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      More than one fungus in the pepper pot: Integrative taxonomy unmasks hidden species within Myriostoma coliforme (Geastraceae, Basidiomycota)

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          Abstract

          Since the nineteenth century, Myriostoma has been regarded as a monotypic genus with a widespread distribution in north temperate and subtropical regions. However, on the basis of morphological characters and phylogenetic evidence of DNA sequences of the internal transcribed spacer (ITS) regions and the large subunit nuclear ribosomal RNA gene (LSU), four species are now delimited: M. areolatum comb. & stat. nov., M. calongei sp. nov., M. capillisporum comb. & stat. nov., and M. coliforme. Myriostoma coliforme is typified by selecting a lectotype (iconotype) and a modern sequenced collection as an epitype. The four species can be discriminated by a combination of morphological characters, such as stomatal form, endoperidial surface texture, and basidiospore size and ornamentation.

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          The general stochastic model of nucleotide substitution.

          DNA sequence evolution through nucleotide substitution may be assimilated to a stationary Markov process. The fundamental equations of the general model, with 12 independent substitution parameters, are used to obtain a formula which corrects the effect of multiple and parallel substitutions on the measure of evolutionary divergence between two homologous sequences. We show that only reversible models, with six independent parameters, allow the calculation of the substitution rates. Simulation experiments on DNA sequence evolution through nucleotide substitution call into question the effectiveness of the general model (and of any other more detailed description); nevertheless, the general model results are slightly superior to any of its particular cases.
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            Markov Chasin Monte Carlo Algorithms for the Bayesian Analysis of Phylogenetic Trees

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              Dimensions of biodiversity in the Earth mycobiome.

              Fungi represent a large proportion of the genetic diversity on Earth and fungal activity influences the structure of plant and animal communities, as well as rates of ecosystem processes. Large-scale DNA-sequencing datasets are beginning to reveal the dimensions of fungal biodiversity, which seem to be fundamentally different to bacteria, plants and animals. In this Review, we describe the patterns of fungal biodiversity that have been revealed by molecular-based studies. Furthermore, we consider the evidence that supports the roles of different candidate drivers of fungal diversity at a range of spatial scales, as well as the role of dispersal limitation in maintaining regional endemism and influencing local community assembly. Finally, we discuss the ecological mechanisms that are likely to be responsible for the high heterogeneity that is observed in fungal communities at local scales.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                7 June 2017
                2017
                : 12
                : 6
                : e0177873
                Affiliations
                [1 ]Programa de Pós-Graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
                [2 ]Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, England
                [3 ]Department of Biology, University of Toronto, Mississagua, Ontario, Canada
                [4 ]Graduação em Ciências Biológicas, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
                [5 ]Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
                [6 ]Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
                [7 ]Departamento de Micología, Real Jardín Botánico-CSIC, Plaza de Murillo 2, Madrid, Spain
                Brigham Young University, UNITED STATES
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                • Conceptualization: JOS LMS MAG AMA IGB MPM.

                • Data curation: JOS LMS AMA IGB MPM.

                • Formal analysis: MPM JOS.

                • Funding acquisition: IGB MPM JOS DSA LMS AMA.

                • Investigation: JOS LMS DSA LMC AMA IGB MPM.

                • Methodology: JOS LMS MAG AMA IGB MPM.

                • Project administration: IGB AMA MPM.

                • Resources: IGB PM AMA MPM.

                • Software: JOS LMS MAG MPM.

                • Supervision: MPM IGB.

                • Validation: MPM JOS LMS AMA MAG IGB.

                • Visualization: JOS LMS DSA LMC AMA IGB MPM.

                • Writing – original draft: JOS LMS AMA IGB MPM.

                • Writing – review & editing: MPM JOS LMS MAG DSA AMA IGB.

                Author information
                http://orcid.org/0000-0002-1235-4418
                Article
                PONE-D-17-05671
                10.1371/journal.pone.0177873
                5462367
                28591150
                8732b5ee-15c8-4a7c-bb88-9619fce87c00
                © 2017 Sousa et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 12 February 2017
                : 1 May 2017
                Page count
                Figures: 7, Tables: 2, Pages: 19
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100002322, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior;
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100002322, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior;
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100003593, Conselho Nacional de Desenvolvimento Científico e Tecnológico;
                Award ID: CNPq_Brazil, Projeto Pesquisador Visitante Especial PVE/407474/2013-7
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100003593, Conselho Nacional de Desenvolvimento Científico e Tecnológico;
                Award ID: CNPq_Brazil, Projeto Pesquisador Visitante Especial PVE/407474/2013-7
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001293, Natural England;
                Award ID: Species Recovery Programme
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001293, Natural England;
                Award ID: Species Recovery Programme
                Award Recipient :
                The authors would like to express their thanks to the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES—Brazil) for the PhD scholarships awarded to Julieth de Oliveira Sousa and Donis S. Alfredo in 2014/2015 and to the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq—Brazil, Projeto Pesquisador Visitante Especial PVE/407474/2013–7 and Projecto de Pesquisa em Biodiversidade do Semiarido PPBio/457476/2012–5; María P. Martín and Iuri G. Baseia) for the scholarship of scientific initiation awarded to Luana Conrado. Natural England (Species Recovery Programme) is thanked for funding part of the sequencing work carried out in England.
                Categories
                Research Article
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Biology and Life Sciences
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Computer and Information Sciences
                Data Management
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Medicine and Health Sciences
                Dermatology
                Warts
                Research and Analysis Methods
                Database and Informatics Methods
                Bioinformatics
                Sequence Analysis
                Sequence Alignment
                Research and Analysis Methods
                Database and Informatics Methods
                Biological Databases
                Sequence Databases
                Research and Analysis Methods
                Database and Informatics Methods
                Bioinformatics
                Sequence Analysis
                Sequence Databases
                Biology and Life Sciences
                Plant Science
                Plant Anatomy
                Leaves
                Stomata
                Biology and Life Sciences
                Plant Science
                Plant Anatomy
                Stem Anatomy
                Stomata
                Research and Analysis Methods
                Database and Informatics Methods
                Bioinformatics
                Sequence Analysis
                Biology and Life Sciences
                Organisms
                Fungi
                Biology and Life Sciences
                Taxonomy
                Computer and Information Sciences
                Data Management
                Taxonomy
                Custom metadata
                All relevant data are within the paper; the new sequences generated in this study are already located in GenBank (Accession Numbers are included in Table 1).

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