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      Revision of Cerinomyces ( Dacrymycetes, Basidiomycota) with notes on morphologically and historically related taxa

      research-article
      1 , 6 , , 2 , 3 , 4 , 5 , 1 , 6 , 4
      Studies in Mycology
      Westerdijk Fungal Biodiversity Institute
      Ceracea, Cerinomycetaceae, Corticioid, New taxa, Phylogeny, Taxonomy, Type studies, Typification, Cerinomyces aeneus A. Savchenko, Miettinen & J.C. Zamora, C. atrans A. Savchenko, C. borealis Miettinen, Spirin & A. Savchenko, C. brevisetus Chikowski, Alvarenga & A. Savchenko, C. concretus A. Savchenko, C. creber J.C. Zamora, A. Savchenko, Trichies & Olariaga, C. enterolaxus Shirouzu & A. Savchenko, C. favonius Spirin, Miettinen & A. Savchenko, C. fugax A. Savchenko, C. hesperidis A. Savchenko, C. inermis A. Savchenko, C. lipoferus J.C. Zamora & A. Savchenko, C. nepalensis A. Savchenko, C. neuhoffii J.C. Zamora & A. Savchenko, C. paulistanus A. Savchenko, C. pinguis A. Savchenko, C. ramosissimus A. Savchenko, C. tristis Miettinen & A. Savchenko, C. verecundus A. Savchenko, C. volaticus A. Savchenko, V. Malysheva & J.C. Zamora, Dacrymyces burdsallii A. Savchenko, D. grandii A. Savchenko & Miettinen, D. sobrius A. Savchenko, D. venustus A. Savchenko, Cerinomyces cokeri (McNabb) A. Savchenko & J.C. Zamora, C. enatus (Berk. & M.A. Curtis) A. Savchenko, C. tortus (Willd.) Miettinen, J.C. Zamora & A. Savchenko, Dacrymyces ceraceus (Ginns) A. Savchenko, D. cereus (Rick) A. Savchenko, D. grandinioides (McNabb) A. Savchenko, D. lagerheimii (Pat.) A. Savchenko, D. pengii (B. Liu & L. Fan) A. Savchenko, D. pulchrus (Lowy) A. Savchenko, Ceracea aureofulva Bres., Ce. cerea Rick, D. confluens P. Karst., Tremella enata Berk. & M.A. Curtis, Tremella torta Willd

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          Abstract

          Cerinomyces (Dacrymycetes, Basidiomycota) is a genus traditionally defined by corticioid basidiocarps, in contrast to the rest of the class, which is characterized by gelatinous ones. In the traditional circumscription the genus is polyphyletic, and the monotypic family Cerinomycetaceae is paraphyletic. Aiming for a more concise delimitation, we revise Cerinomyces s.l. with a novel phylogeny based on sequences of nrDNA (SSU, ITS, LSU) and protein-coding genes (RPB1, RPB2, TEF1-α) . We establish that monophyletic Cerinomyces s.s. is best characterized not by the corticioid morphology, but by a combination of traits: hyphal clamps, predominantly aseptate thin-walled basidiospores, and low content of carotenoid pigments. In our updated definition, Cerinomyces s.s. encompasses five well-supported phylogenetic clades divided into two morphological groups: (i-iii) taxa with arid corticioid basidiocarps, including the generic type C. pallidus; and (iv-v) newly introduced members with gelatinous basidiocarps, like Dacrymyces enatus and D. tortus. The remaining corticioid species of Cerinomyces s.l. are morphologically distinct and belong to the Dacrymycetaceae: our analysis places the carotenoid-rich Cerinomyces canadensis close to Femsjonia, and we transfer the clamps-lacking C. grandinioides group to Dacrymyces. In addition, we address genera related to Cerinomyces s.l. historically and morphologically, such as Ceracea, Dacryonaema and Unilacryma. Overall, we describe twenty-four new species and propose nine new combinations in both Cerinomycetaceae and Dacrymycetaceae.

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          RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

          Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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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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              Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

              Abstract Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) plays a central role in understanding evolutionary history from molecular sequence data. Visualizing and analyzing the MCMC-generated samples from the posterior distribution is a key step in any non-trivial Bayesian inference. We present the software package Tracer (version 1.7) for visualizing and analyzing the MCMC trace files generated through Bayesian phylogenetic inference. Tracer provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, conditional posterior distribution summary, and more. Tracer is open-source and available at http://beast.community/tracer.
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                Author and article information

                Contributors
                Journal
                Stud Mycol
                Stud Mycol
                Studies in Mycology
                Westerdijk Fungal Biodiversity Institute
                0166-0616
                1872-9797
                01 December 2021
                June 2021
                01 December 2021
                : 99
                Affiliations
                [1 ]Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411, Tartu, Estonia
                [2 ]Museum of Evolution, Uppsala University, Norbyvägen 16, SE-75236, Uppsala, Sweden
                [3 ]Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie, 514-8507, Japan
                [4 ]Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014, Helsinki, Finland
                [5 ]Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova str. 2, RU-197376, St. Petersburg, Russia
                [6 ]Natural History Museum, University of Tartu, Vanemuise 46, 51003, Tartu, Estonia
                Author notes
                [] Correspondence: A. Savchenko savchenko.anton.kh@ 123456gmail.com
                Article
                S0166-0616(21)00004-X 100117
                10.1016/j.simyco.2021.100117
                8645972
                c8cbc3db-2709-48e0-8911-2c27b5932904
                © 2021 Westerdijk Fungal Biodiversity Institute. Production and hosting by ELSEVIER B.V.

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                Categories
                Research Paper

                Plant science & Botany
                ceracea,cerinomycetaceae,corticioid,new taxa,phylogeny,taxonomy,type studies,typification,cerinomyces aeneus a. savchenko, miettinen & j.c. zamora,c. atrans a. savchenko,c. borealis miettinen, spirin & a. savchenko,c. brevisetus chikowski, alvarenga & a. savchenko,c. concretus a. savchenko,c. creber j.c. zamora, a. savchenko, trichies & olariaga,c. enterolaxus shirouzu & a. savchenko,c. favonius spirin, miettinen & a. savchenko,c. fugax a. savchenko,c. hesperidis a. savchenko,c. inermis a. savchenko,c. lipoferus j.c. zamora & a. savchenko,c. nepalensis a. savchenko,c. neuhoffii j.c. zamora & a. savchenko,c. paulistanus a. savchenko,c. pinguis a. savchenko,c. ramosissimus a. savchenko,c. tristis miettinen & a. savchenko,c. verecundus a. savchenko,c. volaticus a. savchenko, v. malysheva & j.c. zamora,dacrymyces burdsallii a. savchenko,d. grandii a. savchenko & miettinen,d. sobrius a. savchenko,d. venustus a. savchenko,cerinomyces cokeri (mcnabb) a. savchenko & j.c. zamora,c. enatus (berk. & m.a. curtis) a. savchenko,c. tortus (willd.) miettinen, j.c. zamora & a. savchenko,dacrymyces ceraceus (ginns) a. savchenko,d. cereus (rick) a. savchenko,d. grandinioides (mcnabb) a. savchenko,d. lagerheimii (pat.) a. savchenko,d. pengii (b. liu & l. fan) a. savchenko,d. pulchrus (lowy) a. savchenko,ceracea aureofulva bres.,ce. cerea rick,d. confluens p. karst.,tremella enata berk. & m.a. curtis,tremella torta willd
                Plant science & Botany
                ceracea, cerinomycetaceae, corticioid, new taxa, phylogeny, taxonomy, type studies, typification, cerinomyces aeneus a. savchenko, miettinen & j.c. zamora, c. atrans a. savchenko, c. borealis miettinen, spirin & a. savchenko, c. brevisetus chikowski, alvarenga & a. savchenko, c. concretus a. savchenko, c. creber j.c. zamora, a. savchenko, trichies & olariaga, c. enterolaxus shirouzu & a. savchenko, c. favonius spirin, miettinen & a. savchenko, c. fugax a. savchenko, c. hesperidis a. savchenko, c. inermis a. savchenko, c. lipoferus j.c. zamora & a. savchenko, c. nepalensis a. savchenko, c. neuhoffii j.c. zamora & a. savchenko, c. paulistanus a. savchenko, c. pinguis a. savchenko, c. ramosissimus a. savchenko, c. tristis miettinen & a. savchenko, c. verecundus a. savchenko, c. volaticus a. savchenko, v. malysheva & j.c. zamora, dacrymyces burdsallii a. savchenko, d. grandii a. savchenko & miettinen, d. sobrius a. savchenko, d. venustus a. savchenko, cerinomyces cokeri (mcnabb) a. savchenko & j.c. zamora, c. enatus (berk. & m.a. curtis) a. savchenko, c. tortus (willd.) miettinen, j.c. zamora & a. savchenko, dacrymyces ceraceus (ginns) a. savchenko, d. cereus (rick) a. savchenko, d. grandinioides (mcnabb) a. savchenko, d. lagerheimii (pat.) a. savchenko, d. pengii (b. liu & l. fan) a. savchenko, d. pulchrus (lowy) a. savchenko, ceracea aureofulva bres., ce. cerea rick, d. confluens p. karst., tremella enata berk. & m.a. curtis, tremella torta willd

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