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55. LASSO-based approach to sample sites for phylogenetic tree search.

Author

Ecker, Noa, Azouri, Dana, Bettisworth, Ben, Stamatakis, Alexandros, Mansour, Yishay, Mayrose, Itay, and Pupko, Tal

Subjects
COMPUTER workstation clusters, INTERNET servers, PYTHON programming language, DATABASES, TREES
Abstract

Motivation In recent years, full-genome sequences have become increasingly available and as a result many modern phylogenetic analyses are based on very long sequences, often with over 100 000 sites. Phylogenetic reconstructions of large-scale alignments are challenging for likelihood-based phylogenetic inference programs and usually require using a powerful computer cluster. Current tools for alignment trimming prior to phylogenetic analysis do not promise a significant reduction in the alignment size and are claimed to have a negative effect on the accuracy of the obtained tree. Results Here, we propose an artificial-intelligence-based approach, which provides means to select the optimal subset of sites and a formula by which one can compute the log-likelihood of the entire data based on this subset. Our approach is based on training a regularized Lasso-regression model that optimizes the log-likelihood prediction accuracy while putting a constraint on the number of sites used for the approximation. We show that computing the likelihood based on 5% of the sites already provides accurate approximation of the tree likelihood based on the entire data. Furthermore, we show that using this Lasso-based approximation during a tree search decreased running-time substantially while retaining the same tree-search performance. Availability and implementation The code was implemented in Python version 3.8 and is available through GitHub (https://github.com/noaeker/lasso%5fpositions%5fsampling). The datasets used in this paper were retrieved from Zhou et al. (2018) as described in section 3. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Published
2022
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66. A gentle Introduction to Probabilistic Evolutionary Models

Author

Pupko, Tal, Mayrose, Itay, Bibal, Christine, Scornavacca, Celine, Delsuc, Frédéric, and Galtier, Nicolas

Subjects
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN]
Abstract

A large body of research is dedicated to model sequence evolutionary dynamics. The evolutionary process may vary within groups of genes, among sites within a gene, between populations and among diverged species. Evolutionary models aiming to describe these dynamics must account for base pair substitutions as well as insertion and deletion (indel) events. Here, we explain the fundamental of continuous time Markov models used to describe sequence evolution. We begin by describing discrete Markov models, and slowly progress towards more realistic and more computationally complicated continuous time Markov models. Among other topics, we discuss nucleotide, amino acid, and codon models, among site rate variation, model reversibility, stationary distributions, rate matrix normalization, mixture models, indel models, and models of gene family evolution. Understanding the concepts presented here is vital for various phylogenom-ics analyses such as the inference of positive selection, alignment and phylogeny reconstruction, ancestral sequence reconstruction, and molecular dating.

Published
2020

67. Pepitope: epitope mapping from affinity-selected peptides

Author

Mayrose, Itay, Penn, Osnat, Erez, Elana, Rubinstein, Nimrod D., Shlomi, Tomer, Freund, Natalia Tarnovitski, Bublil, Erez M., Ruppin, Eytan, Sharan, Roded, Gershoni, Jonathan M., Martz, Eric, and Pupko, Tal

Published
2007

70. TRY plant trait database – enhanced coverage and open access

Author

Kattge, Jens, Bönisch, Gerhard, Díaz, Sandra, Lavorel, Sandra, Prentice, Iain Colin, Leadley, Paul, Tautenhahn, Susanne, Werner, Gijsbert D. A., Aakala, Tuomas, Abedi, Mehdi, Acosta, Alicia T. R., Adamidis, George C., Adamson, Kairi, Aiba, Masahiro, Albert, Cécile H., Alcántara, Julio M., Alcázar C, Carolina, Aleixo, Izabela, Ali, Hamada, Amiaud, Bernard, Ammer, Christian, Amoroso, Mariano M., Anand, Madhur, Anderson, Carolyn, Anten, Niels, Antos, Joseph, Apgaua, Deborah Mattos Guimarães, Ashman, Tia-Lynn, Asmara, Degi Harja, Asner, Gregory P., Aspinwall, Michael, Atkin, Owen, Aubin, Isabelle, Baastrup-Spohr, Lars, Bahalkeh, Khadijeh, Bahn, Michael, Baker, Timothy, Baker, William J., Bakker, Jan P., Baldocchi, Dennis, Baltzer, Jennifer, Banerjee, Arindam, Baranger, Anne, Barlow, Jos, Barneche, Diego R., Baruch, Zdravko, Bastianelli, Denis, Battles, John, Bauerle, William, Bauters, Marijn, Bazzato, Erika, Beckmann, Michael, Beeckman, Hans, Beierkuhnlein, Carl, Bekker, Renee, Belfry, Gavin, Belluau, Michael, Beloiu, Mirela, Benavides, Raquel, Benomar, Lahcen, Berdugo-Lattke, Mary Lee, Berenguer, Erika, Bergamin, Rodrigo, Bergmann, Joana, Bergmann Carlucci, Marcos, Berner, Logan, Bernhardt-Römermann, Markus, Bigler, Christof, Bjorkman, Anne D., Blackman, Chris, Blanco, Carolina, Blonder, Benjamin, Blumenthal, Dana, Bocanegra-González, Kelly T., Boeckx, Pascal, Bohlman, Stephanie, Böhning-Gaese, Katrin, Boisvert-Marsh, Laura, Bond, William, Bond-Lamberty, Ben, Boom, Arnoud, Boonman, Coline C. F., Bordin, Kauane, Boughton, Elizabeth H., Boukili, Vanessa, Bowman, David M. J. S., Bravo, Sandra, Brendel, Marco Richard, Broadley, Martin R., Brown, Kerry A., Bruelheide, Helge, Brumnich, Federico, Bruun, Hans Henrik, Bruy, David, Buchanan, Serra W., Bucher, Solveig Franziska, Buchmann, Nina, Buitenwerf, Robert, Bunker, Daniel E., Bürger, Jana, Burrascano, Sabina, Burslem, David F. R. P., Butterfield, Bradley J., Byun, Chaeho, Marques, Marcia, Scalon, Marina C., Caccianiga, Marco, Cadotte, Marc, Cailleret, Maxime, Camac, James, Camarero, Jesús Julio, Campany, Courtney, Campetella, Giandiego, Campos, Juan Antonio, Cano-Arboleda, Laura, Canullo, Roberto, Carbognani, Michele, Carvalho, Fabio, Casanoves, Fernando, Castagneyrol, Bastien, Catford, Jane A., Cavender-Bares, Jeannine, Cerabolini, Bruno E. L., Cervellini, Marco, Chacón-Madrigal, Eduardo, Chapin, Kenneth, Chapin, F. Stuart, Chelli, Stefano, Chen, Si-Chong, Chen, Anping, Cherubini, Paolo, Chianucci, Francesco, Choat, Brendan, Chung, Kyong-Sook, Chytrý, Milan, Ciccarelli, Daniela, Coll, Lluís, Collins, Courtney G., Conti, Luisa, Coomes, David, Cornelissen, Johannes H. C., Cornwell, William K., Corona, Piermaria, Coyea, Marie, Craine, Joseph, Craven, Dylan, Cromsigt, Joris P. G. M., Csecserits, Anikó, Cufar, Katarina, Cuntz, Matthias, da Silva, Ana Carolina, Dahlin, Kyla M., Dainese, Matteo, Dalke, Igor, Dalle Fratte, Michele, Dang-Le, Anh Tuan, Danihelka, Jirí, Dannoura, Masako, Dawson, Samantha, de Beer, Arend Jacobus, De Frutos, Angel, De Long, Jonathan R., Dechant, Benjamin, Delagrange, Sylvain, Delpierre, Nicolas, Derroire, Géraldine, Dias, Arildo S., Diaz-Toribio, Milton Hugo, Dimitrakopoulos, Panayiotis G., Dobrowolski, Mark, Doktor, Daniel, Dřevojan, Pavel, Dong, Ning, Dransfield, John, Dressler, Stefan, Duarte, Leandro, Ducouret, Emilie, Dullinger, Stefan, Durka, Walter, Duursma, Remko, Dymova, Olga, E-Vojtkó, Anna, Eckstein, Rolf Lutz, Ejtehadi, Hamid, Elser, James, Emilio, Thaise, Engemann, Kristine, Erfanian, Mohammad Bagher, Erfmeier, Alexandra, Esquivel-Muelbert, Adriane, Esser, Gerd, Estiarte, Marc, Domingues, Tomas F., Fagan, William F., Fagúndez, Jaime, Falster, Daniel S., Fang, Jingyun, Farris, Emmanuele, Fazlioglu, Fatih, Feng, Yanhao, Fernandez-Mendez, Fernando, Ferrara, Carlotta, Ferreira, Joice, Fidelis, Alessandra, Finegan, Bryan, Firn, Jennifer, Flowers, Timothy J., Flynn, Dan F. B., Fontana, Veronika, Forey, Estelle, Forgiarini, Cristiane, François, Louis, Frangipani, Marcelo, Frank, Dorothea, Frenette-Dussault, Cedric, Freschet, Grégoire T., Fry, Ellen L., Fyllas, Nikolaos M., Mazzochini, Guilherme G., Gachet, Sophie, Gallagher, Rachael, Ganade, Gislene, Ganga, Francesca, García-Palacios, Pablo, Gargaglione, Verónica, Garnier, Eric, Garrido, Jose Luis, de Gasper, André Luís, Gea-Izquierdo, Guillermo, Gibson, David, Gillison, Andrew N., Giroldo, Aelton, Glasenhardt, Mary-Claire, Gleason, Sean, Gliesch, Mariana, Goldberg, Emma, Göldel, Bastian, Gonzalez-Akre, Erika, Gonzalez-Andujar, Jose L., González-Melo, Andrés, González-Robles, Ana, Graae, Bente Jessen, Granda, Elena, Graves, Sarah, Green, Walton A., Gregor, Thomas, Gross, Nicolas, Guerin, Greg R., Günther, Angela, Gutiérrez, Alvaro G., Haddock, Lillie, Haines, Anna, Hall, Jefferson, Hambuckers, Alain, Han, Wenxuan, Harrison, Sandy P., Hattingh, Wesley, Hawes, Joseph E., He, Tianhua, He, Pengcheng, Heberling, Jacob Mason, Helm, Aveliina, Hempel, Stefan, Hentschel, Jörn, Hérault, Bruno, Hereş, Ana-Maria, Herz, Katharina, Heuertz, Myriam, Hickler, Thomas, Hietz, Peter, Higuchi, Pedro, Hipp, Andrew L., Hirons, Andrew, Hock, Maria, Hogan, James Aaron, Holl, Karen, Honnay, Olivier, Hornstein, Daniel, Hou, Enqing, Hough-Snee, Nate, Hovstad, Knut Anders, Ichie, Tomoaki, Igić, Boris, Illa, Estela, Isaac, Marney, Ishihara, Masae, Ivanov, Leonid, Ivanova, Larissa, Iversen, Colleen M., Izquierdo, Jordi, Jackson, Robert B., Jackson, Benjamin, Jactel, Hervé, Jagodzinski, Andrzej M., Jandt, Ute, Jansen, Steven, Jenkins, Thomas, Jentsch, Anke, Jespersen, Jens Rasmus Plantener, Jiang, Guo-Feng, Johansen, Jesper Liengaard, Johnson, David, Jokela, Eric J., Joly, Carlos Alfredo, Jordan, Gregory J., Joseph, Grant Stuart, Junaedi, Decky, Junker, Robert R., Justes, Eric, Kabzems, Richard, Kane, Jeffrey, Kaplan, Zdenek, Kattenborn, Teja, Kavelenova, Lyudmila, Kearsley, Elizabeth, Kempel, Anne, Kenzo, Tanaka, Kerkhoff, Andrew, Khalil, Mohammed I., Kinlock, Nicole L., Kissling, Wilm Daniel, Kitajima, Kaoru, Kitzberger, Thomas, Kjøller, Rasmus, Klein, Tamir, Kleyer, Michael, Klimešová, Jitka, Klipel, Joice, Kloeppel, Brian, Klotz, Stefan, Knops, Johannes M. H., Kohyama, Takashi, Koike, Fumito, Kollmann, Johannes, Komac, Benjamin, Komatsu, Kimberly, König, Christian, Kraft, Nathan J. B., Kramer, Koen, Kreft, Holger, Kühn, Ingolf, Kumarathunge, Dushan, Kuppler, Jonas, Kurokawa, Hiroko, Kurosawa, Yoko, Kuyah, Shem, Laclau, Jean-Paul, Lafleur, Benoit, Lallai, Erik, Lamb, Eric, Lamprecht, Andrea, Larkin, Daniel J., Laughlin, Daniel, Le Bagousse-Pinguet, Yoann, le Maire, Guerric, le Roux, Peter C., le Roux, Elizabeth, Lee, Tali, Lens, Frederic, Lewis, Simon L., Lhotsky, Barbara, Li, Yuanzhi, Li, Xine, Lichstein, Jeremy W., Liebergesell, Mario, Lim, Jun Ying, Lin, Yan-Shih, Linares, Juan Carlos, Liu, Chunjiang, Liu, Daijun, Liu, Udayangani, Livingstone, Stuart, Llusià, Joan, Lohbeck, Madelon, López-García, Álvaro, Lopez-Gonzalez, Gabriela, Lososová, Zdeňka, Louault, Frédérique, Lukács, Balázs A., Lukeš, Petr, Luo, Yunjian, Lussu, Michele, Ma, Siyan, Maciel Rabelo Pereira, Camilla, Mack, Michelle, Maire, Vincent, Mäkelä, Annikki, Mäkinen, Harri, Malhado, Ana Claudia Mendes, Mallik, Azim, Manning, Peter, Manzoni, Stefano, Marchetti, Zuleica, Marchino, Luca, Marcilio-Silva, Vinicius, Marcon, Eric, Marignani, Michela, Markesteijn, Lars, Martin, Adam, Martínez-Garza, Cristina, Martínez-Vilalta, Jordi, Mašková, Tereza, Mason, Kelly, Mason, Norman, Massad, Tara Joy, Masse, Jacynthe, Mayrose, Itay, McCarthy, James, McCormack, M. Luke, McCulloh, Katherine, McFadden, Ian R., McGill, Brian J., McPartland, Mara Y., Medeiros, Juliana S., Medlyn, Belinda, Meerts, Pierre, Mehrabi, Zia, Meir, Patrick, Melo, Felipe P. L., Mencuccini, Maurizio, Meredieu, Céline, Messier, Julie, Mészáros, Ilona, Metsaranta, Juha, Michaletz, Sean T., Michelaki, Chrysanthi, Migalina, Svetlana, Milla, Ruben, Miller, Jesse E. D., Minden, Vanessa, Ming, Ray, Mokany, Karel, Moles, Angela T., Molnár V, Attila, Molofsky, Jane, Molz, Martin, Montgomery, Rebecca A., Monty, Arnaud, Moravcová, Lenka, Moreno-Martínez, Alvaro, Moretti, Marco, Mori, Akira S., Mori, Shigeta, Morris, Dave, Morrison, Jane, Mucina, Ladislav, Mueller, Sandra, Muir, Christopher D., Müller, Sandra Cristina, Munoz, François, Myers-Smith, Isla H., Myster, Randall W., Nagano, Masahiro, Naidu, Shawna, Narayanan, Ayyappan, Natesan, Balachandran, Negoita, Luka, Nelson, Andrew S., Neuschulz, Eike Lena, Ni, Jian, Niedrist, Georg, Nieto, Jhon, Niinemets, Ülo, Nolan, Rachael, Nottebrock, Henning, Nouvellon, Yann, Novakovskiy, Alexander, Network, The Nutrient, Nystuen, Kristin Odden, O'Grady, Anthony, O'Hara, Kevin, O'Reilly-Nugent, Andrew, Oakley, Simon, Oberhuber, Walter, Ohtsuka, Toshiyuki, Oliveira, Ricardo, Öllerer, Kinga, Olson, Mark E., Onipchenko, Vladimir, Onoda, Yusuke, Onstein, Renske E., Ordonez, Jenny C., Osada, Noriyuki, Ostonen, Ivika, Ottaviani, Gianluigi, Otto, Sarah, Overbeck, Gerhard E., Ozinga, Wim A., Pahl, Anna T., Paine, C. E. Timothy, Pakeman, Robin J., Papageorgiou, Aristotelis C., Parfionova, Evgeniya, Pärtel, Meelis, Patacca, Marco, Paula, Susana, Paule, Juraj, Pauli, Harald, Pausas, Juli G., Peco, Begoña, Penuelas, Josep, Perea, Antonio, Peri, Pablo Luis, Petisco-Souza, Ana Carolina, Petraglia, Alessandro, Petritan, Any Mary, Phillips, Oliver L., Pierce, Simon, Pillar, Valério D., Pisek, Jan, Pomogaybin, Alexandr, Poorter, Hendrik, Portsmuth, Angelika, Poschlod, Peter, Potvin, Catherine, Pounds, Devon, Powell, A. Shafer, Power, Sally A., Prinzing, Andreas, Puglielli, Giacomo, Pyšek, Petr, Raevel, Valerie, Rammig, Anja, Ransijn, Johannes, Ray, Courtenay A., Reich, Peter B., Reichstein, Markus, Reid, Douglas E. B., Réjou-Méchain, Maxime, de Dios, Victor Resco, Ribeiro, Sabina, Richardson, Sarah, Riibak, Kersti, Rillig, Matthias C., Riviera, Fiamma, Robert, Elisabeth M. R., Roberts, Scott, Robroek, Bjorn, Roddy, Adam, Rodrigues, Arthur Vinicius, Rogers, Alistair, Rollinson, Emily, Rolo, Victor, Römermann, Christine, Ronzhina, Dina, Roscher, Christiane, Rosell, Julieta A., Rosenfield, Milena Fermina, Rossi, Christian, Roy, David B., Royer-Tardif, Samuel, Rüger, Nadja, Ruiz-Peinado, Ricardo, Rumpf, Sabine B., Rusch, Graciela M., Ryo, Masahiro, Sack, Lawren, Saldaña, Angela, Salgado-Negret, Beatriz, Salguero-Gomez, Roberto, Santa-Regina, Ignacio, Santacruz-García, Ana Carolina, Santos, Joaquim, Sardans, Jordi, Schamp, Brandon, Scherer-Lorenzen, Michael, Schleuning, Matthias, Schmid, Bernhard, Schmidt, Marco, Schmitt, Sylvain, Schneider, Julio V., Schowanek, Simon D., Schrader, Julian, Schrodt, Franziska, Schuldt, Bernhard, Schurr, Frank, Selaya Garvizu, Galia, Semchenko, Marina, Seymour, Colleen, Sfair, Julia C., Sharpe, Joanne M., Sheppard, Christine S., Sheremetiev, Serge, Shiodera, Satomi, Shipley, Bill, Shovon, Tanvir Ahmed, Siebenkäs, Alrun, Sierra, Carlos, Silva, Vasco, Silva, Mateus, Sitzia, Tommaso, Sjöman, Henrik, Slot, Martijn, Smith, Nicholas G., Sodhi, Darwin, Soltis, Pamela, Soltis, Douglas, Somers, Ben, Sonnier, Grégory, Sørensen, Mia Vedel, Sosinski Jr, Enio Egon, Soudzilovskaia, Nadejda A., Souza, Alexandre F., Spasojevic, Marko, Sperandii, Marta Gaia, Stan, Amanda B., Stegen, James, Steinbauer, Klaus, Stephan, Jörg G., Sterck, Frank, Stojanovic, Dejan B., Strydom, Tanya, Suarez, Maria Laura, Svenning, Jens-Christian, Svitková, Ivana, Svitok, Marek, Svoboda, Miroslav, Swaine, Emily, Swenson, Nathan, Tabarelli, Marcelo, Takagi, Kentaro, Tappeiner, Ulrike, Tarifa, Rubén, Tauugourdeau, Simon, Tavsanoglu, Cagatay, te Beest, Mariska, Tedersoo, Leho, Thiffault, Nelson, Thom, Dominik, Thomas, Evert, Thompson, Ken, Thornton, Peter E., Thuiller, Wilfried, Tichý, Lubomír, Tissue, David, Tjoelker, Mark G., Tng, David Yue Phin, Tobias, Joseph, Török, Péter, Tarin, Tonantzin, Torres-Ruiz, José M., Tóthmérész, Béla, Treurnicht, Martina, Trivellone, Valeria, Trolliet, Franck, Trotsiuk, Volodymyr, Tsakalos, James L., Tsiripidis, Ioannis, Tysklind, Niklas, Umehara, Toru, Usoltsev, Vladimir, Vadeboncoeur, Matthew, Vaezi, Jamil, Valladares, Fernando, Vamosi, Jana, van Bodegom, Peter M., van Breugel, Michiel, Van Cleemput, Elisa, van de Weg, Martine, van der Merwe, Stephni, van der Plas, Fons, van der Sande, Masha T., van Kleunen, Mark, Van Meerbeek, Koenraad, Vanderwel, Mark, Vanselow, Kim André, Vårhammar, Angelica, Varone, Laura, Vasquez Valderrama, Maribel Yesenia, Vassilev, Kiril, Vellend, Mark, Veneklaas, Erik J., Verbeeck, Hans, Verheyen, Kris, Vibrans, Alexander, Vieira, Ima, Villacís, Jaime, Violle, Cyrille, Vivek, Pandi, Wagner, Katrin, Waldram, Matthew, Waldron, Anthony, Walker, Anthony P., Waller, Martyn, Walther, Gabriel, Wang, Han, Wang, Feng, Wang, Weiqi, Watkins, Harry, Watkins, James, Weber, Ulrich, Weedon, James T., Wei, Liping, Weigelt, Patrick, Weiher, Evan, Wells, Aidan W., Wellstein, Camilla, Wenk, Elizabeth, Westoby, Mark, Westwood, Alana, White, Philip John, Whitten, Mark, Williams, Mathew, Winkler, Daniel E., Winter, Klaus, Womack, Chevonne, Wright, Ian J., Wright, S. Joseph, Wright, Justin, Pinho, Bruno X., Ximenes, Fabiano, Yamada, Toshihiro, Yamaji, Keiko, Yanai, Ruth, Yankov, Nikolay, Yguel, Benjamin, Zanini, Kátia Janaina, Zanne, Amy E., Zelený, David, Zhao, Yun-Peng, Zheng, Jingming, Zheng, Ji, Ziemińska, Kasia, Zirbel, Chad R., Zizka, Georg, Zo-Bi, Irié Casimir, Zotz, Gerhard, Wirth, Christian, Kattge, Jens, Bönisch, Gerhard, Díaz, Sandra, Lavorel, Sandra, Prentice, Iain Colin, Leadley, Paul, Tautenhahn, Susanne, Werner, Gijsbert D. A., Aakala, Tuomas, Abedi, Mehdi, Acosta, Alicia T. R., Adamidis, George C., Adamson, Kairi, Aiba, Masahiro, Albert, Cécile H., Alcántara, Julio M., Alcázar C, Carolina, Aleixo, Izabela, Ali, Hamada, Amiaud, Bernard, Ammer, Christian, Amoroso, Mariano M., Anand, Madhur, Anderson, Carolyn, Anten, Niels, Antos, Joseph, Apgaua, Deborah Mattos Guimarães, Ashman, Tia-Lynn, Asmara, Degi Harja, Asner, Gregory P., Aspinwall, Michael, Atkin, Owen, Aubin, Isabelle, Baastrup-Spohr, Lars, Bahalkeh, Khadijeh, Bahn, Michael, Baker, Timothy, Baker, William J., Bakker, Jan P., Baldocchi, Dennis, Baltzer, Jennifer, Banerjee, Arindam, Baranger, Anne, Barlow, Jos, Barneche, Diego R., Baruch, Zdravko, Bastianelli, Denis, Battles, John, Bauerle, William, Bauters, Marijn, Bazzato, Erika, Beckmann, Michael, Beeckman, Hans, Beierkuhnlein, Carl, Bekker, Renee, Belfry, Gavin, Belluau, Michael, Beloiu, Mirela, Benavides, Raquel, Benomar, Lahcen, Berdugo-Lattke, Mary Lee, Berenguer, Erika, Bergamin, Rodrigo, Bergmann, Joana, Bergmann Carlucci, Marcos, Berner, Logan, Bernhardt-Römermann, Markus, Bigler, Christof, Bjorkman, Anne D., Blackman, Chris, Blanco, Carolina, Blonder, Benjamin, Blumenthal, Dana, Bocanegra-González, Kelly T., Boeckx, Pascal, Bohlman, Stephanie, Böhning-Gaese, Katrin, Boisvert-Marsh, Laura, Bond, William, Bond-Lamberty, Ben, Boom, Arnoud, Boonman, Coline C. F., Bordin, Kauane, Boughton, Elizabeth H., Boukili, Vanessa, Bowman, David M. J. S., Bravo, Sandra, Brendel, Marco Richard, Broadley, Martin R., Brown, Kerry A., Bruelheide, Helge, Brumnich, Federico, Bruun, Hans Henrik, Bruy, David, Buchanan, Serra W., Bucher, Solveig Franziska, Buchmann, Nina, Buitenwerf, Robert, Bunker, Daniel E., Bürger, Jana, Burrascano, Sabina, Burslem, David F. R. P., Butterfield, Bradley J., Byun, Chaeho, Marques, Marcia, Scalon, Marina C., Caccianiga, Marco, Cadotte, Marc, Cailleret, Maxime, Camac, James, Camarero, Jesús Julio, Campany, Courtney, Campetella, Giandiego, Campos, Juan Antonio, Cano-Arboleda, Laura, Canullo, Roberto, Carbognani, Michele, Carvalho, Fabio, Casanoves, Fernando, Castagneyrol, Bastien, Catford, Jane A., Cavender-Bares, Jeannine, Cerabolini, Bruno E. L., Cervellini, Marco, Chacón-Madrigal, Eduardo, Chapin, Kenneth, Chapin, F. Stuart, Chelli, Stefano, Chen, Si-Chong, Chen, Anping, Cherubini, Paolo, Chianucci, Francesco, Choat, Brendan, Chung, Kyong-Sook, Chytrý, Milan, Ciccarelli, Daniela, Coll, Lluís, Collins, Courtney G., Conti, Luisa, Coomes, David, Cornelissen, Johannes H. C., Cornwell, William K., Corona, Piermaria, Coyea, Marie, Craine, Joseph, Craven, Dylan, Cromsigt, Joris P. G. M., Csecserits, Anikó, Cufar, Katarina, Cuntz, Matthias, da Silva, Ana Carolina, Dahlin, Kyla M., Dainese, Matteo, Dalke, Igor, Dalle Fratte, Michele, Dang-Le, Anh Tuan, Danihelka, Jirí, Dannoura, Masako, Dawson, Samantha, de Beer, Arend Jacobus, De Frutos, Angel, De Long, Jonathan R., Dechant, Benjamin, Delagrange, Sylvain, Delpierre, Nicolas, Derroire, Géraldine, Dias, Arildo S., Diaz-Toribio, Milton Hugo, Dimitrakopoulos, Panayiotis G., Dobrowolski, Mark, Doktor, Daniel, Dřevojan, Pavel, Dong, Ning, Dransfield, John, Dressler, Stefan, Duarte, Leandro, Ducouret, Emilie, Dullinger, Stefan, Durka, Walter, Duursma, Remko, Dymova, Olga, E-Vojtkó, Anna, Eckstein, Rolf Lutz, Ejtehadi, Hamid, Elser, James, Emilio, Thaise, Engemann, Kristine, Erfanian, Mohammad Bagher, Erfmeier, Alexandra, Esquivel-Muelbert, Adriane, Esser, Gerd, Estiarte, Marc, Domingues, Tomas F., Fagan, William F., Fagúndez, Jaime, Falster, Daniel S., Fang, Jingyun, Farris, Emmanuele, Fazlioglu, Fatih, Feng, Yanhao, Fernandez-Mendez, Fernando, Ferrara, Carlotta, Ferreira, Joice, Fidelis, Alessandra, Finegan, Bryan, Firn, Jennifer, Flowers, Timothy J., Flynn, Dan F. B., Fontana, Veronika, Forey, Estelle, Forgiarini, Cristiane, François, Louis, Frangipani, Marcelo, Frank, Dorothea, Frenette-Dussault, Cedric, Freschet, Grégoire T., Fry, Ellen L., Fyllas, Nikolaos M., Mazzochini, Guilherme G., Gachet, Sophie, Gallagher, Rachael, Ganade, Gislene, Ganga, Francesca, García-Palacios, Pablo, Gargaglione, Verónica, Garnier, Eric, Garrido, Jose Luis, de Gasper, André Luís, Gea-Izquierdo, Guillermo, Gibson, David, Gillison, Andrew N., Giroldo, Aelton, Glasenhardt, Mary-Claire, Gleason, Sean, Gliesch, Mariana, Goldberg, Emma, Göldel, Bastian, Gonzalez-Akre, Erika, Gonzalez-Andujar, Jose L., González-Melo, Andrés, González-Robles, Ana, Graae, Bente Jessen, Granda, Elena, Graves, Sarah, Green, Walton A., Gregor, Thomas, Gross, Nicolas, Guerin, Greg R., Günther, Angela, Gutiérrez, Alvaro G., Haddock, Lillie, Haines, Anna, Hall, Jefferson, Hambuckers, Alain, Han, Wenxuan, Harrison, Sandy P., Hattingh, Wesley, Hawes, Joseph E., He, Tianhua, He, Pengcheng, Heberling, Jacob Mason, Helm, Aveliina, Hempel, Stefan, Hentschel, Jörn, Hérault, Bruno, Hereş, Ana-Maria, Herz, Katharina, Heuertz, Myriam, Hickler, Thomas, Hietz, Peter, Higuchi, Pedro, Hipp, Andrew L., Hirons, Andrew, Hock, Maria, Hogan, James Aaron, Holl, Karen, Honnay, Olivier, Hornstein, Daniel, Hou, Enqing, Hough-Snee, Nate, Hovstad, Knut Anders, Ichie, Tomoaki, Igić, Boris, Illa, Estela, Isaac, Marney, Ishihara, Masae, Ivanov, Leonid, Ivanova, Larissa, Iversen, Colleen M., Izquierdo, Jordi, Jackson, Robert B., Jackson, Benjamin, Jactel, Hervé, Jagodzinski, Andrzej M., Jandt, Ute, Jansen, Steven, Jenkins, Thomas, Jentsch, Anke, Jespersen, Jens Rasmus Plantener, Jiang, Guo-Feng, Johansen, Jesper Liengaard, Johnson, David, Jokela, Eric J., Joly, Carlos Alfredo, Jordan, Gregory J., Joseph, Grant Stuart, Junaedi, Decky, Junker, Robert R., Justes, Eric, Kabzems, Richard, Kane, Jeffrey, Kaplan, Zdenek, Kattenborn, Teja, Kavelenova, Lyudmila, Kearsley, Elizabeth, Kempel, Anne, Kenzo, Tanaka, Kerkhoff, Andrew, Khalil, Mohammed I., Kinlock, Nicole L., Kissling, Wilm Daniel, Kitajima, Kaoru, Kitzberger, Thomas, Kjøller, Rasmus, Klein, Tamir, Kleyer, Michael, Klimešová, Jitka, Klipel, Joice, Kloeppel, Brian, Klotz, Stefan, Knops, Johannes M. H., Kohyama, Takashi, Koike, Fumito, Kollmann, Johannes, Komac, Benjamin, Komatsu, Kimberly, König, Christian, Kraft, Nathan J. B., Kramer, Koen, Kreft, Holger, Kühn, Ingolf, Kumarathunge, Dushan, Kuppler, Jonas, Kurokawa, Hiroko, Kurosawa, Yoko, Kuyah, Shem, Laclau, Jean-Paul, Lafleur, Benoit, Lallai, Erik, Lamb, Eric, Lamprecht, Andrea, Larkin, Daniel J., Laughlin, Daniel, Le Bagousse-Pinguet, Yoann, le Maire, Guerric, le Roux, Peter C., le Roux, Elizabeth, Lee, Tali, Lens, Frederic, Lewis, Simon L., Lhotsky, Barbara, Li, Yuanzhi, Li, Xine, Lichstein, Jeremy W., Liebergesell, Mario, Lim, Jun Ying, Lin, Yan-Shih, Linares, Juan Carlos, Liu, Chunjiang, Liu, Daijun, Liu, Udayangani, Livingstone, Stuart, Llusià, Joan, Lohbeck, Madelon, López-García, Álvaro, Lopez-Gonzalez, Gabriela, Lososová, Zdeňka, Louault, Frédérique, Lukács, Balázs A., Lukeš, Petr, Luo, Yunjian, Lussu, Michele, Ma, Siyan, Maciel Rabelo Pereira, Camilla, Mack, Michelle, Maire, Vincent, Mäkelä, Annikki, Mäkinen, Harri, Malhado, Ana Claudia Mendes, Mallik, Azim, Manning, Peter, Manzoni, Stefano, Marchetti, Zuleica, Marchino, Luca, Marcilio-Silva, Vinicius, Marcon, Eric, Marignani, Michela, Markesteijn, Lars, Martin, Adam, Martínez-Garza, Cristina, Martínez-Vilalta, Jordi, Mašková, Tereza, Mason, Kelly, Mason, Norman, Massad, Tara Joy, Masse, Jacynthe, Mayrose, Itay, McCarthy, James, McCormack, M. Luke, McCulloh, Katherine, McFadden, Ian R., McGill, Brian J., McPartland, Mara Y., Medeiros, Juliana S., Medlyn, Belinda, Meerts, Pierre, Mehrabi, Zia, Meir, Patrick, Melo, Felipe P. L., Mencuccini, Maurizio, Meredieu, Céline, Messier, Julie, Mészáros, Ilona, Metsaranta, Juha, Michaletz, Sean T., Michelaki, Chrysanthi, Migalina, Svetlana, Milla, Ruben, Miller, Jesse E. D., Minden, Vanessa, Ming, Ray, Mokany, Karel, Moles, Angela T., Molnár V, Attila, Molofsky, Jane, Molz, Martin, Montgomery, Rebecca A., Monty, Arnaud, Moravcová, Lenka, Moreno-Martínez, Alvaro, Moretti, Marco, Mori, Akira S., Mori, Shigeta, Morris, Dave, Morrison, Jane, Mucina, Ladislav, Mueller, Sandra, Muir, Christopher D., Müller, Sandra Cristina, Munoz, François, Myers-Smith, Isla H., Myster, Randall W., Nagano, Masahiro, Naidu, Shawna, Narayanan, Ayyappan, Natesan, Balachandran, Negoita, Luka, Nelson, Andrew S., Neuschulz, Eike Lena, Ni, Jian, Niedrist, Georg, Nieto, Jhon, Niinemets, Ülo, Nolan, Rachael, Nottebrock, Henning, Nouvellon, Yann, Novakovskiy, Alexander, Network, The Nutrient, Nystuen, Kristin Odden, O'Grady, Anthony, O'Hara, Kevin, O'Reilly-Nugent, Andrew, Oakley, Simon, Oberhuber, Walter, Ohtsuka, Toshiyuki, Oliveira, Ricardo, Öllerer, Kinga, Olson, Mark E., Onipchenko, Vladimir, Onoda, Yusuke, Onstein, Renske E., Ordonez, Jenny C., Osada, Noriyuki, Ostonen, Ivika, Ottaviani, Gianluigi, Otto, Sarah, Overbeck, Gerhard E., Ozinga, Wim A., Pahl, Anna T., Paine, C. E. Timothy, Pakeman, Robin J., Papageorgiou, Aristotelis C., Parfionova, Evgeniya, Pärtel, Meelis, Patacca, Marco, Paula, Susana, Paule, Juraj, Pauli, Harald, Pausas, Juli G., Peco, Begoña, Penuelas, Josep, Perea, Antonio, Peri, Pablo Luis, Petisco-Souza, Ana Carolina, Petraglia, Alessandro, Petritan, Any Mary, Phillips, Oliver L., Pierce, Simon, Pillar, Valério D., Pisek, Jan, Pomogaybin, Alexandr, Poorter, Hendrik, Portsmuth, Angelika, Poschlod, Peter, Potvin, Catherine, Pounds, Devon, Powell, A. Shafer, Power, Sally A., Prinzing, Andreas, Puglielli, Giacomo, Pyšek, Petr, Raevel, Valerie, Rammig, Anja, Ransijn, Johannes, Ray, Courtenay A., Reich, Peter B., Reichstein, Markus, Reid, Douglas E. B., Réjou-Méchain, Maxime, de Dios, Victor Resco, Ribeiro, Sabina, Richardson, Sarah, Riibak, Kersti, Rillig, Matthias C., Riviera, Fiamma, Robert, Elisabeth M. R., Roberts, Scott, Robroek, Bjorn, Roddy, Adam, Rodrigues, Arthur Vinicius, Rogers, Alistair, Rollinson, Emily, Rolo, Victor, Römermann, Christine, Ronzhina, Dina, Roscher, Christiane, Rosell, Julieta A., Rosenfield, Milena Fermina, Rossi, Christian, Roy, David B., Royer-Tardif, Samuel, Rüger, Nadja, Ruiz-Peinado, Ricardo, Rumpf, Sabine B., Rusch, Graciela M., Ryo, Masahiro, Sack, Lawren, Saldaña, Angela, Salgado-Negret, Beatriz, Salguero-Gomez, Roberto, Santa-Regina, Ignacio, Santacruz-García, Ana Carolina, Santos, Joaquim, Sardans, Jordi, Schamp, Brandon, Scherer-Lorenzen, Michael, Schleuning, Matthias, Schmid, Bernhard, Schmidt, Marco, Schmitt, Sylvain, Schneider, Julio V., Schowanek, Simon D., Schrader, Julian, Schrodt, Franziska, Schuldt, Bernhard, Schurr, Frank, Selaya Garvizu, Galia, Semchenko, Marina, Seymour, Colleen, Sfair, Julia C., Sharpe, Joanne M., Sheppard, Christine S., Sheremetiev, Serge, Shiodera, Satomi, Shipley, Bill, Shovon, Tanvir Ahmed, Siebenkäs, Alrun, Sierra, Carlos, Silva, Vasco, Silva, Mateus, Sitzia, Tommaso, Sjöman, Henrik, Slot, Martijn, Smith, Nicholas G., Sodhi, Darwin, Soltis, Pamela, Soltis, Douglas, Somers, Ben, Sonnier, Grégory, Sørensen, Mia Vedel, Sosinski Jr, Enio Egon, Soudzilovskaia, Nadejda A., Souza, Alexandre F., Spasojevic, Marko, Sperandii, Marta Gaia, Stan, Amanda B., Stegen, James, Steinbauer, Klaus, Stephan, Jörg G., Sterck, Frank, Stojanovic, Dejan B., Strydom, Tanya, Suarez, Maria Laura, Svenning, Jens-Christian, Svitková, Ivana, Svitok, Marek, Svoboda, Miroslav, Swaine, Emily, Swenson, Nathan, Tabarelli, Marcelo, Takagi, Kentaro, Tappeiner, Ulrike, Tarifa, Rubén, Tauugourdeau, Simon, Tavsanoglu, Cagatay, te Beest, Mariska, Tedersoo, Leho, Thiffault, Nelson, Thom, Dominik, Thomas, Evert, Thompson, Ken, Thornton, Peter E., Thuiller, Wilfried, Tichý, Lubomír, Tissue, David, Tjoelker, Mark G., Tng, David Yue Phin, Tobias, Joseph, Török, Péter, Tarin, Tonantzin, Torres-Ruiz, José M., Tóthmérész, Béla, Treurnicht, Martina, Trivellone, Valeria, Trolliet, Franck, Trotsiuk, Volodymyr, Tsakalos, James L., Tsiripidis, Ioannis, Tysklind, Niklas, Umehara, Toru, Usoltsev, Vladimir, Vadeboncoeur, Matthew, Vaezi, Jamil, Valladares, Fernando, Vamosi, Jana, van Bodegom, Peter M., van Breugel, Michiel, Van Cleemput, Elisa, van de Weg, Martine, van der Merwe, Stephni, van der Plas, Fons, van der Sande, Masha T., van Kleunen, Mark, Van Meerbeek, Koenraad, Vanderwel, Mark, Vanselow, Kim André, Vårhammar, Angelica, Varone, Laura, Vasquez Valderrama, Maribel Yesenia, Vassilev, Kiril, Vellend, Mark, Veneklaas, Erik J., Verbeeck, Hans, Verheyen, Kris, Vibrans, Alexander, Vieira, Ima, Villacís, Jaime, Violle, Cyrille, Vivek, Pandi, Wagner, Katrin, Waldram, Matthew, Waldron, Anthony, Walker, Anthony P., Waller, Martyn, Walther, Gabriel, Wang, Han, Wang, Feng, Wang, Weiqi, Watkins, Harry, Watkins, James, Weber, Ulrich, Weedon, James T., Wei, Liping, Weigelt, Patrick, Weiher, Evan, Wells, Aidan W., Wellstein, Camilla, Wenk, Elizabeth, Westoby, Mark, Westwood, Alana, White, Philip John, Whitten, Mark, Williams, Mathew, Winkler, Daniel E., Winter, Klaus, Womack, Chevonne, Wright, Ian J., Wright, S. Joseph, Wright, Justin, Pinho, Bruno X., Ximenes, Fabiano, Yamada, Toshihiro, Yamaji, Keiko, Yanai, Ruth, Yankov, Nikolay, Yguel, Benjamin, Zanini, Kátia Janaina, Zanne, Amy E., Zelený, David, Zhao, Yun-Peng, Zheng, Jingming, Zheng, Ji, Ziemińska, Kasia, Zirbel, Chad R., Zizka, Georg, Zo-Bi, Irié Casimir, Zotz, Gerhard, and Wirth, Christian

Abstract

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.

Published
2020

71. A Codon Model for Associating Phenotypic Traits with Altered Selective Patterns of Sequence Evolution

Author

Halabi, Keren, Karin, Eli Levy, Guéguen, Laurent, Mayrose, Itay, Halabi, Keren, Karin, Eli Levy, Guéguen, Laurent, and Mayrose, Itay

Abstract

Detecting the signature of selection in coding sequences and associating it with shifts in phenotypic states can unveil genes underlying complex traits. Of the various signatures of selection exhibited at the molecular level, changes in the pattern of selection at protein-coding genes have been of main interest. To this end, phylogenetic branch-site codon models are routinely applied to detect changes in selective patterns along specific branches of the phylogeny. Many of these methods rely on a prespecified partition of the phylogeny to branch categories, thus treating the course of trait evolution as fully resolved and assuming that phenotypic transitions have occurred only at speciation events. Here, we present TraitRELAX, a new phylogenetic model that alleviates these strong assumptions by explicitly accounting for the uncertainty in the evolution of both trait and coding sequences. This joint statistical framework enables the detection of changes in selection intensity upon repeated trait transitions. We evaluated the performance of TraitRELAX using simulations and then applied it to two case studies. Using TraitRELAX, we found an intensification of selection in the primate SEMG2 gene in polygynandrous species compared to species of other mating forms, as well as changes in the intensity of purifying selection operating on sixteen bacterial genes upon transitioning from a free-living to an endosymbiotic lifestyle.[Evolutionary selection; intensification; $\textbackslashgamma $-proteobacteria; genotype–phenotype; relaxation; SEMG2.]

Published
2020
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76. Probabilistic Model for Indel Evolution: Differentiating Insertions from Deletions.

Author

Loewenthal, Gil, Rapoport, Dana, Avram, Oren, Moshe, Asher, Wygoda, Elya, Itzkovitch, Alon, Israeli, Omer, Azouri, Dana, Cartwright, Reed A, Mayrose, Itay, and Pupko, Tal

Subjects
PROBABILISM, DELETION mutation, INSERTION mutation, EVOLUTIONARY models, EMPIRICAL research
Abstract

Insertions and deletions (indels) are common molecular evolutionary events. However, probabilistic models for indel evolution are under-developed due to their computational complexity. Here, we introduce several improvements to indel modeling: 1) While previous models for indel evolution assumed that the rates and length distributions of insertions and deletions are equal, here we propose a richer model that explicitly distinguishes between the two; 2) we introduce numerous summary statistics that allow approximate Bayesian computation-based parameter estimation; 3) we develop a method to correct for biases introduced by alignment programs, when inferring indel parameters from empirical data sets; and 4) using a model-selection scheme, we test whether the richer model better fits biological data compared with the simpler model. Our analyses suggest that both our inference scheme and the model-selection procedure achieve high accuracy on simulated data. We further demonstrate that our proposed richer model better fits a large number of empirical data sets and that, for the majority of these data sets, the deletion rate is higher than the insertion rate. [ABSTRACT FROM AUTHOR]

Published
2021
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80. Epitopia: a web-server for predicting B-cell epitopes

Author

Martz Eric, Mayrose Itay, Rubinstein Nimrod D, and Pupko Tal

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Detecting candidate B-cell epitopes in a protein is a basic and fundamental step in many immunological applications. Due to the impracticality of experimental approaches to systematically scan the entire protein, a computational tool that predicts the most probable epitope regions is desirable. Results The Epitopia server is a web-based tool that aims to predict immunogenic regions in either a protein three-dimensional structure or a linear sequence. Epitopia implements a machine-learning algorithm that was trained to discern antigenic features within a given protein. The Epitopia algorithm has been compared to other available epitope prediction tools and was found to have higher predictive power. A special emphasis was put on the development of a user-friendly graphical interface for displaying the results. Conclusion Epitopia is a user-friendly web-server that predicts immunogenic regions for both a protein structure and a protein sequence. Its accuracy and functionality make it a highly useful tool. Epitopia is available at http://epitopia.tau.ac.il and includes extensive explanations and example predictions.

Published
2009
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81. A Codon Model for Associating Phenotypic Traits with Altered Selective Patterns of Sequence Evolution.

Author

Halabi, Keren, Karin, Eli Levy, Guéguen, Laurent, and Mayrose, Itay

Subjects
PHENOTYPES, PHENOTYPIC plasticity, GENES, PHYLOGENETIC models, BACTERIAL genes, PHYLOGENY, GENETIC code
Abstract

Detecting the signature of selection in coding sequences and associating it with shifts in phenotypic states can unveil genes underlying complex traits. Of the various signatures of selection exhibited at the molecular level, changes in the pattern of selection at protein-coding genes have been of main interest. To this end, phylogenetic branch-site codon models are routinely applied to detect changes in selective patterns along specific branches of the phylogeny. Many of these methods rely on a prespecified partition of the phylogeny to branch categories, thus treating the course of trait evolution as fully resolved and assuming that phenotypic transitions have occurred only at speciation events. Here, we present TraitRELAX, a new phylogenetic model that alleviates these strong assumptions by explicitly accounting for the uncertainty in the evolution of both trait and coding sequences. This joint statistical framework enables the detection of changes in selection intensity upon repeated trait transitions. We evaluated the performance of TraitRELAX using simulations and then applied it to two case studies. Using TraitRELAX, we found an intensification of selection in the primate SEMG2 gene in polygynandrous species compared to species of other mating forms, as well as changes in the intensity of purifying selection operating on sixteen bacterial genes upon transitioning from a free-living to an endosymbiotic lifestyle.[Evolutionary selection; intensification; |$\gamma $| -proteobacteria; genotype–phenotype; relaxation; SEMG2.] [ABSTRACT FROM AUTHOR]

Published
2021
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83. The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches.

Author

Mayrose, Itay and Lysak, Martin A

Subjects
*CHROMOSOMES, *CHROMOSOMAL rearrangement, *CYTOTAXONOMY, *PHYLOGENETIC models
Abstract

Chromosome numbers have been widely used to describe the most fundamental genomic attribute of an organism or a lineage. Although providing strong phylogenetic signal, chromosome numbers vary remarkably among eukaryotes at all levels of taxonomic resolution. Changes in chromosome numbers regularly serve as indication of major genomic events, most notably polyploidy and dysploidy. Here, we review recent advancements in our ability to make inferences regarding historical events that led to alterations in the number of chromosomes of a lineage. We first describe the mechanistic processes underlying changes in chromosome numbers, focusing on structural chromosomal rearrangements. Then, we focus on experimental procedures, encompassing comparative cytogenomics and genomics approaches, and on computational methodologies that are based on explicit models of chromosome-number evolution. Together, these tools offer valuable predictions regarding historical events that have changed chromosome numbers and genome structures, as well as their phylogenetic and temporal placements. [ABSTRACT FROM AUTHOR]

Published
2021
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84. Phenology and polyploidy in annual Brachypodium species (Poaceae) along the aridity gradient in Israel.

Author

Penner, Shira, Dror, Barak, Aviezer, Iris, Bar‐Lev, Yamit, Salman‐Minkov, Ayelet, Mandakova, Terezie, Šmarda, Petr, Mayrose, Itay, and Sapir, Yuval

Subjects
POLYPLOIDY, BRACHYPODIUM, PHENOLOGY, DESERT plants, PLANT adaptation, GRASSES
Abstract

Local adaptation of plants along environmental gradients provides strong evidence for clinal evolution mediated by natural selection. Plants have developed diverse strategies to mitigate stress, for example, drought escape is a phenological strategy to avoid drought stress, while polyploidy was proposed as a genomic adaptation to stress. Polyploidy as an adaptation to aridity (an environmental parameter integrating temperature and precipitation) was previously documented in annual Brachypodium spp. (Poaceae) in the Western Mediterranean. Here, we examined whether polyploidy or phenology are associated with aridity in annual Brachypodium spp. along the aridity gradient in the Eastern Mediterranean. Using flow cytometry, we determined ploidy levels of plants from natural populations along the Israeli gradient, spanning ∼424 km from mesic Mediterranean to extreme desert climates. In a common garden we recorded time of seedling emergence, flowering and senescence. We tested whether the proportion of allotetraploids in the populations and phenological traits were associated with aridity. Contrary to a previous study in the Western Mediterranean, we found no effect of aridity on the proportion of allotetraploids and diploids within populations. Interestingly, phenology was associated with aridity: time of emergence was later, while flowering and senescence were earlier in desert plants. Our results indicate that in the Eastern Mediterranean, adaptation of Brachypodium to aridity is mediated mainly by phenology, rather than ploidy level. Therefore, we suggest that genome duplication is not the main driver of adaptation to environmental stress; rather, phenological change as a drought escape mechanism may be the major adaptation. [ABSTRACT FROM AUTHOR]

Published
2020
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91. Sex determination: why so many ways of doing it?

Author

Bachtrog, Doris, Mank, Judith E., Peichel, Catherine L., Kirkpatrick, Mark, Otto, Sarah P., Ashman, Tia Lynn, Hahn, Matthew W., Kitano, Jun, Mayrose, Itay, Ming, Ray, Perrin, Nicolas, Ross, Laura, Valenzuela, Nicole, Vamosi, Jana C., Blackmon, Heath, Goldberg, Emma E., and Pennell, Matthew W.

Subjects
Evolutionary Genetics, Male, Hermaphroditic Organisms, X Chromosome, Evolution of sexual reproduction, Essay, QH301-705.5, Biology, Y chromosome, Genome, General Biochemistry, Genetics and Molecular Biology, Cytogenetics, Y Chromosome, Genetics, Sex Determination Process, Animals, Humans, Biology (General), Evolutionary Biology, Evolutionary Theory, Sexual differentiation, Sex Chromosomes, General Immunology and Microbiology, Human evolutionary genetics, General Neuroscience, Biology and Life Sciences, Sex Determination Processes, Biological Evolution, Organismal Evolution, Sexual reproduction, Female, General Agricultural and Biological Sciences, human activities, Population Genetics
Abstract

Sex is universal amongst most eukaryotes, yet a remarkable diversity of sex determining mechanisms exists. We review our current understanding of how and why sex determination evolves in animals and plants., Sexual reproduction is an ancient feature of life on earth, and the familiar X and Y chromosomes in humans and other model species have led to the impression that sex determination mechanisms are old and conserved. In fact, males and females are determined by diverse mechanisms that evolve rapidly in many taxa. Yet this diversity in primary sex-determining signals is coupled with conserved molecular pathways that trigger male or female development. Conflicting selection on different parts of the genome and on the two sexes may drive many of these transitions, but few systems with rapid turnover of sex determination mechanisms have been rigorously studied. Here we survey our current understanding of how and why sex determination evolves in animals and plants and identify important gaps in our knowledge that present exciting research opportunities to characterize the evolutionary forces and molecular pathways underlying the evolution of sex determination.

Published
2014
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96. Clumpak : a program for identifying clustering modes and packaging population structure inferences across K

Author

Kopelman, Naama M., Mayzel, Jonathan, Jakobsson, Mattias, Rosenberg, Noah A., Mayrose, Itay, Kopelman, Naama M., Mayzel, Jonathan, Jakobsson, Mattias, Rosenberg, Noah A., and Mayrose, Itay

Abstract

The identification of the genetic structure of populations from multilocus genotype data has become a central component of modern population-genetic data analysis. Application of model-based clustering programs often entails a number of steps, in which the user considers different modelling assumptions, compares results across different predetermined values of the number of assumed clusters (a parameter typically denoted K), examines multiple independent runs for each fixed value of K, and distinguishes among runs belonging to substantially distinct clustering solutions. Here, we present Clumpak (Cluster Markov Packager Across K), a method that automates the postprocessing of results of model-based population structure analyses. For analysing multiple independent runs at a single K value, Clumpak identifies sets of highly similar runs, separating distinct groups of runs that represent distinct modes in the space of possible solutions. This procedure, which generates a consensus solution for each distinct mode, is performed by the use of a Markov clustering algorithm that relies on a similarity matrix between replicate runs, as computed by the software Clumpp. Next, Clumpak identifies an optimal alignment of inferred clusters across different values of K, extending a similar approach implemented for a fixed K in Clumpp and simplifying the comparison of clustering results across different K values. Clumpak incorporates additional features, such as implementations of methods for choosing K and comparing solutions obtained by different programs, models, or data subsets. Clumpak, available at , simplifies the use of model-based analyses of population structure in population genetics and molecular ecology.

Published
2015
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100. An Integrated Model of Phenotypic Trait Changes and Site-Specific Sequence Evolution.

Author

PUPKO, TAL, KARIN, ELI LEVY, MAYROSE, ITAY, and WICKE, SUSANN

Subjects
PHENOTYPES, PLANT genetics, NUCLEOTIDE sequencing, EVOLUTIONARY models, ORCHIDS, PLASTIDS
Abstract

Recent years have seen a constant rise in the availability of trait data, including morphological features, ecological preferences, and life history characteristics. These phenotypic data provide means to associate genomic regions with phenotypic attributes, thus allowing the identification of phenotypic traits associated with the rate of genome and sequence evolution. However, inference methodologies that analyze sequence and phenotypic data in a unified statistical framework are still scarce. Here, we present TraitRateProp, a probabilistic method that allows testing whether the rate of sequence evolution is associated with a binary phenotypic character trait. The method further allows the detection of specific sequence sites whose evolutionary rate is most noticeably affected following the character transition, suggesting a shift in functional/structural constraints. TraitRateProp is first evaluated in simulations and then applied to study the evolutionary process of plastid plant genomes upon a transition to a heterotrophic lifestyle. To this end,we analyze 20 plastid genes across 85 orchid species, spanning different lifestyles and representing different genera in this large family of flowering plants. Our results indicate higher evolutionary rates following repeated transitions to a heterotrophic lifestyle in all but four of the loci analyzed. [ABSTRACT FROM AUTHOR]

Published
2017
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