Showing papers in "Mycologia in 2006"

Major clades of Agaricales: a multilocus phylogenetic overview

Abstract: An overview of the phylogeny of the Agaricales is presented based on a multilocus analysis of a six-gene region supermatrix. Bayesian analyses of 5611 nucleotide characters of rpb1, rpb1-intron 2, rpb2 and 18S, 25S, and 5.8S ribosomal RNA genes re- covered six major clades, which are recognized informally and labeled the Agaricoid, Tricholoma- toid, Marasmioid, Pluteoid, Hygrophoroid and Plica- turopsidoid clades. Each clade is discussed in terms of key morphological and ecological traits. At least 11 origins of the ectomycorrhizal habit appear to have evolved in the Agaricales, with possibly as many as nine origins in the Agaricoid plus Tricholomatoid clade alone. A family-based phylogenetic classification is sketched for the Agaricales, in which 30 families,

A multigene phylogeny of the Dothideomycetes using four nuclear loci.

Abstract: We present an expanded multigene phylogeny of the Dothideomycetes. The final data matrix consisted of four loci (nuc SSU rDNA, nuc LSU rDNA, TEF1, RPB2) for 96 taxa, representing five of the seven orders in the current classification of Dothideomycetes and several outgroup taxa representative of the major clades in the Pezizomycotina. The resulting phylogeny differentiated two main dothideomycete lineages comprising the pseudoparaphysate Pleosporales and aparaphysate Dothideales. We propose the subclasses Pleosporomycetidae (order Pleosporales) and Dothideomycetidae (orders Dothideales, Capnodiales and Myriangiales). Furthermore we provide strong molecular support for the placement of Mycosphaerellaceae and Piedraiaceae within the Capnodiales and introduce Davidiellaceae as a new family to accommodate species of Davidiella with Cladosporium anamorphs. Some taxa could not be placed with certainty (e.g. Hysteriales), but there was strong support for new groupings. The clade containing members of the genera Botryosphaeria and Guignardia resolved well but without support for any relationship to any other described orders and we hereby propose the new order Botryosphaeriales. These data also are consistent with the removal of Chaetothyriales and Coryneliales from the Dothideomycetes and strongly support their placement in the Eurotiomycetes.

Dating divergences in the Fungal Tree of Life: review and new analyses.

Abstract: The collection of papers in this issue of Mycologia documents considerable improvements in taxon sampling and phylogenetic resolution regarding the Fungal Tree of Life. The new data will stimulate ...

A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota).

Abstract: Chytridiomycota (chytrids) is the only phylum of true Fungi that reproduces with motile spores (zoospores). Chytrids currently are classified into five orders based on habitat, zoospore characters and life cycles. In this paper we estimate the phylogeny of the chytrids with DNA sequences from the ribosomal RNA operon (18S+5.8S+28S subunits). To our surprise the morphologically reduced para- sites Olpidium and Rozella comprise two entirely new, and separate, lineages on the fungal tree. Olpidium brassicae groups among the Zygomycota, and Rozella spp. are the earliest branch to diverge in the fungal kingdom. The phylogeny also suggests that Chytri- diomycota is not monophyletic and there are four major lineages of chytrids: Rozella spp., Olpidium brassicae, the Blastocladiales and a ''core chytrid clade'' containing the remaining orders and families and the majority of flagellated fungi. Within the core chytrid group 11 subclades can be identified, each of which correlates well with zoospore ultrastructure or morphology. We provide a synopsis of each clade and its morphological circumscription. The Blastocla- diales appears to be the sister taxon of most nonflagellated fungi. Based on molecular phyloge- netic and ultrastructural characters this order is elevated to a phylum, the Blastocladiomycota.

A five-gene phylogeny of Pezizomycotina

Abstract: Pezizomycotina is the largest subphylum of Ascomycota and includes the vast majority of filamen- tous, ascoma-producing species. Here we report the results from weighted parsimony, maximum likelihood and Bayesian phylogenetic analyses of five nuclear loci (SSU rDNA, LSU rDNA, RPB1, RPB2 and EF-1a) from 191 taxa. Nine of the 10 Pezizomycotina classes currently recognized were represented in the sam- pling. These data strongly supported the monophyly of Pezizomycotina, Arthoniomycetes, Eurotiomycetes, Orbiliomycetes and Sordariomycetes. Pezizomycetes and Dothideomycetes also were resolved as mono- phyletic but not strongly supported by the data. Lecanoromycetes was resolved as paraphyletic in parsimony analyses but monophyletic in maximum likelihood and Bayesian analyses. Leotiomycetes was polyphyletic due to exclusion of Geoglossaceae. The two most basal classes of Pezizomycotina were Orbilio- mycetes and Pezizomycetes, both of which comprise species that produce apothecial ascomata. The seven

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

Abstract: 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.

New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes

Abstract: The Lecanoromycetes includes most of the lichen-forming fungal species (>13 500) and is therefore one of the most diverse class of all Fungi in terms of phenotypic complexity. We report phylogeneti...

Molecular systematics and biological diversification of Boletales

Abstract: Historical patterns of morphological evo- lution and ecology in the Boletales are largely unresolved but appear to involve extensive conver- gence. We studied phylogenetic relationships of Boletales based on two datasets. The nuc-lsu dataset is broadly sampled and includes roughly 30% of the described species of Boletales and 51 outgroup taxa across the Hymenomycetes. The multigene dataset (nuc-ssu, nuc-lsu, 5.8S, mt-lsu, atp6) sampled 42 key species of Boletales in a framework of 14 representa- tive Hymenomycetes. The Boletales are strongly supported as monophyletic in our analyses on both datasets with parsimony, maximum likelihood and Bayesian approaches. Six major lineages of Boletales that currently are recognized on subordinal level, Boletineae, Paxillineae, Sclerodermatineae, Suilli- neae, Tapinellineae, Coniophorineae, received varied support. The backbone of the Boletales was moder- ately resolved in the analyses with the nuc-lsu dataset, but support was strong for most major groups. Nevertheless, most brown-rot producing forms were placed as a paraphyletic grade at the base of the Boletales. Analyses on the multigene dataset confirm sister group relationships among Boletales, Agaricales and Atheliales. Boletineae and Suillineae received the highest support values; Paxillineae and Scleroderma- tineae were not consistently resolved as monophyletic groups. The Coniophorineae were not monophyletic in any analyses. The Tapinellineae consisting of morphologically diverse brown-rotting fungi forms the basal group in the Boletales. We performed ancestral state reconstruction with BayesMultiState, which suggested that the ancestor of the Boletales was a resupinate or polyporoid saprotrophic fungus, producing a brown-rot.

Eurotiomycetes : Eurotiomycetidae and Chaetothyriomycetidae

Abstract: The class Eurotiomycetes (Ascomycota, Pezizomycotina) is a monophyletic group comprising two major clades of very different ascomycetous fungi: (i) the subclass Eurotiomycetidae, a clade that contains most of the fungi previously recognized as Plectomycetes because of their mostly enclosed ascomata and prototunicate asci; and (ii) the subclass Chaetothyriomycetidae, a group of fungi that produce ascomata with an opening reminiscent of those produced by Dothideomycetes or Sordariomycetes. In this paper we use phylogenetic analyses based on data available from the Assembling the Fungal Tree of Life project (AFTOL), in addition to sequences in GenBank, to outline this important group of fungi. The Eurotiomycetidae include producers of toxic and useful secondary metabolites, fermentation agents used to make food products and enzymes, xerophiles and psychrophiles, and the important genetics model Aspergillus nidulans. The Chaetothyriomycetidae include the common black yeast fungi, some of which are pathogens of humans and animals, as well as some primarily lichenized groups newly found to be phylogenetically associated with this group. The recently proposed order Mycocaliciales shows a sister relationship with Eurotiomycetes. The great majority of human pathogenic Pezizomycotina are Eurotiomycetes, particularly in Eurotiales, Onygenales and Chaetothyriales. Due to their broad importance in basic research, industry and public health, several genome projects have focused on species in Onygenales and Eurotiales.

Phylogeny of the glomeromycota (arbuscular mycorrhizal fungi): recent developments and new gene markers.

Abstract: The fungal symbionts of arbuscular mycorrhiza form a monophyletic group in the true Fungi, the phylum Glomeromycota. Fewer than 200 described species currently are included in this group. The only member of this clade known to form a different type of symbiosis is Geosiphon pyriformis, which associates with cyanobacteria. Because none of these fungi has been cultivated without their plant hosts or cyanobacterial partners, progress in obtaining multigene phylogenies has been slow and the nuclear-encoded ribosomal RNA genes have remained the only widely accessible molecular markers. rDNA phylogenies have revealed considerable polyphyly of some glomeromycotan genera that has been used to reassess taxonomic concepts. Environmental studies using phylogenetic methods for molecular identification have recovered an amazing diversity of unknown phylotypes, suggesting considerable cryptic species diversity. Protein gene sequences that have become available recently have challenged the rDNA-supported sister group relationship of the Glomeromycota with Asco/Basidiomycota. However the number of taxa analyzed with these new markers is still too small to provide a comprehensive picture of intraphylum relationships. We use nuclear-encoded rDNA and rpb1 protein gene sequences to reassess the phylogeny of the Glomeromycota and discuss possible implications.

Phylogeny of the Zygomycota based on nuclear ribosomal sequence data

Abstract: The Zygomycota is an ecologically heter- ogenous assemblage of nonzoosporic fungi compris- ing two classes, Zygomycetes and Trichomycetes. Phylogenetic analyses have suggested that the phylum is polyphyletic; two of four orders of Trichomycetes are related to the Mesomycetozoa (protists) that diverged near the fungal/animal split. Current circumscription of the Zygomycota includes only orders with representatives that produce zygospores. We present a molecular-based phylogeny including recognized representatives of the Zygomycetes and Trichomycetes with a combined dataset for nuclear rRNA 18S (SSU), 5.8S and 28S (LSU) genes. Tree reconstruction by Bayesian analyses suggests the Zygomycota is paraphyletic. Although 12 clades were identified only some of these correspond to the nine orders of Zygomycota currently recognized. A large superordinal clade, comprising the Dimargaritales, Harpellales, Kickxellales and Zoopagales, grouping together many symbiotic fungi, also is identified in part by a unique septal structure. Although Harpel- lales and Kickxellales are not monophyletic, these lineages are distinct from the Mucorales, Endogo- nales and Mortierellales, which appear more closely related to the Ascomycota + Basidiomycota + Glomeromycota. The final major group, the insect- associated Entomophthorales, appears to be poly- phyletic. In the present analyses Basidiobolus and Neozygites group within Zygomycota but not with the Entomophthorales. Clades are discussed with special reference to traditional classifications, mapping mor- phological characters and ecology, where possible, as a snapshot of our current phylogenetic perspective of the Zygomycota.

Molecular phylogenetics of the gomphoid-phalloid fungi with an establishment of the new subclass Phallomycetidae and two new orders.

Abstract: Molecular phylogenetic analyses for the gomphoid-phalloid fungi were conducted based on the five gene dataset with extensive taxon sampling. The monophyly of the gomphoid-phalloid clade was strongly supported, and four well supported major subclades were recognized. Three of the four subclades were represented entirely by gastroid taxa, and only Gomphales contained both gastroid and non-gastroid taxa. While the gastroid morphology is derived from epigeous, nongastroid taxa in Gomphales, the topology of Phallales indicated that truffle-like form is an ancestral morphology of the stinkhorn fruiting bodies. Although basidiospore maturation occurs within the enclosed fruiting bodies of the stinkhorn, the elevation of the mature spore-producing tissue represents an independent origin of the stipe among Basidiomycota. Comparisons are made between previous and new classification schemes, which are based on the results of phylogenetic analyses. Based on the results of these analyses, a new subclass Phallomycetidae, and two new orders, Hysterangiales and Geastrales, are proposed.

A phylogenetic overview of the Agaricomycotina.

Abstract: The Agaricomycotina contains about one- third of the described species of Fungi, including mushrooms, jelly fungi and basidiomycetous yeasts. Recent phylogenetic analyses by P. Matheny and colleagues combining nuclear rRNA genes with the protein-coding genes rpb1, rpb2 and tef1 support the division of Agaricomycotina into Tremellomycetes, Dacrymycetes and Agaricomycetes. There is strong support for the monophyly of the Tremellomycetes, and its position as the sister group of the rest of the Agaricomycotina. Dacrymycetes and Agaricomycetes also are supported strongly, and together they form a clade that is equivalent to the Hymenomycetidae of Swann and Taylor. The deepest nodes in the Agaricomycetes, which are supported only by Bayes- ian measures of confidence, suggest that the Sebaci- nales, Cantharellales and Auriculariales are among the most ancient lineages. For the first time, the Polyporales are strongly supported as monophyletic and are placed as the sister group of the Thelepho- rales. The Agaricales, Boletales and Atheliales are united as the Agaricomycetidae, and the Russulales might be its sister group. There are still some problematical nodes that will require more loci to be resolved. Phylogenomics has promise for recon- structing these difficult backbone nodes, but current genome projects are limited mostly to the Agaricales, Boletales and Polyporales. Genome sequences from other major lineages, especially the early diverging clades, are needed to resolve the most ancient nodes and to assess deep homology in ecological characters

An overview of the higher level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences

Abstract: In this study we provide a phylogenetically based introduction to the classes and orders of Pucciniomycotina (5Urediniomycetes), one of three subphyla of Basidiomycota. More than 8000 species of Pucciniomycotina have been described including putative saprotrophs and parasites of plants, animals and fungi. The overwhelming majority of these (,90%) belong to a single order of obligate plant pathogens, the Pucciniales (5Uredinales), or rust fungi. We have assembled a dataset of previously published and newly generated sequence data from two nuclear rDNA genes (large subunit and small subunit) including exemplars from all known major groups in order to test hypotheses about evolutionary relationships among the Pucciniomycotina. The utility of combining nuc-lsu sequences spanning the entire D1-D3 region with complete nuc-ssu sequences for resolution and support of nodes is discussed. Our study confirms Pucciniomycotina as a monophyletic group of Basidiomycota. In total our results support eight major clades ranked as classes (Agaricostilbo- mycetes, Atractiellomycetes, Classiculomycetes, Cryp- tomycocolacomycetes, Cystobasidiomycetes, Microbo- tryomycetes, Mixiomycetes and Pucciniomycetes) and 18 orders.

Hymenochaetales: a molecular phylogeny for the hymenochaetoid clade.

Abstract: The hymenochaetoid clade is dominated by wood-decaying species previously classified in the artificial families Corticiaceae, Polyporaceae and Stereaceae. The majority of these species cause a white rot. The polypore Bridgeoporus and several corticioid species with inconspicuous basidiomata live in association with brown-rotted wood, but their nutritional strategy is not known. Mycorrhizal habit is reported for Coltricia perennis but needs confirmation. A surprising element in the hymenochaetoid clade is a group of small white to brightly pigmented agarics earlier classified in Omphalina. They form a subclade together with some similarly colored stipitate stereoid and corticioid species. Several are associated with living mosses or one-celled green algae. Hyphoderma pratermissum and some related corticioid species have specialized organs for trapping and killing nematodes as a source of nitrogen. There are no unequivocal morphological synapomorphies known for the hymenochaetoid clade. However almost all species examined ultrastructurally have dolipore septa with continuous parenthesomes while perforate parenthesomes is the normal condition for other homobasidiomycete clades. The agaricoid Hymenochaetales have not been examined. Within Hymenochaetales the Hymenochaetaceae forms a distinct clade but unfortunately all morphological characters supporting Hymenochaetaceae also are found in species outside the clade. Other subclades recovered by the molecular phylogenetic analyses are less uniform, and the overall resolution within the nuclear LSU tree presented here is still unsatisfactory.

The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods

Abstract: We reassessed the circumscription of the cantharelloid clade and identified monophyletic groups by using nLSU, nSSU, mtSSU and RPB2 sequence data. Results agreed with earlier studies that placed the genera Cantharellus, Craterellus, Hydnum, Clavulina, Membranomyces, Multiclavula, Sistotrema, Botryobasidium and the family Ceratobasidiaceae in that clade. Phylogenetic analyses support monophyly of all genera except Sistotrema, which was highly polyphyletic. Strongly supported monophyletic groups were: (i) Cantharellus-Craterellus, Hydnum, and the Sistotrema confluens group; (ii) Clavulina-Membranomyces and the S. brinkmannii-oblongisporum group, with Multiclavula being possibly sister of that clade; (iii) the Sistotrema eximum-octosporum group; (iv) Sistotrema adnatum and S. coronilla. Positions of Sistotrema raduloides and S. athelioides were unresolved, as were basal relationships. Botryobasidium was well supported as the sister taxon of all the above taxa, while Ceratobasidiaceae was the most basal lineage. The relationship between Tulasnella and members of the cantharelloid clade will require further scrutiny, although there is cumulative evidence that they are probably sister groups. The rates of molecular evolution of both the large and small nuclear ribosomal RNA genes (nuc-rDNA) are much higher in Cantharellus, Craterellus and Tulasnella than in the other cantharelloid taxa, and analyses of nuc-rDNA sequences strongly placed Tulasnella close to Cantharellus-Craterellus. In contrast analyses with RPB2 and mtSSU sequences placed Tulasnella at the base of the cantharelloid clade. Our attempt to reconstruct a "supertree" from tree topologies resulting from separate analyses that avoided phylogenetic reconstruction problems associated with missing data and/or unalignable sequences proved unsuccessful.

Toward a phylogenetic classification of the Leotiomycetes based on rDNA data

Abstract: Phylogenetic relationships of one of the largest nonlichen-forming ascomycetous groups, the Leotiomycetes, were inferred from genes encoding three rDNA regions (SSU+LSU+5.8S rDNA). A dataset was prepared with rDNA sequences data from 108 isolates, among which we sampled 85 taxa representing four orders and 16 families in the Leotiomycetes. Equally weighted parsimony and Bayesian analyses were performed. Bootstrap pro- portion and Bayesian posterior probability under the GTR+C+I model were estimated along the branches. Based on our results the Leotiomycetes is relatively well defined as a class and it includes the Cyttariales, Erysiphales, Helotiales, Rhytismatales and two fami- lies of uncertain position, Myxotrichaceae and Pseu- deurotiaceae. The placements of the Thelebolales and Ascocorticiaceae are not examined and are accepted as tentative in the Leotiomycetes. Our results agree with previous studies to remove the Geoglossaceae, including Geoglossum, Trichoglossum and Sarcoleotia, from the Leotiomycetes. Positions of the Erysiphales and Rhytismatales in the Leotiomy- cetes are confirmed. The Helotiales and Myxotricha- ceae are paraphyletic. Close relationships are sup- ported strongly among the Hemiphacidiaceae, Rutstroemiaceae and Sclerotiniaceae, among Lora- mycetaceae, the northern hemisphere Vibrisseaceae, the Dark Septate Endophyte fungus Phialocephala

Three new Lasiodiplodia spp. from the tropics, recognized based on DNA sequence comparisons and morphology

Abstract: Botryosphaeria rhodina (anamorph Lasiodiplodia theobromae) is a common endophyte and opportunistic pathogen on more than 500 tree species in the tropics and subtropics. During routine disease surveys of plantations in Australia and Venezuela several isolates differing from L. theobromae were identified and subsequently characterized based upon morphology and ITS and EF1-alpha nucleotide sequences. These isolates grouped into three strongly supported clades related to but different from the known taxa, B. rhodina and L. gonubiensis, These have been described here as three new species L. venezuelensis sp. nov., L. crassispora sp. nov. and L. rubropurpurea sp. nov. The three could be distinguished easily from each other and the two described species of Lasiodiplodia, thus confirming phylogenetic separations. Furthermore all five Lasiodiplodia spp. now recognized separated from Diplodia spp. and Dothiorella spp. with 100% bootstrap support.

A phylogenetic hypothesis of Ustilaginomycotina based on multiple gene analyses and morphological data.

Abstract: The subphylum Ustilaginomycotina comprises about 1500 species of basidiomycetous plant parasites. They are usually dimorphic, producing a saprobic haploid yeast phase and a parasitic dikaryotic hyphal phase. With only a few exceptions they occur on angiosperms and are found mainly on members of the Poaceae and Cyperaceae. Molecular methods recently have shown that anamorphic species such as members of Malassezia or Tilletiopsis should be included in this group. Here we present the most recent consensus as to the phylogeny of this group and discuss its relevant characteristics. Our morphological, ultrastructural and molecular phylogenetic data point to the existence of three lines of Ustilaginomycotina: Entorrhizomycetes, Ustilaginomycetes and Exobasidiomycetes. Entorrhizomycetes is represented by Entorrhizales, a small group of unusual teliosporic root parasites on Juncaceae and Cyperaceae. Ustilaginomycetes, to which the majority of Ustilaginomycotina belong, is a teliosporic and gastroid group characterized by the presence of enlarged interaction zones. Ustilaginomycetes is dichotomous, consisting of predominantly holobasidiate Urocystales and predominantly phragmobasidiate Ustilaginales. Exobasidiomycetes forms local interaction zones. This group is predominantly holobasidiate and consists of teliosporic Doassansiales, Entylomatales, Georgefischeriales and Tilletiales, nonteliosporic Ceraceosorales, Exobasidiales and Microstromatales, as well as the anamorphic Malasseziales. Entorrhizomycetes, Exobasidiomycetes and Ceraceosorales are proposed as new taxa, and the description of Ustilaginomycetes is emended.

Phylogenetic relationships of Pythium and Phytophthora species based on ITS rDNA, cytochrome oxidase II and beta-tubulin gene sequences.

Abstract: Fifty-eight isolates representing 39 Pythium species and 17 isolates representing nine Phytophthora species were chosen to investigate intra- and intergeneric relationships with sequence analysis of three genomic areas. The internal transcribed spacer regions (ITS1 and ITS2), including the 5.8S gene of the ribosomal DNA were PCR amplified with the universal primers ITS1 and ITS4. On the other hand 563 bp of the cytochrome oxidase II (cox II) gene was amplified with the primer pair FM66 and FM58 for Pythium and FM75 and FM78 for Phytophthora. The 658 bp partial beta-tubulin gene was amplified with the forward primer BT5 and reverse primer BT6. Maximum parsimony analysis of the three DNA regions revealed four major clades, reflective of sporangial morphology. Clade 1 was composed of Pythium isolates that bear filamentous to lobulate sporangia. Clade 2 represents Pythium isolates that bear globose to spherical zoosporangia or spherical hyphal swellings. Meanwhile Phytophthora isolates were lumped into Clade 3 wherein the papillate, semipapillate and nonpapillate species occupied separate subclades. Lastly, Clade 4 was composed of Pythium species that bear subglobose sporangia resembling the papillate sporangia observed in Phytophthora. Hence a number of species (Ph. undulata, P. helicoides, P. ostracodes, P. oedochilum and P. vexans) have been proposed to be the elusive intermediate species in the Pythium-to-Phytophthora evolutionary line.

Systematics of the Pezizomycetes—the operculate discomycetes

Abstract: The Pezizomycetes (order Pezizales) is an early diverging lineage within the Pezizomycotina. A shared derived character, the operculate ascus, supports the Pezizales as monophyletic, although functional opercula have been lost in certain taxa. Phylogenetic relationships within Pezizales were studied using parsimony and Bayesian analyses of partial SSU and LSU rDNA sequences from 100 taxa representing 82 genera and 13 of the 15 families currently recognized. Three primary lineages are identified that more or less correspond to the A, B and C lineages resolved in previous analyses using SSU rDNA: (A) Ascobolaceae and Pezizaceae; (B) Discinaceae-Morchellaceae and Helvellaceae-Tuberaceae; (C) Ascodesmidaceae, Glaziellaceae, Pyronemataceae, Sarcoscyphaceae and Sarcosomataceae. In contrast the monotypic Rhizinaceae and Caloscyphaceae are resolved as two independent lineages. Bayesian analyses support a relationship among Rhizina and two species of Psilopezia (Pyronemataceae). Only lineage C is highly supported. The B and C lineages form a strongly supported monophyletic group. None of these lineages corresponds to earlier proposed suborders. The A and B lineages are supported by certain morphological features (e.g. ascus bluing reaction in iodine, cytology of spores and paraphyses, septal pore structures and excipulum structure); these characters have been subject to homoplasy. Lineage C is the largest and most heterogeneous, and no unifying morphological features support its recognition. The Pyronemataceae, in which almost half of the species in the order are found, is not monophyletic because the Ascodesmidaceae and Glaziellaceae are nested within it. The relationships among all families in the C lineage remain uncertain. The origin of various forms of ascomata, including hypogeous forms (truffles and truffle-like), epigeous cleistothecia, simple reduced apothecia and highly elaborate, stipitate forms (helvelloid and morchelloid), are discussed.

Research Coordination Networks: a phylogeny for kingdom Fungi (Deep Hypha).

Abstract: Research in fungal phylogenetics and systematics progressed rapidly in the past decade due to advances in DNA sequencing technologies and analytical methods. A newfound wealth of sequence data acquired through community-wide initiatives has advanced the process of acquiring a stable phyloge- netic classification of many fungal taxa. Financial support from the National Science Foundation Re- search Coordination Networks: a phylogeny for kingdom Fungi (Deep Hypha) for 5 y enabled more than 100 fungal systematists to assess the taxon sampling, molecular markers and analytical methods necessary to facilitate such a project. Later a second NSF program provided financial support for the Assembling the Fungal Tree of Life (AFTOL) project to accomplish much of the research. Deep Hypha may be viewed as an involved parent of AFTOL with a continuing role as coordinator of likeminded workers. Many questions posed at the beginning of the Deep Hypha project have been addressed, at least in part, although some details remain to be clarified. Many of the main branches of the fungal tree are stable and well supported, often as a result of multigene analyses that involved collaboration of many laboratories. More work is necessary, however, to resolve certain branching events near the base of the tree, as well as to reconstruct relationships in some terminal groups. The phylogenetic classification in this issue of Mycologia is a product of the AFTOL project and many other independent research in- itiatives, and it is an initial synthesis of a working classification designed to be used for all major

Fungal decomposition of Abies needle and Betula leaf litter

Abstract: The effect of litter type and incubation temperature on the ability of fungi to decompose leaf litter of subalpine trees was examined by a pure-culture test. Mass loss of Abies needle and Betula leaf litter and utilization patterns of lignin and carbohydrates were investigated under two temperature conditions (20 C and 10 C) and compared for 29 species in basidiomycetes, ascomycetes and zygomycetes. The decomposing ability was generally higher in basidiomycetes than in ascomycetes and zygomycetes. Mass loss (% original mass) of litter was higher in Betula than in Abies and higher at 20 C than at 10 C. The 29 fungi were divided into lignocellulose decomposers, cellulose decomposers and sugar fungi based on their substrate utilization in Abies and Betula litter. Mass loss of lignin and carbohydrates by lignocellulose and cellulose decomposers was higher in Betula than in Abies. Mass loss of carbohydrates was higher at 20 C than at 10 C, but the temperature did not influence mass loss of lignin, indicating l...

Phylogenetics of Saccharomycetales, the ascomycete yeasts.

Abstract: Ascomycete yeasts (phylum Ascomycota: subphylum Saccharomycotina: class Saccharomycetes: order Saccharomycetales) comprise a monophyletic lineage with a single order of about 1000 known species. These yeasts live as saprobes, often in association with plants, animals and their interfaces. A few species account for most human mycotic infections, and fewer than 10 species are plant pathogens. Yeasts are responsible for important industrial and biotechnological processes, including baking, brewing and synthesis of recombinant proteins. Species such as Saccharomyces cerevisiae are model organisms in research, some of which led to a Nobel Prize. Yeasts usually reproduce asexually by budding, and their sexual states are not enclosed in a fruiting body. The group also is well defined by synapomorphies visible at the ultrastructural level. Yeast identification and classification changed dramatically with the availability of DNA sequencing. Species identification now benefits from a constantly updated sequence database and no longer relies on ambiguous growth tests. A phylogeny based on single gene analyses has shown the order to be remarkably divergent despite morphological similarities among members. The limits of many previously described genera are not supported by sequence comparisons, and multigene phylogenetic studies are under way to provide a stable circumscription of genera, families and orders. One recent multigene study has resolved species of the Saccharomycetaceae into genera that differ markedly from those defined by analysis of morphology and growth responses, and similar changes are likely to occur in other branches of the yeast tree as additional sequences become available.

Perspectives in the new Russulales

Abstract: The Russulales is one of 12 major lineages recently elucidated by molecular sequence data in the homobasidiomycetes. The order is morphologically most diverse, containing a remarkable variety of sporophore forms including resupinate, discoid, effused-reflexed, clavarioid, pileate, or gasteroid and hymenophore configurations from smooth, poroid, hydnoid, lamellate, to labyrinthoid. Functionally these fungi are primarily saprotrophs but others are ectomycorrhizal, root parasites and insect symbionts. A phylogenetic analysis of the nuclear 5.8S, ITS2 and large-subunit rDNA genes comprises the best information to date on relationships of taxa within the Russulales. Two large sister groups encompassing 11-13 major clades have been recovered within the Russulales. Based on molecular and morphological data 12 families and approximately 80 genera have been identified, although placement of many taxa has not yet been determined. The two clades containing ectomycorrhizal taxa, corresponding to the Russulaceae and the Albatrellaceae, represent the greatest diversity of sporophore morphologies. The primarily pileate lamellate family Russulaceae is nested with resupinate species and also contains pileate sequestrate, gasteroid annulate and pleurotoid forms. Albatrellaceae similarly contains resupinate poroid, pileate poroid and pileate labyrinthoid sporophores. Presence of gloeoplerous hyphae containing fluid that typically stains black in sulfoaldehyde compounds is a synapomorphy for the Russulales. Amyloid reactions in spore or hyphal walls that occur frequently throughout the Russulales often are perceived as an obvious synapomorphy but are inconsistent. Approaches including sequencing functional genes, analysis of gene expression and biochemical analysis across the entire order are needed.

Metarhizium frigidum sp. nov.: a cryptic species of M. anisopliae and a member of the M. flavoviride complex

Abstract: The anamorph genus Metarhizium is composed of arthropod pathogens, several with broad geographic and host ranges. Members of the genus, including "M. anisopliae var. frigidum" nomen nudum and Metarhizium flavoviride, have been used as biological insecticides. In a recent revision of the genus the variety "M. anisopliae var. frigidum" was suggested to be a synonym of M. flavoviride based largely on ITS sequence phylogenetic analysis. In this study we conducted morphological evaluations and multigene phylogenetic analyses with EF-1alpha, RPB1 and RPB2 for strains of M. flavoviride and "M. anisopliae var. frigidum." Included in these evaluations were the ex-type of M. flavoviride var. flavoviride and what likely would be considered the "ex-type' of the invalidly published taxon "M. anisopliae var. frigidum". Based on morphological and molecular evidence we conclude that "M. anisopliae var. frigidum" is distinct from M. flavoviride and the taxon M. frigidum sp. nov. is described.

Penicillium species endophytic in coffee plants and ochratoxin A production.

Abstract: Tissues from Coffea arabica, C. congensis, C. dewevrei and C. liberica collected in Colombia, Hawaii and at a local plant nursery in Maryland were sampled for the presence of fungal endophytes. Surface sterilized tissues including roots, leaves, stems and various berry parts were plated on yeast-malt agar. DNA was extracted from a set of isolates visually recognized as Penicillium, and the internal transcribed spacer region and partial LSU-rDNA was amplified and sequenced. Comparison of DNA sequences with GenBank and unpublished sequences revealed the presence of 11 known Penicillium species: P. brevicompactum, P. brocae, P. cecidicola, P. citrinum, P. coffeae, P. crustosum, P. janthinellum, P. olsonii, P. oxalicum, P. sclerotiorum and P. steckii as well as two possibly undescribed species near P. diversum and P. roseopurpureum. Ochratoxin A was produced by only four isolates, one isolate each of P. brevicompactum, P. crustosum, P. olsonii and P. oxalicum. The role these endophytes play in the biology of the coffee plant remains enigmatic.

Aspergillus ibericus: a new species of section Nigri isolated from grapes.

Abstract: As part of a study on the ochratoxin producing mycoflora of grapes, several Aspergillus strains were isolated and tested for their ochratoxin A (OTA) producing abilities. Aspergillus strains of the section Nigri, which did not produce detectable amounts of OTA but which had a similar morphology to A. carbonarius, were isolated from wine grapes and/or dried vine fruit in Portugal and Spain. These strains, however, have characters that allow morphological distinction from the other species in the section, particularly the conidia size (5-7 microm), which allows separation of the species from the two most common biseriate species in section Nigri: A. carbonarius (7-9 microm) and A. niger and its aggregate species (3-5 microm). The strains are described here as belonging to a new species, named A. ibericus. The validation of this new taxon is supported further by analysis of the ITS-5.8S rDNA and calmodulin gene sequences and by analysis of the amplified fragment length polymorphism (AFLP) patterns, which were consistent in separating these strains from other species in the section. A. ibericus strains do not produce OTA therefore they are interesting for biotechnological exploration because many metabolites with commercial value are produced by other species in the section.

Fungal spore diversity of arbuscular mycorrhizal fungi associated with spring wheat: effects of tillage

Abstract: We investigated the influence of tilling, N fertilization and crop stage on arbuscular mycorrhizae (AM) fungal species diversity in a wheat monoculture in the Pampa region of Argentina. Glomalean spores were isolated by wet sieving and decanting from conventionally tilled and nontilled soils cropped with wheat with or without N fertilization, at three phenological stages of the crop (tilling, flowering and grain filling) and fallow. Morphological characterization yielded at least 24 AM fungi taxa in the field samples, belonging to six genera of AMF: Acaulospora Archaeospora, Entrophospora, Gigaspora, Glomus and Scutellospora. Tilling and fertilization treatments did not result in decreased spore biodiversity. Wheat phenology influenced AM communities, with highest spore biodiversity during grain filling.

Early diverging Ascomycota: phylogenetic divergence and related evolutionary enigmas

Abstract: The early diverging Ascomycota lineage, detected primarily from nSSU rDNA sequence-based phylogenetic analyses, includes enigmatic key taxa important to an understanding of the phylogeny and evolution of higher fungi. At the moment six representative genera of early diverging ascomycetes (i.e. Taphrina, Protomyces, Saitoella, Schizosaccharomyces, Pneumocystis and Neolecta) have been assigned to "Archiascomycetes" sensu Nishida and Sugi ama (1994) or the subphylum "Taphrinomycotina" sensu Eriksson and Winka (1997). The group includes fungi that are ecologically and morphologically diverse, and it is difficult therefore to define the group based on common phenotypic characters. Bayesian analyses of nSSU rDNA or combined nSSU and nLSU rDNA sequences supported previously published Ascomycota frameworks that consist of three major lineages (i.e. a group of early diverging Ascomycota. [Taphrinomycotina], Saccharomycotina and Pezizomycotina); Taphrinomycotina is the sister group of Saccharomycotina and Pezizomycotina. The 50% majority rule consensus of 18000 Bayesian MCMCMC-generated trees from multilocus gene sequences of nSSU rDNA, nLSU rDNA (D1/D2), RPB2 and beta-tubulin also showed the monophyly of the three subphyla and the basal position of Taphrinomycotina in Ascomycota with significantly higher statistical support. However to answer controversial questions on the origin, monophyly and evolution of the Taphrinomycotina, additional integrated phylogenetic analyses might be necessary using sequences of more genes with broader taxon sampling from the early diverging Ascomycota.