Taxonomic Utility of Old Names in Current Fungal Classification and Nomenclature: Conflicts, Confusion & Clarifications
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The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service. -
Development and Evaluation of Rrna Targeted in Situ Probes and Phylogenetic Relationships of Freshwater Fungi
Development and evaluation of rRNA targeted in situ probes and phylogenetic relationships of freshwater fungi vorgelegt von Diplom-Biologin Christiane Baschien aus Berlin Von der Fakultät III - Prozesswissenschaften der Technischen Universität Berlin zur Erlangung des akademischen Grades Doktorin der Naturwissenschaften - Dr. rer. nat. - genehmigte Dissertation Promotionsausschuss: Vorsitzender: Prof. Dr. sc. techn. Lutz-Günter Fleischer Berichter: Prof. Dr. rer. nat. Ulrich Szewzyk Berichter: Prof. Dr. rer. nat. Felix Bärlocher Berichter: Dr. habil. Werner Manz Tag der wissenschaftlichen Aussprache: 19.05.2003 Berlin 2003 D83 Table of contents INTRODUCTION ..................................................................................................................................... 1 MATERIAL AND METHODS .................................................................................................................. 8 1. Used organisms ............................................................................................................................. 8 2. Media, culture conditions, maintenance of cultures and harvest procedure.................................. 9 2.1. Culture media........................................................................................................................... 9 2.2. Culture conditions .................................................................................................................. 10 2.3. Maintenance of cultures.........................................................................................................10 -
Molecular Systematics of the Marine Dothideomycetes
available online at www.studiesinmycology.org StudieS in Mycology 64: 155–173. 2009. doi:10.3114/sim.2009.64.09 Molecular systematics of the marine Dothideomycetes S. Suetrong1, 2, C.L. Schoch3, J.W. Spatafora4, J. Kohlmeyer5, B. Volkmann-Kohlmeyer5, J. Sakayaroj2, S. Phongpaichit1, K. Tanaka6, K. Hirayama6 and E.B.G. Jones2* 1Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand; 2Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Paholyothin Road, Khlong 1, Khlong Luang, Pathum Thani, 12120, Thailand; 3National Center for Biothechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, MSC 6510, Bethesda, Maryland 20892-6510, U.S.A.; 4Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, U.S.A.; 5Institute of Marine Sciences, University of North Carolina at Chapel Hill, Morehead City, North Carolina 28557, U.S.A.; 6Faculty of Agriculture & Life Sciences, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan *Correspondence: E.B. Gareth Jones, [email protected] Abstract: Phylogenetic analyses of four nuclear genes, namely the large and small subunits of the nuclear ribosomal RNA, transcription elongation factor 1-alpha and the second largest RNA polymerase II subunit, established that the ecological group of marine bitunicate ascomycetes has representatives in the orders Capnodiales, Hysteriales, Jahnulales, Mytilinidiales, Patellariales and Pleosporales. Most of the fungi sequenced were intertidal mangrove taxa and belong to members of 12 families in the Pleosporales: Aigialaceae, Didymellaceae, Leptosphaeriaceae, Lenthitheciaceae, Lophiostomataceae, Massarinaceae, Montagnulaceae, Morosphaeriaceae, Phaeosphaeriaceae, Pleosporaceae, Testudinaceae and Trematosphaeriaceae. Two new families are described: Aigialaceae and Morosphaeriaceae, and three new genera proposed: Halomassarina, Morosphaeria and Rimora. -
Pt Reyes Species As of 12-1-2017 Abortiporus Biennis Agaricus
Pt Reyes Species as of 12-1-2017 Abortiporus biennis Agaricus augustus Agaricus bernardii Agaricus californicus Agaricus campestris Agaricus cupreobrunneus Agaricus diminutivus Agaricus hondensis Agaricus lilaceps Agaricus praeclaresquamosus Agaricus rutilescens Agaricus silvicola Agaricus subrutilescens Agaricus xanthodermus Agrocybe pediades Agrocybe praecox Alboleptonia sericella Aleuria aurantia Alnicola sp. Amanita aprica Amanita augusta Amanita breckonii Amanita calyptratoides Amanita constricta Amanita gemmata Amanita gemmata var. exannulata Amanita calyptraderma Amanita calyptraderma (white form) Amanita magniverrucata Amanita muscaria Amanita novinupta Amanita ocreata Amanita pachycolea Amanita pantherina Amanita phalloides Amanita porphyria Amanita protecta Amanita velosa Amanita smithiana Amaurodon sp. nova Amphinema byssoides gr. Annulohypoxylon thouarsianum Anthrocobia melaloma Antrodia heteromorpha Aphanobasidium pseudotsugae Armillaria gallica Armillaria mellea Armillaria nabsnona Arrhenia epichysium Pt Reyes Species as of 12-1-2017 Arrhenia retiruga Ascobolus sp. Ascocoryne sarcoides Astraeus hygrometricus Auricularia auricula Auriscalpium vulgare Baeospora myosura Balsamia cf. magnata Bisporella citrina Bjerkandera adusta Boidinia propinqua Bolbitius vitellinus Suillellus (Boletus) amygdalinus Rubroboleus (Boletus) eastwoodiae Boletus edulis Boletus fibrillosus Botryobasidium longisporum Botryobasidium sp. Botryobasidium vagum Bovista dermoxantha Bovista pila Bovista plumbea Bulgaria inquinans Byssocorticium californicum -
Species of Hygrocybe Subgenus Cuphophyllus Hygrophorus Flavipes
PERS OONIA Published by the Rijksherbarium, Leiden 43-46 Volume 14, Part 1, pp. (1989) Notes on Hygrophoraceae — XI. Observations on some species of Hygrocybe subgenus Cuphophyllus Eef Arnolds Biological Station, Wijster (Drente), Netherlands* The nomenclature of the violaceous of grey species Hygrocybe subgenus Cuphophyllus and the taxonomic position of H. subradiata are discussed. One new species is described and onenew combination is made, viz. Hygrocybe radiata and H. flavipes. In Europe usually two species with a grey violaceous to lilac pileus are distinguished within Hygrocybe subgenus Cuphophyllus Donk (= Camarophyllus sensu auct.), named H. subvio- lacea (Peck) Orton & Watl. and H. lacmus (Schum.) Orton & Watl. The former species is characterized by an entirely white stipe and aromatic smell, whereas the latter species has a yellow base of stipe and no characteristic smell. Recently, Raid& Boertmann (1988) demonstrated that the name Agaricus lacmus Schum. has been since Schumacher did mention (1803: 333) currently misinterpreted not a yellow base of stipe in the original description and an unpublished, authentic plate by that author shows white lacmus Schum. is an entirely stipe. Consequently, Agaricus an earlier synonym ofHygrophorus subviolaceus Peck (1900: 82) and H. lacmus sensu auct. (with a yellow stipe base) should have a new name. According to Raid & Boertmann (1988) the oldest available name is Hygrophorus flavipes Britz. This epithet was not yet combinedin Hygrocybe and thereforethe following combina- tion is proposed: Hygrocybe flavipes (Britz.) Arnolds, comb. nov. — Basionym: Hygrophorus flavipes Britz., Hymenomyc. Stidbayern 8: 10, fig. 69. 1891. Some authors (Clemengon, 1982; Bon, 1984) distinguished two species with a yellow base of stipe, differing in spore size only: Camarophyllus lacmus sensu C16mengon with ellip- soid to lacrimiform of 6.5-8 x 4.5-6 and C. -
Phylogenetic Assignment of the Fungicolous Hypoxylon Invadens (Ascomycota, Xylariales) and Investigation of Its Secondary Metabolites
microorganisms Article Phylogenetic Assignment of the Fungicolous Hypoxylon invadens (Ascomycota, Xylariales) and Investigation of its Secondary Metabolites Kevin Becker 1,2 , Christopher Lambert 1,2,3 , Jörg Wieschhaus 1 and Marc Stadler 1,2,* 1 Department of Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany; [email protected] (K.B.); [email protected] (C.L.); [email protected] (J.W.) 2 German Centre for Infection Research Association (DZIF), Partner site Hannover-Braunschweig, Inhoffenstraße 7, 38124 Braunschweig, Germany 3 Department for Molecular Cell Biology, Helmholtz Centre for Infection Research GmbH (HZI) Inhoffenstraße 7, 38124 Braunschweig, Germany * Correspondence: [email protected]; Tel.: +49-531-6181-4240; Fax: +49-531-6181-9499 Received: 23 July 2020; Accepted: 8 September 2020; Published: 11 September 2020 Abstract: The ascomycete Hypoxylon invadens was described in 2014 as a fungicolous species growing on a member of its own genus, H. fragiforme, which is considered a rare lifestyle in the Hypoxylaceae. This renders H. invadens an interesting target in our efforts to find new bioactive secondary metabolites from members of the Xylariales. So far, only volatile organic compounds have been reported from H. invadens, but no investigation of non-volatile compounds had been conducted. Furthermore, a phylogenetic assignment following recent trends in fungal taxonomy via a multiple sequence alignment seemed practical. A culture of H. invadens was thus subjected to submerged cultivation to investigate the produced secondary metabolites, followed by isolation via preparative chromatography and subsequent structure elucidation by means of nuclear magnetic resonance (NMR) spectroscopy and high-resolution mass spectrometry (HR-MS). -
A Translation of the Linnaean Dissertation the Invisible World
BJHS 49(3): 353–382, September 2016. © British Society for the History of Science 2016 doi:10.1017/S0007087416000637 A translation of the Linnaean dissertation The Invisible World JANIS ANTONOVICS* AND JACOBUS KRITZINGER** Abstract. This study presents the first translation from Latin to English of the Linnaean disser- tation Mundus invisibilis or The Invisible World, submitted by Johannes Roos in 1769. The dissertation highlights Linnaeus’s conviction that infectious diseases could be transmitted by living organisms, too small to be seen. Biographies of Linnaeus often fail to mention that Linnaeus was correct in ascribing the cause of diseases such as measles, smallpox and syphilis to living organisms. The dissertation itself reviews the work of many microscopists, especially on zoophytes and insects, marvelling at the many unexpected discoveries. It then discusses and quotes at length the observations of Münchhausen suggesting that spores from fungi causing plant diseases germinate to produce animalcules, an observation that Linnaeus claimed to have confirmed. The dissertation then draws parallels between these findings and the conta- giousness of many human diseases, and urges further studies of this ‘invisible world’ since, as Roos avers, microscopic organisms may cause more destruction than occurs in all wars. Introduction Here we present the first translation from Latin to English of the Linnaean dissertation published in 1767 by Johannes Roos (1745–1828) entitled Dissertatio academica mundum invisibilem, breviter delineatura and republished by Carl Linnaeus (1707– 1778) several years later in the Amoenitates academicae under the title Mundus invisibi- lis or The Invisible World.1 Roos was a student of Linnaeus, and the dissertation is important in highlighting Linnaeus’s conviction that infectious diseases could be trans- mitted by living organisms. -
Amplicon-Based Sequencing of Soil Fungi from Wood Preservative Test Sites
ORIGINAL RESEARCH published: 18 October 2017 doi: 10.3389/fmicb.2017.01997 Amplicon-Based Sequencing of Soil Fungi from Wood Preservative Test Sites Grant T. Kirker 1*, Amy B. Bishell 1, Michelle A. Jusino 2, Jonathan M. Palmer 2, William J. Hickey 3 and Daniel L. Lindner 2 1 FPL, United States Department of Agriculture-Forest Service (USDA-FS), Durability and Wood Protection, Madison, WI, United States, 2 NRS, United States Department of Agriculture-Forest Service (USDA-FS), Center for Forest Mycology Research, Madison, WI, United States, 3 Department of Soil Science, University of Wisconsin-Madison, Madison, WI, United States Soil samples were collected from field sites in two AWPA (American Wood Protection Association) wood decay hazard zones in North America. Two field plots at each site were exposed to differing preservative chemistries via in-ground installations of treated wood stakes for approximately 50 years. The purpose of this study is to characterize soil fungal species and to determine if long term exposure to various wood preservatives impacts soil fungal community composition. Soil fungal communities were compared using amplicon-based DNA sequencing of the internal transcribed spacer 1 (ITS1) region of the rDNA array. Data show that soil fungal community composition differs significantly Edited by: Florence Abram, between the two sites and that long-term exposure to different preservative chemistries National University of Ireland Galway, is correlated with different species composition of soil fungi. However, chemical analyses Ireland using ICP-OES found levels of select residual preservative actives (copper, chromium and Reviewed by: Seung Gu Shin, arsenic) to be similar to naturally occurring levels in unexposed areas. -
Dr. Sahanaj Jamil Associate Professor of Botany M.L.S.M. College, Darbhanga
Subject BOTANY Paper No V Paper Code BOT521 Topic Taxonomy and Diversity of Seed Plant: Gymnosperms & Angiosperms Dr. Sahanaj Jamil Associate Professor of Botany M.L.S.M. College, Darbhanga BOTANY PG SEMESTER – II, PAPER –V BOT521: Taxonomy and Diversity of seed plants UNIT- I BOTANY PG SEMESTER – II, PAPER –V BOT521: Taxonomy and Diversity of seed plants Classification of Gymnosperms. # Robert Brown (1827) for the first time recognized Gymnosperm as a group distinct from angiosperm due to the presence of naked ovules. BENTHAM and HOOKSER (1862-1883) consider them equivalent to dicotyledons and monocotyledons and placed between these two groups of angiosperm. They recognized three classes of gymnosperm, Cyacadaceae, coniferac and gnetaceae. Later ENGLER (1889) created a group Gnikgoales to accommodate the genus giankgo. Van Tieghem (1898) treated Gymnosperm as one of the two subdivision of spermatophyte. To accommodate the fossil members three more classes- Pteridospermae, Cordaitales, and Bennettitales where created. Coulter and chamberlain (1919), Engler and Prantl (1926), Rendle (1926) and other considered Gymnosperm as a division of spermatophyta, Phanerogamia or Embryoptyta and they further divided them into seven orders: - i) Cycadofilicales ii) Cycadales iii) Bennettitales iv) Ginkgoales v) Coniferales vi) Corditales vii) Gnetales On the basis of wood structure steward (1919) divided Gymnosperm into two classes: - i) Manoxylic ii) Pycnoxylic The various classification of Gymnosperm proposed by various workers are as follows: - i) Sahni (1920): - He recognized two sub-divison in gymnosperm: - a) Phylospermae b) Stachyospermae BOTANY PG SEMESTER – II, PAPER –V BOT521: Taxonomy and Diversity of seed plants ii) Classification proposed by chamber lain (1934): - He divided Gymnosperm into two divisions: - a) Cycadophyta b) Coniterophyta iii) Classification proposed by Tippo (1942):- He considered Gymnosperm as a class of the sub- phylum pteropsida and divided them into two sub classes:- a) Cycadophyta b) Coniferophyta iv) D. -
Towards a Phylogenetic Clarification of Lophiostoma / Massarina and Morphologically Similar Genera in the Pleosporales
Fungal Diversity Towards a phylogenetic clarification of Lophiostoma / Massarina and morphologically similar genera in the Pleosporales Zhang, Y.1, Wang, H.K.2, Fournier, J.3, Crous, P.W.4, Jeewon, R.1, Pointing, S.B.1 and Hyde, K.D.5,6* 1Division of Microbiology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P.R. China 2Biotechnology Institute, Zhejiang University, 310029, P.R. China 3Las Muros, Rimont, Ariège, F 09420, France 4Centraalbureau voor Schimmelcultures, Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD, Utrecht, The Netherlands 5School of Science, Mae Fah Luang University, Tasud, Muang, Chiang Rai 57100, Thailand 6International Fungal Research & Development Centre, The Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, Yunnan, P.R. China 650034 Zhang, Y., Wang, H.K., Fournier, J., Crous, P.W., Jeewon, R., Pointing, S.B. and Hyde, K.D. (2009). Towards a phylogenetic clarification of Lophiostoma / Massarina and morphologically similar genera in the Pleosporales. Fungal Diversity 38: 225-251. Lophiostoma, Lophiotrema and Massarina are similar genera that are difficult to distinguish morphologically. In order to obtain a better understanding of these genera, lectotype material of the generic types, Lophiostoma macrostomum, Lophiotrema nucula and Massarina eburnea were examined and are re-described. The phylogeny of these genera is investigated based on the analysis of 26 Lophiostoma- and Massarina-like taxa and three genes – 18S, 28S rDNA and RPB2. These taxa formed five well-supported sub-clades in Pleosporales. This study confirms that both Lophiostoma and Massarina are polyphyletic. Massarina-like taxa can presently be differentiated into two groups – the Lentithecium group and the Massarina group. -
Resurrection and Emendation of the Hypoxylaceae, Recognised from a Multigene Phylogeny of the Xylariales
Mycol Progress DOI 10.1007/s11557-017-1311-3 ORIGINAL ARTICLE Resurrection and emendation of the Hypoxylaceae, recognised from a multigene phylogeny of the Xylariales Lucile Wendt1,2 & Esteban Benjamin Sir3 & Eric Kuhnert1,2 & Simone Heitkämper1,2 & Christopher Lambert1,2 & Adriana I. Hladki3 & Andrea I. Romero4,5 & J. Jennifer Luangsa-ard6 & Prasert Srikitikulchai6 & Derek Peršoh7 & Marc Stadler1,2 Received: 21 February 2017 /Revised: 12 April 2017 /Accepted: 19 April 2017 # The Author(s) 2017. This article is an open access publication Abstract A multigene phylogeny was constructed, including polymerase II (RPB2), and beta-tubulin (TUB2). Specimens a significant number of representative species of the main were selected based on more than a decade of intensive mor- lineages in the Xylariaceae and four DNA loci the internal phological and chemotaxonomic work, and cautious taxon transcribed spacer region (ITS), the large subunit (LSU) of sampling was performed to cover the major lineages of the the nuclear rDNA, the second largest subunit of the RNA Xylariaceae; however, with emphasis on hypoxyloid species. The comprehensive phylogenetic analysis revealed a clear-cut This article is part of the “Special Issue on ascomycete systematics in segregation of the Xylariaceae into several major clades, honor of Richard P. Korf who died in August 2016”. which was well in accordance with previously established morphological and chemotaxonomic concepts. One of these The present paper is dedicated to Prof. Jack D. Rogers, on the occasion of his fortcoming 80th birthday. clades contained Annulohypoxylon, Hypoxylon, Daldinia,and other related genera that have stromatal pigments and a Section Editor: Teresa Iturriaga and Marc Stadler nodulisporium-like anamorph. -
A Higher-Level Phylogenetic Classification of the Fungi
mycological research 111 (2007) 509–547 available at www.sciencedirect.com journal homepage: www.elsevier.com/locate/mycres A higher-level phylogenetic classification of the Fungi David S. HIBBETTa,*, Manfred BINDERa, Joseph F. BISCHOFFb, Meredith BLACKWELLc, Paul F. CANNONd, Ove E. ERIKSSONe, Sabine HUHNDORFf, Timothy JAMESg, Paul M. KIRKd, Robert LU¨ CKINGf, H. THORSTEN LUMBSCHf, Franc¸ois LUTZONIg, P. Brandon MATHENYa, David J. MCLAUGHLINh, Martha J. POWELLi, Scott REDHEAD j, Conrad L. SCHOCHk, Joseph W. SPATAFORAk, Joost A. STALPERSl, Rytas VILGALYSg, M. Catherine AIMEm, Andre´ APTROOTn, Robert BAUERo, Dominik BEGEROWp, Gerald L. BENNYq, Lisa A. CASTLEBURYm, Pedro W. CROUSl, Yu-Cheng DAIr, Walter GAMSl, David M. GEISERs, Gareth W. GRIFFITHt,Ce´cile GUEIDANg, David L. HAWKSWORTHu, Geir HESTMARKv, Kentaro HOSAKAw, Richard A. HUMBERx, Kevin D. HYDEy, Joseph E. IRONSIDEt, Urmas KO˜ LJALGz, Cletus P. KURTZMANaa, Karl-Henrik LARSSONab, Robert LICHTWARDTac, Joyce LONGCOREad, Jolanta MIA˛ DLIKOWSKAg, Andrew MILLERae, Jean-Marc MONCALVOaf, Sharon MOZLEY-STANDRIDGEag, Franz OBERWINKLERo, Erast PARMASTOah, Vale´rie REEBg, Jack D. ROGERSai, Claude ROUXaj, Leif RYVARDENak, Jose´ Paulo SAMPAIOal, Arthur SCHU¨ ßLERam, Junta SUGIYAMAan, R. Greg THORNao, Leif TIBELLap, Wendy A. UNTEREINERaq, Christopher WALKERar, Zheng WANGa, Alex WEIRas, Michael WEISSo, Merlin M. WHITEat, Katarina WINKAe, Yi-Jian YAOau, Ning ZHANGav aBiology Department, Clark University, Worcester, MA 01610, USA bNational Library of Medicine, National Center for Biotechnology Information,