Nuclear Large Subunit rDNA Sequences Research Articles

Polyporus hapalopus sp. nov. (Polyporales, Basidiomycota) from China based on morphological and molecular data

Polyporus sensu lato is understood to be a polyphyletic genus, including two narrowly defined genera (Favolus and Neofavolus), two subclades (Melanopus and Polyporellus), and some scattered species. In this study, Polyporus hapalopus is described and illustrated as a new species on the basis of morphological and molecular evidence. This species is characterized by laterally stipitate, imbricate and large basidiocarps (up to 40 cm diam.), grapefruit odor when fresh, angular pores with lacerate dissepiments, soft (when fresh) to tough (when dry) context, a dimitic hyphal system in context and stipe with variable wide skeleto-binding hyphae, a monomitic hyphal system in trama, and cylindrical basidiospores bearing one or two guttules. Phylogenetically, on the basis of the combined internal transcribed spacer and nuclear large subunit rDNA sequences, P. hapalopus is nested within the Polyporus sensu lato clade, but is separated from four previously established subclades and from other known species.

Evolution of Distorted Pellicle Patterns in Rigid Photosynthetic Euglenids (Phacus Dujardin)

Members of the euglenid genus Phacus are morphologically differentiated from other photosynthetic species by the presence of a rigid cytoskeleton (pellicle) and predominantly dorsoventrally flattened, leaf-shaped cells. In order to better understand the evolutionary history of this lineage, we used scanning electron microscopy to examine patterns of pellicle strips in Phacus acuminatus, Phacus longicauda var. tortus, Phacus triqueter, Phacus segretii, Phacus pleuronectes, Phacus similis, Phacus pusillus, Phacus orbicularis, Phacus warszewiczii, and Discoplastis spathirhyncha, a putative close relative of Phacus and Lepocinclis. Our observations showed that while the earliest diverging species in our analyses, namely P. warszewiczii, has three whorls of exponential reduction, most members of Phacus have clustered patterns of posterior strip reduction that are bilaterally symmetrical distortions of the radially symmetrical "whorled" patterns found in other photosynthetic euglenids. Comparative morphology, interpreted within the context of molecular phylogenetic analyses of combined nuclear small subunit rDNA and partial nuclear large subunit rDNA sequences, demonstrates that clustered patterns of posterior strip reduction arose after the divergence of Phacus from other photosynthetic euglenids and are the result of developmental processes that govern individual strip length. Clustered patterns of pellicle strips in Phacus do not appear to be adaptively significant themselves; they evolved in association with the origin of cell flattening and cell rigidity, which may be adaptations to a planktonic lifestyle.

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.

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.

The phylogenetic distribution of resupinate forms across the major clades of mushroom‐forming fungi (Homobasidiomycetes)

Phylogenetic relationships of resupinate Homobasidiomycetes (Corticiaceae s. lat. and others) were studied using ribosomal DNA (rDNA) sequences from a broad sample of resupinate and nonresupinate taxa. Two datasets were analysed using parsimony, a ‘core’ dataset of 142 species, each of which is represented by four rDNA regions (mitochondrial and nuclear large and small subunits), and a ‘full’ dataset of 656 species, most of which were represented only by nuclear large subunit rDNA sequences. Both datasets were analysed using traditional heuristic methods with bootstrapping, and the full dataset was also analysed with the Parsimony Ratchet, using equal character weights and six‐parameter weighted parsimony. Analyses of both datasets supported monophyly of the eight major clades of Homobasidiomycetes recognised by Hibbett and Thorn, as well as independent lineages corresponding to the Gloeophyllum clade, corticioid clade and Jaapia argillacea. Analyses of the full dataset resolved two additional groups, the athelioid clade and trechisporoid clade (the latter may be nested in the polyporoid clade). Thus, there are at least 12 independent clades of Homobasidiomycetes. Higher‐level relationships among the major clades are not resolved with confidence. Nevertheless, the euagarics clade, bolete clade, athelioid clade and Jaapia argillacea are consistently resolved as a monophyletic group, whereas the cantharelloid clade, gomphoid‐phalloid clade and hymenochaetoid clade are placed at the base of the Homobasidiomycetes, which is consistent with the preponderance of imperforate parenthesomes in those groups. Resupinate forms occur in each of the major clades of Homobasidiomycetes, some of which are composed mostly or exclusively of resupinate forms (athelioid clade, corticioid clade, trechisporoid clade, Jaapia). The largest concentrations of resupinate forms occur in the polyporoid clade, russuloid clade and hymenochaetoid clade. The cantharelloid clade also includes many resupinate forms, including some that have traditionally been regarded as heterobasidiomycetes (Sebacinaceae, Tulasnellales, Ceratobasidiales). The euagarics clade, which is by far the largest clade in the Homobasidiomycetes, has the smallest fraction of resupinate species. Results of the present study are compared with recent phylogenetic analyses, and a table summarising the phylogenetic distribution of resupinate taxa is presented, as well as notes on the ecology of resupinate forms and related Homobasidiomycetes.

A natural classification of Lasiosphaeria based on nuclear LSU rDNA sequences

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

Molecular studies of the Bionectriaceae using large subunit rDNA sequences

Holomorphic species of fifteen genera in the family Bionectriaceae, Hypocreales, and related anamorph species were studied using nuclear large subunit rDNA sequences. Most elements of the Bionectriaceae are shown to form a monophyletic group closely related to representatives of two other families in the Hypocreales, namely the Clavicipitaceae/Hypocreaceae, which is distinct from the Nectriaceae. The genus Bionectria, represented by B. ochroleuca and its anamorph, Clonostachys rosea, and B. cf. aureofulva, appears as a monophyletic lineage that groups with three other species that may also belong to Bionectria. The Bionectria clade is distinct from a second major lineage that includes the perithecial genera Hydropisphaera, Nectriopsis, Ochronectria and Selinia, as well as two cleistothecial genera, Heleococcum and Roumegueriella. Within this lineage the cleistothecial genera, Heleococcum, represented by the nontype species, H. japonense, and the monospecific genus, Roumegueriella, group with the paraphyletic genus Hydropisphaera, including H. peziza, the type species, and H. erubescens. Another lineage includes six cleistothecial genera, namely Bulbithecium, Emericellopsis, Hapsidospora, Leucosphaerina, Mycoarachis, and Nigrosabulum, most of which have Acremonium anamorphs. These genera cluster with the type of Acremonium, A. alternatum, and two anamorph genera, Geosmithia, and Stanjemonium. Both species of Kallichroma, K. tethys and K. glabrum, form a separate lineage within the Bionectriaceae. Kallichroma is the first genus from marine habitats to be confirmed as a member of the Hypocreales. Although classified in the Bionectriaceae based on morphological evidence, species of the tropical genus Peethambara and their Didymostilbe anamorphs and the morphologically similar anamorph genera, Albosynnema and Myrothecium, fall outside of any of the supported clades. These species form a paraphyletic group at the base to the Hypocreaceae/Clavicipitaceae.

Molecular Studies of the Bionectriaceae Using Large Subunit rDNA Sequences

Holomorphic species of fifteen genera in the family Bionectriaceae, Hypocreales, and related anamorph species were studied using nuclear large subunit rDNA sequences. Most elements of the Bionectriaceae are shown to form a monophyletic group closely related to representatives of two other families in the Hypocreales, namely the Clavicipitaceae/Hypocreaceae, which is distinct from the Nectriaceae. The genus Bionectria, represented by B. ochroleuca and its anamorph, Clonostachys rosea, and B. cf. aureofulva, appears as a monophyletic lineage that groups with three other species that may also belong to Bionectria. The Bionectria clade is distinct from a second major lineage that includes the perithecial genera Hydropisphaera, Nectriopsis, Ochronectria and Selinia, as well as two cleistothecial genera, Heleococcum and Roumegueriella. Within this lineage the cleistothecial genera, Heleococcum, represented by the nontype species, H. japonense, and the monospecific genus, Roumegueriella, group with the paraphyletic genus Hydropisphaera, including H. peziza, the type species, and H. erubescens. Another lineage includes six cleistothecial genera, namely Bulbithecium, Emericellopsis, Hapsidospora, Leucosphaerina, Mycoarachis, and Nigrosabulum, most of which have Acremonium anamorphs. These genera cluster with the type of Acremonium, A. alternatum, and two anamorph genera, Geosmithia, and Stanjemonium. Both species of Kallichroma, K. tethys and K. glabrum, form a separate lineage within the Bionectriaceae. Kallichroma is the first genus from marine habitats to be confirmed as a member of the Hypocreales. Although classified in the Bionectriaceae based on morphological evidence, species of the tropical genus Peethambara and their Didymostilbe anamorphs and the morphologically similar anamorph genera, Albosynnema and Myrothecium, fall outside of any of the supported clades. These species form a paraphyletic group at the base to the Hypocreaceae/Clavicipitaceae.