Higher-level phylogenetic relationships of Homobasidiomycetes (mushroom-forming fungi) inferred from four rDNA regions.

Homobasidiomycetes include approximately 13,000 described species of mushroom-forming fungi and related taxa. The higher-level classification of this ecologically important group has been unsettled for over 100 years. The goals of the present study were to evaluate a recent phylogenetic classification by Hibbett and Thorn that divided the homobasidiomycetes into eight major unranked clades, and to infer the higher-order relationships among these clades. A dataset of 93 species that represent all eight previously recognized clades was assembled, with 3800 bp of sequence data from nuclear and mitochondrial large and small subunit rDNAs for each taxon. Parsimony and maximum-likelihood analyses support the monophyly of the eight major clades recognized by Hibbett and Thorn. Most groups are strongly supported in bootstrapped parsimony analyses, but the polyporoid clade remains weakly supported. For the first time, the sister-group relationship of the euagarics clade and bolete clade is strongly supported, and the Hygrophoraceae is strongly supported as the sister group of the rest of the euagarics clade. Nevertheless, the backbone of the homobasidiomycete phylogeny, and the internal structure of several clades, remain poorly resolved.     

Phylogenetic relationships of russuloid basidiomycetes with emphasis on aphyllophoralean taxa

Many homobasidiomycetes are characterized by a combination of gloeocystidia and amyloid basidiospores. They display a great variation in basidioma morphology, including erect and effused forms and gilled and nongilled forms. Earlier studies have shown these taxa to be related, and the group has been named the russuloid clade. Phylogenetic relationships among russuloid basidiomycetes were investigated using sequence data from the nuclear 5.8S, ITS2 and large-subunit rDNA genes. A dataset including 127 ingroup sequences representing 43 genera and ca 120 species were analyzed by maximum-parsimony and neighbor-joining methods. The sampling of taxa had an emphasis on nongilled taxa and two-thirds of the species possessed corticioid basidiomata. Thirteen major well-supported clades were identified within the russuloid clade. All clades except one include corticioid species. Ten characters from basidioma morphology and cultured mycelium were observed and evaluated. Results suggest that gloeocystidia are a synapomorphy for taxa within the russuloid clade while the amyloidity of spores is inconsistent. The ornamentation of spores and type of nuclear behavior seems to be informative characters at genus level. The agaricoid genera Lactarius and Russula are nested in a clade with corticioid species at the basal position. The new combinations Boidinia aculeata, Gloeodontia subasperispora, Gloeocystidiopsis cryptacantha and Megalocystidium wakullum are proposed.     

Evolutionary relationships of Mycaureola dilseae (Agaricales), a basidiomycete pathogen of a subtidal rhodophyte

Mushroom-forming fungi (homobasidiomycetes) are major examples of morphological and ecological diversification in terrestrial habitats. Homobasidiomycetes includes only nine described species that are known from marine environments. Morphological traits that have concealed the ancestry of these fungi include reduced fruiting bodies with hairy surfaces and extremely modified spores, both of which may function as floating devices to aid successful dispersal and adhesion to various substrates such as driftwood. Our previous results suggested that all marine forms as yet investigated are placed in the Nia clade (euagarics) and that they have primarily evolved from cypelloid forms (minute, cup-shaped, terrestrial saprotrophs) via transitions through mangroves to fully marine habitats. We show here that Mycaureola dilseae, which parasitizes the red alga Dilsea carnosa, is a second independent lineage of marine fungi in the euagarics clade that is not related to cyphelloid forms. Phylogenetic reconstructions were based on two data sets: a partial four-region rDNA data set (nuc-ssu, nuc-lsu, mt-ssu, and mt-lsu) with inclusive sampling of 249 taxa and a densely sampled ITS data set including 32 taxa, which formed a clade with Mycaureola in the four-region rDNA analyses. Inferences using constrained and unconstrained six-parameter weighted parsimony, Bayesian Markov chain Monte Carlo methods, and maximum likelihood approaches place M. dilseae in the morphologically diverse /physalacriaceae clade next to Gloiocephala spp., a group of highly reduced stipitate-pileate saprotrophs.     

Stipitate stereoid basidiocarps have evolved multiple times

Stipitate stereoid fungi are Basidiomycetes with a stipe, a spathulate-to funnel-shaped pileus, a smooth hymenophore, and hyaline, smooth spores. Representatives of the genera Cotylidia, Cymatoderma, Muscinupta, Podoscypha and Stereopsis were subjected to molecular phylogenetic analyses based on nuclear ribosomal large subunit, 5.8S and ITS sequences. For four of the genera the type species was included in analyses. Stereopsis radicans, the type species of Stereopsis, forms a lineage with the corticioid species Clavulicium globosum but could not be placed in any of the presently accepted orders within Agaricomycotina. Stereopsis vitellina falls within the Atheliales, making it the first pileus- and stipe-forming fungus recovered in this order. Cotylidia and Muscinupta again are shown to be members of the Hymenochaetales, whereas Cymatoderma and Podoscypha belong in the Polyporales. Cymatoderma is polyphyletic and Cymatoderma sensu stricto is separated from other stipitate stereoid fungi in the Polyporales, whereas the remaining Cymatoderma species are nested within a well supported clade holding all Podoscypha species but also Abortiporus biennis.     

Reconstructing the Clavariaceae using nuclear large subunit rDNA sequences and a new genus segregated from Clavaria

Fungi that produce clavarioid fruit bodies have evolved independently many times in the Basidiomycota. The evolutionary significance of this morphology is difficult to interpret because the phylogenetic positions of many clavarioid fungi are still unknown. In this study we examined the phylogenetic diversity of the Clavariaceae sensu lato among Homobasidiomycetidae by adding partial nuclear large subunit ribosomal DNA sequences from clavarioid and corticioid fungi to a large euagaric dataset and analyzing them both together and separately. Our results indicate that the clavarioid morphology has evolved at least five times in the euagarics while the inclusion of type species enabled us to evaluate the taxonomic consequences of this polyphyletic distribution. Although the sampling available at present is incomplete, a qualitative assessment of our phylogenetic hypotheses indicates that the clavarioid habit might not be as evolutionary labile as previously reported. We propose the new genus Alloclavaria to accommodate Clavaria purpurea, which is not related to Clavaria but is derived within the hymenochaetoid clade. The Physalacriaceae and Clavariaceae are redefined to reflect monophyletic groups, and the limits of Clavaria, Clavulinopsis and Ramariopsis should be reconsidered when additional data are available.     

Tying up loose threads: revised taxonomy and phylogeny of an avian-dispersed Neotropical rhizomorph-forming fungus

Rhizomorpha corynecarpos Kunze was originally described from wet forests in Suriname. This unusual fungus forms white, sterile rhizomorphs bearing abundant club-shaped branches. Its evolutionary origins are unknown because reproductive structures have never been found. Recent collections and observations of R. corynecarpos were made from Belize, Brazil, Ecuador, Guyana, and Peru. Phylogenetic analyses of three nuclear rDNA regions (internal transcribed spacer, large ribosomal subunit, and small ribosomal subunit) were conducted to resolve the phylogenetic relationship of R. corynecarpos. Results show that this fungus is sister to Brunneocorticium bisporum—a widely distributed, tropical crust fungus. These two taxa along with Neocampanella blastanos form a clade within the primarily mushroom-forming Marasmiaceae. Based on phylogenetic evidence and micromorphological similarities, we propose the new combination, Brunneocorticium corynecarpon, to accommodate this species. Brunneocorticium corynecarpon is a pathogen, infecting the crowns of trees and shrubs in the Neotropics; the long, dangling rhizomorphs with lateral prongs probably colonize neighboring trees. Longer-distance dispersal can be accomplished by birds as it is used as construction material in nests of various avian species.     

One hundred and seventeen clades of euagarics

This study provides a first broad systematic treatment of the euagarics as they have recently emerged in phylogenetic systematics. The sample consists of 877 homobasidiomycete taxa and includes approximately one tenth (ca. 700 species) of the known number of species of gilled mushrooms that were traditionally classified in the order Agaricales. About 1000 nucleotide sequences at the 5(') end of the nuclear large ribosomal subunit gene (nLSU) were produced for each taxon. Phylogenetic analyses of nucleotide sequence data employed unequally weighted parsimony and bootstrap methods. Clades revealed by the analyses support the recognition of eight major groups of homobasidiomycetes that cut across traditional lines of classification, in agreement with other recent phylogenetic studies. Gilled fungi comprise the majority of species in the euagarics clade. However, the recognition of a monophyletic euagarics results in the exclusion from the clade of several groups of gilled fungi that have been traditionally classified in the Agaricales and necessitates the inclusion of several clavaroid, poroid, secotioid, gasteroid, and reduced forms that were traditionally classified in other basidiomycete orders. A total of 117 monophyletic groups (clades) of euagarics can be recognized on the basis on nLSU phylogeny. Though many clades correspond to traditional taxonomic groups, many do not. Newly discovered phylogenetic affinities include for instance relationships of the true puffballs (Lycoperdales) with Agaricaceae, of Panellus and the poroid fungi Dictyopanus and Favolaschia with Mycena, and of the reduced fungus Caripia with Gymnopus. Several clades are best supported by ecological, biochemical, or trophic habits rather than by morphological similarities.     

Phylogenetic analyses reveal deeply divergent species lineages in the genus Sphaerobolus (Phallales: Basidiomycota)

Phylogenetic analyses of 27 artillery fungus (Sphaerobolus sp.) isolates were conducted to identify species boundaries in the genus Sphaerobolus. Multiple gene genealogies inferred from maximum likelihood, Bayesian, and maximum-parsimony analyses of sequence data from individual loci (mtSSU, ITS, EF 1-alpha, and LSU) and a combined dataset (mtSSU, ITS, and EF 1-alpha) concordantly indicate the existence of three deeply divergent lineages in the genus Sphaerobolus, each representing a phylogenetic species. These three phylogenetic species correspond to two known species: Sphaerobolus iowensis and Sphaerobolus stellatus, and a newly discovered species. Suprageneric phylogenetic analyses of the mtSSU and LSU datasets containing representatives of related genera of the gomphoid-phalloid clade of Homobasidiomycetes suggested that the undescribed taxon likely is more closely related to S. stellatus than to S. iowensis.     

Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi)

A phylogeny of the fungal phylum Basidiomycota is presented based on a survey of 160 taxa and five nuclear genes. Two genes, rpb2, and tef1, are presented in detail. The rpb2 gene is more variable than tef1 and recovers well-supported clades at shallow and deep taxonomic levels. The tef1 gene recovers some deep and ordinal-level relationships but with greater branch support from nucleotides compared to amino acids. Intron placement is dynamic in tef1, often lineage-specific, and diagnostic for many clades. Introns are fewer in rpb2 and tend to be highly conserved by position. When both protein-coding loci are combined with sequences of nuclear ribosomal RNA genes, 18 inclusive clades of Basidiomycota are strongly supported by Bayesian posterior probabilities and 16 by parsimony bootstrapping. These numbers are greater than produced by single genes and combined ribosomal RNA gene regions. Combination of nrDNA with amino acid sequences, or exons with third codon positions removed, produces strong measures of support, particularly for deep internodes of Basidiomycota, which have been difficult to resolve with confidence using nrDNA data alone. This study produces strong boostrap support and significant posterior probabilities for the first time for the following monophyletic groups: (1) Ustilaginomycetes plus Hymenomycetes, (2) an inclusive cluster of hymenochaetoid, corticioid, polyporoid, Thelephorales, russuloid, athelioid, Boletales, and euagarics clades, (3) Thelephorales plus the polyporoid clade, (4) the polyporoid clade, and (5) the cantharelloid clade. Strong support is also recovered for the basal position of the Dacrymycetales in the Hymenomycetidae and paraphyly of the Exobasidiomycetidae.     

Fruiting body-guided molecular identification of root-tip mantle mycelia provides strong indications of ectomycorrhizal associations in two species of Sistotrema (Basidiomycota)

Fruiting body guided sequence analysis of mycorrhizal root-tip mycelia is a powerful yet relatively sparsely explored method for species-level identification of mycorrhizal fungi. It is used in this study to indicate mycorrhizal associations in the corticioid (resupinate) genus Sistotrema of the cantharelloid clade through phylogenetic analysis of the ITS and nuLSU rDNA regions of two spatiotemporally co-occurring Sistotrema fruiting bodies and ectomycorrhizal root tips. The genus Sistotrema is confirmed to be polyphyletic, and the mycorrhizal species form a strongly supported monophyletic clade together with the stipitate genus Hydnum. The remaining lineages of Sistotrema may well be saprotrophic, the nutritional mode traditionally attributed to the genus, but the phylogenetic analyses show that they should be excluded from Sistotrema. The cantharelloid clade contains several mycorrhizal genera, but no symbiotic associations have previously been demonstrated for Sistotrema.     

Obba and Sebipora, new polypore genera related to Cinereomyces and Gelatoporia (Polyporales, Basidiomycota)

Cinereomyces clade is a newly proposed monophyletic group of polypores containing currently four genera and five species, including two promising biopulping fungi, Ceriporiopsis rivulosa and C. subvermispora. The Cinereomyces clade is well-delimited in nrDNA-based phylogenetic analysis, but its position in Polyporales remains unclear. Its closest relative may be found in the core polyporoid clade. Only a few morphological characters are common for all the species in the clade, e.g. CB– and CRB+ hyphae, white fruiting bodies, presence of oil, and middle-sized spores. Culturally, the species are unified by producing simple-septate generative hyhpae in the margin, which produce simple-clamped hyphae backwards. The genus Gelatoporia is the correct place for Ceriporiopsis subvermispora. Two new genera are described in the group: Obba to incorporate C. rivulosa and a new austral species, Obba valdiviana, known from southern Argentina and recorded here also from Tasmania, and Sebipora to accommodate a new species from tropical Asia, S. aquosa. ITS sequences imply that Eurasian Gelatoporia subvermispora may belong to a different species from the North American one. G. subvermispora is recorded as new to Indonesia.     

Derivation of a polymorphic lineage of Gasteromycetes from boletoid ancestors

The phylogeny of selected gasteromycetes and hymenomycetes was inferred from partial nuclear large subunit rDNA (nuc-lsu, 28S) sequences, delimited by primers LR0R and LR5. Taxon sampling with emphasis on relationships within the Boletales further included some gasteroid groups, which obviously have evolved convergent fruiting body morphology, and therefore remained controversial in taxonomy. This study confirms the close relationship of Geastrales, Gauteriales and Phallales and the presumable derivation of Nidulariales and Tulostomatales within the euagarics clade, as widely accepted. In addition, four Hymenogaster species investigated were found to be in the euagarics clade and a relationship to the Cortinariaceae was indicated. The gasteroid fungus Zelleromyces stephensii is an example for maintaining morphological linkage by a lactiferous hyphal system to the genus Lactarius in the Russulales, and this relationship was affirmed in the sequence analysis. Several previously suggested relationships of gasteromycetes and Boletales were reproducible by analyzing nuc-lsu sequences. As a new result, Astraeus hygrometricus, the barometer earth star, is an additional representative of the Boletales. Together with Boletinellus, Phlebopus, Pisolithus, Calostoma, Gyroporus, Scleroderma, and Veligaster, Astraeus forms an unusual group comprising pileate-stipitate hymenomycetes and polymorphic gasteromycetes. This group is a major lineage within the Boletales and we propose the new suborder Sclerodermatineae, including the six families Boletinellaceae fam. nov. (Boletinellus and Phlebopus), Gyroporaceae (Singer) fam. nov. (Gyroporus), Pisolithaceae (Pisolithus), Astraeaceae (Astraeus), Calostomataceae (Calostoma), and the typus subordinis Sclerodermataceae (Scleroderma and Veligaster). Morphological and ecological characters, and pigment synthesis support the delimitation of the Sclerodermatineae, and indicate the radiation of different lineages in the Boletales originating from fungi with primitive tubular hymenophores. We regard such boletes with gyroid-boletinoid hymenophores, like Boletinellus, Gyrodon, Gyroporus, Paragyrodon and Phlebopus as key taxa in the evolution of Paxillineae, Sclerodermatineae and Boletineae.     

<Emphasis Type="Italic">Purpureocorticium microsporum</Emphasis> (Basidiomycota) gen. et sp. nov. from East Asia

A corticioid fungal species found in mountainous Taiwan, and Yunnan Province of China, is described as a new genus and new species: Purpureocorticium microsporum (Agaricomycetes, Basidiomycota). Morphological study and phylogenetic analyses based on sequence data respectively derived from the large subunit nuclear ribosomal RNA gene (LSU nrDNA) alone and the combined dataset of LSU nrDNA and translation elongation factor 1-α gene (tef1-α) indicated that Purpureocorticium does not belong to any clade of the Agaricomycetes. Purpureocorticium and P. microsporum are characterized by having a resupinate basidiocarp with smooth hymenial surface which turns purple in KOH, and becomes purplish after storage, microscopically having compact texture of subiculum, nodose-septate thin-walled generative hyphae, absence of cystidia, basidia subclavate with a median constriction, or utriform, bearing ovate-ellipsoid small-sized basidiospores, which are smooth and thin-walled, inamyloid, and nondextrinoid. The new combination Rhizochaete rubescens is proposed, based on morphological and phylogenetic evidences.     

Vittatispora, a new melanosporaceous genus from Indian soil

Vittatispora coorgii gen. sp. nov., isolated from soil in India, is described and illustrated. The fungus has morphological characteristics of the genera Melanospora, Sphaerodes and Syspastospora. The most striking feature is the presence of a thick hyaline ridge along the vertical axis of the lemon-shaped ascospores wall. Perithecia also have a long neck composed of adhering hyphae, similar to that of Syspatospora. Phylogenetic studies on the 28S rDNA indicate it is closely related to Melanospora and Sphaerodes and belongs in the Ceratostomataceae. The new genus is based on the distinctive morphology and phylogenetic analyses. The fungus grew in culture only conjointly with a sterile fungus which a BLAST analysis suggested was close to Tetracladium marchalianum.     

<Emphasis Type="Italic">Lecophagus vermicola</Emphasis> sp. nov., a nematophagous hyphomycete with an unusual hunting strategy

Lecophagus vermicola sp. nov. is described and illustrated as a predacious (carnivorous) hyphomycete living in bark fissures of living trees of Platanus and other angiosperm and gymnosperm trees, recorded in Hungary, Luxembourg and France. The fungus captures nematodes unlike other Lecophagus species, which are predators of rotifers and tardigrades. The morphology of the sessile, adhesive knobs differ from all previously described species of the genus which form adhesive pegs. Molecular data confirms that the new species belongs to the Lecophagus clade but without matching existing sequences. The fungus captures victims with adhesive knobs and colonizes its prey with a mycelium of rather broad hyphae on which, again, adhesive knobs are formed which penetrate the cuticule of the victim. Clusters of colonized nematodes form a network utilized to capture more prey. The fungus lives in the xeric, ephemerally aquatic habitat of bark fissures of standing, living or dead, corticated trunks and branches. The genus Haptocara is compared, which has similar adhesive knobs capturing nematodes and similar broad hyphae, but for which no molecular data was available.     

Hymenochaetales: a molecular phylogeny for the hymenochaetoid clade

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 corticicoid 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 confirmttion. 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.     

Pseudotripoconidium, a new anamorph genus connected to Orbilia

A new anamorphic fungus is described based on four isolates from ascospores of Orbilia aff. luteorubella. This fungus differs from previously known Orbilia anamorphs in producing inversely pyramidal, unicellular conidia with several protuberances at their distal end. Conidia produce 1-7 prominent denticles that emerge from a node at the conidiophore apex. Conidiogenesis is holoblastic. Because phylogenetic analysis indicated greater than 90% ITS sequence similarities among the four isolates they are treated here as a single species. In the sequence analysis of the internal transcribed spacer region (ITS) these isolates and other sequences identified as O. aff. luteorubella were nested within Orbilia and formed a clade with 99% bootstrap support. This clade is separated from nematode-trapping species of Orbilia. Based on both morphological and molecular analyses, we propose a new genus, Pseudotripoconidium.     

中国南方两个革菌新种：中国丝皮革菌和棉絮丝皮革菌（丝皮革菌科,多孔菌目）

依据形态学和分子系统学研究结果,描述了产自中国云南省的丝皮革菌属2个新种,即中国丝皮革菌Hyphoderma sinense和棉絮丝皮革菌H. floccosum。中国丝皮革菌以光滑子实层体表面、被结晶和念珠状的囊状体及圆柱形至腊肠状的担孢子（8-11.5×3-5μm）为主要识别特征。棉絮丝皮革菌具有棉絮状至粉状子实层体表面、管状和分隔状囊状体及椭圆形至腊肠状担孢子。对新种的ITS和nLSU片段进行了测序和分析,采用最大似然法、最大简约法和贝叶斯推断法对研究样本的ITS+nLSU nrRNA基因序列进行系统发育分析,结果显示两个新种隶属于丝皮革菌属,其中,中国丝皮革菌与变形丝皮革菌聚在一起;棉絮丝皮革菌与松生丝皮革菌、丝皮革菌和拟丝皮革菌聚为一类。本研究提供了两新种的详细描述、线条图、生态照片及与相似种的区别,同时编写了我国丝皮革菌属23个种的检索表。     

Low host-pathogen specificity in the leaf-cutting ant-microbe symbiosis

Host-parasite associations are shaped by coevolutionary dynamics. One example is the complex fungus-growing ant-microbe symbiosis, which includes ancient host-parasite coevolution. Fungus-growing ants and the fungi they cultivate for food have an antagonistic symbiosis with Escovopsis, a specialized microfungus that infects the ants' fungus gardens. The evolutionary histories of the ant, cultivar and Escovopsis are highly congruent at the deepest phylogenetic levels, with specific parasite lineages exclusively associating with corresponding groups of ants and cultivar. Here, we examine host-parasite specificity at finer phylogenetic levels, within the most derived clade of fungus-growing ants, the leaf-cutters (Atta spp. and Acromyrmex spp.). Our molecular phylogeny of Escovopsis isolates from the leaf-cutter ant-microbe symbiosis confirms specificity at the broad phylogenetic level, but reveals frequent host-switching events between species and genera of leaf-cutter ants. Escovopsis strains isolated from Acromyrmex and Atta gardens occur together in the same clades, and very closely related strains can even infect the gardens of both ant genera. Experimental evidence supports low host-parasite specificity, with phylogenetically diverse strains of Escovopsis being capable of overgrowing all leaf-cutter cultivars examined. Thus, our findings indicate that this host-pathogen association is shaped by the farming ants having to protect their cultivated fungus from phylogenetically diverse Escovopsis garden pathogens.     

Ancestral lineages of arbuscular mycorrhizal fungi (Glomales)

Using new and existing 18S rRNA sequence data, we show that at least five species of glomalean fungi lie outside the previously defined families and diverged very early in the evolution of that group. These five fungi would have been missed by many previous ecological studies because their sequences are not well matched to available taxon-specific primers and they do not stain well with the standard reagents used for morphological analysis. Based upon spore morphology, these species are currently assigned to Glomus and Acaulospora, and two of the species are dimorphic, exhibiting spore stages of both genera. This suggests that dimorphic spores are the ancestral state for the order and that one or the other morphology was lost in various lineages. Our analyses also show that Geosiphon pyriforme, a symbiont with cyanobacteria, is not necessarily a sister group of the Glomales; instead, it may be derived from mycorrhizal ancestors.