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      A multi-gene phylogeny of Lactifluus ( Basidiomycota, Russulales) translated into a new infrageneric classification of the genus

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          Abstract

          Infrageneric relations of the genetically diverse milkcap genus Lactifluus ( Russulales, Basidiomycota) are poorly known. Currently used classification systems still largely reflect the traditional, mainly morphological, characters used for infrageneric delimitations of milkcaps. Increased sampling, combined with small-scale molecular studies, show that this genus is underexplored and in need of revision. For this study, we assembled an extensive dataset of the genus Lactifluus, comprising 80 % of all known species and 30 % of the type collections. To unravel the infrageneric relationships within this genus, we combined a multi-gene molecular phylogeny, based on nuclear ITS, LSU, RPB2 and RPB1, with a morphological study, focussing on five important characteristics (fruit body type, presence of a secondary velum, colour reaction of the latex/context, pileipellis type and presence of true cystidia). Lactifluus comprises four supported subgenera, each containing several supported clades. With extensive sampling, ten new clades and at least 17 new species were discovered, which highlight the high diversity in this genus. The traditional infrageneric classification is only partly maintained and nomenclatural changes are proposed. Our morphological study shows that the five featured characteristics are important at different evolutionary levels, but further characteristics need to be studied to find morphological support for each clade. This study paves the way for a more detailed investigation of biogeographical history and character evolution within Lactifluus.

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          AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics.

          A key element to a successful Markov chain Monte Carlo (MCMC) inference is the programming and run performance of the Markov chain. However, the explicit use of quality assessments of the MCMC simulations-convergence diagnostics-in phylogenetics is still uncommon. Here, we present a simple tool that uses the output from MCMC simulations and visualizes a number of properties of primary interest in a Bayesian phylogenetic analysis, such as convergence rates of posterior split probabilities and branch lengths. Graphical exploration of the output from phylogenetic MCMC simulations gives intuitive and often crucial information on the success and reliability of the analysis. The tool presented here complements convergence diagnostics already available in other software packages primarily designed for other applications of MCMC. Importantly, the common practice of using trace-plots of a single parameter or summary statistic, such as the likelihood score of sampled trees, can be misleading for assessing the success of a phylogenetic MCMC simulation. The program is available as source under the GNU General Public License and as a web application at http://ceb.scs.fsu.edu/awty.
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            Improving phylogenetic inference of mushrooms with RPB1 and RPB2 nucleotide sequences (Inocybe; Agaricales).

            P. Matheny (2005)
            Approximately 3000 bp across 84 taxa have been analyzed for variable regions of RPB1, RPB2, and nLSU-rDNA to infer phylogenetic relationships in the large ectomycorrhizal mushroom genus Inocybe (Agaricales; Basidiomycota). This study represents the first effort to combine variable regions of RPB1 and RPB2 with nLSU-rDNA for low-level phylogenetic studies in mushroom-forming fungi. Combination of the three loci increases non-parametric bootstrap support, Bayesian posterior probabilities, and resolution for numerous clades compared to separate gene analyses. These data suggest the evolution of at least five major lineages in Inocybe-the Inocybe clade, the Mallocybe clade, the Auritella clade, the Inosperma clade, and the Pseudosperma clade. Additionally, many clades nested within each major lineage are strongly supported. These results also suggest the family Crepiodataceae sensu stricto is sister to Inocybe. Recognition of Inocybe at the family level, the Inocybaceae, is recommended.
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              Using RPB1 sequences to improve phylogenetic inference among mushrooms (Inocybe, Agaricales).

              An investigation of mushroom phylogeny using the largest subunit of RNA polymerase II gene sequences (RPB1) was conducted in comparison with nuclear ribosomal large subunit RNA gene sequences (nLSU) for the same set of taxa in the genus Inocybe (Agaricales, Basidiomycota). The two data sets, though not significantly incongruent, exhibit conflict among the placement of two taxa that exhibit long branches in the nLSU data set. In contrast, RPB1 terminal branch lengths are rather uniform. Bootstrap support is increased for clades in RPB1. Combined data sets increase the degree of confidence for several relationships. Overall, nLSU data do not yield a robust phylogeny when independently assessed by RPB1 sequences. This multigene study indicates that Inocybe is a monophyletic group composed of at least four distinct lineages-subgenus Mallocybe, section Cervicolores, section Rimosae, and subgenus Inocybe sensu Kühner, Kuyper, non Singer. Within subgenus Inocybe, two additional lineages, one composed of species with smooth basidiospores (clade I) and a second characterized by nodulose-spored species (clade II), are recovered by RPB1 and combined data. The nLSU data recover only clade I. The genera Astrosporina and Inocybella cannot be recognized phylogenetically. "Supersections" Cortinatae and Marginatae are not monophyletic groups.
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                Author and article information

                Journal
                Persoonia
                Persoonia
                Persoonia
                Persoonia : Molecular Phylogeny and Evolution of Fungi
                Naturalis Biodiversity Center & Centraalbureau voor Schimmelcultures
                0031-5850
                1878-9080
                15 September 2016
                June 2017
                : 38
                : 58-80
                Affiliations
                [1 ] Research group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 32, 9000 Ghent, Belgium; corresponding author e-mail: eske.decrop@ugent.be.
                [2 ] Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands.
                [3 ] Centre of Excellence in Fungal Research, Mae Fah Luang University, 333 Moo 1, Thasud subdistrict, Muang district, Chiang Rai 57100, Thailand.
                [4 ] School of Science, Mae Fah Luang University, 333 Moo 1, Thasud sub-district, Muang district, Chiang Rai 57100, Thailand.
                [5 ] Université Toulouse 3 Paul Sabatier, CNRS, ENFA, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, 31062 Toulouse, France.
                [6 ] Service of Mycology and Aerobiology, BCCM/IHEM Biomedical Fungi and Yeasts Collection, Scientific Institute of Public Health, Brussels, Belgium.
                [7 ] The New York Botanical Garden, Institute of Systematic Botany, Bronx, NY 10458, USA.
                [8 ] EA 4483, Université Lille Nord France, Faculté des Sciences Pharmaceutiques & Biologiques, F-59006 Lille, France.
                [9 ] Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany.
                Author notes
                Article
                10.3767/003158517X693255
                5645188
                29151627
                29ffc8aa-b3d8-43e4-a330-98b13c337344
                © 2016-2017 Naturalis Biodiversity Center & Centraalbureau voor Schimmelcultures

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                History
                : 7 September 2015
                : 12 May 2016
                Categories
                Research Article

                Plant science & Botany
                milkcaps,molecular evolution,morphology,taxonomy
                Plant science & Botany
                milkcaps, molecular evolution, morphology, taxonomy

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