A morphological and phylogenetic evaluation of Marasmius sect. Globulares (Globulares-Sicci complex) with nine new taxa from the Neotropical Atlantic Forest.

The largest and most recently emended Marasmius sect. Globulares (Globulares-Sicci complex) has increased in number of species annually while its infrasectional organization remains inconclusive. During forays in remnants of the Atlantic Rainforest in Brazil, 24 taxa of Marasmius belonging to sect. Globulares were collected from which nine are herein proposed as new: Marasmius altoribeirensis, M. ambicellularis, M. hobbitii, M. luteoolivaceus, M. neotropicalis, M. pallidibrunneus, M. pseudoniveoaffinis, M. rhabarbarinoides and M. venatifolius. We took this opportunity to evaluate sect. Globulares sensu Antonín & Noordel. in particular, combining morphological examination and both single and multilocus phylogenetic analyses using LSU and ITS data, including Neotropical samples to a broader and more globally distributed sampling of over 200 strains. Three different approaches were developed in order to better use the genetic information via Bayesian and Maximum Likelihood analyses. The implementation of these approaches resulted in: i) the phylogenetic placement of the new and known taxa herein studied among the other taxa of a wide sampling of the section; ii) the reconstruction of improved phylogenetic trees presenting more strongly supported resolution especially from intermediate to deep nodes; iii) clearer evidence indicating that the series within sect. Sicci and sect. Globulares in the traditional concept are non-monophyletic by this more stringent evaluation; and iv) the existence of several monophyletic suprespecific groups equivalent to the stirpes of Singer - clusters of morphologically similar species. These two latter points corroborate with findings of previous studies implementing analyses with the entire genus. Based on these results, we proposed a new infrasectional classification elevating Singer's concept of stirpes to series. Thirteen new series, the emendation of three extant series and three subsections gathering these series based on the major clades are proposed.

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.

Polymorphism at the ribosomal DNA spacers and its relation to breeding structure of the widespread mushroom Schizophyllum commune.

The common split-gilled mushroom Schizophyllum commune is found throughout the world on woody substrates. This study addresses the dispersal and population structure of this fungal species by studying the phylogeny and evolutionary dynamics of ribosomal DNA (rDNA) spacer regions. Extensive sampling (n = 195) of sequences of the intergenic spacer region (IGS1) revealed a large number of unique haplotypes (n = 143). The phylogeny of these IGS1 sequences revealed strong geographic patterns and supported three evolutionarily distinct lineages within the global population. The same three geographic lineages were found in phylogenetic analysis of both other rDNA spacer regions (IGS2 and ITS). However, nested clade analysis of the IGS1 phylogeny suggested the population structure of S. commune has undergone recent changes, such as a long distance colonization of western North America from Europe as well as a recent range expansion in the Caribbean. Among all spacer regions, variation in length and nucleotide sequence was observed between but not within the tandem rDNA repeats (arrays). This pattern is consistent with strong within-array and weak among-array homogenizing forces. We present evidence for the suppression of recombination between rDNA arrays on homologous chromosomes that may account for this pattern of concerted evolution.

Multiple origins of sequestrate fungi related to Cortinarius (Cortinariaceae).

The aim of the present study was to investigate the phylogeny and evolution of sequestrate fungi (with gastroid or partially exposed basidiomes) in relation to their gilled relatives from the Cortinariaceae (Basidiomycetes). Phylogenetic analyses of 151 ITS sequences from 77 gilled species and 37 sequestrate taxa were performed using maximum parsimony and maximum likelihood methods. Results show that sequestrate basidiome forms occur in all three major ectomycorrhizal lineages of Cortinariaceae: the clades Cortinarius, Hebeloma/Hymenogaster/Naucoria, and Descolea. However, these forms do not appear within the saprobic outgroup Gymnopilus, indicating multiple origins of sequestrate forms from ectomycorrhizal ancestors. Additionally, within the Cortinarius clade sequestrate forms have multiple origins: emergent Cortinarius spp., Thaxterogaster, Quadrispora, Protoglossum, and two Hymenogaster spp. (H. remyi, H. sublilacinus) share common ancestors with Cortinarius spp., but these sequestrate genera are not closely related to each other (with exception of Thaxterogaster and Quadrispora). Hymenogaster sensu stricto, Setchelliogaster, and Descomyces were placed in the two other major clades. Thus, sequestrate taxa evolved independently many times within brown-spored Agaricales. Furthermore, emergent, secotioid, and gastroid forms have evolved independently from each other, and so are not necessarily intermediate forms. After their establishment, these apparently morphologically stable taxa show a tendency to radiate.

Variation in modes and rates of evolution in nuclear and mitochondrial ribosomal DNA in the mushroom genus Amanita (Agaricales, Basidiomycota): phylogenetic implications.

Modes and rates of molecular evolution, and congruence and combinability for phylogenetic reconstruction, of portions of the nuclear large ribosomal subunit (nLSU-rDNA) and mitochondrial small subunit (mtSSU-rDNA) genes were investigated in the mushroom genus Amanita. The AT content was higher in the mtSSU-rDNA than in the nLSU-rDNA. A transition bias in which AT substitutions were as frequent as transitions was present in the mtSSU-rDNA but not in the nLSU-rDNA. Among-sites rate variation in nucleotide substitutions at variable sites was present in the nLSU-rDNA but not in the mtSSU-rDNA. Likelihood ratio tests indicated very different models of evolution for the two molecules. A molecular clock could be rejected for both data sets. Rates of molecular evolution in the two molecules were uncoupled: faster evolutionary rates in the mtSSU-rDNA and nLSU-rDNA were not observed for the same taxa. In separate phylogenetic analyses, the nLSU-rDNA data set had higher phylogenetic resolution. The partition homogeneity test and statistical bootstrap support for branches indicated absence of conflict in the phylogenetic signal in the two data sets; however, tree topologies produced from the separate data sets were not congruent. Heterogeneity in modes and rates of evolution in the two molecules pose difficulties for a combined analysis of the two data sets: the use of equally weighted parsimony is not fully satisfactory when rate heterogeneity is present, and it is impractical to determine a model for maximum-likelihood analysis that fits simultaneously two heterogeneous data sets. Overall topologies produced from either the separated or the combined analyses using various tree reconstruction methods were identical for nearly all statistically significant branches.

Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences.

Phylogenetic relationships of mushrooms and their relatives within the order Agaricales were addressed by using nuclear large subunit ribosomal DNA sequences. Approximately 900 bases of the 5' end of the nucleus-encoded large subunit RNA gene were sequenced for 154 selected taxa representing most families within the Agaricales. Several phylogenetic methods were used, including weighted and equally weighted parsimony (MP), maximum likelihood (ML), and distance methods (NJ). The starting tree for branch swapping in the ML analyses was the tree with the highest ML score among previously produced MP and NJ trees. A high degree of consensus was observed between phylogenetic estimates obtained through MP and ML. NJ trees differed according to the distance model that was used; however, all NJ trees still supported most of the same terminal groupings as the MP and ML trees did. NJ trees were always significantly suboptimal when evaluated against the best MP and ML trees, by both parsimony and likelihood tests. Our analyses suggest that weighted MP and ML provide the best estimates of Agaricales phylogeny. Similar support was observed between bootstrapping and jackknifing methods for evaluation of tree robustness. Phylogenetic analyses revealed many groups of agaricoid fungi that are supported by moderate to high bootstrap or jackknife values or are consistent with morphology-based classification schemes. Analyses also support separate placement of the boletes and russules, which are basal to the main core group of gilled mushrooms (the Agaricineae of Singer). Examples of monophyletic groups include the families Amanitaceae, Coprinaceae (excluding Coprinus comatus and subfamily Panaeolideae), Agaricaceae (excluding the Cystodermateae), and Strophariaceae pro parte (Stropharia, Pholiota, and Hypholoma); the mycorrhizal species of Tricholoma (including Leucopaxillus, also mycorrhizal); Mycena and Resinomycena; Termitomyces, Podabrella, and Lyophyllum; and Pleurotus with Hohenbuehelia. Several groups revealed by these data to be nonmonophyletic include the families Tricholomataceae, Cortinariaceae, and Hygrophoraceae and the genera Clitocybe, Omphalina, and Marasmius. This study provides a framework for future systematics studies in the Agaricales and suggestions for analyzing large molecular data sets.

Differentiation and grouping of isolates of the Ganoderma lucidum complex by random amplified polymorphic DNA-PCR compared with grouping on the basis of internal transcribed spacer sequences.

Laccate polypores of the Ganoderma lucidum species complex are widespread white rot fungi of economic importance, but isolates cannot be identified by traditional taxonomic methods. Parsimony analysis of nucleotide sequences from the internal transcribed spacers (ITS) of the ribosomal gene (rDNA) distinguished six lineages in this species complex. Each ITS lineage may represent one or more putative species. While some isolates have identical ITS sequences, all of them could be clearly differentiated by genetic fingerprinting using random amplified polymorphic DNA (RAPD). To investigate the suitability of RAPD markers for taxonomic identification and grouping of isolates of the G. lucidum complex, RAPD fragments (RAPDs) were used as phenotypic characters in numerical and parsimony analyses. Results show that data from RAPDS do not distinguish the same clades as ITS data do. Groupings based on analysis of RAPD data were very sensitive to the choice of the grouping method used, and no consistent grouping of isolates could be proposed. However, analysis with RAPDs did resolve several robust terminal clades containing putatively conspecific isolates, suggesting that RAPDs might be helpful for systematics at the lower taxonomic levels that are unresolved by ITS sequence data. The limitations of RAPDs for systematics are briefly discussed. The conclusion of this study is that ITS sequences can be used to identify isolates of the G. lucidum complex, whereas RAPDs can be used to differentiate between isolates having identical ITS sequences. The practical implications of these results are briefly illustrated.