB2) suggest that C. hypodermia and O. suffusa are congeneric within the Gnomoniaceae (Diaporthales). This result is supported by similarities in perithecial, ascal and ascospore morphology, and lifestyles characterized as initially endophytic, becoming saprobic as plant tissues die. Furthermore, both type species produce Disculina anamorphs. A review of the literature indicates that the generic name Cryptosporella has priority over Ophiovalsa and its synonym Winterella sensu Reid & Booth (1987). A redescription of the genus Cryptosporella is included, as well as a description of C. hypodermia, C. suffusa, the type species of Ophiovalsa, a brief account of the other seven species accepted in Cryptosporella, and a key to species of Cryptosporella. Eight new combinations are established: C. alnicola (Fr.) L.C. Mejía & Castleb., comb. nov.; C. betulae (Tul. & C. Tul.) L.C. Mejía & Castleb., comb. nov.; C. confusa (Reid & Booth) L.C. Mejía & Castleb., comb. nov.; C. corylina (Tul. & C. Tul.) L.C. Mejía & Castleb., comb. nov.; C. femoralis (Peck) L.C. Mejía & Castleb., comb. nov.; C. suffusa (Fr.) L.C. Mejía & Castleb., comb. nov.; C. tiliae (Tul. & C. Tul.) L.C. Mejía & Castleb., comb. nov.; and C. wehmeyeriana (Reid & Booth) L.C. Mejía & Castleb., comb. nov.

Widespread occurrence and phylogenetic placement of a soil clone group adds a prominent new branch to the fungal tree of life

Fungi are one of the most diverse groups of Eukarya and play essential roles in terrestrial ecosystems as decomposers, pathogens and mutualists. This study unifies disparate reports of unclassified fungal sequences from soils of diverse origins and anchors many of them in a well-supported clade of the Ascomycota equivalent to a subphylum. We refer to this clade as Soil Clone Group I (SCGI). We expand the breadth of environments surveyed and develop a taxon-specific primer to amplify 2.4kbp rDNA fragments directly from soil. Our results also expand the known range of this group from North America to Europe and Australia. The ancient origin of SCGI implies that it may represent an important transitional form among the basal Ascomycota groups. SCGI is unusual because it currently represents the only major fungal lineage known only from sequence data. This is an important contribution towards building a more complete fungal phylogeny and highlights the need for further work to determine the function and biology of SCGI taxa.

Using the putative asexual fungus Cenococcum geophilum as a model to test how species concepts influence recombination analyses using sequence data from multiple loci

Recent studies have found that three divergent lineages of the ectomycorrhizal fungus Cenococcum geophilum may co-occur within a single soil sample. To test how inference of population structure is affected by species concept, potential recombination in this putative asexual fungus was analyzed by sequencing 10 loci from 44 isolates from within one main lineage that is potentially sub-divisible into two phylogenetic species (A and B). Phylogenetic incongruence between these loci and recombination analyses using six different methods was consistent with recombination. However, most of the incongruence was caused by an apparently reciprocal recombination event between the actin locus and the other loci studied. Extreme divergence between the two types of actin loci suggests either an ancient recombination event or a more recent horizontal inheritance. We also found that random mating could not be rejected when A and B isolates were treated as members of a single species based on multilocus disequilibrium analyses, whereas random mating was rejected when all isolates were pooled. These results are significant and demonstrate that inferences of population structure can be confounded when isolates are pooled together based entirely on a morphological species concept.

The polyphyletic nature of Pleosporales: an example from Massariosphaeria based on rDNA and RBP2 gene phylogenies

Massariosphaeria is a loculoascomycetous fungus currently accommodated within the Pleosporales. However, based on morphology alone, it has been difficult to assess its familial position and its affinities to other fungi with bitunicate asci. In order to establish its evolutionary relationships, two regions of the rDNA (18S and 28S) and two regions of the RPB2 protein-coding gene were sequenced and analysed phylogenetically. Multigene phylogenies revealed that Massariosphaeria is not monophyletic and results are in disagreement with existing morphological-based classification schemes. Characters, such as ascomatal shape and ascospore morphology, have evolved more than once within the Pleosporales. The familial placement of several species is still obscure, except M. grandispora, which could be confidently assigned to the Lophiostomaceae. M. typhicola is closely related to Trematosphaeria hydrela (Melanommataceae), whereas M. triseptata is related to Melanomma radicans but shares close affinities to the Sporormiaceae. The placement of M. roumeguerei is still unresolved, and it does not appear to have any close evolutionary relationship to any known melanommataceous or pleosporaceous genera. Our molecular data also refute the monophyly of Kirschsteiniothelia, Massarina, Melanomma, and Pleospora, and support previous phylogenetic hypotheses that Melanommataceae is polyphyletic. There is a need for more phylogenetic (and taxonomic) studies within the Pleosporales, especially incorporation of more anamorphic taxa and type species.

Diversity of the trifunctional histidine biosynthesis gene (his) in cereal Phaeosphaeria species

Phaeosphaeria species are important causal agents of Stagonospora leaf blotch diseases in cereals. In this study, the nucleotide sequence and deduced polypeptide of the trifunctional histidine biosynthesis gene (his) are used to investigate the phylogenetic relationships and provide molecular identification among cereal Phaeosphaeria species. The full-length sequences of the his gene were obtained by PCR amplification and compared among cereal Phaeosphaeria species. The coding sequence of the his gene in wheat-biotype P. nodorum (PN-w) was 2697 bp. The his genes in barley-biotype P. nodorum (PN-b), two P. avenaria f. sp. triticea isolates (homothallic Pat1 and Pat3), and Phaeosphaeria species from Polish rye and dallis grass were 2694 bp. The his gene in heterothallic isolate Pat2, however, was 2693 bp because the intron had one fewer base. In P. avenaria f. sp. avenaria (Paa), the his gene was only 2670 bp long. The differences in the size of the his gene contributed to the variation in amino acid sequences in the gap region located between the phosphoribosyl-ATP pyrophosphohydrolase and histidinol dehydrogenase sub-domains. Based on nucleotide and deduced amino acid sequences of the his gene, Pat1 was not closely related to either PN-w or the Paa clade. It appears that rates of evolution of the his gene were fast in cereal Phaeosphaeria species. The possible involvement of meiotic recombination in genetic diversity of the his gene in P. nodorum is discussed.

Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: A case study of the Lecanoromycetes (Ascomycota)

The resolving power and statistical support provided by two protein-coding (RPB1 and RPB2) and three ribosomal RNA-coding (nucSSU, nucLSU, and mitSSU) genes individually and in various combinations were investigated based on maximum likelihood bootstrap analyses on lichen-forming fungi from the class Lecanoromycetes (Ascomycota). Our results indicate that the optimal loci (single and combined) to use for molecular systematics of lichen-forming Ascomycota are protein-coding genes (RPB1 and RPB2). RPB1 and RPB2 genes individually were phylogenetically more efficient than all two- and three-locus combinations of ribosomal loci. The 3rd codon position of each of these two loci provided the most characters in support of phylogenetic relationships within the Lecanoromycetes. Of the three ribosomal loci we used in this study, mitSSU contributed the most to phylogenetic analyses when combined with RPB1 and RPB2. Except for the mitSSU, ribosomal genes were the most difficult to recover because they often contain many introns, resulting in PCR bias toward numerous and intronless co-extracted contaminant fungi (mainly Dothideomycetes, Chaetothyriomycetes, and Sordariomycetes in the Ascomycota, and members of the Basidiomycota), which inhabit lichen thalli. Maximum likelihood analysis on the combined five-locus data set for 82 members of the Lecanoromycetes provided a well resolved and well supported tree compared to existing phylogenies. We confirmed the monophyly of three recognized subclasses in the Lecanoromycetes, the Acarosporomycetidae, Ostropomycetidae, and Lecanoromycetideae; the latter delimited as monophyletic for the first time, with the exclusion of the family Umbilicariaceae and Hypocenomyce scalaris. The genus Candelariella (formerly in the Candelariaceae, currently a member of the Lecanoraceae) represents the first evolutionary split within the Lecanoromycetes, before the divergence of the Acarosporomycetidae. This study provides a foundation necessary to guide the selection of loci for future multilocus phylogenetic studies on lichen-forming and allied ascomycetes.

Biogeography of Hysterangiales (Phallomycetidae, Basidiomycota)

To understand the biogeography of truffle-like fungi, DNA sequences were analysed from representative taxa of Hysterangiales. Multigene phylogenies and the results of ancestral area reconstructions are consistent with the hypothesis of an Australian, or eastern Gondwanan, origin of Hysterangiales with subsequent range expansions to the Northern Hemisphere. However, neither Northern Hemisphere nor Southern Hemisphere taxa formed a monophyletic group, which is in conflict with a strictly vicariant scenario. Therefore, the occurrence and importance of long-distance dispersal could not be rejected. Although a pre-Gondwanan origin of Hysterangiales remains as a possibility, this hypothesis requires that Hysterangiales exist prior to the origin of the currently recognized ectomycorrhizal plants, as well as the arrival of mycophagous animals in Australia. This also requires that a basal paraphyletic assemblage represents parallel evolution of the ectomycorrhizal symbiosis, or that Hysterangiales was mycorrhizal with members of the extinct flora of Gondwana. Regardless, models for both ancient and more recent origins of Hysterangiales are consistent with truffle-like fungi being capable of transoceanic dispersal.

Evolution of nematode-trapping cells of predatory fungi of the Orbiliaceae based on evidence from rRNA-encoding DNA and multiprotein sequences

Among fungi, the basic life strategies are saprophytism, parasitism, and predation. Fungi in Orbiliaceae (Ascomycota) prey on animals by means of specialized trapping structures. Five types of trapping devices are recognized, but their evolutionary origins and divergence are not well understood. Based on comprehensive phylogenetic analysis of nucleotide sequences of three protein-coding genes (RNA polymerase II subunit gene, rpb2; elongation factor 1-alpha gene, ef1-alpha; and ss tubulin gene, bt) and ribosomal DNA in the internal transcribed spacer region, we have demonstrated that the initial trapping structure evolved along two lineages yielding two distinct trapping mechanisms: one developed into constricting rings and the other developed into adhesive traps. Among adhesive trapping devices, the adhesive network separated from the others early and evolved at a steady and gentle speed. The adhesive knob evolved through stalk elongation, with a final development of nonconstricting rings. Our data suggest that the derived adhesive traps are at a highly differentiated stage. The development of trapping devices is felicitous proof of adaptive evolution.

Phylogenetic relationships of Nemania plumbea sp. nov. and related taxa based on ribosomal ITS and RPB2 sequences

During a survey fungal diversity of xylariaceous fungi in Thailand, a new Nemania species, N. plumbea, was identified. Nemania plumbea is characterized by soft-textured grey stromata on a persistent mat of white hyphae, pale brown ascospores with a short germ-slit on the more convex side. It also produces a Geniculosporium-like anamorph in culture. In order to evaluate its phylogenetic relationships among related species and genera, ITS-5.8S rDNA and RPB2 were analysed separately and simultaneously. Results from the phylogenetic analyses indicate that there is close phylogenetic association between N. plumbea and N. aenea. A preliminary account into the natural grouping of Xylariaceae based on ITS-5.8S rDNA and RPB2 sequences is also discussed.

A phylogenetic overview of the family Pyronemataceae (Ascomycota, Pezizales)

Partial sequences of nuLSU rDNA were obtained to investigate the phylogenetic relationships of Pyronemataceae, the largest and least studied family of Pezizales. The dataset includes sequences for 162 species from 51 genera of Pyronemataceae, and 39 species from an additional 13 families of Pezizales. Parsimony, ML, and Bayesian analyses suggest that Pyronemataceae is not monophyletic as it is currently circumscribed. Ascodesmidaceae is nested within Pyronemataceae, and several pyronemataceous taxa are resolved outside the family. Glaziellaceae forms the sister group to Pyronemataceae in ML analyses, but this relationship, as well as those of Pyronemataceae to the other members of the lineage, are not resolved with support. Fourteen clades of pyronemataceous taxa are well supported and/or present in all recovered trees. Several pyronemataceous genera are suggested to be non-monophyletic, including Anthracobia, Cheilymenia, Geopyxis, Humaria, Lasiobolidium, Neottiella, Octospora, Pulvinula, Stephensia, Tricharina, and Trichophaea. Cleistothecial and truffle or truffle-like ascomata forms appear to have evolved independently multiple times within Pyronemataceae. Results of these analyses do not support previous classifications of Pyronemataceae, and suggest that morphological characters traditionally used to segregate the family into subfamilial groups are not phylogenetically informative above the genus level.

Phylogenetic evidence for an animal pathogen origin of ergot and the grass endophytes

Grass-associated fungi (grass symbionts) in the family Clavicipitaceae (Ascomycota, Hypocreales) are species whose host range is restricted to the plant family Poaceae and rarely Cyperaceae. The best-characterized species include Claviceps purpurea (ergot of rye) and Neotyphodium coenophialum (endophyte of tall fescue). They have been the focus of considerable research due to their importance in agricultural and grassland ecosystems and the diversity of their bioactive secondary metabolites. Here we show through multigene phylogenetic analyses and ancestral character state reconstruction that the grass symbionts in Clavicipitaceae are a derived group that originated from an animal pathogen through a dynamic process of interkingdom host jumping. The closest relatives of the grass symbionts include the genera Hypocrella, a pathogen of scale insects and white flies, and Metarhizium, a generalist arthropod pathogen. These data do not support the monophyly of Clavicipitaceae, but place it as part of a larger clade that includes Hypocreaceae, a family that contains mainly parasites of other fungi. A minimum of 5-8 independent and unidirectional interkingdom host jumps has occurred among clavicipitaceous fungi, including 3-5 to fungi, 1-2 to animals, and 1 to plants. These findings provide a new evolutionary context for studying the biology of the grass symbionts, their role in plant ecology, and the evolution of host affiliation in fungal symbioses.

Molecular phylogeny of the genus Lecania (Ramalinaceae, lichenized Ascomycota)

The molecular phylogeny of the lichen genus Lecania was investigated using nucleotide sequences from the mt-SSU rRNA, the ITS region of the nu-rDNA, and the RNA polymerase II second largest subunit. Forty-six species representing Lecania and other genera likely to influence the phylogeny were included in the study. Phylogenetic reconstructions were carried out using Bayesian inference, ML, and MP approaches. Lecania, as traditionally circumscribed, is not a monophyletic genus. However, a monophyletic group containing a large number of Lecania species, including the type species L. fuscella, was discovered in the analysis, and recognition of Lecania sensu stricto is suggested. L. baeomma, L. glauca, L. gerlachei, L. brialmontii, L. racovitzae, L. hyalina (alias Biatora globulosa), L. chlorotiza, L. naegelii, and L. furfuracea do not belong in Lecania s. str., although the latter two are closely related to Lecania s. str. Representatives of the genus Bilimbia form a well-supported group, as does the 'Thamnolecania' group containing the Antarctic 'Lecania' species, L. gerlachei, L. brialmontii, and L. racovitzae. An alternative to recognizing these two genera would be a wider circumscription of Bilimbia to include the 'Thamnolecania' group as well as affiliated taxa.

Migration between continents: geographical structure and long-distance gene flow in Porpidia flavicunda (lichen-forming Ascomycota)

Historical and contemporary geographical distribution ranges with their associated gene flow patterns interact to produce the genetic diversity observed today. Often it is not possible to separate out the impacts of historical events, e.g. past fragmentation, and contemporary gene flow, e.g. long-distance dispersal. Porpidia flavicunda is a lichen-forming ascomycete occurring circumpolar in the boreal to arctic zones for which vegetation history suggests that its distribution pattern has stayed broadly the same over the past millennia. DNA-sequence diversity in P. flavicunda can, thus, be expected to predominantly represent geographical population differentiation and its contemporary migration rates. The population sample consists of 110 specimens collected in Northern Québec, Baffin Island, Western Greenland and Northern Scandinavia. DNA-sequence data sets of three nuclear gene fragments (LSU, RPB2 and beta-tubulin) were analysed for genetic diversity within, and differentiation between, geographical regions. Tests of population subdivision employing analyses of molecular variance and exact tests of haplotype frequency distributions showed significant structure between the geographical regions. However, the lack of fixed nucleotide polymorphisms and the wide sharing of identical haplotypes between geographical regions suggest recurrent long-distance gene flow of propagules. Still, the means by which propagules are dispersed remain to be discovered. Inference of migration rates shows that in many cases a sufficiently high amount of migrants is exchanged between geographical regions to prevent drastic population differentiation through genetic drift. The observed haplotype distributions and migration rates point to a gene flow model of isolation by distance.

Evolution of Pleopsidium (Lichenized Ascomycota) S943 Group I Introns and the Phylogeography of an Intron-Encoded Putative Homing Endonuclease

The sporadic distribution of nuclear group I introns among different fungal lineages can be explained by vertical inheritance of the introns followed by successive losses, or horizontal transfers from one lineage to another through intron homing or reverse splicing. Homing is mediated by an intron-encoded homing endonuclease (HE) and recent studies suggest that the introns and their associated HE gene (HEG) follow a recurrent cyclical model of invasion, degeneration, loss, and reinvasion. The purpose of this study was to compare this model to the evolution of HEGs found in the group I intron at position S943 of the nuclear ribosomal DNA of the lichen-forming fungus Pleopsidium. Forty-eight S943 introns were found in the 64 Pleopsidium samples from a worldwide screen, 22 of which contained a full-length HEG that encodes a putative 256-amino acid HE, and 2 contained HE pseudogenes. The HEGs are divided into two closely related types (as are the introns that encode them) that differ by 22.6% in their nucleotide sequences. The evolution of the Pleopsidium intron-HEG element shows strong evidence for a cyclical model of evolution. The intron was likely acquired twice in the genus and then transmitted via two or three interspecific horizontal transfers. Close geographical proximity plays an important role in intron-HEG horizontal transfer because most of these mobile elements were found in Europe. Once acquired in a lineage, the intron-HEG element was also vertically transmitted, and occasionally degenerated or was lost.

Multiple gene genealogies reveal important relationships between species of Phaeophleospora infecting Eucalyptus leaves

The majority of Eucalyptus species are native to Australia, but worldwide there are over 3 million ha of exotic plantations, especially in the tropics and subtropics. Of the numerous known leaf diseases, three species of Phaeophleospora can cause severe defoliation of young Eucalyptus; Phaeophleospora destructans, Phaeophleospora eucalypti and Phaeophleospora epicoccoides. Phaeophleospora destructans has a major impact on seedling survival in Asia and has not, as yet, been found in Australia where it is considered a serious threat to the biosecurity of native eucalypts. It can be difficult to distinguish Phaeophleospora species based on symptoms and micromorphology and an unequivocal diagnostic tool for quarantine purposes would be useful. In this study, a multiple gene genealogy of these Phaeophleospora species and designed specific primers has been constructed to detect their presence from leaf samples. The phylogenetic position of these Phaeophleospora species within Mycosphaerella was established. They are closely related to each other and to other important Eucalyptus pathogens, Mycosphaerella nubilosa, Mycosphaerella cryptica and Colletogloeopsis zuluensis. The specific primers developed can now be used for diagnostic and screening purposes within Australia.

A multistep process gave rise to RNA polymerase IV of land plants

Since their discovery in Metazoa, the three nuclear RNA polymerases (RNAPs) have been found in fungi, plants, and diverse protists. In all eukaryotes studied to date, RNAPs I, II, and III collectively transcribe all major RNAs made in the nucleus. We have found genes for the largest subunit (RPD1/RPE1) of a new DNA-dependent RNAP, RNAP IV, in all major land plant taxa and in closely related green algae. Genes for the second-largest subunit (RPD2) of this enzyme were found in all land plants. Phylogenetic study indicates that RNAP IV genes are sister to the corresponding RNAP II genes. Our results show the genesis of RNAP IV to be a multistep process in which the largest and second-largest subunit genes evolved by independent duplication events in the ancestors of Charales and land plants. These findings provide insights into evolutionary mechanisms that can explain the origin of multiple RNAPs in the eukaryotic nucleus.

Duplication and paralog sorting of RPB2 and RPB1 genes in core eudicots

RPB1 and RPB2, which encode the largest and second largest subunits of RNA polymerase II, respectively, are essential single copy genes in fungi, animals and most plants. Two paralogs of the RPB2 gene have been found in some groups of angioperms [Oxelman, B., Yoshikawa, N., McConaughy, B.L., Luo, J., Denton, A.L., Hall, B.D., 2004. RPB2 gene phylogeny in flowering plants, with particular emphasis on asterids. Mol. Phylogenet. Evol. 32, 462-479]. Here, we report the results of experiments designed to identify the evolutionary origin of the RPB2 duplicate copies. Through careful sampling and phylogenetic analysis, we were able to construct the RPB2 gene tree in angiosperms and infer the phylogenetic positions of the gene duplication and gene loss events that occurred. Our study shows that an RPB2 gene duplication occurred early in core eudicot evolution, at or near the time of the Buxaceae/Trochodendraceae divergence. Subsequently, multiple gene duplication and paralog sorting events happened independently in different core eudicot taxa. Differential expression of the two RPB2 gene paralogs may explain the preservation of both paralogs in the asterids. One gene (RPB2-i) accounts for most of the RPB2 mRNA made in the flower organs while the other gene (RPB2-d) is predominantly used in the vegetative tissues. We also found two paralogs of the RPB1 gene in some core eudicot species. The RPB1 gene duplication occurred before core eudicot divergence, around the time of RPB2 gene duplication. Several independent RPB1 paralog sorting events happened in different core eudicot taxa; their occurrence was independent of the RPB2 paralog sorting events. Our results suggest that a polyploidization event happened at or near the time of the Buxaceae/Trochodendraceae divergence. We propose that this polyploidization and the partial diploidization processes thereafter may have been the driving force of core eudicot radiation.

Resolving the phylogenetic position of the Wallemiomycetes: an enigmatic major lineage of Basidiomycota

The Wallemiomycetes includes three species of molds from the genus Wallemia . These fungi are adapted to environments of high osmotic stress, contaminate various foods, cause respiratory disease, and have an unusual mode of asexual reproduction. Wallemia was recently proposed as a new class based on 18S ribosomal RNA gene sequences to accommodate the isolated position of the clade in the Basidiomycota. We analyzed the phylogenetic position of the Wallemiomycetes using 3451 nucleotide characters of the 18S, 25S, and 5.8S ribosomal RNA genes and 1282 amino acid positions of rpb1, rpb2, and tef1 nuclear protein-coding genes across 91 taxa. Different gene regions and methods of phylogenetic inference produce mildly conflicting placements of the Wallemiomycetes. Parsimony analyses of nrDNA data suggest that the Wallemiomycetes is an early diverging lineage of Basidiomycota, occupying a basal position near the Entorrhizomycetidae. Ultrastructural data, some Bayesian analyses, and amino acid sequences suggest the Wallemiomycetes may be the sister group of the Agaricomycotina or Ustilaginomycotina. The combined gene tree supports the Wallemiomycetes as a lineage basal to a core clade of Pucciniomycotina, Ustilaginomycotina, and Agaricomycotina with robust measures of branch support. This study reinforces the isolated position of Wallemia in the Basidiomycota using molecular data from six nuclear genes. In total, five major lineages of Basidiomycota are recognized: the Agaricomycotina, Ustilaginomycotina, Pucciniomycotina, Entorrhizomycetidae, and the Wallemiomycetes.

Phenotypic and genotypic identification of human pathogenic aspergilli

Human pathogenic aspergilli are identified in the clinical diagnostic laboratory predominantly by macro- and micro-morphology. Such phenotypic characteristics are largely subjective and unstable, as they are influenced by environmental factors, including media and temperature of incubation. Recent advances in molecular biology have impacted the field of mycology; multiple studies have noted new genetically distinct species that are not easily distinguished by phenotypic characteristics. Strengths of molecular typing methods include objectivity and the ability to identify nonsporulating or slowly growing fungi. As such, molecular methods provide powerful tools for the study of the epidemiology, evolution and population biology of fungal pathogens. This review focuses on current and future methods of identifying aspergilli, and implications regarding Aspergillus species/strain identification.

A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis

BACKGROUND

To date, most fungal phylogenies have been derived from single gene comparisons, or from concatenated alignments of a small number of genes. The increase in fungal genome sequencing presents an opportunity to reconstruct evolutionary events using entire genomes. As a tool for future comparative, phylogenomic and phylogenetic studies, we used both supertrees and concatenated alignments to infer relationships between 42 species of fungi for which complete genome sequences are available.

RESULTS

A dataset of 345,829 genes was extracted from 42 publicly available fungal genomes. Supertree methods were employed to derive phylogenies from 4,805 single gene families. We found that the average consensus supertree method may suffer from long-branch attraction artifacts, while matrix representation with parsimony (MRP) appears to be immune from these. A genome phylogeny was also reconstructed from a concatenated alignment of 153 universally distributed orthologs. Our MRP supertree and concatenated phylogeny are highly congruent. Within the Ascomycota, the sub-phyla Pezizomycotina and Saccharomycotina were resolved. Both phylogenies infer that the Leotiomycetes are the closest sister group to the Sordariomycetes. There is some ambiguity regarding the placement of Stagonospora nodurum, the sole member of the class Dothideomycetes present in the dataset. Within the Saccharomycotina, a monophyletic clade containing organisms that translate CTG as serine instead of leucine is evident. There is also strong support for two groups within the CTG clade, one containing the fully sexual species Candida lusitaniae, Candida guilliermondii and Debaryomyces hansenii, and the second group containing Candida albicans, Candida dubliniensis, Candida tropicalis, Candida parapsilosis and Lodderomyces elongisporus. The second major clade within the Saccharomycotina contains species whose genomes have undergone a whole genome duplication (WGD), and their close relatives. We could not confidently resolve whether Candida glabrata or Saccharomyces castellii lies at the base of the WGD clade.

CONCLUSION

We have constructed robust phylogenies for fungi based on whole genome analysis. Overall, our phylogenies provide strong support for the classification of phyla, sub-phyla, classes and orders. We have resolved the relationship of the classes Leotiomyctes and Sordariomycetes, and have identified two classes within the CTG clade of the Saccharomycotina that may correlate with sexual status.

Evolution of helotialean fungi (Leotiomycetes, Pezizomycotina): A nuclear rDNA phylogeny

The highly divergent characters of morphology, ecology, and biology in the Helotiales make it one of the most problematic groups in traditional classification and molecular phylogeny. Sequences of three rDNA regions, SSU, LSU, and 5.8S rDNA, were generated for 50 helotialean fungi, representing 11 out of 13 families in the current classification. Data sets with different compositions were assembled, and parsimony and Bayesian analyses were performed. The phylogenetic distribution of lifestyle and ecological factors was assessed. Plant endophytism is distributed across multiple clades in the Leotiomycetes. Our results suggest that (1) the inclusion of LSU rDNA and a wider taxon sampling greatly improves resolution of the Helotiales phylogeny, however, the usefulness of rDNA in resolving the deep relationships within the Leotiomycetes is limited; (2) a new class Geoglossomycetes, including Geoglossum, Trichoglossum, and Sarcoleotia, is the basal lineage of the Leotiomyceta; (3) the Leotiomycetes, including the Helotiales, Erysiphales, Cyttariales, Rhytismatales, and Myxotrichaceae, is monophyletic; and (4) nine clades can be recognized within the Helotiales.

Phylogenetic utility of protein (RPB2, β-tubulin) and ribosomal (LSU, SSU) gene sequences in the systematics of Sordariomycetes (Ascomycota, Fungi)

The Sordariomycetes is an important group of fungi whose taxonomic relationships and classification is obscure. There is presently no multi-gene molecular phylogeny that addresses evolutionary relationships among different classes and orders. In this study, phylogenetic analyses with a broad taxon sampling of the Sordariomycetes were conducted to evaluate the utility of four gene regions (LSU rDNA, SSU rDNA, beta-tubulin and RPB2) for inferring evolutionary relationships at different taxonomic ranks. Single and multi-gene genealogies inferred from Bayesian and Maximum Parsimony analyses were compared in individual and combined datasets. At the subclass level, SSU rDNA phylogenies demonstrate their utility as a marker to infer phylogenetic relationships at higher levels. All analyses with SSU rDNA alone, combined LSU rDNA and SSU rDNA, and the combined 28 S rDNA, SSU rDNA and RPB2 datasets resulted in three subclasses: Hypocreomycetidae, Sordariomycetidae and Xylariomycetidae, which correspond well to established morphological classification schemes. At the ordinal level, the best resolved phylogeny was obtained from the combined LSU rDNA and SSU rDNA datasets. Individually, the RPB2 gene dataset resulted in significantly higher number of parsimony informative characters. Our results supported the recent separation of Boliniaceae, Chaetosphaeriaceae and Coniochaetaceae from Sordariales and placement of Coronophorales in Hypocreomycetidae. Microascales was found to be paraphyletic and Ceratocystis is phylogenetically associated to Faurelina, while Microascus and Petriella formed another clade and basal to other members of Halosphaeriales. In addition, the order Lulworthiales does not appear to fit in any of the three subclasses. Congruence between morphological and molecular classification schemes is discussed.

RNA polymerase II gene (RPB2) encoding the second largest protein subunit in Phaeosphaeria nodorum and P. avenaria

A 5586 bp sequence (accession no. DQ278491), which includes the RNA polymerase II gene (RPB2) encoding the second largest protein subunit (RPB2), was obtained from the wheat biotype Phaeosphaeria nodorum (PN-w) by PCR amplification. The 3841 bp full length RPB2 gene contains two exons and a 52 bp intron, and encodes a complete 1262 amino acid protein. Similar to the C-terminals of the beta subunits of prokaryotes and yeast RNA polymerases, the deduced RPB2 protein contained many structural features needed for gene transcription. Based on the phylogenetic analysis with the deduced RPB2 polypeptide sequences, the PN-w was closely related to the maize pathogen Cochliobolus heterostrophus. Size differences were found in the full length RPB2 gene of cereal Phaeosphaeria species, mainly due to differences in intron size. No nucleotide substitutions were found in homothallic P. avenaria f.sp. triticea (Pat1) and barley biotype P. nodorum (PN-b) isolates used in this study. The nucleotide and deduced amino acid sequences of the RPB2 gene in Pat1 were closely related to that in PN-w.

Loss of the flagellum happened only once in the fungal lineage: phylogenetic structure of kingdom Fungi inferred from RNA polymerase II subunit genes

Background

At present, there is not a widely accepted consensus view regarding the phylogenetic structure of kingdom Fungi although two major phyla, Ascomycota and Basidiomycota, are clearly delineated. Regarding the lower fungi, Zygomycota and Chytridiomycota, a variety of proposals have been advanced. Microsporidia may or may not be fungi; the Glomales (vesicular-arbuscular mycorrhizal fungi) may or may not constitute a fifth fungal phylum, and the loss of the flagellum may have occurred either once or multiple times during fungal evolution. All of these issues are capable of being resolved by a molecular phylogenetic analysis which achieves strong statistical support for major branches. To date, no fungal phylogeny based upon molecular characters has satisfied this criterion.

Results

Using the translated amino acid sequences of the RPB1 and RPB2 genes, we have inferred a fungal phylogeny that consists largely of well-supported monophyletic phyla. Our major results, each with significant statistical support, are: (1) Microsporidia are sister to kingdom Fungi and are not members of Zygomycota; that is, Microsporidia and fungi originated from a common ancestor. (2) Chytridiomycota, the only fungal phylum having a developmental stage with a flagellum, is paraphyletic and is the basal lineage. (3) Zygomycota is monophyletic based upon sampling of Trichomycetes, Zygomycetes, and Glomales. (4) Zygomycota, Basidiomycota, and Ascomycota form a monophyletic group separate from Chytridiomycota. (5) Basidiomycota and Ascomycota are monophyletic sister groups.

Conclusion

In general, this paper highlights the evolutionary position and significance of the lower fungi (Zygomycota and Chytridiomycota). Our results suggest that loss of the flagellum happened only once during early stages of fungal evolution; consequently, the majority of fungi, unlike plants and animals, are nonflagellated. The phylogeny we infer from gene sequences is the first one that is congruent with the widely accepted morphology-based classification of Fungi. We find that, contrary to what has been published elsewhere, the four morphologically defined phyla (Ascomycota, Basidiomycota, Zygomycota and Chytridiomycota) do not overlap with one another. Microsporidia are not included within kingdom Fungi; rather they are a sister-group to the Fungi. Our study demonstrates the applicability of protein sequences from large, slowly-evolving genes to the derivation of well-resolved and highly supported phylogenies across long evolutionary distances.

Phylogenetic relationships of Neonectria/Cylindrocarpon on Fagus in North AmericaMention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture

The relationship of two species of Neonectria associated with beech bark canker in North America was evaluated by comparing isolates of these and additional species of the Neonectria coccinea (Pers.:Fr.) Rossman & Samuels group found on Fagus. Gene regions in the translation elongation factor 1-alpha (EF1-α), RNA polymerase II second largest subunit (RPB2), and β-tubulin were sequenced and analyzed. Results indicate that the fungus associated with beech bark disease previously known as Neonectria coccinea var. faginata Lohman et al. (≡ Nectria coccinea (Pers.:Fr.) Fr. var. faginata Lohman et al.) should be recognized as a separate species, Neonectria faginata , distinct from Neonectria coccinea . Neonectria faginata including its anamorphic state, Cylindrocarpon faginatum C. Booth, is known only on Fagus in North America. A second species associated with beech bark disease in North America is Neonectria ditissima (Tul. & C. Tul.) Samuels & Rossman, which can be distinguished morphologically from Neonectria faginata based on ascospore size, conidial size and shape, and colony pigmentation. Morphological and molecular data indicate that Neonectria ditissima represents an older name for Neonectria galligena Bres. Similarly, the anamorphic state of Neonectria ditissima is the older epithet Cylindrocarpon heteronema with Cylindrocarpon willkommii as a synonym. Neonectria ditissima occurs on a variety of hardwood trees in North America and Europe. Neonectria coccinea occurs only on Fagus in Europe. Neonectria major (Wollenw.) Castl. & Rossman is recognized as a species that occurs only on Alnus in Canada (British Columbia), France, Norway, and the United States (Washington). The following nomenclatural changes are proposed: Neonectria faginata comb. and stat. nov., Neonectria fuckeliana comb. nov., Neonectria hederae comb. nov., Neonectria major comb. and stat. nov., and Neonectria punicea comb. nov.

Multilocus sequence analysis of Penicillium and Eupenicillium species

Taxonomy of Hyphomycetes has always been a challenging problem, with experts viewing species in different ways and modifying the taxonomy of groups to reflect their best evaluation of species limits and concepts. The advent of phylogenetic analysis, relatively easy DNA sequencing techniques and PCR has provided an opportunity for mycology to move from a strictly morphological analysis of species to phylogenetic analysis of DNA sequences. Phylogenetic theory dictates that data from different loci will produce congruent or at least non-contradictory evolutionary histories of a clonal lineage. Tests of tree congruence such as the index of association can show whether lineages are clonal, and has revealed that some species long thought to be clonal are cryptically recombining. Genealogical concordance phylogenetic species recognition allows unambiguous identification of species boundaries.

A taxonomic revision of the insect biocontrol fungus Aschersonia aleyrodis, its allies with white stromata and their Hypocrella sexual states

A revision of a monophyletic group of Hypocrella species and their Aschersonia anamorphs with white effuse stromata is presented. In addition to taxon descriptions, distributions, and nomenclature, a synoptic key and a molecular phylogenetic analysis are also provided. A new holomorph, Hypocrella rhombispora sp. nov., is described. This study presents a revisionary treatment of Aschersonia aleyrodis (teleomorph: Hypocrella libera) and its allies. These fungi parasitize whiteflies and are promising candidates for whitefly biological control. Four species of Aschersonia and their Hypocrella teleomorphs are treated in detail: Aschersonia aleyrodis/Hypocrella libera; A. andropogonis/H. andropogonis, A. placenta/H. raciborskii, and A. sp./H. rhombispora sp. nov. A synoptic key including these and six other morphologically similar species is presented to facilitate identification in the field and laboratory. Phylogenetic analyses of partial DNA sequences from three genes (LSU, mtSSU, and RPB2) suggest that Aschersonia species with effuse white stromata form a monophyletic group of whitefly pathogens. Phylogenetically informative characters in the group include the colour and shape of the stromata, the arrangement of tubercles containing perithecia, the arrangement of conidial masses on the stromata, and the shape of conidia and part spores.