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      Phylogenetic study and taxonomic revision of the Xanthoparmeliamexicana group, including the description of a new species (Parmeliaceae, Ascomycota)

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          Abstract

          Abstract

          Xanthoparmelia ( Parmeliaceae , Ascomycota ) is the most species-rich genus of lichen-forming fungi. Species boundaries are based on morphological and chemical features, varying reproductive strategies and, more recently, molecular sequence data. The isidiate Xanthoparmelia mexicana group is common in arid regions of North and Central America and includes a range of morphological variation and variable secondary metabolites – salazinic or stictic acids mainly. In order to better understand the evolutionary history of this group and potential taxonomic implications, a molecular phylogeny representing 58 ingroup samples was reconstructed using four loci, including ITS, mtSSU, nuLSU rDNA and MCM7. Results indicate the existence of multiple, distinct lineages phenotypically agreeing with X. mexicana. One of these isidiate, salazinic acid-containing lineages is described here as a new species, X. pedregalensis sp. nov., including populations from xerophytic scrub vegetation in Pedregal de San Angel, Mexico City. X. mexicana s. str. is less isidiate than X. pedregalensis and has salazinic and consalazinic acid, occasionally with norstictic acid; whereas X. pedregalensis contains salazinic and norstictic acids and an unknown substance. Samples from the Old World, morphologically agreeing with X. mexicana , are only distantly related to X. mexicana s. str. Our results indicate that X. mexicana is likely less common than previously assumed and ongoing taxonomic revisions are required for isidiate Xanthoparmelia species.

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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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            SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

            We present SequenceMatrix, software that is designed to facilitate the assembly and analysis of multi-gene datasets. Genes are concatenated by dragging and dropping FASTA, NEXUS, or TNT files with aligned sequences into the program window. A multi-gene dataset is concatenated and displayed in a spreadsheet; each sequence is represented by a cell that provides information on sequence length, number of indels, the number of ambiguous bases ("Ns"), and the availability of codon information. Alternatively, GenBank numbers for the sequences can be displayed and exported. Matrices with hundreds of genes and taxa can be concatenated within minutes and exported in TNT, NEXUS, or PHYLIP formats, preserving both character set and codon information for TNT and NEXUS files. SequenceMatrix also creates taxon sets listing taxa with a minimum number of characters or gene fragments, which helps assess preliminary datasets. Entire taxa, whole gene fragments, or individual sequences for a particular gene and species can be excluded from export. Data matrices can be re-split into their component genes and the gene fragments can be exported as individual gene files. SequenceMatrix also includes two tools that help to identify sequences that may have been compromised through laboratory contamination or data management error. One tool lists identical or near-identical sequences within genes, while the other compares the pairwise distance pattern of one gene against the pattern for all remaining genes combined. SequenceMatrix is Java-based and compatible with the Microsoft Windows, Apple MacOS X and Linux operating systems. The software is freely available from http://code.google.com/p/sequencematrix/. © The Willi Hennig Society 2010.
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              Taxonomic bias in biodiversity data and societal preferences

              Studying and protecting each and every living species on Earth is a major challenge of the 21st century. Yet, most species remain unknown or unstudied, while others attract most of the public, scientific and government attention. Although known to be detrimental, this taxonomic bias continues to be pervasive in the scientific literature, but is still poorly studied and understood. Here, we used 626 million occurrences from the Global Biodiversity Information Facility (GBIF), the biggest biodiversity data portal, to characterize the taxonomic bias in biodiversity data. We also investigated how societal preferences and taxonomic research relate to biodiversity data gathering. For each species belonging to 24 taxonomic classes, we used the number of publications from Web of Science and the number of web pages from Bing searches to approximate research activity and societal preferences. Our results show that societal preferences, rather than research activity, strongly correlate with taxonomic bias, which lead us to assert that scientists should advertise less charismatic species and develop societal initiatives (e.g. citizen science) that specifically target neglected organisms. Ensuring that biodiversity is representatively sampled while this is still possible is an urgent prerequisite for achieving efficient conservation plans and a global understanding of our surrounding environment.
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                Author and article information

                Journal
                MycoKeys
                MycoKeys
                MycoKeys
                MycoKeys
                Pensoft Publishers
                1314-4057
                1314-4049
                2018
                18 September 2018
                : 40
                : 13-28
                Affiliations
                [1 ] Science & Education, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605-2496, USA The Field Museum Chicago United States of America
                [2 ] Department of Biology and M.L. Bean Life Science Museum, Brigham Young University, 4102 Life Science Building, Provo, UT 84602, USA Brigham Young University Provo United States of America
                Author notes
                Corresponding author: H. Thorsten Lumbsch ( tlumbsch@ 123456fieldmuseum.org )

                Academic editor: Pradeep Divakar

                Article
                10.3897/mycokeys.40.26724
                6160798
                5a6ec7ca-d993-4a37-b019-0d6c2c9c7117
                Alejandrina Barcenas-Peña, Steven D. Leavitt, Jen-Pan Huang, Felix Grewe, H. Thorsten Lumbsch

                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
                : 16 May 2018
                : 2 September 2018
                Categories
                Research Article
                Ascomycota
                Lichenized Fungi
                Molecular Systematics
                Phylogeny
                Taxonomy
                Americas

                cryptic species,lichenised fungi,mexico,phylogeny,taxonomy,fungi,lecanorales,parmeliaceae

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