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

Author

Zamora, Juan Carlos, Svensson, Måns, 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., Jr., 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., Ekman, Stefan, Zamora, Juan Carlos, Svensson, Måns, 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., Jr., 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., 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 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.

Published
2018

3. Beyond ectomycorrhizal bipartite networks: projected networks demonstrate contrasted patterns between early- and late-successional plants in Corsica

Author

Taudiere, Adrien, Munoz, Francois, Lesne, Annick, Monnet, Anne-Christine, Bellanger, Jean-Michel, Selosse, Marc-Andre, Moreau, Pierre-Arthur, Richard, Franck, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut Français de Pondichéry (IFP), Centre National de la Recherche Scientifique (CNRS)-Ministère de l'Europe et des Affaires étrangères (MEAE), Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut de Génétique Moléculaire de Montpellier (IGMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Université de Lille, Droit et Santé, Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Ministère de l'Europe et des Affaires étrangères (MEAE)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre d’Ecologie Fonctionnelle et Evolutive ( CEFE ), Université Paul-Valéry - Montpellier 3 ( UM3 ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -École pratique des hautes études ( EPHE ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Botanique et Modélisation de l'Architecture des Plantes et des Végétations ( UMR AMAP ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ), French Institute of Pondicherry, Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Physique Théorique de la Matière Condensée ( LPTMC ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Génétique Moléculaire de Montpellier ( IGMM ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Origine, structure et évolution de la biodiversité ( OSEB ), Muséum National d'Histoire Naturelle ( MNHN ) -Centre National de la Recherche Scientifique ( CNRS ), and Département de botanique, Faculté des sciences pharmaceutiques et biologiques, Université de Lille

Subjects
[ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, [ SDV.BV.BOT ] Life Sciences [q-bio]/Vegetal Biology/Botanics, ecological mycorrhizal network, fungi, food and beverages, Plant Science, bipartite networks, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, ecological strategies, ectomycorrhiza, projected networks, Mediterranean forests, host-specificity, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; The ectomycorrhizal (ECM) symbiosis connects mutualistic plants and fungal species into bipartite networks. While links between one focal ECM plant and its fungal symbionts have been widely documented, systemic views of ECM networks are lacking, in particular, concerning the ability of fungal species to mediate indirect ecological interactions between ECM plant species (projected-ECM networks). We assembled a large dataset of plant–fungi associations at the species level and at the scale of Corsica using molecular data and unambiguously host-assigned records to: (i) examine the correlation between the number of fungal symbionts of a plant species and the average specialization of these fungal species, (ii) explore the structure of the plant–plant projected network and (iii) compare plant association patterns in regard to their position along the ecological succession. Our analysis reveals no trade-off between specialization of plants and specialization of their partners and a saturation of the plant projected network. Moreover, there is a significantly lower-than-expected sharing of partners between early- and late-successional plant species, with fewer fungal partners for early-successional ones and similar average specialization of symbionts of early- and late-successional plants. Our work paves the way for ecological readings of Mediterranean landscapes that include the astonishing diversity of below-ground interactions.

Published
2015

4. A global meta-analysis of the relative extent of intraspecific trait variation in plant communities

Author

Siefert, Andrew, Violle, Cyrille, Chalmandrier, Loic, Albert, Cecile H., Taudiere, Adrien, Fajardo, Alex, Aarssen, Lonnie W., Baraloto, Christopher, Carlucci, Marcos B., Cianciaruso, Marcus V., Dantas, Vinicius de L., de Bello, Francesco, Duarte, Leandro D. S., Fonseca, Carlos R., Freschet, Gregoire T., Gaucherand, Stephanie, Gross, Nicolas, Hikosaka, Kouki, Jackson, Benjamin, Jung, Vincent, Kamiyama, Chiho, Katabuchi, Masatoshi, Kembel, Steven W., Kichenin, Emilie, Kraft, Nathan J. B., Lagerstrom, Anna, Le Bagousse-Pinguet, Yoann, Li, Yuanzhi, Mason, Norman, Messier, Julie, Nakashizuka, Tohru, McC Overton, Jacob, Peltzer, Duane A., Perez-Ramos, I. M., Pillar, Valerio D., Prentice, Honor C., Richardson, Sarah, Sasaki, Takehiro, Schamp, Brandon S., Schoeb, Christian, Shipley, Bill, Sundqvist, Maja, Sykes, Martin T., Vandewalle, Marie, Wardle, David A., Siefert, Andrew, Violle, Cyrille, Chalmandrier, Loic, Albert, Cecile H., Taudiere, Adrien, Fajardo, Alex, Aarssen, Lonnie W., Baraloto, Christopher, Carlucci, Marcos B., Cianciaruso, Marcus V., Dantas, Vinicius de L., de Bello, Francesco, Duarte, Leandro D. S., Fonseca, Carlos R., Freschet, Gregoire T., Gaucherand, Stephanie, Gross, Nicolas, Hikosaka, Kouki, Jackson, Benjamin, Jung, Vincent, Kamiyama, Chiho, Katabuchi, Masatoshi, Kembel, Steven W., Kichenin, Emilie, Kraft, Nathan J. B., Lagerstrom, Anna, Le Bagousse-Pinguet, Yoann, Li, Yuanzhi, Mason, Norman, Messier, Julie, Nakashizuka, Tohru, McC Overton, Jacob, Peltzer, Duane A., Perez-Ramos, I. M., Pillar, Valerio D., Prentice, Honor C., Richardson, Sarah, Sasaki, Takehiro, Schamp, Brandon S., Schoeb, Christian, Shipley, Bill, Sundqvist, Maja, Sykes, Martin T., Vandewalle, Marie, and Wardle, David A.

Abstract

Recent studies have shown that accounting for intraspecific trait variation (ITV) may better address major questions in community ecology. However, a general picture of the relative extent of ITV compared to interspecific trait variation in plant communities is still missing. Here, we conducted a meta-analysis of the relative extent of ITV within and among plant communities worldwide, using a data set encompassing 629 communities (plots) and 36 functional traits. Overall, ITV accounted for 25% of the total trait variation within communities and 32% of the total trait variation among communities on average. The relative extent of ITV tended to be greater for whole-plant (e.g. plant height) vs. organ-level traits and for leaf chemical (e.g. leaf N and P concentration) vs. leaf morphological (e.g. leaf area and thickness) traits. The relative amount of ITV decreased with increasing species richness and spatial extent, but did not vary with plant growth form or climate. These results highlight global patterns in the relative importance of ITV in plant communities, providing practical guidelines for when researchers should include ITV in trait-based community and ecosystem studies.

Published
2015
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5. A global meta‐analysis of the relative extent of intraspecific trait variation in plant communities

Author

Siefert, Andrew, primary, Violle, Cyrille, additional, Chalmandrier, Loïc, additional, Albert, Cécile H., additional, Taudiere, Adrien, additional, Fajardo, Alex, additional, Aarssen, Lonnie W., additional, Baraloto, Christopher, additional, Carlucci, Marcos B., additional, Cianciaruso, Marcus V., additional, L. Dantas, Vinícius, additional, Bello, Francesco, additional, Duarte, Leandro D. S., additional, Fonseca, Carlos R., additional, Freschet, Grégoire T., additional, Gaucherand, Stéphanie, additional, Gross, Nicolas, additional, Hikosaka, Kouki, additional, Jackson, Benjamin, additional, Jung, Vincent, additional, Kamiyama, Chiho, additional, Katabuchi, Masatoshi, additional, Kembel, Steven W., additional, Kichenin, Emilie, additional, Kraft, Nathan J. B., additional, Lagerström, Anna, additional, Bagousse‐Pinguet, Yoann Le, additional, Li, Yuanzhi, additional, Mason, Norman, additional, Messier, Julie, additional, Nakashizuka, Tohru, additional, Overton, Jacob McC., additional, Peltzer, Duane A., additional, Pérez‐Ramos, I. M., additional, Pillar, Valério D., additional, Prentice, Honor C., additional, Richardson, Sarah, additional, Sasaki, Takehiro, additional, Schamp, Brandon S., additional, Schöb, Christian, additional, Shipley, Bill, additional, Sundqvist, Maja, additional, Sykes, Martin T., additional, Vandewalle, Marie, additional, and Wardle, David A., additional

Published
2015
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8. cati: an R package using functional traits to detect and quantify multi-level community assembly processes.

Author

Taudiere, Adrien and Violle, Cyrille

Subjects
*BIOTIC communities, *SPECIES diversity, *ECOLOGISTS, *PLANT phylogeny, *NULL models (Ecology), *COMPETITION (Biology)
Abstract

Community ecologists are active in describing species by their functional traits, quantifying the functional structure of plant and animal assemblages and inferring community assembly processes with null-model analyses of trait distribution and functional diversity indices. Intraspecific variation in traits and effects of spatial scale are potentially important in these analyses. Here, we introduce the R package cati (Community Assembly by Traits: Individuals and beyond) available on CRAN, for the analysis of community assembly with functional traits. cati builds on a recent approach to community assembly that explicitly incorporates individual differences in community assembly analyses and decomposes phenotypic variations across scales and organizational levels, based on three phenotypic variance ratios, termed the T-statistics. More generally, the cati package 1) calculates a variety of single-trait and multi-trait indices from interspecific and intraspecific trait measures; 2) it partitions functional trait variation among spatial and taxonomic levels; 3) it implements a palette of flexible null models for detecting non-random patterns of functional traits. These patterns can be used to draw inferences about hypotheses of community assembly such as environmental filtering and species interactions. The basic input for cati is a data frame in which columns are traits, rows are species or individuals, and entries are the measured trait values. The cati package can also incorporate a square distance matrix into analyses, which could include phylogenetic or genetic distances among individuals or species. Users select from a variety of functional trait metrics and analyze these relative to a null model that specifies trait distributions in a regional source pool. [ABSTRACT FROM AUTHOR]

Published
2016
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9. Drivers of fungal community composition in Corsican forests : role of perturbations and vegetation composition

Author

Adrien Taudière, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), École pratique des hautes études (EPHE), École pratique des hautes études - EPHE PARIS, Christopher Carcaillet, Franck Richard, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Conservatoire Botanique National de Corse & Pres Hésam, EPHE, Taudiere, Adrien, STAR, ABES, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
canopy gaps, Decomposition, Champignons, Ecology, Pinus nigra subsp. laricio, Décomposition, Écologie des communautés, Fungi, Windfall, Forestry, [SDV.EE.IEO] Life Sciences [q-bio]/Ecology, environment/Symbiosis, [SDV.MP.MYC] Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Mycorhizes, régime de feu, Mixed forest, Forêt mixte, Chablis, fire regime, Community ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Mycorrhiza, Ecology, Evolution, Behavior and Systematics, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Study of micro-organisms ecology arose recently despite its intrinsic importance -- both practical and theoretical --, but also despite its overriding role in the niches of macro-organisms. Plant-fungi interactions offer a relevant model to study the ecology of micro-organisms interacting with macro-organisms because of their considerable ecological and economical values in addition to their high taxonomic and ecological diversity. Using next-generation sequencing (NGS) and network analysis, we explore some drivers of fungal community composition in Corsica, at various scales and through three guilds: ectomycorrhizal, endophytic and saprotrophic fungi. We investigate the effect of disturbance (e.g. fire and treefall), environmental variables (e.g. soil depth), constraints due to the interacting plants (e.g. taxonomy) and dispersion on fungal communities. Some community assembly rules are similar across guilds. For instance, forests in different micro-regions of Corsica harbor dissimilar fungal communities. However relative importance of processes and the scales at which they occur vary across guilds. In Corsican pine forests, fifteen years after fire occurrence, soil fungal diversity is close to the level of diversity in unburnt stand. Despite the absence of effect on diversity, fire induces marked shifts in soil fungal community composition, in particular for soil saprobic fungi. We discuss the implication of this work for ecologists -- both plant and fungal ecologist -- and stakeholders., L'étude de l'écologie des micro-organismes est récente malgré son importance pratique et théorique intrinsèque mais également son rôle central dans la niche des macro-organismes. Les interactions plantes-champignons, de par leur importance socio-écologique et de leur diversité -- du mutualisme au parasitisme en passant par le commensalisme --, offrent un modèle judicieux pour étudier l'écologie des communautés de micro-organismes en interaction avec des macro-organismes. À l'aide de techniques de séquençage à haut débit (NGS) et d'analyse des réseaux, nous explorons certains déterminants de la structure des champignons des forêts corses à travers trois guildes : les champignons ectomycorhiziens, endophytiques et saprotrophes. Ce travail considère les processus de dispersion, les perturbations (feux et chablis), les facteurs environnementaux (par ex. la profondeur du sol) et les contraintes dérivées de l'interaction avec les hôtes (par ex. taxinomie). Les assemblages des communautés des différentes guildes présentent des patrons communs qui pourraient être issus de mécanismes identiques. Ainsi, l'ensemble des guildes étudiées présentent des variations fortes à l’échelle des micro-régions de Corse et entre forêts ayant des histoires de feux différentes. En revanche, l'importance des différents processus d'assemblage et les échelles spatiales auxquelles ils s'appliquent varient selon les guildes. Nous discutons des implications que suscitent ce travail pour les écologues des communautés et pour les gestionnaires d'espaces naturels.

Published
2016

10. Beyond ectomycorrhizal bipartite networks: projected networks demonstrate contrasted patterns between early- and late-successional plants in Corsica.

Author

Taudiere A, Munoz F, Lesne A, Monnet AC, Bellanger JM, Selosse MA, Moreau PA, and Richard F

Abstract

The ectomycorrhizal (ECM) symbiosis connects mutualistic plants and fungal species into bipartite networks. While links between one focal ECM plant and its fungal symbionts have been widely documented, systemic views of ECM networks are lacking, in particular, concerning the ability of fungal species to mediate indirect ecological interactions between ECM plant species (projected-ECM networks). We assembled a large dataset of plant-fungi associations at the species level and at the scale of Corsica using molecular data and unambiguously host-assigned records to: (i) examine the correlation between the number of fungal symbionts of a plant species and the average specialization of these fungal species, (ii) explore the structure of the plant-plant projected network and (iii) compare plant association patterns in regard to their position along the ecological succession. Our analysis reveals no trade-off between specialization of plants and specialization of their partners and a saturation of the plant projected network. Moreover, there is a significantly lower-than-expected sharing of partners between early- and late-successional plant species, with fewer fungal partners for early-successional ones and similar average specialization of symbionts of early- and late-successional plants. Our work paves the way for ecological readings of Mediterranean landscapes that include the astonishing diversity of below-ground interactions.

Published
2015
Full Text
View/download PDF

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