Considerations and consequences of allowing DNA sequence data as types of fungal taxa

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Zamora , J C , Svensson , M , Kirschner , R , Olariaga , I , Ryman , S , Alberto Parra , L , Geml , J , Rosling , A , Adamcik , S , Ahti , T , Aime , M C , Ainsworth , A M , Albert , L , Alberto , E , Garcia , A A , Ageev , D , Agerer , R , Aguirre-Hudson , B , Ammirati , J , Andersson , H , Angelini , C , Antonin , V , Aoki , T , Aptroot , A , Argaud , D , Sosa , B I A , Aronsen , A , Arup , U , Asgari , B , Assyov , B , Atienza , V , Bandini , D , Baptista-Ferreira , J L , Baral , H-O , Baroni , T , Barreto , R W , Baker , H , Bell , A , Bellanger , J-M , Bellu , F , Bemmann , M , Bendiksby , M , Bendiksen , E , Bendiksen , K , Benedek , L , Beresova-Guttova , A , Berger , F , Berndt , R , Bernicchia , A , Biketova , A Y , Bizio , E , Bjork , C , Boekhout , T , Boertmann , D , Bohning , T , Boittin , F , Boluda , C G , Boomsluiter , M W , Borovicka , J , Brandrud , T E , Braun , U , Brodo , I , Bulyonkova , T , Burdsall , H H , Buyck , B , Burgaz , A R , Calatayud , V , Callac , P , Campo , E , Candusso , M , Capoen , B , Carbo , J , Carbone , M , Castaneda-Ruiz , R F , Castellano , M A , Chen , J , Clerc , P , Consiglio , G , Corriol , G , Courtecuisse , R , Crespo , A , Cripps , C , Crous , P W , da Silva , G A , da Silva , M , Dam , M , Dam , N , Dammrich , F , Das , K , Davies , L , De Crop , E , De Kesel , A , De Lange , R , Bonzi , B D M , dela Cruz , T E E , Delgat , L , Demoulin , V , Desjardin , D E , Diederich , P , Dima , B , Dios , M M , Divakar , P K , Douanla-Meli , C , Douglas , B , Drechsler-Santos , E R , Dyer , P S , Eberhardt , U , Ertz , D , Esteve-Raventos , F , Salazar , J A E , Evenson , V , Eyssartier , G , Farkas , E , Favre , A , Fedosova , A G , Filippa , M , Finy , P , Flakus , A , Fos , S , Fournier , J , Fraiture , A , Franchi , P , Molano , A E F , Friebes , G , Frisch , A , Fryday , A , Furci , G , Marquez , R G , Garbelotto , M , Garcia-Martin , J M , Otalora , M A G , Sanchez , D G , Gardiennet , A , Garnica , S , Benavent , I G , Gates , G , Gerlach , A D C L , Ghobad-Nejhad , M , Gibertoni , T B , Grebenc , T , Greilhuber , I , Grishkan , B , Groenewald , J Z , Grube , M , Gruhn , G , Gueidan , C , Gulden , G , Gusmao , L F P , Hafellner , J , Hairaud , M , Halama , M , Hallenberg , N , Halling , R E , Hansen , K , Harder , C B , Heilmann-Clausen , J , Helleman , S , Henriot , A , Hernandez-Restrepo , M , Herve , R , Hobart , C , Hoffmeister , M , Hoiland , K , Holec , J , Holien , H , Hughes , K , Hubka , V , Huhtinen , S , Ivancevic , B , Jagers , M , Jaklitsch , W , Jansen , A , Jayawardena , R S , Jeppesen , T S , Jeppson , M , Johnston , P , Jorgensen , P M , Karnefelt , I , Kalinina , L B , Kantvilas , G , Karadelev , M , Kasuya , T , Kautmanova , I , Kerrigan , R W , Kirchmair , M , Kiyashko , A , Knapp , D G , Knudsen , H , Knudsen , K , Knutsson , T , Kolarik , M , Koljalg , U , Kosuthova , A , Koszka , A , Kotiranta , H , Kotkova , V , Koukol , O , Kout , J , Kovacs , G M , Kriz , M , Kruys , A , Kudera , V , Kudzma , L , Kuhar , F , Kukwa , M , Kumar , T K A , Kunca , V , Kusan , I , Kuyper , T W , Lado , C , Laessoe , T , Laine , P , Langer , E , Larsson , E , Larsson , K-H , Laursen , G , Lechat , C , Lee , S , Lendemer , J C , Levin , L , Lindemann , U , Lindstrom , H , Liu , X , Hernandez , R C L , Llop , E , Locsmandi , C , Lodge , D J , Loizides , M , Lokos , L , Luangsa-ard , J , Luderitz , M , Lumbsch , T , Lutz , M , Mahoney , D , Malysheva , E , Malysheva , V , Manimohan , P , Mann-Felix , Y , Marques , G , Martinez-Gil , R , Marson , G , Mata , G , Matheny , P B , Mathiassen , G H , Matocec , N , Mayrhofer , H , Mehrabi , M , Melo , I , Mesic , A , Methven , A S , Miettinen , O , Romero , A M M , Miller , A N , Mitchell , J K , Moberg , R , Moreau , P-A , Moreno , G , Morozova , O , Morte , A , Muggia , L , Gonzalez , G M , Myllys , L , Nagy , I , Nagy , L G , Neves , M A , Niemela , T , Nimis , P L , Niveiro , N , Noordeloos , M E , Nordin , A , Noumeur , S R , Novozhilov , Y , Nuytinck , J , Ohenoja , E , Fiuza , P O , Orange , A , Ordynets , A , Ortiz-Santana , B , Pacheco , L , Pal-Fam , F , Palacio , M , Palice , Z , Papp , V , Partel , K , Pawlowska , J , Paz , A , Peintner , U , Pennycook , S , Pereira , O L , Daniels , P P , Capella , M A P-D-G , del Amo , C M P , Gorjon , S P , Perez-Ortega , S , Perez-Vargas , I , Perry , B A , Petersen , J H , Petersen , R H , Pfister , D H , Phukhamsakda , C , Piatek , M , Piepenbring , M , Pino-Bodas , R , Esquivel , J P P , Pirot , P , Popov , E S , Popoff , O , Alvaro , M P , Printzen , C , Psurtseva , N , Purahong , W , Quijada , L , Rambold , G , Ramirez , N A , Raja , H , Raspe , O , Raymundo , T , Reblova , M , Rebriev , Y A , Garcia , J D D R , Ripoll , M A R , Richard , F , Richardson , M J , Rico , V J , Robledo , G L , Barbosa , F R , Rodriguez-Caycedo , C , Rodriguez-Flakus , P , Ronikier , A , Casas , L R , Rusevska , K , Saar , G , Saar , I , Salcedo , I , Martinez , S M S , Montoya , C A S , Sanchez-Ramirez , S , Sandoval-Sierra , J V , Santamaria , S , Monteiro , J S , Schroers , H J , Schulz , B , Schmidt-Stohn , G , Schumacher , T , Senn-Irlet , B , Sevcikova , H , Shchepin , O , Shirouzu , T , Shiryaev , A , Siepe , K , Sir , E B , Sohrabi , M , Soop , K , Spirin , V , Spribille , T , Stadler , M , Stalpers , J , Stenroos , S , Suija , A , Sunhede , S , Svantesson , S , Svensson , S , Svetasheva , T Y , Swierkosz , K , Tamm , H , Taskin , H , Taudiere , A , Tedebrand , J-O , Lahoz , R T , Temina , M , Thell , A , Thines , M , Thor , G , Thus , H , Tibell , L , Tibell , S , Timdal , E , Tkalcec , Z , Tonsberg , T , Trichies , G , Triebel , D , Tsurykau , A , Tulloss , R E , Tuovinen , V , Sosa , M U , Urcelay , C , Valade , F , Garza , R V , van den Boom , P , Van Vooren , N , Vasco-Palacios , A M , Vauras , J , Santos , J M V , 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 , O , Westberg , M , Yurchenko , E , Zehnalek , P , Zhang , H , Zhurbenko , M P & Ekmani , S 2018 , ' Considerations and consequences of allowing DNA sequence data as types of fungal taxa ' , IMA Fungus , vol. 9 , no. 1 , pp. 167-175 . https://doi.org/10.5598/imafungus.2018.09.01.10

Title: Considerations and consequences of allowing DNA sequence data as types of fungal taxa
Author: Zamora, Juan Carlos; Svensson, Mans; Kirschner, Roland; Olariaga, Ibai; Ryman, Svengunnar; Alberto Parra, Luis; Geml, Jozsef; Rosling, Anna; Adamcik, Slavomir; Ahti, Teuvo; Aime, M. Catherine; Ainsworth, A. Martyn; Albert, Laszlo; Alberto, Edgardo; Garcia, Alberto Altes; Ageev, Dmitry; Agerer, Reinhard; Aguirre-Hudson, Begona; Ammirati, Joe; Andersson, Harry; Angelini, Claudio; Antonin, Vladimir; Aoki, Takayuki; Aptroot, Andre; Argaud, Didier; Sosa, Blanca Imelda Arguello; Aronsen, Arne; Arup, Ulf; Asgari, Bita; Assyov, Boris; Atienza, Violeta; Bandini, Ditte; Baptista-Ferreira, Joao Luis; Baral, Hans-Otto; Baroni, Tim; Barreto, Robert Weingart; Baker, Henry; Bell, Ann; Bellanger, Jean-Michel; Bellu, Francesco; Bemmann, Martin; Bendiksby, Mika; Bendiksen, Egil; Bendiksen, Katriina; Benedek, Lajos; Beresova-Guttova, Anna; Berger, Franz; Berndt, Reinhard; Bernicchia, Annarosa; Biketova, Alona Yu; Bizio, Enrico; Bjork, Curtis; Boekhout, Teun; Boertmann, David; Bohning, Tanja; Boittin, Florent; Boluda, Carlos G.; Boomsluiter, Menno W.; Borovicka, Jan; Brandrud, Tor Erik; Braun, Uwe; Brodo, Irwin; Bulyonkova, Tatiana; Burdsall, Harold H.; Buyck, Bart; Burgaz, Ana Rosa; Calatayud, Vicent; Callac, Philippe; Campo, Emanuele; Candusso, Massimo; Capoen, Brigitte; Carbo, Joaquim; Carbone, Matteo; Castaneda-Ruiz, Rafael F.; Castellano, Michael A.; Chen, Jie; Clerc, Philippe; Consiglio, Giovanni; Corriol, Gilles; Courtecuisse, Regis; Crespo, Ana; Cripps, Cathy; Crous, Pedro W.; da Silva, Gladstone Alves; da Silva, Meiriele; Dam, Marjo; Dam, Nico; Dammrich, Frank; Das, Kanad; Davies, Linda; De Crop, Eske; De Kesel, Andre; De Lange, Ruben; Bonzi, Barbara De Madrignac; dela Cruz, Thomas Edison E.; Delgat, Lynn; Demoulin, Vincent; Desjardin, Dennis E.; Diederich, Paul; Dima, Balint; Dios, Maria Martha; Divakar, Pradeep Kumar; Douanla-Meli, Clovis; Douglas, Brian; Drechsler-Santos, Elisandro Ricardo; Dyer, Paul S.; Eberhardt, Ursula; Ertz, Damien; Esteve-Raventos, Fernando; Salazar, Javier Angel Etayo; Evenson, Vera; Eyssartier, Guillaume; Farkas, Edit; Favre, Alain; Fedosova, Anna G.; Filippa, Mario; Finy, Peter; Flakus, Adam; Fos, Simon; Fournier, Jacques; Fraiture, Andre; Franchi, Paolo; Molano, Ana Esperanza Franco; Friebes, Gernot; Frisch, Andreas; Fryday, Alan; Furci, Giuliana; Marquez, Ricardo Galan; Garbelotto, Matteo; Garcia-Martin, Joaquina Maria; Otalora, Monica A. Garcia; Sanchez, Dania Garcia; Gardiennet, Alain; Garnica, Sigisfredo; Benavent, Isaac Garrido; Gates, Genevieve; Gerlach, Alice da Cruz Lima; Ghobad-Nejhad, Masoomeh; Gibertoni, Tatiana B.; Grebenc, Tine; Greilhuber, Irmgard; Grishkan, Bella; Groenewald, Johannes Z.; Grube, Martin; Gruhn, Gerald; Gueidan, Cecile; Gulden, Gro; Gusmao, Luis F. P.; Hafellner, Josef; Hairaud, Michel; Halama, Marek; Hallenberg, Nils; Halling, Roy E.; Hansen, Karen; Harder, Christoffer Bugge; Heilmann-Clausen, Jacob; Helleman, Stip; Henriot, Alain; Hernandez-Restrepo, Margarita; Herve, Raphael; Hobart, Caroline; Hoffmeister, Mascha; Hoiland, Klaus; Holec, Jan; Holien, Hakon; Hughes, Karen; Hubka, Vit; Huhtinen, Seppo; Ivancevic, Boris; Jagers, Marian; Jaklitsch, Walter; Jansen, AnnaElise; Jayawardena, Ruvishika S.; Jeppesen, Thomas Stjernegaard; Jeppson, Mikael; Johnston, Peter; Jorgensen, Per Magnus; Karnefelt, Ingvar; Kalinina, Liudmila B.; Kantvilas, Gintaras; Karadelev, Mitko; Kasuya, Taiga; Kautmanova, Ivona; Kerrigan, Richard W.; Kirchmair, Martin; Kiyashko, Anna; Knapp, Daniel G.; Knudsen, Henning; Knudsen, Kerry; Knutsson, Tommy; Kolarik, Miroslav; Koljalg, Urmas; Kosuthova, Alica; Koszka, Attila; Kotiranta, Heikki; Kotkova, Vera; Koukol, Ondrej; Kout, Jiri; Kovacs, Gabor M.; Kriz, Martin; Kruys, Asa; Kudera, Viktor; Kudzma, Linas; Kuhar, Francisco; Kukwa, Martin; Kumar, T. K. Arun; Kunca, Vladimir; Kusan, Ivana; Kuyper, Thomas W.; Lado, Carlos; Laessoe, Thomas; Laine, Patrice; Langer, Ewald; Larsson, Ellen; Larsson, Karl-Henrik; Laursen, Gary; Lechat, Christian; Lee, Serena; Lendemer, James C.; Levin, Laura; Lindemann, Uwe; Lindstrom, Hakan; Liu, Xingzhong; Hernandez, Regulo Carlos Llarena; Llop, Esteve; Locsmandi, Csaba; Lodge, Deborah Jean; Loizides, Michael; Lokos, Laszlo; Luangsa-ard, Jennifer; Luderitz, Matthias; Lumbsch, Thorsten; Lutz, Matthias; Mahoney, Dan; Malysheva, Ekaterina; Malysheva, Vera; Manimohan, Patinjareveettil; Mann-Felix, Yasmina; Marques, Guilhermina; Martinez-Gil, Ruben; Marson, Guy; Mata, Gerardo; Matheny, P. Brandon; Mathiassen, Geir Harald; Matocec, Neven; Mayrhofer, Helmut; Mehrabi, Mehdi; Melo, Ireneia; Mesic, Armin; Methven, Andrew S.; Miettinen, Otto; Romero, Ana M. Millanes; Miller, Andrew N.; Mitchell, James K.; Moberg, Roland; Moreau, Pierre-Arthur; Moreno, Gabriel; Morozova, Olga; Morte, Asuncion; Muggia, Lucia; Gonzalez, Guillermo Munoz; Myllys, Leena; Nagy, Istvan; Nagy, Laszlo G.; Neves, Maria Alice; Niemela, Tuomo; Nimis, Pier Luigi; Niveiro, Nicolas; Noordeloos, Machiel E.; Nordin, Anders; Noumeur, Sara Raouia; Novozhilov, Yuri; Nuytinck, Jorinde; Ohenoja, Esteri; Fiuza, Patricia Oliveira; Orange, Alan; Ordynets, Alexander; Ortiz-Santana, Beatriz; Pacheco, Leticia; Pal-Fam, Ferenc; Palacio, Melissa; Palice, Zdenek; Papp, Viktor; Partel, Kadri; Pawlowska, Julia; Paz, Aurelia; Peintner, Ursula; Pennycook, Shaun; Pereira, Olinto Liparini; Daniels, Pablo Perez; Capella, Miguel A. Perez-De-Gregorio; del Amo, Carlos Manuel Perez; Gorjon, Sergio Perez; Perez-Ortega, Sergio; Perez-Vargas, Israel; Perry, Brian A.; Petersen, Jens H.; Petersen, Ronald H.; Pfister, Donald H.; Phukhamsakda, Chayanard; Piatek, Marcin; Piepenbring, Meike; Pino-Bodas, Raquel; Esquivel, Juan Pablo Pinzon; Pirot, Paul; Popov, Eugene S.; Popoff, Orlando; Alvaro, Maria Prieto; Printzen, Christian; Psurtseva, Nadezhda; Purahong, Witoon; Quijada, Luis; Rambold, Gerhard; Ramirez, Natalia A.; Raja, Huzefa; Raspe, Olivier; Raymundo, Tania; Reblova, Martina; Rebriev, Yury A.; Garcia, Juan de Dios Reyes; Ripoll, Miguel Angel Ribes; Richard, Franck; Richardson, Mike J.; Rico, Victor J.; Robledo, Gerardo Lucio; Barbosa, Flavia Rodrigues; Rodriguez-Caycedo, Cristina; Rodriguez-Flakus, Pamela; Ronikier, Anna; Casas, Luis Rubio; Rusevska, Katerina; Saar, Gunter; Saar, Irja; Salcedo, Isabel; Martinez, Sergio M. Salcedo; Montoya, Carlos A. Salvador; Sanchez-Ramirez, Santiago; Sandoval-Sierra, J. Vladimir; Santamaria, Sergi; Monteiro, Josiane Santana; Schroers, Hans Josef; Schulz, Barbara; Schmidt-Stohn, Geert; Schumacher, Trond; Senn-Irlet, Beatrice; Sevcikova, Hana; Shchepin, Oleg; Shirouzu, Takashi; Shiryaev, Anton; Siepe, Klaus; Sir, Esteban B.; Sohrabi, Mohammad; Soop, Karl; Spirin, Viacheslav; Spribille, Toby; Stadler, Marc; Stalpers, Joost; Stenroos, Soili; Suija, Ave; Sunhede, Stellan; Svantesson, Sten; Svensson, Sigvard; Svetasheva, Tatyana Yu; Swierkosz, Krzysztof; Tamm, Heidi; Taskin, Hatira; Taudiere, Adrien; Tedebrand, Jan-Olof; Lahoz, Raul Tena; Temina, Marina; Thell, Arne; Thines, Marco; Thor, Goren; Thus, Holger; Tibell, Leif; Tibell, Sanja; Timdal, Einar; Tkalcec, Zdenko; Tonsberg, Tor; Trichies, Gerard; Triebel, Dagmar; Tsurykau, Andrei; Tulloss, Rodham E.; Tuovinen, Veera; Sosa, Miguel Ulloa; Urcelay, Carlos; Valade, Francois; Garza, Ricardo Valenzuela; van den Boom, Pieter; Van Vooren, Nicolas; Vasco-Palacios, Aida M.; Vauras, Jukka; Santos, Juan Manuel Velasco; Vellinga, Else; Verbeken, Annemieke; Vetlesen, Per; Vizzini, Alfredo; Voglmayr, Hermann; Volobuev, Sergey; von Brackel, Wolfgang; Voronina, Elena; Walther, Grit; Watling, Roy; Weber, Evi; Wedin, Mats; Weholt, Oyvind; Westberg, Martin; Yurchenko, Eugene; Zehnalek, Petr; Zhang, Huang; Zhurbenko, Mikhail P.; Ekmani, Stefan
Contributor: University of Helsinki, Finnish Museum of Natural History
University of Helsinki, Plant Biology
University of Helsinki, Finnish Museum of Natural History
University of Helsinki, Finnish Museum of Natural History
University of Helsinki, Botany
University of Helsinki, Botany
University of Helsinki, Finnish Museum of Natural History
Date: 2018-06
Language: eng
Number of pages: 9
Belongs to series: IMA Fungus
ISSN: 2210-6340
URI: http://hdl.handle.net/10138/258264
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.
Subject: IMC11
nomenclature
speciation
taxonomy
typification
voucherless fungi
INTERNAL TRANSCRIBED SPACER
IN-SITU HYBRIDIZATION
CY3-LABELED OLIGONUCLEOTIDE PROBES
OPERATIONAL TAXONOMIC UNITS
FRESH-WATER FUNGI
SPECIES DELIMITATION
GENE TREES
RIBOSOMAL-RNA
INTEGRATIVE TAXONOMY
POSITIVE SELECTION
1184 Genetics, developmental biology, physiology
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