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Zamora JC, Svensson M, Kirschner R, Olariaga I, Ryman S, Parra LA, Geml J, Rosling A, Adamčík S, Ahti T, Aime MC, Ainsworth AM, Albert L, Albertó E, García AA, Ageev D, Agerer R, Aguirre-Hudson B, Ammirati J, Andersson H, Angelini C, Antonín V, Aoki T, Aptroot A, Argaud D, Sosa BIA, Aronsen A, Arup U, Asgari B, Assyov B, Atienza V, Bandini D, Baptista-Ferreira JL, Baral HO, Baroni T, Barreto RW, Beker H, Bell A, Bellanger JM, Bellù F, Bemmann M, Bendiksby M, Bendiksen E, Bendiksen K, Benedek L, Bérešová-Guttová A, Berger F, Berndt R, Bernicchia A, Biketova AY, Bizio E, Bjork C, Boekhout T, Boertmann D, Böhning T, Boittin F, Boluda CG, Boomsluiter MW, Borovička J, Brandrud TE, Braun U, Brodo I, Bulyonkova T, Burdsall HH, Buyck B, Burgaz AR, Calatayud V, Callac P, Campo E, Candusso M, Capoen B, Carbó J, Carbone M, Castañeda-Ruiz RF, Castellano MA, Chen J, Clerc P, Consiglio G, Corriol G, Courtecuisse R, Crespo A, Cripps C, Crous PW, da Silva GA, da Silva M, Dam M, Dam N, Dämmrich F, Das K, Davies L, De Crop E, De Kesel A, De Lange R, De Madrignac Bonzi B, dela Cruz TEE, Delgat L, Demoulin V, Desjardin DE, Diederich P, Dima B, Dios MM, Divakar PK, Douanla-Meli C, Douglas B, Drechsler-Santos ER, Dyer PS, Eberhardt U, Ertz D, Esteve-Raventós F, Salazar JAE, Evenson V, Eyssartier G, Farkas E, Favre A, Fedosova AG, Filippa M, Finy P, Flakus A, Fos S, Fournier J, Fraiture A, Franchi P, Molano AEF, Friebes G, Frisch A, Fryday A, Furci G, Márquez RG, Garbelotto M, García-Martín JM, Otálora MAG, Sánchez DG, Gardiennet A, Garnica S, Benavent IG, Gates G, da Cruz Lima Gerlach A, Ghobad-Nejhad M, Gibertoni TB, Grebenc T, Greilhuber I, Grishkan B, Groenewald JZ, Grube M, Gruhn G, Gueidan C, Gulden G, Gusmão LFP, Hafellner J, Hairaud M, Halama M, Hallenberg N, Halling RE, Hansen K, Harder CB, Heilmann-Clausen J, Helleman S, Henriot A, Hernandez-Restrepo M, Herve R, Hobart C, Hoffmeister M, Høiland K, Holec J, Holien H, Hughes K, Hubka V, Huhtinen S, Ivančević B, Jagers M, Jaklitsch W, Jansen A, Jayawardena RS, Jeppesen TS, Jeppson M, Johnston P, Jørgensen PM, Kärnefelt I, Kalinina LB, Kantvilas G, Karadelev M, Kasuya T, Kautmanová I, Kerrigan RW, Kirchmair M, Kiyashko A, Knapp DG, Knudsen H, Knudsen K, Knutsson T, Kolařík M, Kõljalg U, Košuthová A, Koszka A, Kotiranta H, Kotkova V, Koukol O, Kout J, Kovács GM, Kříž M, Kruys Å, Kučera V, Kudzma L, Kuhar F, Kukwa M, Arun Kumar TK, Kunca V, Kušan I, Kuyper TW, Lado C, Læssøe T, Lainé P, Langer E, Larsson E, Larsson KH, Laursen G, Lechat C, Lee S, Lendemer JC, Levin L, Lindemann U, Lindström H, Liu X, Hernandez RCL, Llop E, Locsmándi C, Lodge DJ, Loizides M, Lőkös L, Luangsa-ard J, Lüderitz M, Lumbsch T, Lutz M, Mahoney D, Malysheva E, Malysheva V, Manimohan P, Marin-Felix Y, Marques G, Martínez-Gil R, Marson G, Mata G, Matheny PB, Mathiassen GH, Matočec N, Mayrhofer H, Mehrabi M, Melo I, Mešić A, Methven AS, Miettinen O, Romero AMM, Miller AN, Mitchell JK, Moberg R, Moreau PA, Moreno G, Morozova O, Morte A, Muggia L, González GM, Myllys L, Nagy I, Nagy LG, Neves MA, Niemelä T, Nimis PL, Niveiro N, Noordeloos ME, Nordin A, Noumeur SR, Novozhilov Y, Nuytinck J, Ohenoja E, Fiuza PO, Orange A, Ordynets A, Ortiz-Santana B, Pacheco L, Pál-Fám F, Palacio M, Palice Z, Papp V, Pärtel K, Pawlowska J, Paz A, Peintner U, Pennycook S, Pereira OL, Daniëls PP, Pérez-De-Gregorio Capella MÀ, del Amo CMP, Gorjón SP, Pérez-Ortega S, Pérez-Vargas I, Perry BA, Petersen JH, Petersen RH, Pfister DH, Phukhamsakda C, Piątek M, Piepenbring M, Pino-Bodas R, Esquivel JPP, Pirot P, Popov ES, Popoff O, Álvaro MP, Printzen C, Psurtseva N, Purahong W, Quijada L, Rambold G, Ramírez NA, Raja H, Raspé O, Raymundo T, Réblová M, Rebriev YA, de Dios Reyes García J, Ripoll MÁR, Richard F, Richardson MJ, Rico VJ, Robledo GL, Barbosa FR, Rodriguez-Caycedo C, Rodriguez-Flakus P, Ronikier A, Casas LR, Rusevska K, Saar G, Saar I, Salcedo I, Martínez SMS, Montoya CAS, Sánchez-Ramírez S, Sandoval-Sierra JV, Santamaria S, Monteiro JS, Schroers HJ, Schulz B, Schmidt-Stohn G, Schumacher T, Senn-Irlet B, Ševčíková H, Shchepin O, Shirouzu T, Shiryaev A, Siepe K, Sir EB, Sohrabi M, Soop K, Spirin V, Spribille T, Stadler M, Stalpers J, Stenroos S, Suija A, Sunhede S, Svantesson S, Svensson S, Svetasheva TY, Świerkosz K, Tamm H, Taskin H, Taudière A, Tedebrand JO, Lahoz RT, Temina M, Thell A, Thines M, Thor G, Thüs H, Tibell L, Tibell S, Timdal E, Tkalčec Z, Tønsberg T, Trichies G, Triebel D, Tsurykau A, Tulloss RE, Tuovinen V, Sosa MU, Urcelay C, Valade F, Garza RV, van den Boom P, Van Vooren N, Vasco-Palacios AM, Vauras J, Velasco Santos JM, Vellinga E, Verbeken A, Vetlesen P, Vizzini A, Voglmayr H, Volobuev S, von Brackel W, Voronina E, Walther G, Watling R, Weber E, Wedin M, Weholt Ø, Westberg M, Yurchenko E, Zehnálek P, Zhang H, Zhurbenko MP, Ekman S. Considerations and consequences of allowing DNA sequence data as types of fungal taxa. IMA Fungus 2018; 9:167-175. [PMID: 30018877 PMCID: PMC6048565 DOI: 10.5598/imafungus.2018.09.01.10] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 05/21/2018] [Indexed: 11/11/2022] Open
Abstract
Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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Affiliation(s)
- Juan Carlos Zamora
- Museum of Evolution, Uppsala University, Norbyvägen 16, 75236 Uppsala, Sweden
| | - Måns Svensson
- Museum of Evolution, Uppsala University, Norbyvägen 16, 75236 Uppsala, Sweden
| | | | - Ibai Olariaga
- Universidad Rey Juan Carlos, 28933 Móstoles, Madrid, Spain
| | - Svengunnar Ryman
- Museum of Evolution, Uppsala University, Norbyvägen 16, 75236 Uppsala, Sweden
| | | | - József Geml
- Naturalis Biodiversity Center, Vondellaan 55, 2332AA Leiden, The Netherlands
| | - Anna Rosling
- Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
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- Museum of Evolution, Uppsala University, Norbyvägen 16, 75236 Uppsala, Sweden
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Miadlikowska J, Kauff F, Hofstetter V, Fraker E, Grube M, Hafellner J, Reeb V, Hodkinson BP, Kukwa M, Lücking R, Hestmark G, Otalora MG, Rauhut A, Büdel B, Scheidegger C, Timdal E, Stenroos S, Brodo I, Perlmutter GB, Ertz D, Diederich P, Lendemer JC, May P, Schoch CL, Arnold AE, Gueidan C, Tripp E, Yahr R, Robertson C, Lutzoni F. New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832636] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | | | | | - Emily Fraker
- Department of Biology, Duke University, Durham, North Carolina 27708-0338
| | | | - Josef Hafellner
- Institut für Botanik, Karl-Franzens-Universität, Holteigasse 6, A-8010, Graz, Austria
| | | | | | - Martin Kukwa
- Department of Plant Taxonomy and Nature Conservation, Gdansk University, A. Legionow 9, 80-441 Gdansk, Poland
| | - Robert Lücking
- Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, Illinois 60605-2496
| | - Geir Hestmark
- Department of Biology, University of Oslo, P.O. Box 1066 Blindern, NO-0316 Oslo, Norway
| | - Monica Garcia Otalora
- Área de Biodiversidad y Conservación, ESCET, Universidad Rey Juan Carlos, c/ Tulipán s/n, 28933-Móstoles, Madrid, Spain
| | | | - Burkhard Büdel
- Fachbereich Biologie, Abt. Pflanzenökologie und Systematik, University of Kaiserslautern, Postfach 3049, 67653 Kaiserslautern, Germany
| | - Christoph Scheidegger
- Swiss Federal Institute for Forest, Snow and Landscape Research (WSL/FNP), Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Einar Timdal
- Botanical Museum, University of Oslo, Sars’ gate 1, N-1162 Oslo, Norway
| | - Soili Stenroos
- Botanical Museum, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014 Finland
| | - Irwin Brodo
- Canadian Museum of Nature, P.O. Box 3443, Station D, Ottawa, Ontario, K1P 6P4 Canada
| | - Gary B. Perlmutter
- North Carolina Botanical Garden, University of North Carolina at Chapel Hill, CB 3375, Totten Center, Chapel Hill, North Carolina 27599-3375
| | - Damien Ertz
- National Botanic Garden of Belgium, Department of Bryophytes-Thallophytes, Domaine de Bouchout, B-1860 Meise, Belgium
| | - Paul Diederich
- Musée national d’histoire naturelle, 25 rue Munster, L-2160 Luxembourg, Luxembourg
| | - James C. Lendemer
- Department of Botany, Academy of Natural Sciences of Philadelphia, 1900 Benjamin Franklin Parkway, Philadelphia, Pennsylvania 19103
| | - Philip May
- Farlow Herbarium, Harvard University, 22 Divinity Avenue, Cambridge, Massachusetts 02138
| | - Conrad L. Schoch
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon
| | - A. Elizabeth Arnold
- Department of Plant Sciences, University of Arizona, 1140 E. South Campus Drive, Forbes 204, Tucson, Arizona 85721
| | | | | | | | | | - François Lutzoni
- Department of Biology, Duke University, Durham, North Carolina 27708-0338
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Miadlikowska J, Kauff F, Hofstetter V, Fraker E, Grube M, Hafellner J, Reeb V, Hodkinson BP, Kukwa M, Lücking R, Hestmark G, Otalora MG, Rauhut A, Büdel B, Scheidegger C, Timdal E, Stenroos S, Brodo I, Perlmutter GB, Ertz D, Diederich P, Lendemer JC, May P, Schoch CL, Arnold AE, Gueidan C, Tripp E, Yahr R, Robertson C, Lutzoni F. New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. Mycologia 2006; 98:1088-103. [PMID: 17486983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The Lecanoromycetes includes most of the lichen-forming fungal species (> 13500) and is therefore one of the most diverse class of all Fungi in terms of phenotypic complexity. We report phylogenetic relationships within the Lecanoromycetes resulting from Bayesian and maximum likelihood analyses with complementary posterior probabilities and bootstrap support values based on three combined multilocus datasets using a supermatrix approach. Nine of 10 orders and 43 of 64 families currently recognized in Eriksson's classification of the Lecanoromycetes (Outline of Ascomycota--2006 Myconet 12:1-82) were represented in this sampling. Our analyses strongly support the Acarosporomycetidae and Ostropomycetidae as monophyletic, whereas the delimitation of the largest subclass, the Lecanoromycetidae, remains uncertain. Independent of future delimitation of the Lecanoromycetidae, the Rhizocarpaceae and Umbilicariaceae should be elevated to the ordinal level. This study shows that recent classifications include several nonmonophyletic taxa at different ranks that need to be recircumscribed. Our phylogenies confirm that ascus morphology cannot be applied consistently to shape the classification of lichen-forming fungi. The increasing amount of missing data associated with the progressive addition of taxa resulted in some cases in the expected loss of support, but we also observed an improvement in statistical support for many internodes. We conclude that a phylogenetic synthesis for a chosen taxonomic group should include a comprehensive assessment of phylogenetic confidence based on multiple estimates using different methods and on a progressive taxon sampling with an increasing number of taxa, even if it involves an increasing amount of missing data.
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