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      A phylogeny of species near Agrostis supporting the recognition of two new genera, Agrostula and Alpagrostis ( Poaceae , Pooideae , Agrostidinae ) from Europe

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          Abstract

          Based on a molecular DNA phylogeny of three plastid ( rpl32-trnK, rps16 intron, and rps16-trnK) and nuclear ITS regions investigating 32 species of Agrostidinae , we describe two new genera, Agrostula gen. nov. with a single species and Alpagrostis gen. nov. with four species; provide support for five species in a monophyletic Podagrostis ; and include a small sample of 12 species of a monophyletic Agrostis s.s. (including the type and most species of Neoschischkinia ), that separates into two clades corresponding to A. subg. Agrostis and A. subg. Vilfa . Agrostula differs from Agrostis in having leaf blades with pillars of sclerenchyma which are continuous between the adaxial and abaxial surface of the blades, dorsally rounded glumes with blunt to truncate and erose to denticulate apices, florets ½ the length of the glumes, lemmas equally wide as long, widest at (or near) apex, apices broadly truncate, irregularly 5 to 7 denticulate to erose, awnless, anthers longer than the lemmas, and rugose-papillose caryopses. Alpagrostis differs from Agrostis in having geniculate basally inserted awns and truncate lemma apices with lateral veins prolonged from the apex in (2)4 setae. The following eight new combinations are made: Agrostula truncatula , Agrostula truncatula subsp. durieui , Alpagrostis alpina , Alpagrostis alpina var. flavescens , Alpagrostis barceloi , Alpagrostis setacea , Alpagrostis setacea var. flava , and Alpagrostis schleicheri . In addition, we provide a key separating Agrostula and Alpagrostis from Agrostis s.s. and other genera previously considered as synonyms of Agrostis ; lectotypify Agrostis alpina Scop., A. schleicheri Jord. & Verl., A. truncatula Parl., and A. truncatula var. durieui Henriq.; and neotypify A. setacea Curtis.

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          Resumen

          Sobre la base de una filogenia molecular de ADN de tres regiones plastidiales ( rpl32-trnK, rps16 intrón y rps16-trnK) e ITS nuclear de 32 especies de Agrostidinae , describimos dos nuevos géneros, Agrostula gen. nov. con una sola especie, y Alpagrostis gen. nov. con cuatro especies; mostramos el apoyo para las cinco especies dentro de Podagrostis monofilético; e incluimos una pequeña muestra de 12 especies de Agrostis s.s (que incluye el tipo y la mayoría de las especies de Neoschischkinia ), este último dividido en dos subclados que corresponden a A. subg. Agrostis y A. subg. Vilfa . Agrostula se diferencia de otras especies de Agrostis por tener láminas foliares con haces de esclerénquima continuos entre las superficies adaxial y abaxial de los limbos, glumas de dorso redondeado y ápice embotado a truncado y eroso a denticulado, antecios de ½ de la longitud de las glumas, lemas tan anchas como largas, lo más ancho en o cerca del ápice, ápices anchamente truncados, irregularmente 5 a 7 denticulados o erosos, sin arista, anteras más largas que los lemas y cariopsis rugosa-papilosa. Alpagrostis se diferencia de otras especies de Agrostis por tener aristas geniculadas insertas basalmente y ápices de lema truncados con venas laterales que se prolongan en (2)4 arístulas apicales. Presentamos las siguientes ocho nuevas combinaciones: Agrostula truncatula , Agrostula truncatula subsp. durieui , Alpagrostis alpina , Alpagrostis alpina var. flavescens , Alpagrostis barceloi , Alpagrostis setacea , Alpagrostis setacea var. flava y Alpagrostis schleicheri . Además, proporcionamos una clave que separa Agrostula y Alpagrostis de Agrostis s.s. y otros géneros previamente considerados como sinónimos de Agrostis , lectotipificamos Agrostis alpina Scop., A. schleicheri Jord. & Verl., A. truncatula Parl. y A. truncatula var. durieui Henriq. y neotipificamos A. setacea Curtis.

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          MUSCLE: multiple sequence alignment with high accuracy and high throughput.

          We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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            Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

            Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com
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              MRBAYES: Bayesian inference of phylogenetic trees.

              The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
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                Author and article information

                Contributors
                Journal
                PhytoKeys
                PhytoKeys
                3
                urn:lsid:arphahub.com:pub:F7FCE910-8E78-573F-9C77-7788555F8AAD
                PhytoKeys
                Pensoft Publishers
                1314-2011
                1314-2003
                2020
                20 November 2020
                : 167
                : 57-82
                Affiliations
                [1 ] Department of Botany MRC-166, National Museum of Natural History, Smithsonian Institution, Washington DC 20013-7012, USA
                [2 ] College of Biology and the Environment, Nanjing Forestry University, Long Pan Road No. 159, Nanjing, 210037, China
                [3 ] Department of Africa and Madagascar, Missouri Botanical Garden, St. Louis, Missouri 63110-2291, USA
                [4 ] Herbarium MA, Unidad de Herbarios, Real Jardín Botánico, Consejo Superior de Investigaciones Científicas, 28014, Madrid, Spain
                [5 ] Department of Biodiversity and Conservation, Real Jardín Botánico, Consejo Superior de Investigaciones Científicas, 28014, Madrid, Spain
                Author notes
                Corresponding author: Paul M. Peterson ( peterson@ 123456si.edu )

                Academic editor: Marcin Nobis

                Author information
                https://orcid.org/0000-0001-9405-5528
                https://orcid.org/0000-0001-5577-8782
                https://orcid.org/0000-0002-8358-4915
                Article
                PMC7695677 PMC7695677 7695677 55171
                10.3897/phytokeys.167.55171
                7695677
                33306060
                b216ff48-3d74-49df-a783-b8957d7d28d3

                This is an open access article distributed under the terms of the CC0 Public Domain Dedication.

                History
                : 06 June 2020
                : 31 July 2020
                Funding
                Funded by: Smithsonian Institution 100000014 http://doi.org/10.13039/100000014
                Categories
                Research Article
                Poaceae
                Molecular Systematics
                Nomenclature
                Phylogeny
                Taxonomy
                Cenozoic
                Europe

                Podagrostis ,plastid DNA sequences, Agrostis , Agrostula ,taxonomy,phylogeny, Alpagrostis ,classification,ITS, Neoschischkinia

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