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

Author

Zamora, Juan, Svensson, Måns, Kirschner, Roland, Olariaga, Ibai, Ryman, Svengunnar, Parra, Luis, Geml, József, Rosling, Anna, Adamčík, Slavomír, Ahti, Teuvo, Aime, M., Ainsworth, A., Albert, László, Albertó, Edgardo, García, Alberto, Ageev, Dmitry, Agerer, Reinhard, Aguirre-Hudson, Begoña, Ammirati, Joe, Andersson, Harry, Angelini, Claudio, Antonín, Vladimír, Aoki, Takayuki, Aptroot, André, Argaud, Didier, Sosa, Blanca, Aronsen, Arne, Arup, Ulf, Asgari, Bita, Assyov, Boris, Atienza, Violeta, Bandini, Ditte, Baptista-Ferreira, João, Baral, Hans-Otto, Baroni, Tim, Barreto, Robert, Beker, Henry, Bell, Ann, Bellanger, Jean-Michel, Bellù, Francesco, Bemmann, Martin, Bendiksby, Mika, Bendiksen, Egil, Bendiksen, Katriina, Benedek, Lajos, Bérešová-Guttová, Anna, Berger, Franz, Berndt, Reinhard, Bernicchia, Annarosa, Biketova, Alona, Bizio, Enrico, Bjork, Curtis, Boekhout, Teun, Boertmann, David, Böhning, Tanja, Boittin, Florent, Boluda, Carlos, Boomsluiter, Menno, Borovička, Jan, Brandrud, Tor, Braun, Uwe, Brodo, Irwin, Bulyonkova, Tatiana, Burdsall, Harold, Buyck, Bart, Burgaz, Ana, Calatayud, Vicent, Callac, Philippe, Campo, Emanuele, Candusso, Massimo, Capoen, Brigitte, Carbó, Joaquim, Carbone, Matteo, Castañeda-Ruiz, Rafael, Castellano, Michael, Chen, Jie, Clerc, Philippe, Consiglio, Giovanni, Corriol, Gilles, Courtecuisse, Régis, Crespo, Ana, Cripps, Cathy, Crous, Pedro, da Silva, Gladstone, da Silva, Meiriele, Dam, Marjo, Dam, Nico, Dämmrich, Frank, Das, Kanad, Davies, Linda, De Crop, Eske, De Kesel, Andre, De Lange, Ruben, De Madrignac Bonzi, Bárbara, dela Cruz, Thomas, Delgat, Lynn, Demoulin, Vincent, Desjardin, Dennis, Diederich, Paul, Dima, Bálint, Dios, Maria, Divakar, Pradeep, Douanla-Meli, Clovis, Douglas, Brian, Drechsler-Santos, Elisandro, Dyer, Paul, Eberhardt, Ursula, Ertz, Damien, Esteve-Raventós, Fernando, Salazar, Javier, Evenson, Vera, Eyssartier, Guillaume, Farkas, Edit, Favre, Alain, Fedosova, Anna, Filippa, Mario, Finy, Péter, Flakus, Adam, Fos, Simón, Fournier, Jacques, Fraiture, André, Franchi, Paolo, Molano, Ana, Friebes, Gernot, Frisch, Andreas, Fryday, Alan, Furci, Giuliana, Márquez, Ricardo, Garbelotto, Matteo, García-Martín, Joaquina, Otálora, Mónica, Sánchez, Dania, Gardiennet, Alain, Garnica, Sigisfredo, Benavent, Isaac, Gates, Genevieve, da Gerlach, Alice, Ghobad-Nejhad, Masoomeh, Gibertoni, Tatiana, Grebenc, Tine, Greilhuber, Irmgard, Grishkan, Bella, Groenewald, Johannes, Grube, Martin, Gruhn, Gérald, Gueidan, Cécile, Gulden, Gro, Gusmão, Luis, Hafellner, Josef, Hairaud, Michel, Halama, Marek, Hallenberg, Nils, Halling, Roy, Hansen, Karen, Harder, Christoffer, Heilmann-Clausen, Jacob, Helleman, Stip, Henriot, Alain, Hernandez-Restrepo, Margarita, Herve, Raphaël, Hobart, Caroline, Hoffmeister, Mascha, Høiland, Klaus, Holec, Jan, Holien, Håkon, Hughes, Karen, Hubka, Vit, Huhtinen, Seppo, Ivančević, Boris, Jagers, Marian, Jaklitsch, Walter, Jansen, AnnaElise, Jayawardena, Ruvishika, Jeppesen, Thomas, Jeppson, Mikael, Johnston, Peter, Jørgensen, Per, Kärnefelt, Ingvar, Kalinina, Liudmila, Kantvilas, Gintaras, Karadelev, Mitko, Kasuya, Taiga, Kautmanová, Ivona, Kerrigan, Richard, Kirchmair, Martin, Kiyashko, Anna, Knapp, Dániel, Knudsen, Henning, Knudsen, Kerry, Knutsson, Tommy, Kolařík, Miroslav, Kõljalg, Urmas, Košuthová, Alica, Koszka, Attila, Kotiranta, Heikki, Kotkova, Vera, Koukol, Ondřej, Kout, Jiří, Kovács, Gábor, Kříž, Martin, Kruys, Åsa, Kučera, Viktor, Kudzma, Linas, Kuhar, Francisco, Kukwa, Martin, Kumar, T., Kunca, Vladimír, Kušan, Ivana, Kuyper, Thomas, Lado, Carlos, Læssøe, Thomas, Lainé, Patrice, Langer, Ewald, Larsson, Ellen, Larsson, Karl-Henrik, Laursen, Gary, Lechat, Christian, Lee, Serena, Lendemer, James, Levin, Laura, Lindemann, Uwe, Lindström, Håkan, Liu, Xingzhong, Hernandez, Regulo, Llop, Esteve, Locsmándi, Csaba, Lodge, Deborah, Loizides, Michael, Lőkös, László, Luangsa-ard, Jennifer, Lüderitz, Matthias, Lumbsch, Thorsten, Lutz, Matthias, Mahoney, Dan, Malysheva, Ekaterina, Malysheva, Vera, Manimohan, Patinjareveettil, Marin-Felix, Yasmina, Marques, Guilhermina, Martínez-Gil, Rubén, Marson, Guy, Mata, Gerardo, Matheny, P., Mathiassen, Geir, Matočec, Neven, Mayrhofer, Helmut, Mehrabi, Mehdi, Melo, Ireneia, Mešić, Armin, Methven, Andrew, Miettinen, Otto, Romero, Ana, Miller, Andrew, Mitchell, James, Moberg, Roland, Moreau, Pierre-Arthur, Moreno, Gabriel, Morozova, Olga, Morte, Asunción, Muggia, Lucia, González, Guillermo, Myllys, Leena, Nagy, István, Nagy, László, Neves, Maria, Niemelä, Tuomo, Nimis, Pier, Niveiro, Nicolas, Noordeloos, Machiel, Nordin, Anders, Noumeur, Sara, Novozhilov, Yuri, Nuytinck, Jorinde, Ohenoja, Esteri, Fiuza, Patricia, Orange, Alan, Ordynets, Alexander, Ortiz-Santana, Beatriz, Pacheco, Leticia, Pál-Fám, Ferenc, Palacio, Melissa, Palice, Zdeněk, Papp, Viktor, Pärtel, Kadri, Pawlowska, Julia, Paz, Aurelia, Peintner, Ursula, Pennycook, Shaun, Pereira, Olinto, Daniëls, Pablo, Capella, Miquel, Amo, Carlos, Gorjón, Sergio, Pérez-Ortega, Sergio, Pérez-Vargas, Israel, Perry, Brian, Petersen, Jens, Petersen, Ronald, Pfister, Donald, Phukhamsakda, Chayanard, Piątek, Marcin, Piepenbring, Meike, Pino-Bodas, Raquel, Esquivel, Juan, Pirot, Paul, Popov, Eugene, Popoff, Orlando, Álvaro, María, Printzen, Christian, Psurtseva, Nadezhda, Purahong, Witoon, Quijada, Luis, Rambold, Gerhard, Ramírez, Natalia, Raja, Huzefa, Raspé, Olivier, Raymundo, Tania, Réblová, Martina, Rebriev, Yury, García, Juan, Ripoll, Miguel, Richard, Franck, Richardson, Mike, Rico, Víctor, Robledo, Gerardo, Barbosa, Flavia, Rodriguez-Caycedo, Cristina, Rodriguez-Flakus, Pamela, Ronikier, Anna, Casas, Luis, Rusevska, Katerina, Saar, Günter, Saar, Irja, Salcedo, Isabel, Martínez, Sergio, Montoya, Carlos, Sánchez-Ramírez, Santiago, Sandoval-Sierra, J., Santamaria, Sergi, Monteiro, Josiane, Schroers, Hans, Schulz, Barbara, Schmidt-Stohn, Geert, Schumacher, Trond, Senn-Irlet, Beatrice, Ševčíková, Hana, Shchepin, Oleg, Shirouzu, Takashi, Shiryaev, Anton, Siepe, Klaus, Sir, Esteban, Sohrabi, Mohammad, Soop, Karl, Spirin, Viacheslav, Spribille, Toby, Stadler, Marc, Stalpers, Joost, Stenroos, Soili, Suija, Ave, Sunhede, Stellan, Svantesson, Sten, Svensson, Sigvard, Svetasheva, Tatyana, Świerkosz, Krzysztof, Tamm, Heidi, Taskin, Hatira, Taudière, Adrien, Tedebrand, Jan-Olof, Lahoz, Raúl, Temina, Marina, Thell, Arne, Thines, Marco, Thor, Göran, Thüs, Holger, Tibell, Leif, Tibell, Sanja, Timdal, Einar, Tkalčec, Zdenko, Tønsberg, Tor, Trichies, Gérard, Triebel, Dagmar, Tsurykau, Andrei, Tulloss, Rodham, Tuovinen, Veera, Sosa, Miguel, Urcelay, Carlos, Valade, François, Garza, Ricardo, Boom, Pieter, Van Vooren, Nicolas, Vasco-Palacios, Aida, Vauras, Jukka, Santos, Juan, 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, Øyvind, Westberg, Martin, Yurchenko, Eugene, Zehnálek, Petr, Zhang, Huang, Zhurbenko, Mikhail, and Ekman, Stefan

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 11thInternational 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.

Published
2018
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4. Six novelties to European bryosymbiotic discomycetes

Author

Huhtinen, Seppo, Laukka, Tomi, Döbbeler, Peter, and Stenroos, Soili

Abstract

Six new species of bryosymbiotic discomycetes are described from various bryophytes collected in Europe. The new discomycetous (Helotiales, Leotiomycetes) species are: Fuscolachnum necatoron Polytrichum juniperinum, Hyphodiscus delitescenson Bazzania trilobata, Microscypha cajaniensison Ptilidium pulcherrinumand Lophoziasp., Chlorociboria lamellicolaon Polytrichastrum alpinumand P. formosum, Belonioscyphella pluriseptataon Dicranum polysetum, and Pezoloma scanicumon Sphagnum squarrosum. In all, four new genera of fungi are added to those containing bryosymbiotic species.

Published
2010

5. New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes

Author

Miadlikowska, Jolanta, Kauff, Frank, Hofstetter, Valérie, Fraker, Emily, Grube, Martin, Hafellner, Josef, Reeb, Valérie, Hodkinson, Brendan P., Kukwa, Martin, Lücking, Robert, Hestmark, Geir, Otalora, Monica Garcia, Rauhut, Alexandra, Büdel, Burkhard, Scheidegger, Christoph, Timdal, Einar, Stenroos, Soili, Brodo, Irwin, Perlmutter, Gary B., Ertz, Damien, Diederich, Paul, Lendemer, James C., May, Philip, Schoch, Conrad L., Arnold, A. Elizabeth, Gueidan, Cécile, Tripp, Erin, Yahr, Rebecca, Robertson, Connie, and Lutzoni, François

Published
2006
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6. Phylogenetic relationships of Stereocaulaceae based on simultaneous analysis of beta-tubulin, GAPDH and SSU rDNA sequences

Author

Myllys, Leena, Högnabba, Filip, Lohtander, Katileena, Thell, Arne, Stenroos, Soili, and Hyvönen, Jaakko

Abstract

The phylogenetic relationships of the lichenised ascomycete family Stereocaulaceae were investigated with partial beta-tubulin, partial glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and SSU rDNA sequence data. Due to the marked length variation in the SSU rDNA sequences, the analyses were performed with direct optimization. The combined analysis of the beta-tubulin, GAPDH and SSU rDNA sequences as well as the separate analyses of beta-tubulin and GAPDH data recognized the monophyletic group comprising Lepraria, Muhriaand Stereocaulon. In the combined analysis Stereocaulon tornenseappears as a basal taxon in the Stereocaulonclade, suggesting that the crustose growth form and the absence of cephalodia are primitive features within the genus. Muhriais nested in Stereocaulonand groups with the crustose S. cumulatumand S. leucophaeopsis. The genus Leprariais monophyletic if Leprolomais included, but species that were represented by several specimens in our study, i.e., Lepraria jackiiand Leproloma membranaceum, do not appear as monophyletic entities. The genus Pilophorusis included in Cladoniaceae. Combined analysis of the three datasets clearly led to an increase in support values compared to the separate analyses, showing high support for the monophyly of families Cladoniaceae and Stereocaulaceae and for the sistergroup relation for the two families. The relationships between higher groupings did not reach high support values probably due to the incongruencies among the three datasets.

Published
2005
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7. Configuration and location of pycnidia in the lichen genus Cladonia section Perviae

Author

Stenroos, Soili

Abstract

The size, form and location of pycnidia in the genus Cladonia section Perviae has been examined. The members of the section Perviae can produce pycnidia either basally on primary squamules, terminally on podetial tips or on funnel margins. Basal pycnidia are more rare. The most common ontogenetic type in Perviae is the one with primordia born on mature podetia but some other types can also be found. The size and shape of pycnidia are rather variable but offer useful characters in some species, e. g. in C. sphacelata, which has big pycnidia or in C. santensis in which the pycnidia are more or less ovoid. Pycnidia belong to the regular ontogeny of hymenial discs in Cladonia, apparently representing spermogonia. In Perviae the pycnidial jelly which contains pycnoconidia can be either red or hyaline.

Published
1998
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