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      Taxonomic revision of the Plagiothecium curvifolium complex

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      1 , * , , 2 , 3
      PLOS ONE
      Public Library of Science

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          Abstract

          Supported by the examination of specimens from the entire range and by the analysis of type specimens and the diagnosis of individual names, morphological and genetic studies of the Plagiothecium curvifolium complex resulted in the conclusion that this taxon should be recognized as four separate taxa. In addition to P. curvifolium s.str., there is a variety that is proposed as a new combination– P. curvifolium var. recurvum; resurrection of the forgotten P. decursivifolium; and the description of a new species– P. imbricatum. The features that distinguish individual taxa focus primarily on: plant size; arrangement of leaves on the stem; the symmetry, dimensions, shape, concavity and folding of leaves; cell length; serration of the leaf apex; the shape of the decurrencies; the length of the sporophyte and the shape of the operculum. For all described taxa, the distribution, ecological preferences, key to their identification and detailed photographic documentation have been provided.

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          Most cited references46

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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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            UFBoot2: Improving the Ultrafast Bootstrap Approximation

            Abstract The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches. Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested data sets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
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              MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

              Abstract This article describes several features in the MAFFT online service for multiple sequence alignment (MSA). As a result of recent advances in sequencing technologies, huge numbers of biological sequences are available and the need for MSAs with large numbers of sequences is increasing. To extract biologically relevant information from such data, sophistication of algorithms is necessary but not sufficient. Intuitive and interactive tools for experimental biologists to semiautomatically handle large data are becoming important. We are working on development of MAFFT toward these two directions. Here, we explain (i) the Web interface for recently developed options for large data and (ii) interactive usage to refine sequence data sets and MSAs.

                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: InvestigationRole: Project administrationRole: SupervisionRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: InvestigationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: InvestigationRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                PLOS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                9 November 2022
                2022
                : 17
                : 11
                : e0275665
                Affiliations
                [1 ] Faculty of Biology and Environmental Protection, Department of Geobotany and Plant Ecology, University of Lodz, Lodz, Poland
                [2 ] Faculty of Biology and Environmental Protection, Department of Algology and Mycology, University of Lodz, Lodz, Poland
                [3 ] Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY, United States of America
                Universite de Liege, BELGIUM
                Author notes

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

                Author information
                https://orcid.org/0000-0003-1480-8003
                https://orcid.org/0000-0002-7722-9132
                Article
                PONE-D-22-12166
                10.1371/journal.pone.0275665
                9645594
                36350818
                0419c80d-9955-4421-8ee9-3c1b3fc0243e
                © 2022 Wolski 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
                : 25 April 2022
                : 19 September 2022
                Page count
                Figures: 15, Tables: 1, Pages: 24
                Funding
                The research was funded by a grant "Genetic study on variability of selected taxa of the genus Plagiothecium" NCN Miniatura 4 – DEC-020/04/X/NZ8/00420.
                Categories
                Research Article
                Biology and Life Sciences
                Plant Science
                Plant Anatomy
                Leaves
                Biology and Life Sciences
                Taxonomy
                Computer and Information Sciences
                Data Management
                Taxonomy
                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
                Biology and Life Sciences
                Ecology
                Ecosystems
                Forests
                Ecology and Environmental Sciences
                Ecology
                Ecosystems
                Forests
                Ecology and Environmental Sciences
                Terrestrial Environments
                Forests
                Biology and Life Sciences
                Organisms
                Eukaryota
                Plants
                Trees
                Pines
                Biology and Life Sciences
                Ecology
                Forest Ecology
                Ecology and Environmental Sciences
                Ecology
                Forest Ecology
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Research and Analysis Methods
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Biology and Life Sciences
                Genetics
                Custom metadata
                All relevant data are within the paper and its Supporting information files, including public repositories linked directly to the paper: the raw data sequences, the alignment file, the evolutionary model set for the partition and the tree files have been uploaded to the figshare online database ( https://doi.org/10.6084/m9.figshare.16570353).

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