@article {4519, title = {Re-evaluation of the morphological variability of Microglossum viride and M. griseoviride sp. nov.}, journal = {Mycologia}, volume = {106}, year = {2014}, month = {2014 Mar-Apr}, pages = {282-90}, abstract = {

Studies in Microglossum viride (Pers.) Gillet revealed that the name was used incorrectly for two similar but different taxa. Analyses of morphological, ecological and molecular (sequences of ITS and LSU region of rRNA gene) characters of type and voucher specimens of M. viride and related taxa resulted in delimitation and description of a new species, Microglossum griseoviride V. Ku{\v c}era, Lizo{\v n} \& M. Tom\šovsk\ý. Lectotypes of Geoglossum viride Pers., and epitype of Geoglossum viride are designated. Species Microglossum minus Velen. and Microglossum lutescens Boud. are confirmed to be conspecific to M. viride.

}, keywords = {Ascomycota, DNA, Fungal, DNA, Ribosomal, Molecular Sequence Data, Phylogeny, Soil Microbiology, Spores, Fungal}, issn = {0027-5514}, doi = {10.3852/106.2.282}, author = {Ku{\v c}era, Viktor and Lizo{\v n}, Pavel and Tom{\v s}ovsk{\'y}, Michal and Ku{\v c}era, Jarom{\'\i}r and Gaisler, Jan} } @article {4507, title = {Molecular phylogeny of Hypoxylon and closely related genera}, journal = {Mycologia}, volume = {97}, year = {2005}, pages = {844-865}, abstract = {

Phylogenetic relationships were inferred among several xylariaceous genera with Nodulisporium or nodulisporium-like anamorphs based on the analyses of beta-tubulin and alpha-actin sequences. One hundred nine cultures and three specimens of 83 representatives of these four genera were included in the study. Biscogniauxia taxa formed a well supported clade that was basal to the other taxa, while taxa of Hypoxylon and Daldinia comprised a large monophyletic group that contained two subclades. The first subclade encompassed Hypoxylon sect. Annulata and is accepted here as the new genus Annulohypoxylon. The second subclade contained taxa of Hypoxylon sect. Hypoxylon and Daldinia. Hypoxylon is restricted to include only those taxa in sect. Hypoxylon. Thirty-three epithets are made in Annulohypoxylon. Hypoxylon cohaerens var. microsporum is raised to the species level and accepted as A. minutellum. Hypoxylon polyporoideum is recognized as distinct from H. crocopeplum. Hypoxylon placentiforme is accepted as Daldinia placentiformis.

}, keywords = {Actins, DNA, Fungal, Molecular Sequence Data, Phylogeny, Sequence Analysis, DNA, Species Specificity, Tubulin, Xylariales}, issn = {0027-5514}, author = {Hsieh, H.M. and Ju, Y.-M. and Rogers, J.D.} } @article {4255, title = {Molecular evidence supports the distinction between Xanthoria parietina and X. aureola (Teloschistaceae, lichenized Ascomycota).}, journal = {Mycological Research}, volume = {109}, year = {2005}, pages = {187-199}, abstract = {

This study aims to clarify taxonomic relationships within the current concept of Xanthoria parietina in northern Europe. For comparison, X. calcicola was also included in the study. Morphological as well as molecular data were utilized. Morphology indicated the presence of three species, Xanthoria parietina, X. calcicola, and X. aureola, the latter of which is resurrected here from synonymy. The most important separating characters involve colour and thickness of the thallus, lobe width, morphology of laminar structures, and the texture of the upper surface. X. aureola, as recognized here, mostly occurs on seashore rocks. Part of the IGS region as well as the complete ITS were sequenced in 70 individual thalli representing ten geographical regions in Europe. In total, 19 different IGS haplotypes and 20 different ITS haplotypes were present in the data set. Owing to indications of possible recombination between the IGS and the ITS, the two data sets were analyzed separately. Haplotype networks were estimated, both of which indicate that X. parietina is distinct from X. aureola and X. calcicola. In our sample, the two latter do not share haplotypes, but are only separated by a few mutational steps.

}, keywords = {Ascomycota, Base Sequence, DNA, Fungal, DNA, Ribosomal, DNA, Ribosomal Spacer, Haplotypes, Lichens, Molecular Sequence Data, Mycological Typing Techniques, Phylogeny, Recombination, Genetic, Sequence Analysis, DNA, Spores, Fungal}, issn = {0953-7562}, doi = {https://doi.org/10.1017/S0953756204001790}, author = {Lindblom, L. and Ekman, S.} } @article {4204, title = {Disintegration of the Micareaceae (lichenized Ascomycota): a molecular phylogeny based on mitochondrial rDNA sequences.}, journal = {Mycological Research}, volume = {109}, year = {2005}, pages = {21-30}, abstract = {

The phylogeny of the family Micareaceae and the genus Micarea was studied using mitochondrial small subunit ribosomal DNA sequences. Phylogenetic reconstructions were performed using Bayesian MCMC tree sampling and a maximum likelihood approach. The Micareaceae in its current sense is highly heterogeneous, and Helocarpon, Psilolechia, and Scutula, all thought to be close relatives of Micarea, are shown to be only distantly related. The genus Micarea is paraphyletic unless the entire Pilocarpaceae and Ectolechiaceae are included, as also indicated by an expected likelihood weights test. It is suggested that the Micareaceae is reduced to synonymy with the Pilocarpaceae, which also includes the Ectolechiaceae, and that Micarea may have to be divided into a series of smaller genera in the future. Micarea species with a \&$\#$39;non-micareoid\&$\#$39; photobiont group with Psora and the Ramalinaceae, whereas Micarea intrusa appears to belong in Scoliciosporum. Three species fall inside the paraphyletic Micarea: Szczawinskia tsugae, Catillaria contristans, and Fellhaneropsis vezdae. Tropical foliicolous taxa are nested within groups of mainly temperate and arctic-alpine distribution. A \&$\#$39;micareoid\&$\#$39; photobiont appears to be plesiomorphic in the Pilocarpaceae but has been lost a few times.

}, keywords = {Ascomycota, DNA, Fungal, DNA, Mitochondrial, DNA, Ribosomal, Evolution, Molecular, Lichens, Phylogeny, Sequence Analysis, DNA}, issn = {0953-7562}, url = {http://www.reelab.net/phylografter/study/download/study_file.file.aff47904dbea7823.3737355f7064662e706466.pdf}, author = {Andersen, H.L. and Ekman, S.} } @article {4188, title = {A phylogenetic overview of the family Pyronemataceae (Ascomycota, Pezizales)}, journal = {Mycological Research}, volume = {111}, year = {2007}, pages = {549-571}, abstract = {

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

}, keywords = {Ascomycota, DNA, Fungal, DNA, Ribosomal, Evolution, Molecular, Genes, Fungal, Phenotype, Phylogeny, Sequence Alignment}, issn = {0953-7562}, doi = {10.1016/j.mycres.2007.03.014}, author = {Perry, B.A. and Hansen, K. and Pfister, D.H.} } @article {4186, title = {The phylogenetic placement of Ostropales within Lecanoromycetes (Ascomycota) revisited}, journal = {Mycological Research}, volume = {111}, year = {2007}, pages = {257-267}, abstract = {

Results of molecular studies regarding the phylogenetic placement of the order Ostropales and related taxa within Lecanoromycetes were thus far inconclusive. Some analyses placed the order as sister to the rest of Lecanoromycetes, while others inferred a position nested within Lecanoromycetes. We assembled a data set of 101 species including sequences from nuLSU rDNA, mtSSU rDNA, and the nuclear protein-coding RPB1 for each species to examine the cause of incongruencies in previously published phylogenies. MP, minimum evolution, and Bayesian analyses were performed using the combined three-region data set and the single-gene data sets. The position of Ostropales nested in Lecanoromycetes is confirmed in all single-gene and concatenated analyses, and a placement as sister to the rest of Lecanoromycetes is significantly rejected using two independent methods of alternative topology testing. Acarosporales and related taxa (Acarosporaceae group) are basal in Lecanoromycetes. However, if the these basal taxa are excluded from the analyses, Ostropales appear to be sister to the rest of Lecanoromycetes, suggesting different ingroup rooting as the cause for deviating topologies in previously published phylogenies.

}, keywords = {Ascomycota, Fungal Proteins, Genes, Fungal, Phylogeny, Species Specificity}, issn = {0953-7562}, doi = {10.1016/j.mycres.2007.01.006}, author = {Lumbsch, H.T. and Schmitt, I. and L{\"u}cking, R. and Wiklund, E. and Wedin, M.} } @article {2970, title = {Phylogenetic relationships and convergence of helicosporous fungi inferred from ribosomal DNA sequences.}, journal = {Molecular Phylogenetics and Evolution}, volume = {39}, year = {2006}, pages = {587-597}, abstract = {

Helicosporous fungi form elegant, coiled, and multicellular mitotic spores (conidia). In this paper, we investigate the phylogenetic relationships among helicosporous fungi in the asexual genera Helicoma, Helicomyces, Helicosporium, Helicodendron, Helicoon, and in the sexual genus Tubeufia (Tubeufiaceae, Dothideomycetes, and Ascomycota). We generated ribosomal small subunit and partial large subunit sequences from 39 fungal cultures. These and related sequences from GenBank were analyzed using parsimony, likelihood, and Bayesian analysis. Results showed that helicosporous species arose convergently from six lineages of fungi in the Ascomycota. The Tubeufiaceae s. str. formed a strongly supported monophyletic lineage comprising most species from Helicoma, Helicomyces, and Helicosporium. However, within the Tubeufiaceae, none of the asexual genera were monophyletic. Traditional generic characters, such as whether conidiophores were conspicuous or reduced, the thickness of the conidial filament, and whether or not conidia were hygroscopic, were more useful for species delimitation than for predicting higher level relationships. In spite of their distinctive, barrel-shaped spores, Helicoon species were polyphyletic and had evolved in different ascomycete orders. Helicodendron appeared to be polyphyletic although most representatives occurred within Leotiomycetes. We speculate that some of the convergent spore forms may represent adaptation to dispersal in aquatic environments.

}, keywords = {DNA, Ribosomal, Fungi, Phylogeny, Polymerase Chain Reaction}, issn = {1055-7903}, doi = {10.1016/j.ympev.2006.01.025}, author = {Tsui, C.K.M. and Berbee, M.L.} }