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      When mycologists describe new species, not all relevant information is provided (clearly enough)

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          Abstract

          Taxonomic mycology struggles with what seems to be a perpetual shortage of resources. Logically, fungal taxonomists should therefore leverage every opportunity to highlight and visualize the importance of taxonomic work, the usefulness of taxonomic data far beyond taxonomy, and the integrative and collaborative nature of modern taxonomy at large. Is mycology really doing that, though? In this study, we went through ten years’ worth (2009–2018) of species descriptions of extant fungal taxa – 1,097 studies describing at most ten new species – in five major mycological journals plus one plant journal. We estimated the frequency at which a range of key words, illustrations, and concepts related to ecology, geography, taxonomy, molecular data, and data availability were provided with the descriptions. We also considered a range of science-demographical aspects such as gender bias and the rejuvenation of taxonomy and taxonomists as well as public availability of the results. Our results show that the target audience of fungal species descriptions appears to be other fungal taxonomists, because many aspects of the new species were presented only implicitly, if at all. Although many of the parameters we estimated show a gradual, and in some cases marked, change for the better over time, they still paint a somewhat bleak picture of mycological taxonomy as a male-dominated field where the wants and needs of an extended target audience are often not understood or even considered. This study hopes to leave a mark on the way fungal species are described by putting the focus on ways in which fungal taxonomy can better anticipate the end users of species descriptions – be they mycologists, other researchers, the public at large, or even algorithms. In the end, fungal taxonomy, too, is likely to benefit from such measures.

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          Taxonomic triage and the poverty of phylogeny.

          Revisionary taxonomy is frequently dismissed as merely descriptive, which belies its strong intellectual content and hypothesis-driven nature. Funding for taxonomy is inadequate and largely diverted to studies of phylogeny that neither improve classifications nor nomenclature. Phylogenetic classifications are optimal for storing and predicting information, but phylogeny divorced from taxonomy is ephemeral and erodes the accuracy and information content of the language of biology. Taxonomic revisions and monographs are efficient, high-throughput species hypothesis-testing devices that are ideal for the World Wide Web. Taxonomic knowledge remains essential to credible biological research and is made urgent by the biodiversity crisis. Theoretical and technological advances and threats of mass species extinctions indicate that this is the time for a renaissance in taxonomy. Clarity of vision and courage of purpose are needed from individual taxonomists and natural history museums to bring about this evolution of taxonomy into the information age.
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            Cloudy, increasingly FAIR; revisiting the FAIR Data guiding principles for the European Open Science Cloud

            The FAIR Data Principles propose that all scholarly output should be Findable, Accessible, Interoperable, and Reusable. As a set of guiding principles, expressing only the kinds of behaviours that researchers should expect from contemporary data resources, how the FAIR principles should manifest in reality was largely open to interpretation. As support for the Principles has spread, so has the breadth of these interpretations. In observing this creeping spread of interpretation, several of the original authors felt it was now appropriate to revisit the Principles, to clarify both what FAIRness is, and is not.
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              Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences

              Molecular data form an important research tool in most branches of mycology. A non-trivial proportion of the public fungal DNA sequences are, however, compromised in terms of quality and reliability, contributing noise and bias to sequence-borne inferences such as phylogenetic analysis, diversity assessment, and barcoding. In this paper we discuss various aspects and pitfalls of sequence quality assessment. Based on our observations, we provide a set of guidelines to assist in manual quality management of newly generated, near-full-length (Sanger-derived) fungal ITS sequences and to some extent also sequences of shorter read lengths, other genes or markers, and groups of organisms. The guidelines are intentionally non-technical and do not require substantial bioinformatics skills or significant computational power. Despite their simple nature, we feel they would have caught the vast majority of the severely compromised ITS sequences in the public corpus. Our guidelines are nevertheless not infallible, and common sense and intuition remain important elements in the pursuit of compromised sequence data. The guidelines focus on basic sequence authenticity and reliability of the newly generated sequences, and the user may want to consider additional resources and steps to accomplish the best possible quality control. A discussion on the technical resources for further sequence quality management is therefore provided in the supplementary material.
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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
                2020
                10 September 2020
                : 72
                : 109-128
                Affiliations
                [1 ] Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden University of Gothenburg Gothenburg Sweden
                [2 ] Department of Forest Mycology and Plant Pathology, Uppsala Biocentre, Swedish University of Agricultural Sciences, Uppsala, Sweden wedish University of Agricultural Sciences Uppsala Sweden
                [3 ] Nofima – Norwegian Institute of Food, Fisheries and Aquaculture Research, P.O. Box 210, 1431 Ås, Norway Norwegian Institute of Food, Fisheries and Aquaculture Research Oslo Norway
                [4 ] Department of Organismal Biology, Uppsala University, Uppsala, Sweden Uppsala University Uppsala Sweden
                [5 ] Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden University of Technology and University of Gothenburg Gothenburg Sweden
                Author notes
                Corresponding author: R. Henrik Nilsson ( henrik.nilsson@ 123456bioenv.gu.se )

                Academic editor: T. Lumbsch

                Author information
                https://orcid.org/0000-0002-6795-4349
                https://orcid.org/0000-0002-8052-0107
                Article
                56691
                10.3897/mycokeys.72.56691
                7498475
                32982558
                4249aec3-8968-495d-b16e-929eb8458135
                Louisa Durkin, Tobias Jansson, Marisol Sanchez, Maryia Khomich, Martin Ryberg, Erik Kristiansson, R. Henrik Nilsson

                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
                : 19 July 2020
                : 24 August 2020
                Categories
                Research Article
                Ascomycota
                Basidiomycota
                Chytridiomycota
                Glomeromycota
                Zygomycota
                Taxonomy
                World

                collaboration,gender equality,metadata,reproducibility,species description,taxonomy

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