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      Notes on Trochila (Ascomycota, Leotiomycetes), with new species and combinations

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          Abstract

          Studies of Trochila ( Leotiomycetes , Helotiales , Cenangiaceae ) are scarce. Here, we describe two new species based on molecular phylogenetic data and morphology. Trochila bostonensis was collected at the Boston Harbor Islands National Recreation Area, Massachusetts. It was found on the stem of Asclepias syriaca , representing the first report of any Trochila species from a plant host in the family Apocynaceae . Trochila urediniophila is associated with the uredinia of the rust fungus Cerotelium fici . It was discovered during a survey for rust hyperparasites conducted at the Arthur Fungarium, in a single sample from 1912 collected in Trinidad. Macro- and micromorphological descriptions, illustrations, and molecular phylogenetic analyses are presented. The two new species are placed in Trochila with high support in both our six-locus (SSU, ITS, LSU, rpb1, rpb2, tef1) and two-locus (ITS, LSU) phylogenetic reconstructions. In addition, two species are combined in Trochila : Trochila colensoi (formerly placed in Pseudopeziza ) and T. xishuangbanna (originally described as the only species in Calycellinopsis ). This study reveals new host plant families, a new ecological strategy, and a new country record for the genus Trochila . Finally, our work emphasizes the importance of specimens deposited in biological collections such as fungaria.

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          MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

          We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
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            IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

            Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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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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                Author and article information

                Contributors
                Journal
                MycoKeys
                MycoKeys
                11
                urn:lsid:arphahub.com:pub:C004A564-9D6A-5F9F-B058-6A3815DFE9C3
                MycoKeys
                Pensoft Publishers
                1314-4057
                1314-4049
                2021
                11 February 2021
                : 78
                : 21-47
                Affiliations
                [1 ] Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA Purdue University West Lafayette United States of America
                [2 ] Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA Harvard University Cambridge United States of America
                [3 ] Farlow Herbarium and Reference Library of Cryptogamic Botany, Harvard University Herbaria, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA Harvard University Herbaria Cambridge United States of America
                [4 ] Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic University of South Bohemia České Budějovice Czech Republic
                Author notes
                Corresponding author: Paula Andrea Gómez-Zapata ( pgomezza@ 123456purdue.edu ), Danny Haelewaters ( danny.haelewaters@ 123456gmail.com ), M. Catherine Aime ( maime@ 123456purdue.edu )

                Academic editor: N. Wijayawardene

                Author information
                https://orcid.org/0000-0002-6424-0834
                https://orcid.org/0000-0002-9018-8646
                Article
                62046
                10.3897/mycokeys.78.62046
                9849072
                36761369
                9385421a-410b-4694-aa2e-951d3cd039db
                Paula Andrea Gómez-Zapata, Danny Haelewaters, Luis Quijada, Donald H. Pfister, M. Catherine Aime

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 15 December 2020
                : 07 January 2021
                Funding
                Funded by: Fundación Ramón Areces 100008054 http://doi.org/10.13039/100008054
                Categories
                Research Article
                Ascomycota
                Leotiomycetes
                Biodiversity & Conservation
                DNA barcoding
                Molecular systematics
                Phylogeny
                Taxonomy
                Americas

                4 new taxa,biological collections,boston harbor islands,fungarium specimens,fungicolous fungi,south america,taxonomy,trinidad

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