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      The taxonomy of the model filamentous fungus Podospora anserina

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          The filamentous fungus Podospora anserina has been used as a model organism for more than 100 years and has proved to be an invaluable resource in numerous areas of research. Throughout this period, P. anserina has been embroiled in a number of taxonomic controversies regarding the proper name under which it should be called. The most recent taxonomic treatment proposed to change the name of this important species to Triangularia anserina . The results of past name changes of this species indicate that the broader research community is unlikely to accept this change, which will lead to nomenclatural instability and confusion in literature. Here, we review the phylogeny of the species closely related to P. anserina and provide evidence that currently available marker information is insufficient to resolve the relationships amongst many of the lineages. We argue that it is not only premature to propose a new name for P. anserina based on current data, but also that every effort should be made to retain P. anserina as the current name to ensure stability and to minimise confusion in scientific literature. Therefore, we synonymise Triangularia with Podospora and suggest that either the type species of Podospora be moved to P. anserina from P. fimiseda or that all species within the Podosporaceae be placed in the genus Podospora .

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          Most cited references 42

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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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            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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              ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates

              Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. The improvement is achieved by incorporating a model of rate-heterogeneity across sites not previously considered in this context, and by allowing concurrent searches of model-space and tree-space.

                Author and article information

                Pensoft Publishers
                25 November 2020
                : 75
                : 51-69
                [1 ] Systematic Biology, Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden Uppsala Univeristy Uppsala Sweden
                [2 ] Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91400, Orsay, France Université Paris-Saclay Orsay France
                [3 ] Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France Université Paris-Saclay Gif-sur-Yvette France
                [4 ] IBGC, UMR 5095, CNRS Université de Bordeaux, 1 rue Camille Saint Saëns, 33077, Bordeaux, France Université de Bordeaux Bordeaux France
                [5 ] Laboratory of Genetics, Wageningen University, Arboretumlaan 4, 6703 BD, Wageningen, Netherlands Wageningen University Wageningen Netherlands
                [6 ] Instituto de Fisiología Celular, Departamento de Bioquímica y Biología Estructural, Universidad Nacional Autónoma de México, Mexico City, Mexico Universidad Nacional Autónoma de México Mexico City Mexico
                [7 ] UMR BGPI, Université de Montpellier, INRAE, CIRAD, Institut Agro, F-34398, Montpellier, France Université de Montpellier Montpellier France
                [8 ] Museum of Evolution, Botany, Uppsala University, Norbyvägen 18, 752 36, Uppsala, Sweden Uppsala University Uppsala Sweden
                [9 ] Université de Paris, Laboratoire Interdisciplinaire des Energies de Demain (LIED), F-75006, Paris, France Université de Paris Paris France
                [10 ] Botany Department, The Field Museum, Chicago, Illinois 60605, USA The Field Museum Chicago United States of America
                [11 ] Illinois Natural History Survey, University of Illinois, Champaign, IL 61820, USA University of Illinois Champaign United States of America
                Author notes
                Corresponding author: Aaron A. Vogan ( aaron.vogan@ 123456ebc.uu.se )

                Academic editor: T. Lumbsch

                S. Lorena Ament-Velásquez, Hanna Johannesson, Tatiana Giraud, Robert Debuchy, Sven J. Saupe, Alfons J. M. Debets, Eric Bastiaans, Fabienne Malagnac, Pierre Grognet, Leonardo Peraza-Reyes, Pierre Gladieux, Åsa Kruys, Philippe Silar, Sabine M. Huhndorf, Andrew N. Miller, Aaron A. Vogan

                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.

                Funded by: Vetenskapsrådet 501100004359 http://doi.org/10.13039/501100004359
                Research Article
                Molecular Systematics

                taxonomy, podosporaceae , podospora , phylogenetics


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