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Collybiopsis bambusicola sp. nov. in Yunnan Province, Southwestern China
Abstract
Collybiopsis bambusicola sp. nov. is described and illustrated from Yunnan Province, Southwestern China, based on morphology and molecular phylogenetic analyses. It is characterized by its minute, cream to cinnamon basidiomata, short, eccentric stipe, forked lamellae, nearly poroid hymenophore which are radially arranged from the base of the stipe, 2–spored basidia, oblong ellipsoid basidiospores (6–8.3 × 3–4.3 μm), and gregarious on dead bamboo. In ITS + nLSU based phylogeny, the new species formed a distinct lineage nested within Collybiopsis ramealis complex clade.
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Collybiopsis is a genus of the gymnopoid/marasmioid complex of the family Omphalotaceae. The classification system of Collybiopsis has recently undergone large changes through molecular approaches. The new classification system has not been applied for Collybiopsis in the Republic of Korea, and general research on this genus was also lacking. In this study, we analyzed the Collybiopsis species in the Republic of Korea by assessing all gymnopoid/marasmioid specimens collected nationwide for ten years by combining morphological approaches and multilocus (ITS + nrLSU) phylogenetic analysis. We thus confirmed that 16 species of Collybiopsis are present in the Republic of Korea, including two previously unreported species ( Co. nonnulla and Co. dichroa ) and seven new species ( Co. albicantipes sp. nov. , Co. clavicystidiata sp. nov. , Co. fulva sp. nov. , Co. orientisubnuda sp. nov. , Co. subumbilicata sp. nov. , Co. undulata sp. nov. , and Co. vellerea sp. nov. ). A thorough examination of the Collybiopsis suggested that it is difficult to distinguish or identify the species based on morphological characteristics only; a combined molecular approach is needed for accurate identification. The Collybiopsis database of the Republic of Korea is updated, and information on the new species is provided. Five new combinations from Marasmiellus to Collybiopsis are also proposed ( Co. istanbulensis comb. nov. , Co. koreana comb. nov. , Co. omphalodes comb. nov. , Co. pseudomphalodes comb. nov. , and Co. ramuliciola comb. nov. ).
Molecular analyses have revealed a clade which equates with the genus name Mycetinis Earle. An overall survey of this genus, however, has not been forthcoming. The current study summarizes taxa which are placed in Mycetinis based on morphological and/or molecular data. Fifteen taxa are accepted: Mycetinis scorodonius f. diminutivus and Mycetinis yunnanensis are proposed as new, while Mycetinis cinnamomeus, Mycetinis olidus, Mycetinis prasiosmus, Mycetinis subalpinus and Myctinis virgultorum are newly recombined binomials. Phylogenies based on molecular data show overall disposition in Omphalotaceae, Gymnopus and allied genera, and taxa of Mycetinis.
Collections of four Gymnopus taxa are proposed as new species: G. barbipes, G. disjunctus, G. micromphaleoides and G. pseudoluxurians. All are placed in subg. Vestipedes and all are compared with taxa producing similar basidiomata.
Five species of gymnopoid/marasmioid fungi from Eastern India are described based on morphological and molecular (nuclear ribosomal internal transcribed spacer regions and large subunit DNA) sequence data. Of the taxa described, one represents a new species (Marasmiellus foliiphilus), and two (Gymnopus melanopus and Gymnopus menehune) represent first distribution reports from India. Comprehensive descriptions and illustrations are provided for all of the five species. An artificial key of currently reported species of Gymnopus and Marasmiellus from India is provided.
Based on recent collections from Ecuador and Panama and on type studies, 16 species of Favolaschia (Mycenaceae, Agaricales), including one new to science, are presented with detailed descriptions and illustrations. Favolaschia macropora is described as new from a bamboo
species from Panama. Favolaschia cinnabarina and F. gaillardii probably are synonyms. Six species are recorded from Ecuador and seven from Panama with F. andina, F. aurantiaca, and F. gaillardii being new to Ecuador and F. andina, F. aurantiaca, F. cinnabarina
and F. heliconiae to Panama. A synoptic key is presented containing data from this study and the literature. New DNA sequences (nuc LSU rDNA) from five species from Panama are used in molecular-phylogenetic analyses. Standards for future species descriptions are outlined. Problems with
literature, concepts on species diversity, and distinguishing characteristics are discussed.
Phylogeographic data indicate that DNA differences consistently exist between the North American and European allopatric populations of Gymnopus confluens. Conversely, pairing experiments show that collections from both populations were sexually compatible in vitro and detailed morphological examinations of numerous fresh and dried basidiomata do not produce qualitative differences. Percent ITS sequence divergence between Europe and North American collections of G. confluens was 3.25%. Species delineation metrics including Rosenberg's PAB statistic, PID metrics, RRD (randomly distributed) and PTP (Poisson Tree Processes) gave mixed indications that North American and European populations were distinct at species rank. The North American populations are described as Gymnopus confluens subsp. campanulatus (Peck) R.H. Petersen.
Bootstrapping is a common method for assessing confidence in phylogenetic analyses. Although bootstrapping was first applied in phylogenetics to assess the repeatability of a given result, bootstrap results are commonly interpreted as a measure of the probability that a phylogenetic estimate represents the true phylogeny. Here we use computer simulations and a laboratory-generated phylogeny to test bootstrapping results of parsimony analyses, both as measures of repeatability (i.e., the probability of repeating a result given a new sample of characters) and accuracy (i.e., the probability that a result represents the true phylogeny). Our results indicate that any given bootstrap proportion provides an unbiased but highly imprecise measure of repeatability, unless the actual probability of replicating the relevant result is nearly one. The imprecision of the estimate is great enough to render the estimate virtually useless as a measure of repeatability. Under conditions thought to be typical of most phylogenetic analyses, however, bootstrap proportions in majority-rule consensus trees provide biased but highly conservative estimates of the probability of correctly inferring the corresponding clades. Specifically, under conditions of equal rates of change, symmetric phylogenies, and internodal change of less-than-or-equal-to 20% of the characters, bootstrap proportions of greater-than-or-equal-to 70% usually correspond to a probability of greater-than-or-equal-to 95% that the corresponding clade is real. However, under conditions of very high rates of internodal change (approaching randomization of the characters among taxa) or highly unequal rates of change among taxa, bootstrap proportions >50% are overestimates of accuracy.
Phylogenies based on ITS and LSU nrDNA sequences show Agaricus (Gymnopus) acervatus as unique within the Gymnopus/Rhodocollybia complex. These phylogenies imply that a separate genus is necessary, and Connopus is proposed. Infraspecific morphological and DNA-based variation within C. acervatus suggests that a western North American clade might be reproductively isolated from the eastern North American/Scandinavian clade and that in this species complex the European and eastern North American clade might be conspecific. A Scandinavian exemplar is selected for bar-coding. Two GenBank sequences with name-phylogenetic placement inconsistencies are identified.
No abstract available.
The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein
sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not
only the accuracy of the results, but also the robustness, portability and user-friendliness of the programs. New features
include NEXUS and FASTA format output, printing range numbers and faster tree calculation. Although, Clustal was originally
developed to run on a local computer, numerous Web servers have been set up, notably at the EBI (European Bioinformatics Institute)
(http://www.ebi.ac.uk/clustalw/).
MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types—e.g. morphological, nucleotide, and protein—and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
Availability: http://morphbank.ebc.uu.se/mrbayes
Contact: fredrik.ronquist@ebc.uu.se
*
To whom correspondence should be addressed.
Three distinct lineages of gymnopoid and marasmioid fungi are recognized in parsimony and Bayesian analyses of nLSU rDNA sequences. One lineage contains the genera Lentinula, Rhodocollybia, Tetrapyrgos, a resurrected and redefined Mycetinis, and two unresolved clades designated /marasmiellus and /gymnopus. /marasmiellus includes the type species of Marasmiellus and is dominated by members of Gymnopus sect. Vestipedes. /gymnopus includes the type species of Gymnopus, Micromphale and Setulipes, and members of Gymnopus sect. Levipedes. A second lineage includes the genera Marasmius s.s. and Crinipellis and represents a redefined /marasmiaceae. A third lineage includes the genera Cylindrobasidium, Flammulina, Gloiocephala, Physalacria, Strobilurus, Xerula and Marasmius sect. Epiphylli and represents /physalacriaceae. One new combination in Rhodocollybia and four new combinations in Mycetinis are proposed. A discussion of the taxonomic implications resulting from the phylogenetic reconstruction is presented.
Unlabelled:
RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Gamma yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets > or =4000 taxa it also runs 2-3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively.
Availability:
icwww.epfl.ch/~stamatak
Collybiopsis ( Omphalotaceae , Agaricales ) is accepted as the correct genus name for a large clade of non-typical Gymnopus . The type species of Collybiopsis ( Agaricus ramealis ) is shown to be a genetic complex. Collybiopsis filamentipes , Co. furtiva , Co. hasanskyensis , and Co. minor are proposed as spp. nov. and Co. californica as a stat. nov. Thirty-four additional Collybiopsis comb. nov. are proposed in Appendix I.
Four species of Collybia sensu lato are reported from the Hawaiian Islands: Rhodocollybia laulaha and Gymnopus menehune represent new species, while G. luxurians and G. subpruinosus are first reports. All four Hawaiian taxa are fully described, illustrated and compared with allied taxa. Marasmius subpruinosus, M. subcyathiformis and Clitocybe collybioides are formally transferred to Gymnopus. An artificial dichotomous key to Hawaiian Rhodocollybia and Gymnopus is presented.
Polyporaceae is one of the most important families of Basidiomycota. Investigations on the species diversity, taxonomy and phylogeny of Polyporaceae in China are carried out. So far 217 species belonging to 42 genera are reported from China. Two new genera: Amylosporia gen. nov. and Murinicarpus gen. nov., twelve new species: Coriolopsis dendriformis sp. nov., C. hainanensis sp. nov., Funalia cystidiata sp. nov., Haploporus microsporus sp. nov., Perenniporia citrinoalba sp. nov., P. yinggelingensis sp. nov., Picipes hainanensis sp. nov., P. jiajinensis sp. nov., P. pseudovarius sp. nov., Trametes duplexa sp. nov., T. ellipsoidea sp. nov. and T. stiptica sp. nov., and six new combinations, Amylosporia hattorii comb. nov., Hornodermoporus latissimus comb. nov., Murinicarpus subadustus comb. nov., Picipes pumilus comb. nov., Vanderbylia delavayi comb. nov. and Vanderbylia robiniophila comb. nov., are proposed. All the species are described based on the Chinese collections. Keys to genera of Polyporaceae occurring in China and keys to species of each genus are provided. This monograph provides a revised classification of Polyporaceae in China according to the modern taxonomy. The phylogeny of Polyporaceae from China are reconstructed based on DNA sequences of multiple loci including the internal transcribed spacer (ITS) regions, the large subunit nuclear ribosomal RNA gene (nLSU), the small subunit nuclear ribosomal RNA gene (nSSU), the small subunit mitochondrial rRNA gene sequences (mtSSU), the translation elongation factor 1-α gene (TEF1), the β-tubulin gene (TBB1), the RNA polymerase II largest subunit (RPB1) and second largest subunit (RPB2) genes. In addition, full morphological descriptions, illustrations, color photographs, taxonomic notes, ecology and all the available sequences of Polyporaceae species found from China are provided.
Omphalotaceae is the family of widely distributed and morphologically diverse marasmioid and gymnopoid agaric genera. Phylogenetic studies have included the family in Agaricales, grouping many traditionally and recently described genera of saprotrophic or parasitic mushroom-producing fungi. However, some genera in Omphalotaceae have not reached a stable concept that reflects monophyletic groups with identifiable morphological circumscription. This is the case of Gymnopus and Marasmiellus, which have been the target of two opposing views: (1) a more inclusive Gymnopus encompassing Marasmiellus, or (2) a more restricted Gymnopus (s. str.) while Marasmiellus remains a distict genus; both genera still await a more conclusive phylogenetic hypothesis coupled with morphological recognition. Furthermore, some new genera or undefined clades need more study. In the present paper, a phylogenetic study was conducted based on nrITS and nrLSU in single and multilocus analyses including members of the Omphalotaceae, more specifically of the genera belonging to the /letinuloid clade. The resulting trees support the view of a more restricted Gymnopus and a distinct Marasmiellus based on monophyletic and strongly supported clades on which their morphological circumscriptions and taxonomic treatments are proposed herein. The results also provide evidence for the description of two new genera: Paragymnopus and Pusillomyces. Pusillomyces manuripioides sp. nov. (type species of the genus) is described with morphological description, taxonomic and ecological remarks, and illustrations.
Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
Detailed restriction analyses of many samples often require substantial amounts of time and effort for DNA extraction, restriction digests, Southern blotting, and hybridization. We describe a novel approach that uses the polymerase chain reaction (PCR) for rapid simplified restriction typing and mapping of DNA from many different isolates. DNA fragments up to 2 kilobase pairs in length were efficiently amplified from crude DNA samples of several pathogenic Cryptococcus species, including C. neoformans, C. albidus, C. laurentii, and C. uniguttulatus. Digestion and electrophoresis of the PCR products by using frequent-cutting restriction enzymes produced complex restriction phenotypes (fingerprints) that were often unique for each strain or species. We used the PCR to amplify and analyze restriction pattern variation within three major portions of the ribosomal DNA (rDNA) repeats from these fungi. Detailed mapping of many restriction sites within the rDNA locus was determined by fingerprint analysis of progressively larger PCR fragments sharing a common primer site at one end. As judged by PCR fingerprints, the rDNA of 19 C. neoformans isolates showed no variation for four restriction enzymes that we surveyed. Other Cryptococcus spp. showed varying levels of restriction pattern variation within their rDNAs and were shown to be genetically distinct from C. neoformans. The PCR primers used in this study have also been successfully applied for amplification of rDNAs from other pathogenic and nonpathogenic fungi, including Candida spp., and ought to have wide applicability for clinical detection and other studies.
Taxonomy and systematics of Lentinula, Gymnopus and Rhodocollybia (Agaricales, Fungi) with emphasis on oak forests of southern Costa Rica
- J L Mata
Mata, J.L. (2002) Taxonomy and systematics of Lentinula, Gymnopus and Rhodocollybia (Agaricales, Fungi) with emphasis on oak forests
of southern Costa Rica. PhD Thesis, University of Tennessee, Knoxville.
the Danish mycological society's colour-chart. Foreningen til Svampekundskabens Fremme
- J H Petersen
Petersen, J.H. (1996) the Danish mycological society's colour-chart. Foreningen til Svampekundskabens Fremme, Greve.
https://doi.org/10.1093/bioinformatics/12.4.357