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      Global Diversity and Taxonomy of Sidera (Hymenochaetales, Basidiomycota): Four New Species and Keys to Species of the Genus

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      Journal of Fungi
      MDPI
      phylogenetic analysis, Rickenellaceae, wood-rotting fungi

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          Abstract

          The genus Sidera is a polypore genus with resupinate, white to cream or buff fresh basidioma, poroid or hydnoid hymenophore, a monomitic or dimitic hyphal system with generative hyphae bearing clamp connections, the presence of rosette-like crystals and allantoid to lunate basidiospores. We study the phylogeny and diversity of Sidera herein by using both morphological and molecular methods. Phylogenetic analyses are based on the ITS dataset, the combined 2-locus dataset (5.8S + nLSU) and 7-locus dataset (ITS + nLSU + RPB1 + RPB2 + TEF1 + mtSSU + nSSU) of 15 taxa of Sidera all over the world. Among them, four species are new to science and described and illustrated in this paper, viz. S. inflata, S. malaysiana, S. punctata and S. roseo-bubalina. In addition, three taxa were treated as Sidera vulgaris sensu lato. An identification key of the 14 accepted species of Sidera worldwide is provided.

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          MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

          Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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            AMPLIFICATION AND DIRECT SEQUENCING OF FUNGAL RIBOSOMAL RNA GENES FOR PHYLOGENETICS

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              BioEdit - a user friendly biological sequence alignment editor and analysis program for Windows 95/98/NT

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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                J Fungi (Basel)
                J Fungi (Basel)
                jof
                Journal of Fungi
                MDPI
                2309-608X
                26 March 2021
                April 2021
                : 7
                : 4
                : 251
                Affiliations
                Institute of Microbiology, School of Ecology and Nature Conservation, PO Box 61, Beijing Forestry University, Beijing 100083, China; zhanboliu@ 123456bjfu.edu.cn (Z.-B.L.); zhoumeng9612@ 123456bjfu.edu.cn (M.Z.)
                Author notes
                [* ]Correspondence: yuanyuan1018@ 123456bjfu.edu.cn (Y.Y.); yuchengdai@ 123456bjfu.edu.cn (Y.-C.D.); Tel.: +86-10-6233-6709 (Y.-C.D.)
                Author information
                https://orcid.org/0000-0002-3894-5398
                https://orcid.org/0000-0002-9343-7513
                https://orcid.org/0000-0001-6674-9848
                Article
                jof-07-00251
                10.3390/jof7040251
                8066320
                33810364
                217ca832-14bd-402c-b36d-fbde34358db5
                © 2021 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 19 January 2021
                : 23 March 2021
                Categories
                Article

                phylogenetic analysis,rickenellaceae,wood-rotting fungi

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