Author: "Department of Integrative Biology" - Searchworks@Jio Institute Digital Library Search Results

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12,090 results on '"Department of Integrative Biology"'

1. The evolutionary loss and regain of lipid synthesis

Author: UCL - SST/ELI/ELIB - Biodiversity, Visser, Bertanne, Department of Integrative Biology, University of California, UCL - SST/ELI/ELIB - Biodiversity, Visser, Bertanne, and Department of Integrative Biology, University of California
Published: 2017

2. Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments

Author: UCL - SST/ELI/ELIM - Applied Microbiology, Berg, Maureen, Stenuit, Benoît, Ho, Joshua, Wang, Andrew, Parke, Caitlin, Knight, Matthew, Alvarez-Cohen, Lisa, Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA, UCL - SST/ELI/ELIM - Applied Microbiology, Berg, Maureen, Stenuit, Benoît, Ho, Joshua, Wang, Andrew, Parke, Caitlin, Knight, Matthew, Alvarez-Cohen, Lisa, and Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
Abstract: It is now well accepted that the gut microbiota contributes to our health. However, what determines the microbiota composition is still unclear. Whereas it might be expected that the intestinal niche would be dominant in shaping the microbiota, studies in vertebrates have repeatedly demonstrated dominant effects of external factors such as host diet and environmental microbial diversity. Hypothesizing that genetic variation may interfere with discerning contributions of host factors, we turned to Caenorhabditis elegans as a new model, offering the ability to work with genetically homogenous populations. Deep sequencing of 16S rDNA was used to characterize the (previously unknown) worm gut microbiota as assembled from diverse produce-enriched soil environments under laboratory conditions. Comparisons of worm microbiotas with those in their soil environment revealed that worm microbiotas resembled each other even when assembled from different microbial environments, and enabled defining a shared core gut microbiota. Community analyses indicated that species assortment in the worm gut was non-random and that assembly rules differed from those in their soil habitat, pointing at the importance of competitive interactions between gut-residing taxa. The data presented fills a gap in C. elegans biology. Furthermore, our results demonstrate a dominant contribution of the host niche in shaping the gut microbiota.
Published: 2016

3. RHex: A Biologically Inspired Hexapod Runner

Author: Artificial Intelligence Laboratory, University of Michigan, Ann Arbor, MI, 48109, USA, Ambulatory Robotics Laboratory, Department of Mechanical Engineering, McGill University, Montr??al, Qu??bec, Canada, H2A 2A7, The Robotics Institute, Carnegie Mellon University, Pittsburgh, PA, 15213, USA, Department of Integrative Biology, University of California at Berkeley, Berkeley, CA, 94720, USA, Ann Arbor, Altendorfer, R., Moore, N., Komsuoglu, H., Buehler, M., Brown, H.B., McMordie, D., Saranli, U., Full, R., Koditschek, D.E., Artificial Intelligence Laboratory, University of Michigan, Ann Arbor, MI, 48109, USA, Ambulatory Robotics Laboratory, Department of Mechanical Engineering, McGill University, Montr??al, Qu??bec, Canada, H2A 2A7, The Robotics Institute, Carnegie Mellon University, Pittsburgh, PA, 15213, USA, Department of Integrative Biology, University of California at Berkeley, Berkeley, CA, 94720, USA, Ann Arbor, Altendorfer, R., Moore, N., Komsuoglu, H., Buehler, M., Brown, H.B., McMordie, D., Saranli, U., Full, R., and Koditschek, D.E.
Abstract: RHex is an untethered, compliant leg hexapod robot that travels at better than one body length per second over terrain few other robots can negotiate at all. Inspired by biomechanics insights into arthropod locomotion, RHex uses a clock excited alternating tripod gait to walk and run in a highly maneuverable and robust manner. We present empirical data establishing that RHex exhibits a dynamical (???bouncing???) gait???its mass center moves in a manner well approximated by trajectories from a Spring Loaded Inverted Pendulum (SLIP)???characteristic of a large and diverse group of running animals, when its central clock, body mass, and leg stiffnesses are appropriately tuned. The SLIP template can function as a useful control guide in developing more complex autonomous locomotion behaviors such as registration via visual servoing, local exploration via visual odometry, obstacle avoidance, and, eventually, global mapping and localization.
Published: 2006

4. Black Bears of Utah's East Tavaputs Plateau

Author: Utah. Division of Wildlife Resources, Brigham Young University. Department of Integrative Biology, Black, Hal L., Auger, Janene, Utah. Division of Wildlife Resources, Brigham Young University. Department of Integrative Biology, Black, Hal L., and Auger, Janene
Abstract: In 1985 the Utah Division of Wildlife Resources (UDWR) began a study of black bears (Ursus americanus) in central Utah largely centered in the drainages of Hobble Creek and Diamond Fork along the Wasatch Front (Bates 1991). A short-term study was also conducted in the La Sal Mountains of southeastern Utah between 1987 and 1991 (Richardson 1991, Frost 1990, Ogborn 1990). In 1991 the UDWR, under the direction of Mammal Coordinator Dr. Jordan Pederson, proposed that a long-term study be conducted in a black bear hunting unit that was distant from urban settings and in a large expanse of contiguous habitat. Additionally this new study site was to be in a hunting unit with a history of high hunter success. The most remote hunting unit that fit these criteria was the East Tavaputs Plateau (Plateau), 70–80 miles (112–128 km) from the towns of Roosevelt and Vernal in Utah and Grand Junction in Colorado. The Plateau continues into Colorado on the east and is bordered to the west by Desolation Canyon through which the Green River flows. The Plateau, while remote from urban areas, isnone-the-less frequented by sportsmen hunting deer, elk, mountain lions, and black bears. Additionally, cattle operations use the high-elevation summer ranges and low-elevation winter ranges to the north and south of the Plateau. Natural gas fields and the numerous secondary roads that provide access to well-heads are almost daily traveled by personnel from various companies. Thus, anthropogenic activities on the Plateau are common but unlike those seen in the Wasatch Front study site located near the highly populated Utah Valley and the La Sal study site adjacent to Moab, Utah. Accordingly the Plateau was selected as the most remote, large area of contiguous bear habitat free of extensive human activity. Here we initiated a long-term study designed to determine population characteristics of black bears with special emphasis on the productivity of breeding-age females. It was unofficially agreed th
Published: 2004

5. Discovery of the first Asian plethodontid salamander.

Author: Conservation Genome Resource Bank for Korean Wildlife, and Brain Korea 21, School of Agricultural Biotechnology, Seoul National University, Seoul 151-742, South Korea., Department of Biology, Inha University, Incheon 402-751, South Korea., Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California 94720, USA., Department of Zoology, Southern Illinois University, Carbondale, Illinois 62901, USA., Min, M. S., Yang, S. Y., Bonett, R. M., Vieites, D. R., Brandon, R. A., and Wake, D. B.
Subjects: SALAMANDERS, AMPHIBIANS, EXTREMITIES (Anatomy), AMPHIUMIDAE, AMBYSTOMATIDAE, CRYPTOBRANCHIDAE
Abstract: Nearly 70% of the 535 species of salamanders in the world are members of a single family, the Plethodontidae, or lungless salamanders. The centre of diversity for this clade is North and Middle America, where the vast majority (99%) of species are found. We report the discovery of the first Asian plethodontid salamander, from montane woodlands in southwestern Korea. The new species superficially resembles members of North American genera, in particular the morphologically conservative genus Plethodon. However, phylogenetic analysis of the nuclear encoded gene Rag-1 shows the new taxon to be widely divergent from Plethodon. The new salamander differs osteologically from putative relatives, especially with respect to the tongue (attached protrusible) and the derived tarsus. We place the species in a new genus on the basis of the morphological and molecular data. The distribution of the new salamander adds to the enigma of Old World plethodontids, which are otherwise restricted to the western Mediterranean region, suggesting a more extensive past distribution of the family. [ABSTRACT FROM AUTHOR]
Published: 2005
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6. Phylogenetic Relationships of the Liverworts (Hepaticae), a Basal Embryophyte Lineage, Inferred from Nucleotide Sequence Data of the Chloroplast GenerbcL

Author: Lewis, Louise A., Mishler, Brent D., and Vilgalys, Rytas
Published: 1997
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7. Microsatellite Behavior with Range Constraints: Parameter Estimation and Improved Distances for Use in Phylogenetic Reconstruction

Author: Pollock, David D., Bergman, Aviv, Feldman, Marcus W., and Goldstein, David B.
Published: 1998
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8. Increased Accuracy in Analytical Molecular Distance Estimation

Author: Pollock, David D
Published: 1998
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9. Rarity of monodominance in hyperdiverse Amazonian forests

Author: ter Steege, Hans, Henkel, Terry, Helal, Nora, Marimon, Beatriz, Hur Marimon-Junior, Ben, Huth, Andreas, Groeneveld, Jürgen, Sabatier, Daniel, de Souza Coelho, Luiz, De, Diogenes, Lima Filho, Andrade, Salomão, Rafael, Amaral, Leão, Dionízia, Francisca, Matos, Almeida, Castilho, Carolina, Phillips 12, Oliver, Guevara, Juan, De, Marcelo, Veiga, Jesus, 15, Carim, Cárdenas López, Dairon, Magnusson, William, Wittmann, Florian, Victória Irume, Mariana, Pires Martins, Maria, da Silva Guimarães, José Renan, Guimarães, Silva, Molino, Jean-François, Banki, Olaf, Teresa Fernandez Piedade, Maria, Pitman, Nigel, Mendoza, Abel, Ferreira Ramos, José, Luize, Bruno, Márcia, Evlyn, de Leão Novo, Moraes, Sanna, Thiago, Silva, Freire, Martins Venticinque, Eduardo, Manzatto, Angelo, Farias, Neidiane, Reis, Costa, Terborgh, John, Regina Casula, Katia, Honorio Coronado, Euridice, Montero, Juan, Feldpausch, Ted, Duque, Alvaro, Costa, Flávia, Castaño Arboleda, Nicolás, Schöngart, Jochen, Killeen, Timothy, Vasquez, Rodolfo, Mostacedo, Bonifacio, Demarchi, Layon, Assis, Rafael, Baraloto, Chris, Engel, Julien, Petronelli, Pascal, Castellanos 42, Hernán, Brilhante de Medeiros, Marcelo, Quaresma, Adriano, Fragomeni Simon, Marcelo, Andrade, Ana, 44, Camargo, Laurance, Susan, Laurance, William, Rincón, Lorena, Schietti, Juliana, Sousa, Thaiane, De, Emanuelle, Farias, Sousa, Lopes, Maria, Leonardo, José, Magalhães, Lima, Mendonça Nascimento, Henrique, Lima de Queiroz, Helder, Aymard, Gerardo, 51, C, Brienen, Roel, David, Juan, Revilla, Cardenas, Célia, Ima, Vieira, Guimarães, Barçante, Bruno, Cintra, Ladvocat, Stevenson, Pablo, Oliveira Feitosa 53, Yuri, Duivenvoorden, Joost, Mogollón, Hugo, Araujo-Murakami, Alejandro, Valle Ferreira 10, Leandro, Lozada, José, Comiskey, James, Julio de Toledo, José, Damasco, Gabriel, Dávila, Nallarett, Draper, Freddie, Garcia-Villacorta, Roosevelt, Lopes, Aline, Vicentini, Alberto, Alonso, Alfonso, Dallmeier, Francisco, Gomes, Vitor, Lloyd, Jon, Neill, David, Praia, Daniel, de Aguiar, Portela, Arroyo, Luzmila, Antunes Carvalho, Fernanda, Coelho de Souza, Fernanda, Dantas Do Amaral, Dário, Feeley, Kenneth, Gribel, Rogério, Petratti Pansonato, Marcelo, Barlow, Jos, Berenguer, Erika, Ferreira, Joice, Fine 61, Paul, Guedes, Marcelino, Jimenez, Eliana, Licona, Juan, Cristina, Maria, Mora, Peñuela, Villa, Boris, Cerón, Carlos, Maas, Paul, Silveira, Marcos, Stropp, Juliana, Thomas 84, Raquel, Baker, Tim, Daly, Doug, Dexter, Kyle, Huamantupa-Chuquimaco, Isau, Milliken, William, Pennington, Toby, Paredes, Marcos, Fuentes, Alfredo, Klitgaard, Bente, Pena, Marcelo, Peres 93, Carlos, Silman, Miles, Sebastián Tello 90, J, Chave, Jérôme, Cornejo Valverde, Fernando, Di Fiore 97, Anthony, Hilário, Renato, Fernando Phillips 98, Juan, Rivas-Torres, Gonzalo, van Andel, Tinde, von Hildebrand, Patricio, Noronha, Janaína, Marques Barbosa, Edelcilio, Rodrigues Barbosa, Flávia, Carlos de Matos Bonates, Luiz, de Sá Carpanedo 102, Rainiellen, Paulette, Hilda, Doza, Dávila, Fonty, Emile, Gómezárate Z 104, Ricardo, Gonzales, Therany, Pepe, George, Gonzales, Gallardo, Hoffman, Bruce, Junqueira, André, Malhi, Yadvinder, Paula de Andrade Miranda, Ires, Linder, Felipe, Mozombite Pinto 88, Adriana, De, Domingos, Rodrigues, Jesus, Rudas, Agustin, Ruschel, Ademir, Marimon-Junior, Ben Hur, Coelho, Luiz de Souza, Filho, Diogenes de Andrade Lima, Amaral, Iêda Leão, Matos, Francisca Dionízia de Almeida, Phillips, Oliver, Guevara, Juan Ernesto, Carim, Marcelo de Jesus Veiga, Irume, Mariana Victória, Martins, Maria Pires, Guimarães, José Renan da Silva, Piedade, Maria Teresa Fernandez, Mendoza, Abel Monteagudo, Ramos, José Ferreira, Luize, Bruno Garcia, Moraes de Leão Novo, Evlyn Márcia, Nunez Vargas, Percy, Silva, Thiago Sanna Freire, Venticinque, Eduardo Martins, Manzatto, Angelo Gilberto, Reis, Neidiane Farias Costa, Casula, Katia Regina, Montero, Juan Carlos, Arboleda, Nicolás Castaño, Castellanos, Hernán, de Medeiros, Marcelo Brilhante, Simon, Marcelo Fragomeni, Camargo, José Luís, de Sousa Farias, Emanuelle, Lopes, Maria Aparecida, Magalhães, José Leonardo Lima, Mendonça Nascimento, Henrique Eduardo, Aymard C., Gerardo, Revilla, Juan David Cardenas, Vieira, Ima Célia Guimarães, Cintra, Bruno Barçante Ladvocat, Feitosa, Yuri Oliveira, Ferreira, Leandro Valle, Lozada, José Rafael, de Toledo, José Julio, de Aguiar, Daniel Praia Portela, Carvalho, Fernanda Antunes, de Souza, Fernanda Coelho, Do Amaral, Dário Dantas, Pansonato, Marcelo Petratti, Fine, Paul, Guedes, Marcelino Carneiro, Licona, Juan Carlos, Peñuela Mora, Maria Cristina, Thomas, Raquel, Ríos Paredes, Marcos, Pena, José Luis Marcelo, Peres, Carlos, Tello, J. Sebastián, Di Fiore, Anthony, Hilário, Renato Richard, Phillips, Juan Fernando, Noronha, Janaína Costa, Barbosa, Edelcilio Marques, Barbosa, Flávia Rodrigues, de Matos Bonates, Luiz Carlos, Carpanedo, Rainiellen de Sá, Dávila Doza, Hilda Paulette, Gómezárate Z, Ricardo, Gallardo Gonzales, George Pepe, Junqueira, André Braga, Miranda, Ires Paula de Andrade, Pinto, Linder Felipe Mozombite, Prieto, Adriana, Rodrigues, Domingos de Jesus, Silva, Natalino, Vela, César, Vos, Vincent Antoine, Zent, Egleé, Zent, Stanford, Weiss Albuquerque, Bianca, Cano, Angela, Carrero Márquez, Yrma Andreina, Correa, Diego, Costa, Janaina Barbosa Pedrosa, Flores, Bernardo Monteiro, Galbraith, David, Holmgren, Milena, Kalamandeen, Michelle, Nascimento, Marcelo Trindade, Oliveira, Alexandre, Ramirez-Angulo, Hirma, Rocha, Maira, Scudeller, Veridiana Vizoni, Sierra, Rodrigo, Tirado, Milton, Umaña Medina, Maria Natalia, van Der Heijden, Geertje, Vilanova Torre, Emilio, Vriesendorp, Corine, Wang, Ophelia, Young, Kenneth, Ahuite Reategui, Manuel Augusto, Baider, Cláudia, Balslev, Henrik, Cárdenas, Sasha, Casas, Luisa Fernanda, Farfan-Rios, William, Ferreira, Cid, Linares-Palomino, Reynaldo, Mendoza, Casimiro, Mesones, Italo, Torres-Lezama, Armando, Giraldo, Ligia Estela Urrego, Villarroel, Daniel, Zagt, Roderick, Alexiades, Miguel, de Oliveira, Edmar Almeida, Garcia-Cabrera, Karina, Hernandez, Lionel, Palacios Cuenca, Walter, Pansini, Susamar, Pauletto, Daniela, Ramirez Arevalo, Freddy, Sampaio, Adeilza Felipe, Sandoval, Elvis, Valenzuela Gamarra, Luis, Levesley, Aurora, Pickavance, Georgia, Melgaço, Karina, Systems Ecology, HANS TER STEEGE, NATURALIS BIODIVERSITY CENTER, THE NETHERLANDS, IRES PAULA DE ANDRADE MIRANDA, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, BIANCA WEISS ALBUQUERQUE, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, MAIRA ROCHA, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, VERIDIANA VIZONI SCUDELLER, UNIVERSIDADE FEDERAL DO AMAZONAS, BRAZIL, MARIA CRISTINA PEÑUELA MORA, UNIVERSIDAD REGIONAL AMAZÓNICA, ECUADOR, KARINA MELGAÇO, UNIVERSITY OF LEEDS, UK., FRANCISCO DALLMEIER, SMITHSONIAN CONSERVATION BIOLOGY INSTITUTE, USA, TERRY W. HENKEL, HUMBOLDT STATE UNIVERSITY, USA, NORA HELAL, NATURALIS BIODIVERSITY CENTER, THE NETHERLANDS, BEATRIZ S. MARIMON, UNIVERSIDADE DO ESTADO DE MATO GROSSO, BRAZIL, BEN HUR MARIMON-JUNIOR, UNIVERSIDADE DO ESTADO DE MATO GROSSO, BRAZIL, ANDREAS HUTH, HELMHOLTZ CENTRE FOR ENVIRONMENTAL RESEARCH - UFZ, GERMANY, JÜRGEN GROENEVELD, HELMHOLTZ CENTRE FOR ENVIRONMENTAL RESEARCH - UFZ, GERMANY, DANIEL SABATIER, UNIVERSITÉ DE MONTPELLIER, FRANCE, LUIZ DE SOUZA COELHO, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, BRAZIL, DIOGENES DE ANDRADE LIMA FILHO, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, BRAZIL, RAFAEL P. SALOMÃO, UNIVERSIDADE FEDERAL RURAL DA AMAZÔNIA, BRAZIL, IÊDA LEÃO AMARAL, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, BRAZIL, FRANCISCA DIONÍZIA DE ALMEIDA MATOS, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, BRAZIL, CAROLINA V. CASTILHO, EMBRAPA, CPA DE RORAIMA, BRAZIL, OLIVER L. PHILLIPS, UNIVERSITY OF LEEDS, UK, JUAN ERNESTO GUEVARA, UNIVERSIDAD DE LAS AMÉRICAS, ECUADOR, MARCELO DE JESUS VEIGA CARIM, INSTITUTO DE PESQUISAS CIENTÍFICAS E TECNOLÓGICAS DO AMAPÁ - IEPA, BRAZIL, DAIRON CÁRDENAS LÓPEZ, INSTITUTO SINCHI, COLOMBIA, WILLIAM E. MAGNUSSON, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, BRAZIL, FLORIAN WITTMANN, KARLSRUHE INSTITUTE OF TECHNOLOGY - KIT, GERMANY, MARIANA VICTÓRIA IRUME, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, BRAZIL, MARIA PIRES MARTINS, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, BRAZIL, JOSÉ RENAN DA SILVA GUIMARÃES, INSTITUTO DE PESQUISAS CIENTÍFICAS E TECNOLÓGICAS DO AMAPÁ - IEPA, BRAZIL, JEAN-FRANÇOIS MOLINO, UNIVERSITÉ DE MONTPELLIER, FRANCE, OLAF S. BÁNKI, NATURALIS BIODIVERSITY CENTER, NETHERLANDS, MARIA TERESA FERNANDEZ PIEDADE, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, BRAZIL, NIGEL C. A. PITMAN, THE FIELD MUSEUM, USA, ABEL MONTEAGUDO MENDOZA, JARDÍN BOTÁNICO DE MISSOURI, PERU, JOSÉ FERREIRA RAMOS, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, BRAZIL, BRUNO GARCIA LUIZE, UNESP, BRAZIL, ALFONSO ALONSO, SMITHSONIAN CONSERVATION BIOLOGY INSTITUTE, USA, PERCY NÚÑEZ VARGAS, INSTITUTO NACIONAL DE PESQUISAS ESPACIAIS-INPE, BRAZIL, THIAGO SANNA FREIRE SILVA, UNESP, BRAZIL, EDUARDO MARTINS VENTICINQUE, UNIVERSIDADE FEDERAL DO RIO GRANDE DO NORTE, BRAZIL, ANGELO GILBERTO MANZATTO, UNIVERSIDADE FEDERAL DE RONDÔNIA, BRAZIL, NEIDIANE FARIAS COSTA REIS, UNIVERSIDADE FEDERAL DE RONDÔNIA, BRAZIL, JOHN TERBORGH, UNIVERSITY OF FLORIDA, USA, KATIA REGINA CASULA, UNIVERSIDADE FEDERAL DE RONDÔNIA, BRAZIL, EURIDICE N. HONORIO CORONADO, IIAP, PERU, JUAN CARLOS MONTERO, INSTITUTO BOLIVIANO DE INVESTIGACION FORESTAL, BOLIVIA, TED R. FELDPAUSCH, UNIVERSITY OF EXETER, UK, ALVARO DUQUE, UNIVERSIDAD NACIONAL DE COLOMBIA, COLOMBIA, FLÁVIA R. C. COSTA, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, BRAZIL, NICOLÁS CASTAÑO ARBOLEDA, INSTITUTO SINCHI, COLOMBIA, JOCHEN SCHÖNGART, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, BRAZIL, TIMOTHY J. KILLEEN, AGTECA-AMAZONICA, BOLIVIA, RODOLFO VASQUEZ, JARDÍN BOTÁNICO DE MISSOURI, PERU, BONIFACIO MOSTACEDO, UNIVERSIDAD AUTÓNOMA GABRIEL RENÉ MORENO, BOLIVIA, LAYON O. DEMARCHI, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, BRAZIL, RAFAEL L. ASSIS, UNIVERSITY OF OSLO, NORWAY, CHRIS BARALOTO, FLORIDA INTERNATIONAL UNIVERSITY, USA, JULIEN ENGEL, FLORIDA INTERNATIONAL UNIVERSITY, USA, PASCAL PETRONELLI, INRA, FRANCE, HERNÁN CASTELLANOS, UNIVERSIDAD NACIONAL EXPERIMENTAL DE GUAYANA, VENEZUELA, MARCELO BRILHANTE DE MEDEIROS, Cenargen, ADRIANO QUARESMA, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, MARCELO FRAGOMENI SIMON, Cenargen, ANA ANDRADE, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, JOSÉ LUÍS CAMARGO, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, SUSAN G. W. LAURANCE, JAMES COOK UNIVERSITY, AUSTRALIA, WILLIAM F. LAURANCE, JAMES COOK UNIVERSITY, AUSTRALIA, LORENA M. RINCÓN, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, JULIANA SCHIETTI, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, THAIANE R. SOUSA, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, EMANUELLE DE SOUSA FARIAS, INSTITUTO LEÔNIDAS E MARIA DEANE, MARIA APARECIDA LOPES, UNIVERSIDADE FEDERAL DO PARÁ, JOSÉ LEONARDO LIMA MAGALHÃES, UNIVERSIDADE FEDERAL DO PARÁ, HENRIQUE EDUARDO MENDONÇA NASCIMENTO, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, HELDER LIMA DE QUEIROZ, INSTITUTO DE DESENVOLVIMENTO SUSTENTÁVEL MAMIRAUÁ, GERARDO A. AYMARD C., HERBARIO UNIVERSITARIO (PORT), VENEZUELA, ROEL BRIENEN, UNIVERSITY OF LEEDS, UK, JUAN DAVID CARDENAS REVILLA, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, IMA CÉLIA GUIMARÃES VIEIRA, MUSEU PARAENSE EMÍLIO GOELDI, BRUNO BARÇANTE LADVOCAT CINTRA, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, PABLO R. STEVENSON, UNIVERSIDAD DE LOS ANDES, COLOMBIA, YURI OLIVEIRA FEITOSA, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, JOOST F. DUIVENVOORDEN, UNIVERSITY OF AMSTERDAM, THE NETHERLANDS, HUGO F. MOGOLLÓN, ENDANGERED SPECIES COALITION, USA, ALEJANDRO ARAUJO-MURAKAMI, UNIVERSIDAD AUTÓNOMA GABRIEL RENE MORENO, BOLIVIA, LEANDRO VALLE FERREIRA, MUSEU PARAENSE EMÍLIO GOELDI, JOSÉ RAFAEL LOZADA, UNIVERSIDAD DE LOS ANDES, VENEZUELA, JAMES A. COMISKEY, NATIONAL PARK SERVICE, USA, JOSÉ JULIO DE TOLEDO, UNIVERSIDADE FEDERAL DO AMAPÁ, GABRIEL DAMASCO, UNIVERSITY OF CALIFORNIA, USA, NÁLLARETT DÁVILA, UNIVERSIDADE ESTADUAL DE CAMPINAS, FREDDIE DRAPER, CARNEGIE INSTITUTION FOR SCIENCE, USA, ROOSEVELT GARCÍA-VILLACORTA, UNIVERSITY OF EDINBURGH, UK, ALINE LOPES, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, ALBERTO VICENTINI, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, BRAZIL, VITOR H. F. GOMES, MUSEU PARAENSE EMÍLIO GOELDI, JON LLOYD, IMPERIAL COLLEGE LONDON, UK, DAVID NEILL, UNIVERSIDAD ESTATAL AMAZÓNICA, ECUADOR, DANIEL PRAIA PORTELA DE AGUIAR, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, LUZMILA ARROYO, UNIVERSIDAD AUTÓNOMA GABRIEL RENE MORENO, BOLIVIA, FERNANDA ANTUNES CARVALHO, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, BRAZIL, FERNANDA COELHO DE SOUZA, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, BRAZIL, DÁRIO DANTAS DO AMARAL, MUSEU PARAENSE EMÍLIO GOELDI, KENNETH J. FEELEY, UNIVERSITY OF MIAMI, USA, ROGERIO GRIBEL, INSTITUTO DE PESQUISAS JARDIM BOTÂNICO DO RIO DE JANEIRO, MARCELO PETRATTI PANSONATO, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, JOS BARLOW, LANCASTER UNIVERSITY, UK, ERIKA BERENGUER, UNIVERSITY OF OXFORD, UK, JOICE NUNES FERREIRA, CPATU, PAUL V. A. FINE, UNIVERSITY OF CALIFORNIA, USA, MARCELINO CARNEIRO GUEDES, CPAF-AP, ELIANA M. JIMENEZ, INSTITUCIÓN UNIVERSITARIA, COLOMBIA, JUAN CARLOS LICONA, INSTITUTO BOLIVIANO DE INVESTIGACION FORESTAL, BOLIVIA, BORIS VILLA, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, CARLOS CERÓN, UNIVERSIDAD CENTRAL, ECUADOR, PAUL MAAS, NATURALIS BIODIVERSITY CENTER, THE NETHERLANDS, MARCOS SILVEIRA, UNIVERSIDADE FEDERAL DO ACRE, JULIANA STROPP, FEDERAL UNIVERSITY OF ALAGOAS, RAQUEL THOMAS, IWOKRAMA INTERNATIONAL CENTRE FOR RAINFOREST CONSERVATION, GUYANA, TIM R. BAKER, UNIVERSITY OF LEEDS, UK, DOUG DALY, NEW YORK BOTANICAL GARDEN, USA, KYLE G. DEXTER, UNIVERSITY OF EDINBURGH, UK, ISAU HUAMANTUPA-CHUQUIMACO, UNIVERSIDAD NACIONAL DE SAN ANTONIO ABAD DEL CUSCO, PERU, WILLIAM MILLIKEN, ROYAL BOTANIC GARDENS, UK, TOBY PENNINGTON, UNIVERSITY OF EXETER, UK, MARCOS RÍOS PAREDES, SERVICIOS DE BIODIVERSIDAD EIRL, PERU, ALFREDO FUENTES, UNIVERSITARIO UMSA, BOLIVIA, BENTE KLITGAARD, ROYAL BOTANIC GARDENS, UK, JOSÉ LUIS MARCELO PENA, UNIVERSIDAD NACIONAL AGRARIA LA MOLINA, PERU, MILES R. SILMAN, WAKE FOREST UNIVERSITY, USA, J. SEBASTIÁN TELLO, MISSOURI BOTANICAL GARDEN, USA, JEROME CHAVE, CNRS AND UNIVERSITÉ PAUL SABATIER, FRANCE, FERNANDO CORNEJO VALVERDE, ANDES TO AMAZON BIODIVERSITY PROGRAM, PERU, ANTHONY DI FIORE, UNIVERSITY OF TEXAS AT AUSTIN, USA, RENATO RICHARD HILÁRIO, UNIVERSIDADE FEDERAL DO AMAPÁ, JUAN FERNANDO PHILLIPS, FUNDACIÓN PUERTO RASTROJO, COLOMBIA, GONZALO RIVAS-TORRES, UNIVERSIDAD SAN FRANCISCO DE QUITO-USFQ, ECUADOR, TINDE R. VAN ANDEL, NATURALIS BIODIVERSITY CENTER, THE NETHERLANDS, PATRICIO VON HILDEBRAND, FUNDACIÓN ESTACIÓN DE BIOLOGÍA, COLOMBIA, JANAÍNA COSTA NORONHA, ICNHS, FEDERAL UNIVERSITY OF MATO GROSSO, EDELCILIO MARQUES BARBOSA, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, FLÁVIA RODRIGUES BARBOSA, ICNHS, FEDERAL UNIVERSITY OF MATO GROSSO, LUIZ CARLOS DE MATOS BONATES, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, RAINIELLEN DE SÁ CARPANEDO, ICNHS, FEDERAL UNIVERSITY OF MATO GROSSO, HILDA PAULETTE DÁVILA DOZA, SERVICIOS DE BIODIVERSIDAD EIRL, PERU, ÉMILE FONTY, DIRECTION RÉGIONALE DE LA GUYANE, FRENCH GUIANA, RICARDO GÓME ZÁRATEZ, PROTERRA - IIAP, PERU, THERANY GONZALES, ACEER FOUNDATION, PERU, GEORGE PEPE GALLARDO GONZALES, SERVICIOS DE BIODIVERSIDAD EIRL, PERU, BRUCE HOFFMAN, AMAZON CONSERVATION TEAM, SURINAME, ANDRÉ BRAGA JUNQUEIRA, UNIVERSITAT AUTÒNOMA DE BARCELONA, SPAIN, YADVINDER MALHI, OXFORD UNIVERSITY CENTRE FOR THE ENVIRONMENT, UK, LINDER FELIPE MOZOMBITE PINTO, SERVICIOS DE BIODIVERSIDAD EIRL, PERU, ADRIANA PRIETO, UNIVERSIDAD NACIONAL DE COLOMBIA, COLOMBIA, DOMINGOS DE JESUS RODRIGUES, ICNHS, FEDERAL UNIVERSITY OF MATO GROSSO, AGUSTÍN RUDAS, UNIVERSIDAD NACIONAL DE COLOMBIA, COLOMBIA, ADEMIR ROBERTO RUSCHEL, CPATU, NATALINO SILVA, UNIVERSIDADE FEDERAL RURAL DA AMAZÔNIA, BRAZIL, CÉSAR I. A. VELA, UNIVERSIDAD NACIONAL DE SAN ANTONIO ABAD DEL CUSCO, PERU, VINCENT ANTOINE VOS, UNIVERSIDAD AUTÓNOMA DEL BENI JOSÉ BALLIVIÁN, BOLIVIA, EGLEÉ L. ZENT, INSTITUTO VENEZOLANO DE INVESTIGACIONES CIENTÍFICAS, VENEZUELA, STANFORD ZENT, INSTITUTO VENEZOLANO DE INVESTIGACIONES CIENTÍFICAS, VENEZUELA, ANGELA CANO, UNIVERSIDAD DE LOS ANDES, COLOMBIA, YRMA ANDREINA CARRERO MÁRQUEZ, UNIVERSIDAD DE LOS ANDES, VENEZUELA, DIEGO F. CORREA, UNIVERSIDAD DE LOS ANDES, COLOMBIA, JANAINA BARBOSA PEDROSA COSTA, BERNARDO MONTEIRO FLORES, UNIVERSITY OF CAMPINAS, BRAZIL, DAVID GALBRAITH, UNIVERSITY OF LEEDS, UK, MILENA HOLMGREN, WAGENINGEN UNIVERSITY & RESEARCH, THE NETHERLANDS, MICHELLE KALAMANDEEN, UNIVERSITY OF LEEDS, UK, MARCELO TRINDADE NASCIMENTO, UNIVERSIDADE ESTADUAL DO NORTE FLUMINENSE, BRAZIL, ALEXANDRE A. OLIVEIRA, USP, HIRMA RAMIREZ-ANGULO, UNIVERSIDAD DE LOS ANDES, VENEZUELA, RODRIGO SIERRA, GEOIS, ECUADOR, MILTON TIRADO, GEOIS, ECUADOR, MARIA NATALIA UMAÑA MEDINA, UNIVERSIDAD DE LOS ANDES, COLOMBIA, GEERTJE VAN DER HEIJDEN, UNIVERSITY OF NOTTINGHAM, UK, EMILIO VILANOVA TORRE, UNIVERSIDAD DE LOS ANDES, VENEZUELA, CORINE VRIESENDORP, THE FIELD MUSEUM, USA, OPHELIA WANG, NORTHERN ARIZONA UNIVERSITY, USA, KENNETH R. YOUNG, UNIVERSITY OF TEXAS AT AUSTIN, USA, MANUEL AUGUSTO AHUITE REATEGUI, LORETO, PERU, CLÁUDIA BAIDER, MINISTRY OF AGRO-INDUSTRY AND FOOD SECURITY, MAURITIUS, HENRIK BALSLEV, AARHUS UNIVERSITY, DENMARK, SASHA CÁRDENAS, UNIVERSIDAD DE LOS ANDES, COLOMBIA, LUISA FERNANDA CASAS, UNIVERSIDAD DE LOS ANDES, COLOMBIA, WILLIAM FARFAN-RIOS, WAKE FOREST UNIVERSITY, USA, CID FERREIRA, INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA - INPA, REYNALDO LINARES-PALOMINO, SMITHSONIAN CONSERVATION BIOLOGY INSTITUTE, USA, CASIMIRO MENDOZA, FOMABO, BOLIVIA, ITALO MESONES, UNIVERSITY OF CALIFORNIA, USA, ARMANDO TORRES-LEZAMA, UNIVERSIDAD DE LOS ANDES, VENEZUELA, LIGIA ESTELA URREGO GIRALDO, UNIVERSIDAD NACIONAL DE COLOMBIA, COLOMBIA, DANIEL VILLARROEL, UNIVERSIDAD AUTÓNOMA GABRIEL RENE MORENO, BOLIVIA, RODERICK ZAGT, TROPENBOS INTERNATIONAL, THE NETHERLANDS, MIGUEL N. 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PERES, UNIVERSITY OF EAST ANGLIA, UK, EVLYN MÁRCIA MORAES DE LEÃO NOVO, INSTITUTO NACIONAL DE PESQUISAS ESPACIAIS - INPE, BRAZIL, Naturalis Biodiversity Center [Leiden], Humboldt State University (HSU), Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Department of Ecological Modelling [UFZ Leipzig], Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), 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]), Museu Paraense Emílio Goeldi [Belém, Brésil] (MPEG), Centro de Pesquisa Agroflorestal de Roraima, Brazilian Agricultural Research Corporation (Embrapa), Coordenac Bao de Pesquisas em Ecologia, Instituto Nacional de Pesquisas da Amazônia (INPA), Department of Biochemistry [Mainz], Max Planck Institute for Chemistry (MPIC), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam [Amsterdam] (UvA), Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University [Durham], Departamento de Ciencias Forestales, Universidad Nacional de Colombia, Missouri Botanical Garden, Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), James Cook University (JCU), Royal Welsh College of Music & Drama (RWCMD), Herbario Universitario PORT, School of Geography [Leeds], University of Leeds, Laboratorio de Botánica & Sistemática, Universidad de Los Andes [Venezuela] (ULA), Universidad Autonoma Gabriel René Moreno (UAGRM), Département Intelligence Ambiante et Systèmes Interactifs (DIASI), Laboratoire d'Intégration des Systèmes et des Technologies (LIST), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Department of Integrative Biology, Department of Integrative Biology [Berkeley] (IB), University of California [Berkeley], University of California-University of California, University of Edinburgh, Smithsonian Conservation Biology Institute, Smithsonian Conservation Biology Institute, Center for Conservation Education and Sustainability, MRC 705, Box 37012, Washington, DC, VA 20013-7012, USA, Imperial College London, Universidad Estatal Amazonica, Chercheur indépendant, Laboratório de Genética e Biologia Reprodutiva de Plantas, Lancaster Environment Centre, Lancaster University, Embrapa Amapa, Instituto Boliviano de Investigacion Forestal (IBIF), CREPAL - Centre de recherches sur les pays lusophones - EA 3421 (CREPAL), Université Sorbonne Nouvelle - Paris 3, Herbario Nacional del Ecuador, Department of Botany, Naturalis Biodiversity Center, Museu Univ, Universidade Federal do Acre (UFAC), JRC Institute for Environment and Sustainability (IES), European Commission - Joint Research Centre [Ispra] (JRC), Universidad Nacional de San Antonio Abad del Cusco (UNSAAC), Royal Botanic Garden , Kew, Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Andes to Amazon Biodiversity Program [Madre de Dios], Universidad San Francisco de Quito (EQUATEUR), Universidade Federal de Vicosa (UFV), University of Oxford [Oxford], Universidad Nacional de Colombia [Bogotà] (UNAL), Universidad de Las Américas [Ecuador] (UDLA), Iwokrama International Centre for Rainforest Conservation and Development, Dpt of Anthropology [Austin], University of Texas at Austin [Austin], Instituto de Medicina Tropical 'Alexander von Humboldt' (IMT AvH), Universidad Peruana Cayetano Heredia (UPCH), Resource Ecology Group, Wageningen University and Research [Wageningen] (WUR), Universidad de los Andes [Bogota] (UNIANDES), Geoinformática y Sistemas , Cia. Ltda (GeoIS), School of Geography, University of Oxford, Sch Earth Sci & Environm Sustainabil, Northern Arizona University [Flagstaff], Instituto de Manejo Forestal, Department of integrative biology, University of California, University of Kent [Canterbury], Universidade Federal do Mato Grosso (UFMT), Ecosystem and Landscape Dynamics (IBED, FNWI), 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]), Universidad de Los Andes [Mérida, Venezuela] (ULA), Laboratoire d'Intégration des Systèmes et des Technologies (LIST (CEA)), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Royal Botanic Gardens [Kew], Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Universidad San Francisco de Quito (USFQ), Universidade Federal de Viçosa = Federal University of Viçosa (UFV), University of Oxford, University of California (UC), Helmholtz Centre for Environmental Research (UFZ), Department of Ecological Modelling, Museu Paraense Emílio Goeldi, Missouri Bot Garden, 4344 Shaw Blvd, Missouri Botanical Garden (USA), Universidad de los Andes, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Technologique (CEA) (DRT (CEA)), Universidad Nacional San Antonio Abad del Cusco, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Departamento de Ingeniería Electrónica, Universidad Peruana Cayetano Heredia, Wageningen University and Research Centre [Wageningen] (WUR), Universidad de los Andes [Bogota], Free University, Humboldt State University, Universidade do Estado de Mato Grosso, Helmholtz Centre for Environmental Research - UFZ, Technische Universitaet Dresden, Université de Montpellier, Instituto Nacional de Pesquisas da Amazônia - INPA, Universidade Federal Rural da Amazônia, Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Universidad de las Américas, The Field Museum, Instituto de Pesquisas Científicas e Tecnológicas do Amapá - IEPA, Instituto SINCHI, Karlsruhe Institute of Technology - KIT, Max Planck Institute for Chemistry, Jardín Botánico de Missouri, Universidade Estadual Paulista (Unesp), Instituto Nacional de Pesquisas Espaciais – INPE, Universidad Nacional de San Antonio Abad del Cusco, Universidade Federal do Rio Grande do Norte, Universidade Federal de Rondônia, University of Florida, James Cook University, Instituto de Investigaciones de la Amazonía Peruana (IIAP), Instituto Boliviano de Investigacion Forestal, University of Exeter, Agteca-Amazonica, Universidad Autónoma Gabriel René Moreno, University of Oslo, Florida International University, Univ Guyane, Universidad Nacional Experimental de Guayana, Fiocruz, Pav. Arthur Neiva – Térreo, Universidade Federal do Pará (UFPA), Instituto de Desenvolvimento Sustentável Mamirauá, UNELLEZ-Guanare, University of Amsterdam, Endangered Species Coalition, Universidad Autónoma Gabriel Rene Moreno, Inventory and Monitoring Program, Ciências Ambientais, Universidade Estadual de Campinas (UNICAMP), Carnegie Institution for Science, Royal Botanic Garden Edinburgh, University of Brasilia, Universidad Estatal Amazónica, Universidade Federal de Minas Gerais (UFMG), University of Miami, Fairchild Tropical Botanic Garden, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Universidade de São Paulo (USP), Instituto Tecnológico de Antioquia - Institución Universitaria, Universidad Regional Amazónica IKIAM, Universidad Central, Universidade Federal do Acre, Federal University of Alagoas, Iwokrama International Centre for Rainforest Conservation, New York Botanical Garden, Kew, Servicios de Biodiversidad EIRL, Universitario UMSA, Universidad Nacional Agraria La Molina, University of East Anglia, Wake Forest University, UMR 5174 EDB, Andes to Amazon Biodiversity Program, University of Texas at Austin, Fundación Puerto Rastrojo, Universidad San Francisco de Quito-USFQ, Fundación Estación de Biología, Federal University of Mato Grosso, ONF, ACEER Foundation, Amazon Conservation Team, Universitat Autònoma de Barcelona, Dyson Perrins Building, Universidad Autónoma del Beni José Ballivián, Instituto Venezolano de Investigaciones Científicas - IVIC, 1 Brookside., The University of Queensland, Wageningen University & Research, Universidade Estadual do Norte Fluminense, Conjunto Forestal, Universidade Federal do Amazonas - UFAM – Instituto de Ciências Biológicas – ICB1, 3° Piso, University of Maryland, University Park, University of Washington, Northern Arizona University, Ministry of Agro-Industry and Food Security, Aarhus University, Manejo Forestal en las Tierras Tropicales de Bolivia, Universidad Mayor de San Simon (UMSS), Tropenbos International, University of Kent, Universidad Técnica del Norte, Universidade Federal do Oeste do Pará, Universidad Nacional de la Amazonia Peruana, University of Missouri, University of St Andrews. School of Geography & Sustainable Development, Université des Antilles (UA)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Ter Steege, Hans [0000-0002-8738-2659], and Apollo - University of Cambridge Repository
Subjects: 0106 biological sciences, Aquatic Ecology and Water Quality Management, Geography & travel, QH301 Biology, Biodiversity, lcsh:Medicine, forêt tropicale, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Coppicing, Tropical forest, Bosques amazónicos, K01 - Foresterie - Considérations générales, Seed Weight, lcsh:Science, SDG 15 - Life on Land, ddc:910, Multidisciplinary, Amazon rainforest, Ecology, Inventaire forestier, 3103 Ecology, 3007 Forestry Sciences, Edaphic, F70 - Taxonomie végétale et phytogéographie, Soil Biology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, PE&RC, Biosystematiek, Amazonian forests, Monodominance, Sprout, Rhizobium, F40 - Écologie végétale, 30 Agricultural, Veterinary and Food Sciences, Life History Trait, Nodulation, Biology, 010603 evolutionary biology, Article, Mining, Life history theory, QH301, Écologie forestière, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Amazonia, Forest ecology, Life Science, Forest, Bodembiologie, 13 Climate Action, lcsh:R, Tropics, DAS, Aquatische Ecologie en Waterkwaliteitsbeheer, Nonhuman, biodiversité forestière, Espèce dominante, Amazon Tree Diversity Network (ATDN), Wildlife Ecology and Conservation, Biosystematics, lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Population végétale, 31 Biological Sciences, 010606 plant biology & botany
Abstract: Made available in DSpace on 2020-12-12T01:40:04Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-12-01 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Tropical forests are known for their high diversity. Yet, forest patches do occur in the tropics where a single tree species is dominant. Such “monodominant” forests are known from all of the main tropical regions. For Amazonia, we sampled the occurrence of monodominance in a massive, basin-wide database of forest-inventory plots from the Amazon Tree Diversity Network (ATDN). Utilizing a simple defining metric of at least half of the trees ≥ 10 cm diameter belonging to one species, we found only a few occurrences of monodominance in Amazonia, and the phenomenon was not significantly linked to previously hypothesized life history traits such wood density, seed mass, ectomycorrhizal associations, or Rhizobium nodulation. In our analysis, coppicing (the formation of sprouts at the base of the tree or on roots) was the only trait significantly linked to monodominance. While at specific locales coppicing or ectomycorrhizal associations may confer a considerable advantage to a tree species and lead to its monodominance, very few species have these traits. Mining of the ATDN dataset suggests that monodominance is quite rare in Amazonia, and may be linked primarily to edaphic factors. Biodiversity Dynamics Naturalis Biodiversity Center, PO Box 9517 Systems Ecology Free University, De Boelelaan 1087 Department of Biological Sciences Humboldt State University, 1 Harpst Street Programa de Pós-Graduação em Ecologia e Conservação Universidade do Estado de Mato Grosso Department of Ecological Modelling Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15 Institute of Forest Growth and Computer Sciences Technische Universitaet Dresden, Postfach 1117 AMAP IRD CIRAD CNRS INRA Université de Montpellier, TA A-51/PS2, Bd. de la Lironde, A comprehensive Coordenação de Biodiversidade Instituto Nacional de Pesquisas da Amazônia - INPA, Av. André Araújo, 2936, Petrópolis Programa Professor Visitante Nacional Sênior na Amazônia - CAPES Universidade Federal Rural da Amazônia, Av. Perimetral, s/n Coordenação de Botânica Museu Paraense Emílio Goeldi, Av. Magalhães Barata 376, C.P. 399 EMBRAPA – Centro de Pesquisa Agroflorestal de Roraima, BR 174, km 8 – Distrito Industrial School of Geography University of Leeds, Woodhouse Lane Grupo de Investigación en Biodiversidad Medio Ambiente y Salud-BIOMAS Universidad de las Américas, Campus Queri Keller Science Action Center The Field Museum, 1400S. Lake Shore Drive Departamento de Botânica Instituto de Pesquisas Científicas e Tecnológicas do Amapá - IEPA, Rodovia JK, Km 10, Campus do IEPA da Fazendinha Herbario Amazónico Colombiano Instituto SINCHI, Calle 20 No 5-44 Coordenação de Pesquisas em Ecologia Instituto Nacional de Pesquisas da Amazônia - INPA, Av. André Araújo, 2936, Petrópolis Dep. of Wetland Ecology Institute of Geography and Geoecology Karlsruhe Institute of Technology - KIT, Josefstr.1 Biogeochemistry Max Planck Institute for Chemistry, Hahn-Meitner Weg 1 Naturalis Biodiversity Center, PO Box 9517 Coordenação de Dinâmica Ambiental Instituto Nacional de Pesquisas da Amazônia - INPA, Av. André Araújo, 2936, Petrópolis Science and Education The Field Museum, 1400S. Lake Shore Drive Jardín Botánico de Missouri Departamento de Ecologia Universidade Estadual Paulista - UNESP – Instituto de Biociências – IB, Av. 24A, 1515, Bela Vista Divisao de Sensoriamento Remoto – DSR Instituto Nacional de Pesquisas Espaciais – INPE, Av. dos Astronautas, 1758, Jardim da Granja Herbario Vargas Universidad Nacional de San Antonio Abad del Cusco, Avenida de la Cultura, Nro 733 Departamento de Geografia Universidade Estadual Paulista -UNESP – Instituto de Geociências e Ciências Extas – IGCE Bela Vista Centro de Biociências Departamento de Ecologia Universidade Federal do Rio Grande do Norte, Av. Senador Salgado Filho, 3000 Departamento de Biologia Universidade Federal de Rondônia, Rodovia BR 364s/n Km 9,5 - Sentido Acre, Unir Programa de Pós- Graduação em Biodiversidade e Biotecnologia PPG- Bionorte Universidade Federal de Rondônia, Campus Porto Velho Km 9,5 bairro Rural Department of Biology and Florida Museum of Natural History University of Florida Centre for Tropical Environmental and Sustainability Science and College of Science and Engineering James Cook University Instituto de Investigaciones de la Amazonía Peruana (IIAP), Av. A. Quiñones km 2,5 Instituto Boliviano de Investigacion Forestal, Av. 6 de agosto #28, Km. 14, Doble via La Guardia, Casilla 6204 Geography College of Life and Environmental Sciences University of Exeter, Rennes Drive Departamento de Ciencias Forestales Universidad Nacional de Colombia, Calle 64 x Cra 65 Agteca-Amazonica Facultad de Ciencias Agrícolas Universidad Autónoma Gabriel René Moreno Natural History Museum University of Oslo, Postboks 1172 International Center for Tropical Botany (ICTB) Department of Biological Sciences Florida International University, 11200 SW 8th Street, OE 243 Cirad UMR Ecofog AgrosParisTech CNRS INRA Univ Guyane, Campus agronomique Centro de Investigaciones Ecológicas de Guayana Universidad Nacional Experimental de Guayana, Calle Chile, urbaniz Chilemex Prédio da Botânica e Ecologia Embrapa Recursos Genéticos e Biotecnologia Parque Estação Biológica, Av. W5 Norte Projeto Dinâmica Biológica de Fragmentos Florestais Instituto Nacional de Pesquisas da Amazônia - INPA, Av. André Araújo, 2936, Petrópolis Laboratório de Ecologia de Doenças Transmissíveis da Amazônia (EDTA) Instituto Leônidas e Maria Deane Fiocruz, Rua Terezina, 476, Adrianópolis Programa de Pós-graduação em Biodiversidade e Saúde Instituto Oswaldo Cruz - IOC/FIOCRUZ Pav. Arthur Neiva – Térreo, Av. Brasil, 4365 – Manguinhos Instituto de Ciências Biológicas Universidade Federal do Pará, Av. Augusto Corrêa 01 Programa de Pós-Graduação em Ecologia Universidade Federal do Pará, Av. Augusto Corrêa 01 Embrapa Amazônia Oriental, Trav. Dr. Enéas Pinheiro s/no. Diretoria Técnico-Científica Instituto de Desenvolvimento Sustentável Mamirauá, Estrada do Bexiga, 2584 Programa de Ciencias del Agro y el Mar Herbario Universitario (PORT) UNELLEZ-Guanare Laboratorio de Ecología de Bosques Tropicales y Primatología Universidad de los Andes, Carrera 1 # 18a- 10 Programa de Pós-Graduação em Biologia (Botânica) Instituto Nacional de Pesquisas da Amazônia - INPA, Av. André Araújo, 2936, Petrópolis Institute of Biodiversity and Ecosystem Dynamics University of Amsterdam, Sciencepark 904 Endangered Species Coalition, 8530 Geren Rd. Museo de Historia Natural Noel Kempff Mercado Universidad Autónoma Gabriel Rene Moreno, Avenida Irala 565 Casilla Post al 2489 Facultad de Ciencias Forestales y Ambientales Instituto de Investigaciones para el Desarrollo Forestal Universidad de los Andes, Via Chorros de Milla Inventory and Monitoring Program, National Park Service, 120 Chatham Lane Center for Conservation and Sustainability Smithsonian Conservation Biology Institute, 1100 Jefferson Dr. SW, Suite 3123 Universidade Federal do Amapá Ciências Ambientais, Rod. Juscelino Kubitschek km2 Department of Integrative Biology University of California Biologia Vegetal Universidade Estadual de Campinas, Caixa Postal 6109 Department of Global Ecology Carnegie Institution for Science, 260 Panama St. Institute of Molecular Plant Sciences University of Edinburgh, Mayfield Rd Tropical Diversity Section Royal Botanic Garden Edinburgh, 20a Inverleith Row Department of Ecology University of Brasilia Programa de Pós-Graduação em Ciência Ambientais Universidade Federal do Pará, Rua Augusto Corrêa 01 Faculty of Natural Sciences Department of Life Sciences Imperial College London, Silwood Park, South Kensington Campus Ecosistemas Biodiversidad y Conservación de Especies Universidad Estatal Amazónica, Km. 2 1/2 vía a Tena (Paso Lateral) Universidade Federal de Minas Gerais Instituto de Ciências Biológicas Departamento de Genética Ecologia e Evolução, Av. Antônio Carlos, 6627 Pampulha Department of Biology University of Miami Fairchild Tropical Botanic Garden Diretoria de Pesquisas Científicas Instituto de Pesquisas Jardim Botânico do Rio de Janeiro Instituto de Biociências - Dept. Ecologia Universidade de Sao Paulo - USP Rua do Matão, Trav. 14, no. 321, Cidade Universitária Lancaster Environment Centre Lancaster University Environmental Change Institute University of Oxford Empresa Brasileira de Pesquisa Agropecuária Embrapa Amapá, Rod. Juscelino Kubitschek km 5 Grupo de Investigación en Tecnologías de la Información y Medio Ambiente Instituto Tecnológico de Antioquia - Institución Universitaria, Calle 78B No. 72A-220 Universidad Regional Amazónica IKIAM, Km 7 via Muyuna Escuela de Biología Herbario Alfredo Paredes Universidad Central, Ap. Postal 17.01.2177 Taxonomy and Systematics Naturalis Biodiversity Center, PO Box 9517 Museu Universitário/Centro de Ciências Biológicas e da Natureza/Laboratório de Botânica e Ecologia Vegetal Universidade Federal do Acre Institute of Biological and Health Sciences Federal University of Alagoas, Av. Lourival Melo Mota, s/n, Tabuleiro do Martins Iwokrama International Centre for Rainforest Conservation New York Botanical Garden, 2900 Southern Blvd, Bronx School of Geosciences University of Edinburgh, 201 Crew Building, King’s Buildings Natural Capital and Plant Health Royal Botanic Gardens Kew Servicios de Biodiversidad EIRL, Jr. Independencia 405 Herbario Nacional de Bolivia Universitario UMSA, Casilla 10077 Correo Central Center for Conservation and Sustainable Development Missouri Botanical Garden, P.O. Box 299 Department for Identification & Naming Royal Botanic Gardens Kew Department of Forestry Management Universidad Nacional Agraria La Molina, Avenido La Molina, Apdo. 456, La Molina School of Environmental Sciences University of East Anglia Biology Department and Center for Energy Environment and Sustainability Wake Forest University, 1834 Wake Forest Rd Laboratoire Evolution et Diversité Biologique CNRS and Université Paul Sabatier UMR 5174 EDB Andes to Amazon Biodiversity Program Department of Anthropology University of Texas at Austin, SAC 5.150, 2201 Speedway Stop C3200 Fundación Puerto Rastrojo, Cra 10 No. 24-76 Oficina 1201 Colegio de Ciencias Biológicas y Ambientales-COCIBA & Galapagos Institute for the Arts and Sciences-GAIAS Universidad San Francisco de Quito-USFQ Department of Wildlife Ecology and Conservation University of Florida, 110 Newins-Ziegler Hall Fundación Estación de Biología, Cra 10 No. 24-76 Oficina 1201 ICNHS Federal University of Mato Grosso, Av. Alexandre Ferronato 1200, Setor Industrial Direction régionale de la Guyane ONF PROTERRA Instituto de Investigaciones de la Amazonía Peruana (IIAP), Av. A. Quiñones km 2,5 ACEER Foundation, Jirón Cusco No. 370 Amazon Conservation Team, Doekhieweg Oost #24 Institut de Ciència i Tecnologia Ambientals Universitat Autònoma de Barcelona Environmental Change Institute Oxford University Centre for the Environment Dyson Perrins Building, South Parks Road Instituto de Ciencias Naturales Universidad Nacional de Colombia, Apartado 7945 Instituto de Ciência Agrárias Universidade Federal Rural da Amazônia, Av. Presidente Tancredo Neves 2501 Escuela Profesional de Ingeniería Forestal Universidad Nacional de San Antonio Abad del Cusco, Jirón San Martín 451 Universidad Autónoma del Beni José Ballivián, Campus Universitario Final, Av. Ejercito Laboratory of Human Ecology Instituto Venezolano de Investigaciones Científicas - IVIC, Ado 20632 Cambridge University Botanic Garden 1 Brookside. School of Agriculture and Food Sciences - ARC Centre of Excellence for Environmental Decisions CEED The University of Queensland University of Campinas Plant Biology Department, Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Barão Geraldo, Campinas Resource Ecology Group Wageningen University & Research, Droevendaalsesteeg 3a, Lumen, building number 100 Laboratório de Ciências Ambientais Universidade Estadual do Norte Fluminense, Av. Alberto Lamego 2000 Instituto de Investigaciones para el Desarrollo Forestal (INDEFOR) Universidad de los Andes Conjunto Forestal Departamento de Biologia Universidade Federal do Amazonas - UFAM – Instituto de Ciências Biológicas – ICB1, Av General Rodrigo Octavio 6200 GeoIS El Día 369y El Telégrafo 3° Piso Department of Biology University of Maryland University of Nottingham University Park School of Environmental and Forest Sciences University of Washington Environmental Science and Policy Northern Arizona University Geography and the Environment University of Texas at Austin, 305 E. 23rd Street, CLA building Medio Ambiente PLUSPRETOL The Mauritius Herbarium Agricultural Services Ministry of Agro-Industry and Food Security Department of Bioscience Aarhus University, Building 1540 Ny Munkegade, Aarhus C FOMABO Manejo Forestal en las Tierras Tropicales de Bolivia Escuela de Ciencias Forestales (ESFOR) Universidad Mayor de San Simon (UMSS) Tropenbos International, Lawickse Allee 11 PO Box 232 School of Anthropology and Conservation University of Kent, Marlowe Building Herbario Nacional del Ecuador Universidad Técnica del Norte Instituto de Biodiversidade e Floresta Universidade Federal do Oeste do Pará, Rua Vera Paz, Campus Tapajós Facultad de Biologia Universidad Nacional de la Amazonia Peruana, Pevas 5ta cdra Department of Biology University of Missouri Departamento de Ecologia Universidade Estadual Paulista - UNESP – Instituto de Biociências – IB, Av. 24A, 1515, Bela Vista Departamento de Geografia Universidade Estadual Paulista -UNESP – Instituto de Geociências e Ciências Extas – IGCE Bela Vista
Published: 2019
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10. Determination of genetic relatedness from low-coverage human genome sequences using pedigree simulations

Author: Michael D. Martin, Montgomery Slatkin, Sergi Castellano, Flora Jay, Center for Theoretical Evolutionary Genomics [Berkeley] (CTEG), Department of Integrative Biology [Berkeley] (IB), University of California [Berkeley], University of California-University of California-University of California [Berkeley], University of California-University of California, Bioinformatique (LRI) (BioInfo - LRI), Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, and Department of Integrative Biology
Subjects: 0301 basic medicine, Genotype, [SDV]Life Sciences [q-bio], Genomics, Computational biology, Biology, Genome, Polymorphism, Single Nucleotide, Deep sequencing, DNA sequencing, Article, 03 medical and health sciences, Genetics, Humans, Computer Simulation, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, [STAT.AP]Statistics [stat]/Applications [stat.AP], Models, Genetic, Genome, Human, Pedigree, 030104 developmental biology, Ancient DNA, Pairwise comparison, Human genome, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Software
Abstract: We develop and evaluate methods for inferring relatedness among individuals from low-coverage DNA sequences of their genomes, with particular emphasis on sequences obtained from fossil remains. We suggest the major factors complicating the determination of relatedness among ancient individuals are sequencing depth, the number of overlapping sites, the sequencing error rate and the presence of contamination from present-day genetic sources. We develop a theoretical model that facilitates the exploration of these factors and their relative effects, via measurement of pairwise genetic distances, without calling genotypes, and determine the power to infer relatedness under various scenarios of varying sequencing depth, present-day contamination and sequencing error. The model is validated by a simulation study as well as the analysis of aligned sequences from present-day human genomes. We then apply the method to the recently published genome sequences of ancient Europeans, developing a statistical treatment to determine confidence in assigned relatedness that is, in some cases, more precise than previously reported. As the majority of ancient specimens are from animals, this method would be applicable to investigate kinship in nonhuman remains. The developed software grups (Genetic Relatedness Using Pedigree Simulations) is implemented in Python and freely available.
Published: 2017
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11. Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments

Author: Mikkel Schubert, Saleh A. Alquraishi, Andaine Seguin-Orlando, Clio Der Sarkissian, Tomas Marques-Bonet, Catherine Thèves, Eugenia S. Boulygina, Ruslan Popov, Cecilie Mortensen, Svetlana V. Tsygankova, Melinda A. Yang, Montgomery Slatkin, Eric Crubézy, Molly E. McCue, Alexei Tikhonov, Bent O. Petersen, Vidhya Jagannathan, Egor Prokhortchouk, Edward M. Rubin, Tosso Leeb, Markus Neuditschko, Matteo Fumagalli, Cristina Gamba, Anatoly N. Alekseev, Cindi A. Hoover, Rasmus Nielsen, Belen Lorente-Galdos, Juha Kantanen, Eske Willerslev, Semyon Grigoriev, Hakon Jonsson, Luca Ermini, Khaled A. S. Al-Rasheid, Pablo Librado, Stefan Rieder, Ludovic Orlando, Artem V. Nedoluzhko, Ahmed H. Alfarhan, Thomas Sicheritz-Pontén, Anders Albrechtsen, Danish Council for Independent Research, Danish National Research Foundation, European Commission, Université de Toulouse, German Research Foundation, King Abdulaziz University, King Saud University, Villum Fonden, Eurostat, Lundbeck Foundation, National Science Foundation (US), Human Frontier Science Program, National Institutes of Health (US), Academy of Finland, Ministère des Affaires étrangères (France), North-Eastern Federal University, Institut Polaire Français, Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Bioinformatics Centre, Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Science [Copenhagen], Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), Department of Integrative Biology, National High-Throughput DNA Sequencing Centre, University of Copenhagen = Københavns Universitet (KU), Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark [Lyngby] (DTU), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Universitat Pompeu Fabra [Barcelona] (UPF), Centro Nacional de Análisis Genómico, National Research Centre Kurchatov Institute, Agroscope, Swiss National Stud Farm, Institute of Genetics, University of Bern, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), King Saud University [Riyadh] (KSU), Yakutian Research Institute of Agriculture, College of Veterinary Medicine, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Zoological Institute of Russian Academy of Sciences, Russian Academy of Sciences [Moscow] (RAS), Center for Theoretical Evolutionary Genomics [Berkeley] (CTEG), Department of Integrative Biology [Berkeley] (IB), University of California [Berkeley], University of California-University of California-University of California [Berkeley], University of California-University of California, Agrifood Research Finland, Department of Biology, University of Eastern Finland, and University of Eastern Finland
Subjects: Pleistocene, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Population, Zoology, Population genetics, adaptation, Biology, Horse, regulatory changes, Evolution, Molecular, ancient genomics, Convergent evolution, MD Multidisciplinary, Animals, Horses, Adaptation, Domestication, education, education.field_of_study, Genome, Multidisciplinary, 630 Agriculture, Arctic Regions, Regulatory changes, Adaptation, Physiological, population discontinuity, horse, Cold Temperature, Siberia, Ancient genomics, Ancient DNA, PNAS Plus, Evolutionary developmental biology, 590 Animals (Zoology), 570 Life sciences, biology, Adaption, Population discontinuity
Abstract: Librado, Pablo et al., Yakutia is among the coldest regions in the Northern Hemisphere, showing ∼40% of its territory above the Arctic Circle. Native horses are particularly adapted to this environment, with body sizes and thick winter coats minimizing heat loss. We sequenced complete genomes of two ancient and nine present-day Yakutian horses to elucidate their evolutionary origins. We find that the contemporary population descends from domestic livestock, likely brought by early horse-riders who settled in the region a few centuries ago. The metabolic, anatomical, and physiological adaptations of these horses therefore emerged on very short evolutionary time scales. We show the relative importance of regulatory changes in the adaptive process and identify genes independently selected in cold-adapted human populations and woolly mammoths., This work was supported by the Danish Council for Independent Research, Natural Sciences (Grant 4002-00152B); the Danish National Research Foundation (Grant DNRF94); a Marie-Curie Career Integration grant (Grant FP7 CIG-293845); Initiative d'Excellence Chaires d'attractivité, Université de Toulouse (OURASI); and the International Research Group Program (Grant IRG14-08), Deanship of Scientific Research, King Saud University. P.L. was supported by a Villum Fonden Blokstipendier grant (primary investigator: L.O.); H.J. by a Marie-Curie Initial Training Network grant [EUROTAST (Exploring the History, Archeology, and New Genetics of the Transatlantic Slave Trade); Grant FP7 ITN-290344]; C.G. and L.E. by Marie-Curie Intra-European fellowships (FP7-IEF-328024 and FP7 IEF-302617); M. Schubert by a Lundbeck Foundation grant (Grant R52-A5062); M.A.Y. by a National Science Foundation Graduate Research fellowship; M.F. by a Human Frontier Science Program fellowship (LT000320/2014); A.A. by a Villum Fonden Blokstipendier grant; M. Schubert by an NIH grant (Grant R01-GM40282); and J.K. by the Academy of Finland (Grant 286040). Research work on the ancient Yakut population was supported by the French Archaeological Mission in Oriental Siberia (Ministry of Foreign and European Affairs, France), the North-Eastern Federal University (Yakutsk, Sakha Republic), and the Human Adaptation Program of the French Polar Institute Paul Emile Victor [HUMAD MAFSO (Missions Archéologiques Françaises en Sibérie Orientale) 1038].
Published: 2015
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12. Estimating the global conservation status of more than 15,000 Amazonian tree species

Author: Ted R. Feldpausch, Naara Ferreira da Silva, A C Gerardo Aymard, Henrique E. M. Nascimento, Milton Tirado, Egleé L. Zent, Nállarett Dávila, Ligia Estela Urrego Giraldo, Therany Gonzales, Dário Dantas do Amaral, Francisco Dallmeier, Maria Natalia Umaña Medina, William Milliken, Susan G. Laurance, Marcos Silveira, Rafael L. Assis, Natalia Targhetta, César I.A. Vela, Miguel Alexiades, Rafael de Paiva Salomão, Henrik Balslev, Ophelia Wang, Patricio von Hildebrand, E. M. Jimenez, Rodolfo Vasquez, José Ferreira Ramos, Alfonso Alonso, Alexandre Adalardo de Oliveira, Nicolás Castaño Arboleda, Leandro Valle Ferreira, Luis Valenzuela Gamarra, Bruce Hoffman, Roosevelt García-Villacorta, Jean-Louis Guillaumet, Alberto Vincentini, Bruno Garcia Luize, Bruno Barçante Ladvocat Cintra, Corine Vriesendorp, José Luís Camargo, Cláudia Baider, Dairon Cárdenas López, Álvaro Javier Duque Montoya, Adriana Prieto, Natalino Silva, Juan David Cardenas Revilla, Christopher Baraloto, Walter Palacios Cuenca, Hans ter Steege, Deborah de Castro, Geertje M. F. van der Heijden, Fernanda Carvalho, Ademir R. Ruschell, Tinde van Andel, Maria Pires Martins, Yadvinder Malhi, Beatriz Schwantes Marimon, Fernando Cornejo Valverde, Pablo Roberto Stevenson Diaz, Eduardo Martins Venticinque, Agustín Rudas, Marisol Toledo, Luiz de Souza Coelho, Mariana Victória Irume, Terry W. Henkel, Fernanda Coelho de Souza, Peter M. Jørgensen, Ben-Hur Marimon, Juliana Stropp, Francisca Dionízia de Almeida Matos, Daniel Sabatier, Alejandro Araujo-Murakami, Elvis H. Valderrama Sandoval, James A. Comiskey, Thaise Emilio, Roderick Zagt, Gabriel Damasco, Luiz Carlos de Matos Bonates, Neidiane Farias Costa Reis, Karina Garcia-Cabrera, Lionel Hernández, Marcelo Brilhante de Medeiros, William Farfan-Rios, Rodrigo Sierra, Florian Wittmann, Ima Célia Guimarães Vieira, William E. Magnusson, Miles R. Silman, Anthony Di Fiore, Diogenes de Andrade Lima Filho, Daniel Villarroel, Carolina Levis, Nigel C. A. Pitman, Isau Huamantupa-Chuquimaco, Italo Mesones, Priscila Souza, Carolina V. Castilho, Alfredo F. Fuentes, Katia Regina Casula, Jochen Schöngart, Adeilza Felipe Sampaio, Juan Fernando Phillips, Iêda Leão do Amaral, Carlos Cerón, Eurídice N. Honorio Coronado, Flávia R. C. Costa, Maria Cristina Peñuela Mora, Stanford Zent, Daniela Pauletto, Emanuelle de Sousa Farias, Ana Andrade, Bonifacio Mostacedo, Juan Ernesto Guevara, Raquel Thomas-Caesar, Paul V. A. Fine, Timothy R. Baker, Carlos A. Peres, Marcelo Trindade Nascimento, Hernán Castellanos, M. P. Pansonato, Armando Torres-Lezama, David A. Neill, Marcelo F. Simon, Casimiro Mendoza, José Renan da Silva Guimarães, William F. Laurance, Jean-François Molino, Ángela Cano, Juliana Schietti, Edelcilio Marques Barbosa, Joost F. Duivenvoorden, Angelo Gilberto Manzatto, Luzmila Arroyo, Doug Daly, Julien Engel, Natalia de Castro, Marcos Ríos Paredes, Cid Ferreira, Hirma Ramírez-Angulo, Oliver L. Phillips, Marcelo de Jesus Veiga Carim, Kenneth R. Young, Pascal Petronelli, Maria Teresa Fernandez Piedade, Abel Monteagudo Mendoza, Ires Paula de Andrade Miranda, Timothy J. Killeen, Susamar Pansini, Paul J. M. Maas, Charles E. Zartman, Vincent A. Vos, Emilio Vilanova Torre, Freddy Ramirez Arevalo, Percy Núñez Vargas, John Terborgh, Rogério Gribel, Roel J. W. Brienen, Juan Carlos Montero, Hugo Mogollón, Naturalis Biodiversity Center [Leiden], Duke University [Durham], Universidad de Las Américas [Ecuador] (UDLA), Museu Paraense Emílio Goeldi, Centro de Pesquisa Agroflorestal de Roraima, Brazilian Agricultural Research Corporation (Embrapa), Coordenac Bao de Pesquisas em Ecologia, Instituto Nacional de Pesquisas da Amazônia (INPA), Ecology and Global Change, School of Geography, University of Leeds, 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]), Universidad Nacional San Antonio Abad del Cusco, Division of Marine Science and Conservation, Nicholas School of the Environment, Missouri Bot Garden, 4344 Shaw Blvd, Missouri Botanical Garden (USA), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, James Cook University (JCU), School of Geography [Leeds], Department of Integrative Biology, Bot Grad Program, Inst Nacl de Pesquisas da Amazonia, University of Edinburgh, Smithsonian Conservation Biology Institute, Smithsonian Conservation Biology Institute, Center for Conservation Education and Sustainability, MRC 705, Box 37012, Washington, DC, VA 20013-7012, USA, Universidad Estatal Amazonica, Museo de Historia Natural Noel Kempff Mercado, Universidad Autonoma Gabriel René Moreno, Laboratório de Genética e Biologia Reprodutiva de Plantas, Department of Integrative Biology [Berkeley] (IB), University of California [Berkeley], University of California-University of California, Universidad Autonoma Gabriel René Moreno (UAGRM), Herbario Nacional del Ecuador, Humboldt State University (HSU), Universidad Nacional de Colombia, Department of Botany, Naturalis Biodiversity Center, Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Universidade Federal do Acre (UFAC), Utrecht University [Utrecht], Chercheur indépendant, Andes to Amazon Biodiversity Program, University of Texas at Austin [Austin], Muséum national d'Histoire naturelle (MNHN), Centre for the Environment, University of Oxford [Oxford], Instituto de Medicina Tropical 'Alexander von Humboldt' (IMT AvH), Universidad Peruana Cayetano Heredia, Universidad Nacional de Colombia [Bogotà] (UNAL), Instituto de Investigaciones para el Desarrollo Forestal, Universidad de los Andes [Bogota], Geoinformática y Sistemas , Cia. Ltda (GeoIS), School of Geography, University of Oxford, Sch Earth Sci & Environm Sustainabil, Northern Arizona University [Flagstaff], Instituto de Manejo Forestal, University of Kent [Canterbury], Royal Botanic Garden , Kew, Museu Paraense Emílio Goeldi [Belém, Brésil] (MPEG), 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]), Universidad Nacional de San Antonio Abad del Cusco (UNSAAC), Missouri Botanical Garden, Universidad Peruana Cayetano Heredia (UPCH), Universidad de los Andes [Bogota] (UNIANDES), Alberta Mennega Stichting, ALCOA Suriname, Amazon Conservation Association, Banco de la Republica, CELOS Suriname, CAPES (PNPG), Conselho Nacional de Desenvovimento Cientifico e Tecnologico of Brazil (CNPq), PELD [558069/2009-6, 403792/2012-6], PRONEX-FAPEAM [1600/2006], Areas Umidas, MAUA, PPBio, PVE [004/2012], Universal [479599/2008-4, 3078072009-6], FAPEAM [DCR/2006], Hidroveg, FAPESP, PRONEX, Colciencias, CONICIT, Duke University, Ecopetrol, FEPIM [044/2003], The Field Museum, Conservation International/DC, Gordon and Betty Moore Foundation, Guyana Forestry Commission, Investissement d'Avenir grant of the French ANR [ANR-10-LABX-0025], IVIC, Margaret Mee Amazon Trust, Miquel fonds, MCTI-Museu Paraense Emilio Goeldi-Proc [407232/2013-3-PVE-MEC/MCTI/CAPES/CNPq], National Geographic Society [7754-04, 8047-06, 6679-99, 7435-03, 8481-08], NSF Dissertation Improvement, Netherlands Foundation for the Advancement of Tropical Research WOTRO [WB85-335, W84-581], Primate Conservation Inc., Programme Ecosystemes Tropicaux (French Ministry of Ecology and Sustainable Development), Shell Prospecting and Development Peru, Smithsonian Institution's Biological Diversity of the Guiana Shield Program, Stichting het van Eeden-fonds, The Body Shop, The Ministry of the Environment of Ecuador, TROBIT, Tropenbos International, U.S. National Science Foundation [NSF-0743457, NSF0101775, NSF-0918591], USAID, Variety Woods Guyana, Wenner-Gren Foundation, WWF-Brazil, WWF-Guianas, Xlleme Contrat de Plan Etat Region-Guyane (French Government and European Union), European Union, UK Natural Environment Research Council, Gordon and BettyMoore Foundation, European Research Council Advanced Grant, Royal Society Wolfson Research Merit Award, [NSF-0726797], University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), University of Oxford, Royal Botanic Gardens [Kew], AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Université des Antilles (UA)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Paleoecology and Landscape Ecology (IBED, FNWI), ter Steege, Hans, Hans ter Steege, Biodiversity Dynamics, Naturalis Biodiversity Center / Utrecht University, Nigel C. A. Pitman, The Field Museum / Duke University, Timothy J. Killeen, Agteca-Amazonica, William F. Laurance, James Cook University, Carlos A. Peres, University of East Anglia, Juan Ernesto Guevara, University of California / Museo Ecuatoriano de Ciencias Naturales, Rafael P. Salomão, MPEG, CAROLINA VOLKMER DE CASTILHO, CPAF-RR, Iêda Leão Amaral, INPA, Francisca Dionízia de Almeida Matos, INPA, Luiz de Souza Coelho, INPA, William E. Magnusson, INPA, Oliver L. Phillips, University of Leeds, Diogenes de Andrade Lima Filho, INPA, Marcelo de Jesus Veiga Carim, IEPA, Mariana Victória Irume, INPA, Maria Pires Martins, INPA, Jean-François Molino, Institut de Recherche pour le Développement (IRD), Daniel Sabatier, Institut de Recherche pour le Développement (IRD), Florian Wittmann, Max Planck Institute for Chemistry, Dairon Cárdenas López, Herbario Amazónico Colombiano, Instituto SINCHI, José Renan da Silva Guimarães, IEPA, Abel Monteagudo Mendoza, Jardín Botánico de Missouri, Percy Núñez Vargas, Universidad Nacional de San Antonio Abad del Cusco, Angelo Gilberto Manzatto, UFRO, Neidiane Farias Costa Reis, UFRO, John Terborgh, Duke University, Katia Regina Casula, UFRO, Juan Carlos Montero, INPA / Instituto Boliviano de Investigacion Forestal, Universidad Autónoma Gabriel René Moreno, Ted R. Feldpausch, University of Leeds / University of Exeter, Euridice N. Honorio Coronado, University of Leeds / Instituto de Investigaciones de la Amazonía Peruana, Alvaro Javier Duque Montoya, Universidad Nacional de Colombia, Charles Eugene Zartman, INPA, Bonifacio Mostacedo, Universidad Autónoma Gabriel René Moreno, Rodolfo Vasquez, Jardín Botánico de Missouri, Rafael L. Assis, INPA, MARCELO BRILHANTE DE MEDEIROS, CENARGEN, MARCELO FRAGOMENI SIMON, CENARGEN, Ana Andrade, INPA, José Luís Camargo, INPA, Susan G. W. Laurance, James Cook University, Henrique Eduardo Mendonça Nascimento, INPA, Beatriz S. Marimon, Universidade do Estado de Mato Grosso, Ben-Hur Marimon Jr., Universidade do Estado de Mato Grosso, Flávia Costa, INPA, Natalia Targhetta, INPA, Ima Célia Guimarães Vieira, MPEG, Roel Brienen, University of Leeds, Hernán Castellanos, Universidad Nacional Experimental de Guayana, Joost F. Duivenvoorden, University of Amsterdam, Hugo F. Mogollón, Endangered Species Coalition, Maria Teresa Fernandez Piedade, INPA, Gerardo A. Aymard C., Herbario Universitario (PORT), UNELLEZ-Guanare, James A. Comiskey, National Park Service, Gabriel Damasco, University of California, Nállarett Dávila, Universidade Estadual de Campinas, Roosevelt García-Villacorta, University of Edinburgh / Royal Botanic Garden of Edinburgh, Pablo Roberto Stevenson Diaz, Universidad de los Andes, Alberto Vincentini, INPA, Thaise Emilio, INPA / Royal Botanic Gardens, Carolina Levis, INPA / University of Wageningen, Juliana Schietti, INPA, Priscila Souza, INPA, Alfonso Alonso, Smithsonian Conservation Biology Institute, National Zoological Park, Francisco Dallmeier, Smithsonian Conservation Biology Institute, National Zoological Park, Leandro Valle Ferreira, MPEG, David Neill, Universidad Estatal Amazónica, Alejandro Araujo-Murakami, Universidad Autónoma Gabriel Rene Moreno, Luzmila Arroyo, Universidad Autónoma Gabriel Rene Moreno, Fernanda Antunes Carvalho, INPA, Fernanda Coelho Souza, INPA, Dário Dantas do Amaral, MPEG, Rogerio Gribel, Jardim Botânico do Rio de Janeiro, Bruno Garcia Luize, INPA, Marcelo Petrati Pansonato, INPA, Eduardo Venticinque, UFRN, Paul Fine, University of California, Marisol Toledo, Universidad Autónoma Gabriel René Moreno, Chris Baraloto, INRA / Florida International University, Carlos Cerón, Escuela de Biología Herbario Alfredo Paredes, Universidad Central, Julien Engel, UMR Ecologie des Forêts de Guyane, CNRS, Terry W. Henkel, Humboldt State University, Eliana M. Jimenez, Universidad Nacional de Colombia Sede Amazonía, Paul Maas, Taxonomy and Systematics, Naturalis Biodiversity Center, Maria Cristina Peñuela Mora, Universidad Regional Amazónica IKIAM, Pascal Petronelli, INRA, Juan David Cardenas Revilla, INPA, Marcos Silveira, UFAC, Juliana Stropp, Joint Research Centre of the European Commission / Federal University of Alagoas, Raquel Thomas-Caesar, Iwokrama International Programme for Rainforest Conservation, Tim R. Baker, University of Leeds, Doug Daly, New York Botanical Garden, Marcos Ríos Paredes, Servicios de Biodiversidad EIRL, Naara Ferreira da Silva, INPA, Alfredo Fuentes, Herbario Nacional de Bolivia, Universitario UMSA, Peter Møller Jørgensen, Missouri Botanical Garden, Jochen Schöngart, Max Planck Institute for Chemistry, Miles R. Silman, Wake Forest University, Nicolás Castaño Arboleda, Herbario Amazónico Colombiano, Instituto SINCHI, Bruno Barçante Ladvocat Cintra, INPA, Fernando Cornejo Valverde, Andes to Amazon Biodiversity Program, Anthony Di Fiore, University of Texas at Austin, Juan Fernando Phillips, Fundación Puerto Rastrojo, Tinde R. van Andel, Biodiversity Dynamics, Naturalis Biodiversity Center, Patricio von Hildebrand, Fundación Estación de Biología, Edelcilio Marques Barbosa, INPA, Luiz Carlos de Matos Bonates, INPA, Deborah de Castro, INPA, Emanuelle de Sousa Farias, Instituto Leônidas e Maria Deane, Therany Gonzales, ACEER Foundation, Jean-Louis Guillaumet, Muséum national d’histoire naturelle de Paris, Bruce Hoffman, Amazon Conservation Team, Yadvinder Malhi, Oxford University Centre for the Environment, Ires Paula de Andrade Miranda, INPA, Adriana Prieto, Universidad Nacional de Colombia, Agustín Rudas, Universidad Nacional de Colombia, ADEMIR ROBERTO RUSCHEL, CPATU, Natalino Silva, UFRA, César I. A. Vela, Universidad Nacional de San Antonio Abad del Cusco, Vincent A. Vos, Universidad Autónoma del Beni / Centro de Investigación y Promoción del Campesinado, Eglée L. Zent, Instituto Venezolano de Investigaciones Científicas - IVIC, Stanford Zent, Instituto Venezolano de Investigaciones Científicas - IVIC, Angela Cano, Universidad de los Andes, Marcelo Trindade Nascimento, Universidade Estadual do Norte Fluminense, Alexandre A. Oliveira, USP, Hirma Ramirez-Angulo, Instituto de Investigaciones para el Desarrollo Forestal (INDEFOR), Universidad de los Andes, José Ferreira Ramos, INPA, Rodrigo Sierra, GeoIS, Milton Tirado, GeoIS, Maria Natalia Umaña Medina, University of Maryland, Geertje van der Heijden, University ofWisconsin-Milwaukee, Emilio Vilanova Torre, Instituto de Investigaciones para el Desarrollo Forestal (INDEFOR), Universidad de los Andes, Corine Vriesendorp, The Field Museum, Ophelia Wang, Northern Arizona University, Kenneth R. Young, University of Texas at Austin, Claudia Baider, USP / Agricultural Services, Ministry of Agro-Industry and Food Security, The Mauritius Herbarium, Henrik Balslev, Aarhus University, Natalia de Castro, INPA, William Farfan-Rios, Wake Forest University, Cid Ferreira, INPA, Casimiro Mendoza, FOMABO, Manejo Forestal en las Tierras Tropicales de Bolivia / UniversidadMayor de San Simon, Italo Mesones, University of California, Armando Torres-Lezama, Instituto de Investigaciones para el Desarrollo Forestal (INDEFOR), Universidad de los Andes, Ligia Estela Urrego Giraldo, Universidad Nacional de Colombia, Daniel Villarroel, Universidad Autónoma Gabriel Rene Moreno, Roderick Zagt, Tropenbos International, Miguel N. Alexiades, University of Kent, Karina Garcia-Cabrera, Wake Forest University, Lionel Hernandez, Universidad Nacional Experimental de Guayana, Isau Huamantupa-Chuquimaco, Universidad Nacional de San Antonio Abad del Cusco, William Milliken, Royal Botanic Gardens, Walter Palacios Cuenca, Herbario Nacional del Ecuador, Universidad Técnica del Norte, Susamar Pansini, UFRO, Daniela Pauletto, Universidade Federal do Oeste do Pará, Freddy Ramirez Arevalo, Universidad Nacional de laAmazonia Peruana, Adeilza Felipe Sampaio, UFRO, Elvis H. Valderrama Sandoval, Universidad Nacional de laAmazonia Peruana / University of Missouri, Luis Valenzuela Gamarra, Jardín Botánico de Missouri., HANS TER STEEGE, Biodiversity Dynamics, Naturalis Biodiversity Center / Utrecht University, NIGEL C. A. PITMAN, The Field Museum / Duke University, TIMOTHY J. KILLEEN, Agteca-Amazonica, WILLIAM F. LAURANCE, James Cook University, CARLOS A. PERES, University of East Anglia, JUAN ERNESTO GUEVARA, University of California / Museo Ecuatoriano de Ciencias Naturales, RAFAEL P. SALOMÃO, MPEG, IÊDA LEÃO AMARAL, INPA, FRANCISCA DIONÍZIA DE ALMEIDA MATOS, INPA, LUIZ DE SOUZA COELHO, INPA, WILLIAM E. MAGNUSSON, INPA, OLIVER L. PHILLIPS, University of Leeds, DIOGENES DE ANDRADE LIMA FILHO, INPA, MARCELO DE JESUS VEIGA CARIM, IEPA, MARIANA VICTÓRIA IRUME, INPA, MARIA PIRES MARTINS, INPA, JEAN-FRANÇOIS MOLINO, Institut de Recherche pour le Développement (IRD), DANIEL SABATIER, Institut de Recherche pour le Développement (IRD), FLORIAN WITTMANN, Max Planck Institute for Chemistry, DAIRON CÁRDENAS LÓPEZ, Herbario Amazónico Colombiano, Instituto SINCHI, JOSÉ RENAN DA SILVA GUIMARÃES, IEPA, ABEL MONTEAGUDO MENDOZA, Jardín Botánico de Missouri, PERCY NÚÑEZ VARGAS, Universidad Nacional de San Antonio Abad del Cusco, ANGELO GILBERTO MANZATTO, UFRO, NEIDIANE FARIAS COSTA REIS, UFRO, JOHN TERBORGH, Duke University, KATIA REGINA CASULA, UFRO, JUAN CARLOS MONTERO, INPA / Instituto Boliviano de Investigacion Forestal, Universidad Autónoma Gabriel René Moreno, TED R. FELDPAUSCH, University of Leeds / University of Exeter, EURIDICE N. HONORIO CORONADO, University of Leeds / Instituto de Investigaciones de la Amazonía Peruana, ALVARO JAVIER DUQUE MONTOYA, Universidad Nacional de Colombia, CHARLES EUGENE ZARTMAN, INPA, BONIFACIO MOSTACEDO, Universidad Autónoma Gabriel René Moreno, RODOLFO VASQUEZ, Jardín Botánico de Missouri, RAFAEL L. ASSIS, INPA, ANA ANDRADE, INPA, JOSÉ LUÍS CAMARGO, INPA, SUSAN G. W. LAURANCE, James Cook University, HENRIQUE EDUARDO MENDONÇA NASCIMENTO, INPA, BEATRIZ S. MARIMON, Universidade do Estado de Mato Grosso, BEN-HUR MARIMON JR., Universidade do Estado de Mato Grosso, FLÁVIA COSTA, INPA, NATALIA TARGHETTA, INPA, IMA CÉLIA GUIMARÃES VIEIRA, MPEG, ROEL BRIENEN, University of Leeds, HERNÁN CASTELLANOS, Universidad Nacional Experimental de Guayana, JOOST F. DUIVENVOORDEN, University of Amsterdam, HUGO F. MOGOLLÓN, Endangered Species Coalition, MARIA TERESA FERNANDEZ PIEDADE, INPA, GERARDO A. AYMARD C., Herbario Universitario (PORT), UNELLEZ-Guanare, JAMES A. COMISKEY, National Park Service, GABRIEL DAMASCO, University of California, NÁLLARETT DÁVILA, Universidade Estadual de Campinas, ROOSEVELT GARCÍA-VILLACORTA, University of Edinburgh / Royal Botanic Garden of Edinburgh, PABLO ROBERTO STEVENSON DIAZ, Universidad de los Andes, ALBERTO VINCENTINI, INPA, THAISE EMILIO, INPA / Royal Botanic Gardens, CAROLINA LEVIS, INPA / University of Wageningen, JULIANA SCHIETTI, INPA, PRISCILA SOUZA, INPA, ALFONSO ALONSO, Smithsonian Conservation Biology Institute, National Zoological Park, FRANCISCO DALLMEIER, Smithsonian Conservation Biology Institute, National Zoological Park, LEANDRO VALLE FERREIRA, MPEG, DAVID NEILL, Universidad Estatal Amazónica, ALEJANDRO ARAUJO-MURAKAMI, Universidad Autónoma Gabriel Rene Moreno, LUZMILA ARROYO, Universidad Autónoma Gabriel Rene Moreno, FERNANDA ANTUNES CARVALHO, INPA, FERNANDA COELHO SOUZA, INPA, DÁRIO DANTAS DO AMARAL, MPEG, ROGERIO GRIBEL, Jardim Botânico do Rio de Janeiro, BRUNO GARCIA LUIZE, INPA, MARCELO PETRATI PANSONATO, INPA, EDUARDO VENTICINQUE, UFRN, PAUL FINE, University of California, MARISOL TOLEDO, Universidad Autónoma Gabriel René Moreno, CHRIS BARALOTO, INRA / Florida International University, CARLOS CERÓN, Escuela de Biología Herbario Alfredo Paredes, Universidad Central, JULIEN ENGEL, UMR Ecologie des Forêts de Guyane, CNRS, TERRY W. HENKEL, Humboldt State University, ELIANA M. JIMENEZ, Universidad Nacional de Colombia Sede Amazonía, PAUL MAAS, Taxonomy and Systematics, Naturalis Biodiversity Center, MARIA CRISTINA PEÑUELA MORA, Universidad Regional Amazónica IKIAM, PASCAL PETRONELLI, INRA, JUAN DAVID CARDENAS REVILLA, INPA, MARCOS SILVEIRA, UFAC, JULIANA STROPP, Joint Research Centre of the European Commission / Federal University of Alagoas, RAQUEL THOMAS-CAESAR, Iwokrama International Programme for Rainforest Conservation, TIM R. BAKER, University of Leeds, DOUG DALY, New York Botanical Garden, MARCOS RÍOS PAREDES, Servicios de Biodiversidad EIRL, NAARA FERREIRA DA SILVA, INPA, ALFREDO FUENTES, Herbario Nacional de Bolivia, Universitario UMSA, PETER MØLLER JØRGENSEN, Missouri Botanical Garden, JOCHEN SCHÖNGART, Max Planck Institute for Chemistry, MILES R. SILMAN, Wake Forest University, NICOLÁS CASTAÑO ARBOLEDA, Herbario Amazónico Colombiano, Instituto SINCHI, BRUNO BARÇANTE LADVOCAT CINTRA, INPA, FERNANDO CORNEJO VALVERDE, Andes to Amazon Biodiversity Program, ANTHONY DI FIORE, University of Texas at Austin, JUAN FERNANDO PHILLIPS, Fundación Puerto Rastrojo, TINDE R. VAN ANDEL, Biodiversity Dynamics, Naturalis Biodiversity Center, PATRICIO VON HILDEBRAND, Fundación Estación de Biología, EDELCILIO MARQUES BARBOSA, INPA, LUIZ CARLOS DE MATOS BONATES, INPA, DEBORAH DE CASTRO, INPA, EMANUELLE DE SOUSA FARIAS, Instituto Leônidas e Maria Deane, THERANY GONZALES, ACEER Foundation, JEAN-LOUIS GUILLAUMET, Muséum national d’histoire naturelle de Paris, BRUCE HOFFMAN, Amazon Conservation Team, YADVINDER MALHI, Oxford University Centre for the Environment, IRES PAULA DE ANDRADE MIRANDA, INPA, ADRIANA PRIETO, Universidad Nacional de Colombia, AGUSTÍN RUDAS, Universidad Nacional de Colombia, NATALINO SILVA, UFRA, CÉSAR I. A. VELA, Universidad Nacional de San Antonio Abad del Cusco, VINCENT A. VOS, Universidad Autónoma del Beni / Centro de Investigación y Promoción del Campesinado, EGLÉE L. ZENT, Instituto Venezolano de Investigaciones Científicas - IVIC, STANFORD ZENT, Instituto Venezolano de Investigaciones Científicas - IVIC, ANGELA CANO, Universidad de los Andes, MARCELO TRINDADE NASCIMENTO, Universidade Estadual do Norte Fluminense, ALEXANDRE A. OLIVEIRA, USP, HIRMA RAMIREZ-ANGULO, Instituto de Investigaciones para el Desarrollo Forestal (INDEFOR), Universidad de los Andes, JOSÉ FERREIRA RAMOS, INPA, RODRIGO SIERRA, GeoIS, MILTON TIRADO, GeoIS, MARIA NATALIA UMAÑA MEDINA, University of Maryland, GEERTJE VAN DER HEIJDEN, University ofWisconsin-Milwaukee, EMILIO VILANOVA TORRE, Instituto de Investigaciones para el Desarrollo Forestal (INDEFOR), Universidad de los Andes, CORINE VRIESENDORP, The Field Museum, OPHELIA WANG, Northern Arizona University, KENNETH R. YOUNG, University of Texas at Austin, CLAUDIA BAIDER, USP / Agricultural Services, Ministry of Agro-Industry and Food Security, The Mauritius Herbarium, HENRIK BALSLEV, Aarhus University, NATALIA DE CASTRO, INPA, WILLIAM FARFAN-RIOS, Wake Forest University, CID FERREIRA, INPA, CASIMIRO MENDOZA, FOMABO, Manejo Forestal en las Tierras Tropicales de Bolivia / UniversidadMayor de San Simon, ITALO MESONES, University of California, ARMANDO TORRES-LEZAMA, Instituto de Investigaciones para el Desarrollo Forestal (INDEFOR), Universidad de los Andes, LIGIA ESTELA URREGO GIRALDO, Universidad Nacional de Colombia, DANIEL VILLARROEL, Universidad Autónoma Gabriel Rene Moreno, RODERICK ZAGT, Tropenbos International, MIGUEL N. ALEXIADES, University of Kent, KARINA GARCIA-CABRERA, Wake Forest University, LIONEL HERNANDEZ, Universidad Nacional Experimental de Guayana, ISAU HUAMANTUPA-CHUQUIMACO, Universidad Nacional de San Antonio Abad del Cusco, WILLIAM MILLIKEN, Royal Botanic Gardens, WALTER PALACIOS CUENCA, Herbario Nacional del Ecuador, Universidad Técnica del Norte, SUSAMAR PANSINI, UFRO, DANIELA PAULETTO, Universidade Federal do Oeste do Pará, FREDDY RAMIREZ AREVALO, Universidad Nacional de laAmazonia Peruana, ADEILZA FELIPE SAMPAIO, UFRO, ELVIS H. VALDERRAMA SANDOVAL, Universidad Nacional de laAmazonia Peruana / University of Missouri, and LUIS VALENZUELA GAMARRA, Jardín Botánico de Missouri.
Subjects: Conservation Status, Land Use Policy, Geography & travel, Amazonian, Threatened Species, Conservation-dependent species, Protected Areas, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Conservation Planning, Land Use, IUCN Red List, Deforestation, Research Articles, ddc:910, Multidisciplinary, Near-threatened species, Extinction Risks, Ecology, Conservação, Amazonia, Conservation, Protected areas, Indigenous areas, Tree species, SciAdv r-articles, Gap analysis (conservation), Forestry, Tropical Tree Species, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, PE&RC, Geography, Research Article, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Life Science, Bosecologie en Bosbeheer, Indigenous People, Tropics, 15. Life on land, Forest Ecology and Forest Management, Espécie, 13. Climate action, Threatened species, Conservation status, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Environmental Protection, Desmatamento
Abstract: Analyses of forest loss and protected areas suggest that 36 to 57% of Amazonian tree flora may qualify as “globally threatened.”, Estimates of extinction risk for Amazonian plant and animal species are rare and not often incorporated into land-use policy and conservation planning. We overlay spatial distribution models with historical and projected deforestation to show that at least 36% and up to 57% of all Amazonian tree species are likely to qualify as globally threatened under International Union for Conservation of Nature (IUCN) Red List criteria. If confirmed, these results would increase the number of threatened plant species on Earth by 22%. We show that the trends observed in Amazonia apply to trees throughout the tropics, and we predict that most of the world’s >40,000 tropical tree species now qualify as globally threatened. A gap analysis suggests that existing Amazonian protected areas and indigenous territories will protect viable populations of most threatened species if these areas suffer no further degradation, highlighting the key roles that protected areas, indigenous peoples, and improved governance can play in preventing large-scale extinctions in the tropics in this century.
Published: 2015
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13. The phylogeny and taxonomy of Hippopotamidae (Mammalia: Artiodactyla): a review based on morphology and cladistic analysis

Author: Jean-Renaud Boisserie, Laboratoire de géobiologie, biochronologie et paléontologie humaine (LGBPH), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Department of Integrative Biology & Museum of Vertebrate Zoology, and Department of Integrative Biology
Subjects: 0106 biological sciences, Paraphyly, Hippopotamus sp, Pliocene, Sous-continent indien, cladistique, aff. Hippopotamus sp, 01 natural sciences, Hippopotamidae, Afrique, Genus, actuel, Ungulata, ComputingMilieux_MISCELLANEOUS, Moyen Orient, Phylogeny, Méditerranée occidentale, Diversity, biology, Choeropsis liberiensis, Cladistics, Europe, Eukaryotae, Diagnose, Hexaprotodon sp, Mammalia, Taxonomy (biology), Neogene, Anatomy, Cénozoïque, Néogène, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Morphology, Systematics, Archaeopotamus sp, 010506 paleontology, Asia, Miocène récent, Hexaprotodon ? sp, Evolution, taxonomie, Asie, Zoology, biométrie, 010603 evolutionary biology, Pliocène, systématique, phylogénie, Pléistocène, Cetartiodactyla, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Vertebrata, Metazoa, Hexaprotodon, Miocene, biology.organism_classification, anatomie descriptive et comparée, Afrique centrale, Taxon, Africa, Afrique orientale, Animal Science and Zoology
Abstract: The phylogeny and taxonomy of the whole family Hippopotamidae is in need of reconsideration, the present confusion obstructing palaeoecology and palaeobiogeography studies of these Neogene mammals. The revision of the Hippopotamidae initiated here deals with the last 8 Myr of African and Asian species. The first thorough cladistic analysis of the family is presented here. The outcome of this analysis, including 37 morphological characters coded for 15 extant and fossil taxa, as well as non-coded features of mandibular morphology, was used to reconstruct broad outlines of hippo phylogeny. Distinct lineages within the paraphyletic genus Hexaprotodon are recognized and characterized. In order to harmonize taxonomy and phylogeny, two new genera are created. The genus name Choeropsis is re-validated for the extant Liberian hippo. The nomen Hexaprotodon is restricted to the fossil lineage mostly known in Asia, but also including at least one African species. The genus Hippopotamus is confirmed. These changes represent substantial advances for understanding the evolutionary history of the Hippopotamidae, and provide a new framework for future studies. © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society, 2005, 143, 1–26.
Published: 2005
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14. Effects of acute and chronic exercise on sarcolemmal MCT1 and MCT4 contents in human skeletal muscles: current status

Author: George A. Brooks, Claire Thomas, Karen Lambert, David Bishop, Jacques Mercier, French Institute of Sport (INSEP), Research Department, Laboratory Sport, Expertise and Performance (EA7370) (SEP (EA7370)), Institut national du sport, de l'expertise et de la performance (INSEP), Physiologie & médecine expérimentale du Cœur et des Muscles [U 1046] (PhyMedExp), Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université d'Évry-Val-d'Essonne (UEVE), Institute of Sport, Exercise and Active Living (ISEAL), School of Sport and Exercise Science, Victoria University, Melbourne, Victoria University [Melbourne], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Department of Integrative Biology [Berkeley] (IB), University of California [Berkeley], University of California-University of California, French Institute of Sport (INSEP), Laboratory Sport, Expertise and Performance (EA7370) (SEP (EA7370)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Département STAPS - UFR Sciences Fondamentales Appliquées, Université d'Évry-Val-d'Essonne ( UEVE ), French Institute of Sport (INSEP), Research Department, Laboratory Sport, Expertise and Performance (EA7370) ( SEP (EA7370) ), Institut national du sport, de l'expertise et de la performance ( INSEP ), Physiologie & médecine expérimentale du Cœur et des Muscles [U 1046] ( PhyMedExp ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Centre Hospitalier Universitaire de Montpellier ( CHU Montpellier ), Department of Integrative Biology, University of California, and INSEP, documentation
Subjects: Monocarboxylic Acid Transporters, Gene isoform, Lactate transport, medicine.medical_specialty, [SDV.MHEP.PHY] Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Physiology, Muscle Proteins, [ SHS.SPORT ] Humanities and Social Sciences/Sport, 03 medical and health sciences, Sarcolemma, 0302 clinical medicine, lactate transport capacity, Physiology (medical), Internal medicine, medicine, [SDV.MHEP.PHY]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Humans, Exercise physiology, Muscle, Skeletal, Exercise, monocarboxylate transporters, 030304 developmental biology, 0303 health sciences, Messenger RNA, training, Symporters, business.industry, [ SHS.SPORT.PS ] Humanities and Social Sciences/Sport/Sport physiology, Skeletal muscle, Transporter, Hydrogen-Ion Concentration, Hypoxia (medical), Endocrinology, medicine.anatomical_structure, Lactates, medicine.symptom, Cotransporter, business, 030217 neurology & neurosurgery
Abstract: Two lactate/proton cotransporter isoforms (monocarboxylate transporters, MCT1 and MCT4) are present in the plasma (sarcolemmal) membranes of skeletal muscle. Both isoforms are symports and are involved in both muscle pH and lactate regulation. Accordingly, sarcolemmal MCT isoform expression may play an important role in exercise performance. Acute exercise alters human MCT content, within the first 24 h from the onset of exercise. The regulation of MCT protein expression is complex after acute exercise, since there is not a simple concordance between changes in mRNA abundance and protein levels. In general, exercise produces greater increases in MCT1 than in MCT4 content. Chronic exercise also affects MCT1 and MCT4 content, regardless of the initial fitness of subjects. On the basis of cross-sectional studies, intensity would appear to be the most important factor regulating exercise-induced changes in MCT content. Regulation of skeletal muscle MCT1 and MCT4 content by a variety of stimuli inducing an elevation of lactate level (exercise, hypoxia, nutrition, metabolic perturbations) has been demonstrated. Dissociation between the regulation of MCT content and lactate transport activity has been reported in a number of studies, and changes in MCT content are more common in response to contractile activity, whereas changes in lactate transport capacity typically occur in response to changes in metabolic pathways. Muscle MCT expression is involved in, but is not the sole determinant of, muscle H+and lactate anion exchange during physical activity.
Published: 2012
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15. Disentangling stand and environmental correlates of aboveground biomass in Amazonian forests

Author: Baraloto, Christopher, Rabaud, Suzanne, Molto, Quentin, Blanc, Lilian, FORTUNEL, Claire, Hérault, Bruno, DÁVILA, NALLARETT, Mesones, Italo, Rios, Marcos, Valderrama, Elvis, Fine, Paul V. A., Ecologie des forêts de Guyane (ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université des Antilles et de la Guyane (UAG)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Department of Integrative Biology [Berkeley] (IB), University of California [Berkeley], University of California-University of California, Universidad Nacional de la Amazonía Peruana [Loreto, Perou] (UNAP), Universidad nacional de la amazonia peruana, Départment of biology, University of Central Florida [Orlando] (UCF), Department of biology, University of Florida [Gainesville] (UF), Université des Antilles et de la Guyane (UAG), Botany Graduate Program, Instituto Nacional de Pesquisas da Amazônia (INPA), Department of integrative biology, University of California, and Departement of integrative biology
Subjects: Carbone, P40 - Météorologie et climatologie, REDD, [SDE.MCG]Environmental Sciences/Global Changes, Climate, [SDV]Life Sciences [q-bio], Stockage, F62 - Physiologie végétale - Croissance et développement, Forêt inondée, Facteur climatique, Flooded forest, K01 - Foresterie - Considérations générales, Biomasse, Peru, Tropical rainforest, Propriété physicochimique du sol, Forêt tropicale humide, White sand forest, ComputingMilieux_MISCELLANEOUS, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, U10 - Informatique, mathématiques et statistiques, White-sand forest, P35 - Fertilité du sol, Wood specific gravity, Facteur édaphique, French Guiana, Carbon stocks, Gravité, Soil properties, Modèle mathématique, forest structure
Abstract: Tropical forests contain an important proportion of the carbon stored in terrestrial vegetation, but estimated aboveground biomass (AGB) in tropical forests varies two-fold, with little consensus on the relative importance of climate, soil and forest structure in explaining spatial patterns. Here, we present analyses from a plot network designed to examine differences among contrasting forest habitats (terra firme, seasonally flooded, and white-sand forests) that span the gradient of climate and soil conditions of the Amazon basin. We installed 0.5-ha plots in 74 sites representing the three lowland forest habitats in both Loreto, Peru and French Guiana, and we integrated data describing climate, soil physical and chemical characteristics and stand variables, including local measures of wood specific gravity (WSG). We use a hierarchical model to separate the contributions of stand variables from climate and soil variables in explaining spatial variation in AGB. AGB differed among both habitats and regions, varying from 78 Mg ha−1 in white-sand forest in Peru to 605 Mg ha−1 in terra firme clay forest of French Guiana. Stand variables including tree size and basal area, and to a lesser extent WSG, were strong predictors of spatial variation in AGB. In contrast, soil and climate variables explained little overall variation in AGB, though they did co-vary to a limited extent with stand parameters that explained AGB. Our results suggest that positive feedbacks in forest structure and turnover control AGB in Amazonian forests, with richer soils (Peruvian terra firme and all seasonally flooded habitats) supporting smaller trees with lower wood density and moderate soils (French Guianan terra firme) supporting many larger trees with high wood density. The weak direct relationships we observed between soil and climate variables and AGB suggest that the most appropriate approaches to landscape scale modeling of AGB in the Amazon would be based on remote sensing methods to map stand structure.
Published: 2011
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16. Analysis of waveform and amplitude of mouse rod and cone flash responses

Author: Jürgen Reingruber, Gordon L. Fain, Annia Abtout, Reingruber, Juergen, Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Integrative Biology and Physiology, University of California [Los Angeles] (UCLA), University of California (UC)-University of California (UC), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of California-University of California, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris
Subjects: 0301 basic medicine, genetic structures, Physiology, Phase (waves), [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Article, Feedback, Mice, 03 medical and health sciences, 0302 clinical medicine, Retinal Rod Photoreceptor Cells, Animals, Waveform, Invariant (mathematics), Physics, Intensity (physics), [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Light intensity, 030104 developmental biology, Amplitude, Retinal Cone Photoreceptor Cells, sense organs, Biological system, Transduction (physiology), Photic Stimulation, 030217 neurology & neurosurgery, Signal Transduction, Visual phototransduction
Abstract: Most vertebrate eyes have rod and cone photoreceptors, which use a signal transduction pathway consisting of many biological processes to transform light into an electrical response. We dissect and quantify the contribution of each of these processes to the photoreceptor light response by using a novel method of analysis that provides an analytical solution for the entire time course of the dim-flash light response. We find that the shape of the light response is exclusively controlled by deactivation parameters. Activation parameters scale this shape and alter the response amplitude. We show that the rising phase of the response depends on CaVertebrate eyes have rod and cone photoreceptors, which use a complex transduction pathway comprising many biological processes to transform the absorption of light into an electrical response. A fundamental question in sensory transduction is how these processes contribute to the response. To study this question, we use a well-accepted phototransduction model, which we analyse with a novel method based on the log transform of the current. We derive an analytical solution that describes the entire time course of the photoreceptor response to dim flashes of light. We use this solution to dissect and quantify the contribution of each process to the response. We find that the entire dim-flash response is proportional to the flash intensity. By normalizing responses to unit amplitude, we define a waveform that is independent of the light intensity and characterizes the invariant shape of dim-flash responses. We show that this waveform is exclusively determined by deactivation rates; activation rates only scale the waveform and affect the amplitude. This analysis corrects a previous assumption that the rising phase is determined entirely by activation rates. We further show that the rising phase depends on Ca
Published: 2021
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17. New paleoanthropological research in the Plio-Pleistocene Omo-Group, Lower Omo Valley, SNNPR (Southern Nations, Nationalities and People Regions), Ethiopia

Author: Leslea J. Hlukso, Jean-Renaud Boisserie, Anne Delagnes, Claude Guillemot, Franck Guy, Faysal Bibi, Yonas Beyene, Paléobiodiversité et paléoenvironnements, Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut International de Paléoprimatologie, Paléontologie Humaine : Evolution et Paléoenvironnement (IPHEP), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Department of Integrative Biology & Museum of Vertebrate Zoology, Department of Integrative Biology, Department of Geology & Geophysics, Yale University [New Haven], Department of Archaeology and Paleontology, Authority for Research and Conservation of Cultural Heritage, Muséum national d'Histoire naturelle (MNHN), and Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 010506 paleontology, Hominids, Pleistocene, Environmental change, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Archaeological record, Biostratigraphy, 01 natural sciences, Paléolithique ancien, Stone Age, Theria, Paleontology, Shungura Formation, Eutheria, 0601 history and archaeology, Field work, Pliocène récent, 0105 earth and related environmental sciences, Late Pliocene, Fossil vertebrates, 060101 anthropology, biology, Travaux de terrain, General Engineering, Plio-Pleistocene, 06 humanities and the arts, 15. Life on land, biology.organism_classification, Archaeology, Hominidés, Early Stone Age, Vertébrés fossiles, Afrique orientale, Eastern Africa, Formation de Shungura, Geology
Abstract: International audience; Through previousworks in the early 1930s by C. Arambourg and in the 1960–1970s by the InternationalOmoResearch Expedition (IORE) initiated by F. C. Howell, the Omo Group deposits of the Lower Omo Valley provided decisive data on Plio-Pleistocene environmental change and hominid evolution in eastern Africa. Y. Coppens directed the IORE French component with Arambourg, then alone from 1970 to 1976. After 30-year hiatus, the Omo Group Research Expedition reinitiated field work on Shungura Formation deposits aged between 3Ma and 2 Ma. In 2006 and 2007, renewed methods led to the collection of more than 600 vertebrate specimens with a particularly precise record of contextual data. These specimens include significant hominid remains dated to 2.5 Ma and slightly older. Changes in faunal distributions were also recorded. Additionally, the Shungura Formation archaeological record is reconsidered. These first results are indicative of future advances in the study of biodiversity evolution and its relationship with global and regional environmental changes.; Les travaux menés par C. Arambourg (1932–1933) et les Expéditions Internationales de l'Omo (IORE) initiées par F. C. Howell (1967–1976) ont placé les dépôts du Groupe Omo au coeur des recherches sur l'évolution des hominidés et des environnements plio-pléistocènes. Y. Coppens dirigea l'équipe franc¸aise avec C. Arambourg, puis seul de 1970 à 1976. Après 30 années de « jachère », les Expéditions de Recherche dans le Groupe Omo ont repris les travaux sur les dépôts de la Formation de Shungura. En 2006 et 2007, de nouvelles méthodes ont permis de collecter plus de 600 fossiles de vertébrés, avec des données contextuelles particulièrement détaillées. Ces fossiles incluent des restes d'hominidés datés entre 2,5 Ma et 3,0 Ma. Des modifications dans la composition des faunes ont été observées entre membres. Une révision du registre archéologique de la formation de Shungura a été entamée. Ces premiers résultats permettent d'envisager de prochaines avancées sur les liens entre évolution de la biodiversité et changements globaux et régionaux.
Published: 2008
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18. The Sphagnum microbiome: new insights from an ancient plant lineage

Author: Turetsky, Merritt [Department of Integrative Biology University of Guelph Guelph ON N1G 2W1 Canada]
Published: 2016
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19. Emergence of Hippopotamidae : new scenarios

Author: Fabrice Lihoreau, Jean-Renaud Boisserie, Paléobiodiversité et paléoenvironnements, Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Laboratoire de géobiologie, biochronologie et paléontologie humaine (LGBPH), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Department of Integrative Biology & Museum of Vertebrate Zoology, Department of Integrative Biology, Université de N'Djaména, and Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 010506 paleontology, Anthracotheriidae, 010603 evolutionary biology, 01 natural sciences, bilan, Hippopotamidae, Paleontology, Afrique, extinctions, phylogénie, Ungulata, évolution, Cetartiodactyla, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, review et commentaires, Vertebrata, biology, Selenodont, Metazoa, General Engineering, Eukaryotae, biology.organism_classification, Miocène, Mammalia, (paléo)biogéographie, Néogène, Cénozoïque, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, (paléo)environnement
Abstract: Molecular data analyses blew the problem of hippo origins up to the level of a broader question: cetacean and artiodactyl relationships. Recently, new morphology-based studies strongly supported a hippo origin within Miocene bothriodontines, which are selenodont anthracotheres. Based on these results, two new scenarios for hippo emergence are proposed here. Palaeoenvironmental and evolutionary issues related to these scenarios are discussed. To cite this article: J.-R. Boisserie, C. R. Palevol 5 (2006) .
Published: 2006
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20. The position of Hippopotamidae within Cetartiodactyla

Author: Michel Brunet, Jean-Renaud Boisserie, Fabrice Lihoreau, Laboratoire de géobiologie, biochronologie et paléontologie humaine (LGBPH), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Department of Integrative Biology & Museum of Vertebrate Zoology, Department of Integrative Biology, and Université de N'Djaména
Subjects: 0106 biological sciences, Paraphyly, Libycosaurus, Lineage (evolution), Anthracotheriidae, Zoology, cladistique, 010603 evolutionary biology, 01 natural sciences, Ruminantia, Suoidea, Hippopotamidae, Suidae, 03 medical and health sciences, suoïdes, phylogénie, Animals, Ungulata, Cetartiodactyla, ComputingMilieux_MISCELLANEOUS, Phylogeny, 030304 developmental biology, Artiodactyla, tous continents, Vertebrata, 0303 health sciences, Multidisciplinary, biology, Fossils, Metazoa, Biological Sciences, biology.organism_classification, anatomie descriptive et comparée, Eukaryotae, Sister group, Archaeology, Mammalia, Molecular phylogenetics, Cetacea, Cénozoïque, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Tayassuidae
Abstract: The origin of late Neogene Hippopotamidae (Artiodactyla) involves one of the most serious conflicts between comparative anatomy and molecular biology: is Artiodactyla paraphyletic? Molecular comparisons indicate that Cetacea should be the modern sister group of hippos. This finding implies the existence of a fossil lineage linking cetaceans (first known in the early Eocene) to hippos (first known in the middle Miocene). The relationships of hippos within Artiodactyla are challenging, and the immediate affinities of Hippopotamidae have been studied by biologists for almost two centuries without resolution. Here, we compare opposing hypotheses implicating several “suiform” families. This morphological analysis of a comprehensive set of taxa and characters offers a robust solution to the origins of Hippopotamidae. This family appears to be deeply nested within the otherwise extinct artiodactyl family Anthracotheriidae, most precisely within the most advanced selenodont forms. The proposed sister group of hippos is the middle to late Miocene African semiaquaticLibycosaurus. Any close relationships of hippos with suoids, particularly with Tayassuidae, are rejected. Furthermore, the clade (Hippopotamidae, Anthracotheriidae) is proposed as the sister group of the Cetacea, offering broad morphological support for a molecular phylogeny, such support being also consistent with the fossil record. Corroboration of this relationship requires an exploration of anthracothere affinities with other Paleogene artiodactyls. Among those, the position of Ruminantia is a central question, still to be solved. Further progress in this debate is likely to come from morphological studies of paleontological data, whether known or still to be discovered.
Published: 2005
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21. Origins of Hippopotamidae (Mammalia, Cetartiodactyla): Towards Resolution

Author: Jean-Renaud Boisserie, Fabrice Lihoreau, Michel Brunet, Laboratoire de géobiologie, biochronologie et paléontologie humaine (LGBPH), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Department of Integrative Biology & Museum of Vertebrate Zoology, Department of Integrative Biology, and Université de N'Djaména
Subjects: 0106 biological sciences, 010506 paleontology, Lineage (evolution), Anthracotheriidae, Zoology, cladistique, 010603 evolutionary biology, 01 natural sciences, Hippopotamidae, Suoidea, Dichobunidae, biology.animal, Genetics, phylogénie, suoïdes, Ungulata, Molecular Biology, Cetartiodactyla, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Vertebrata, tous continents, biology, Phylogenetic tree, Metazoa, biology.organism_classification, anatomie descriptive et comparée, Cladistics, Hippopotamus amphibius, Eukaryotae, Evolutionary biology, Hippopotamus, Mammalia, Animal Science and Zoology, Identification (biology), Cénozoïque, Néogène, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Tayassuidae
Abstract: The old debate on hippopotamid origins is still unresolved, balancing between two main phylogenetic hypotheses: origins within the Anthracotheriidae vs. origins within the Tayassuidae. The characters used in the literature to support one, the other, or both hypotheses were re-examined in light of a better known primitive hippopotamid morphology. A cladistic analysis was performed on the basis of these characters. On the one hand, although many features similar in hippopotamuses and anthracotheres appear to have evolved in parallel, the family Anthracotheriidae remains the best putative hippopotamus stem group on the basis of the reviewed characters. However, the precise identification of a stem group within this family is still uncertain. On the other hand, the lineage proposed in the tayassuid hypothesis should not be retained, being mostly based on some incorrect observations and without taking into account the derived or primitive nature of the features. The anatomic similarities seen between modern peccaries and Hippopotamus amphibius are the results of convergences between advanced species of both families.
Published: 2005
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22. Stratigraphic, Chronological and Behavioural Contexts of Pleistocene Homo Sapiens from Middle Awash, Ethiopia

Author: Shigehiro Katoh, Yonas Beyene, William K. Hart, Gen Suwa, Giday WoldeGabriel, Paul R. Renne, J. Desmond Clark, Henry Gilbert, Alban Defleur, Kenneth R. Ludwig, Berhane Asfaw, Tim D. White, Jean-Renaud Boisserie, Department of Integrative Biology & Museum of Vertebrate Zoology, Department of Integrative Biology, Laboratoire de géobiologie, biochronologie et paléontologie humaine (LGBPH), and Université de Poitiers-Centre National de la Recherche Scientifique (CNRS)
Subjects: Primates, Pleistocene, Bouri Herto, Pléistocène moyen, Middle Awash, archéozoologie, Afar, Ruminantia, géochronologie, 03 medical and health sciences, Paleontology, Afrique, Homo sapiens idaltu, 0601 history and archaeology, éthologie, Ungulata, Middle Stone Age, Cetartiodactyla, ComputingMilieux_MISCELLANEOUS, Perissodactyla, 030304 developmental biology, Vertebrata, 0303 health sciences, 060101 anthropology, Multidisciplinary, Crania, biology, Hominoidea, archéologie, Bouri Formation, Metazoa, 06 humanities and the arts, biology.organism_classification, taphonomie, Geography, Eukaryotae, Homo sapiens, Hippopotamus, Mammalia, Hippopotamidae, Afrique orientale, Cénozoïque, Néogène, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Acheulean, Ethiopie, (paléo)environnement
Abstract: Clarifying the geographic, environmental and behavioural contexts in which the emergence of anatomically modern Homo sapiens occurred has proved difficult, particularly because Africa lacked adequate geochronological, palaeontological and archaeological evidence. The discovery of anatomically modern Homo sapiens fossils at Herto, Ethiopia, changes this. Here we report on stratigraphically associated Late Middle Pleistocene artefacts and fossils from fluvial and lake margin sandstones of the Upper Herto Member of the Bouri Formation, Middle Awash, Afar Rift, Ethiopia. The fossils and artefacts are dated between 160,000 and 154,000 years ago by precise age determinations using the 40Ar/39Ar method. The archaeological assemblages contain elements of both Acheulean and Middle Stone Age technocomplexes. Associated faunal remains indicate repeated, systematic butchery of hippopotamus carcasses. Contemporary adult and juvenile Homo sapiens fossil crania manifest bone modifications indicative of deliberate mortuary practices.
Published: 2003
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23. A compact E × B filter: A multi-collector cycloidal focusing mass spectrometer

Author: Ostrom, Peggy [Department of Integrative Biology, Michigan State University, 288 Farm Lane RM 203, East Lansing, Michigan 48824 (United States)]
Published: 2015
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24. Decreasing Phanerozoic extinction intensity as a consequence of Earth surface oxygenation and metazoan ecophysiology

Author: Erik A. Sperling, Richard G. Stockey, Andy Ridgwell, Alexandre Pohl, Seth Finnegan, Department of Geological Sciences [Stanford] (GS), Stanford EARTH, Stanford University-Stanford University, Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), University of California [Riverside] (UC Riverside), University of California (UC), Department of Integrative Biology [Berkeley] (IB), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), European Project: 838373,BioSIGNAL, Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), University of California [Riverside] (UCR), University of California, University of California [Berkeley], University of California-University of California, Pohl, Alexandre, Marie Sklodowska-Curie grant agreement No. 838373 - BioSIGNAL - 838373 - INCOMING, and Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement
Subjects: [SDE] Environmental Sciences, Aquatic Organisms, Hot Temperature, 010504 meteorology & atmospheric sciences, Paleozoic, Earth system evolution, ecophysiology, Earth, Planet, Climate, Oceans and Seas, Effects of global warming on oceans, Biodiversity, Extinction, Biological, Atmospheric sciences, 01 natural sciences, Carbon Cycle, temperature-dependent hypoxia, 03 medical and health sciences, Phanerozoic, Animals, Seawater, Background extinction rate, 14. Life underwater, Ecosystem, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0105 earth and related environmental sciences, Extinction event, 0303 health sciences, Multidisciplinary, Extinction, extinction, Atmosphere, Fossils, Hypoxia (environmental), Earth, 15. Life on land, Biological, Biological Evolution, Oxygen, 13. Climate action, Physical Sciences, [SDE]Environmental Sciences, Environmental science, Planet, geographic locations
Abstract: The decline in background extinction rates of marine animals through geologic time is an established but unexplained feature of the Phanerozoic fossil record. There is also growing consensus that the ocean and atmosphere did not become oxygenated to near-modern levels until the mid-Paleozoic, coinciding with the onset of generally lower extinction rates. Physiological theory provides us with a possible causal link between these two observations-predicting that the synergistic impacts of oxygen and temperature on aerobic respiration would have made marine animals more vulnerable to ocean warming events during periods of limited surface oxygenation. Here, we evaluate the hypothesis that changes in surface oxygenation exerted a first-order control on extinction rates through the Phanerozoic using a combined Earth system and ecophysiological modeling approach. We find that although continental configuration, the efficiency of the biological carbon pump in the ocean, and initial climate state all impact the magnitude of modeled biodiversity loss across simulated warming events, atmospheric oxygen is the dominant predictor of extinction vulnerability, with metabolic habitat viability and global ecophysiotype extinction exhibiting inflection points around 40% of present atmospheric oxygen. Given this is the broad upper limit for estimates of early Paleozoic oxygen levels, our results are consistent with the relative frequency of high-magnitude extinction events (particularly those not included in the canonical big five mass extinctions) early in the Phanerozoic being a direct consequence of limited early Paleozoic oxygenation and temperature-dependent hypoxia responses.
Published: 2021

25. Mitochondrial Genetic Diversity among Farmed Stocks of Oreochromis spp. (Perciformes, Cichlidae) in Madagascar

Author: Elodie Pepey, Diana Edithe Andria-Mananjara, Dirk Steinke, Nicolas Hubert, Jean-Michel Mortillaro, Hugues de Verdal, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), 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, Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), FOFIFA DRZVP, Department of Integrative Biology (University of Guelph), and University of Guelph
Subjects: 0106 biological sciences, tilapia, Introduced species, Broodstock, 01 natural sciences, DNA barcoding, Nucleotide diversity, Aquaculture, Biology (General), 2. Zero hunger, 0303 health sciences, Ecology, biology, Diversité génétique (comme ressource), Oreochromis, Ecological Modeling, Agricultural and Biological Sciences (miscellaneous), génétique animale, aquaculture, Biodiversité, exotic species, management, QH301-705.5, Génétique mitochondriale, Zoology, 010603 evolutionary biology, 03 medical and health sciences, domestication, Variation génétique, 14. Life underwater, Domestication, 030304 developmental biology, Nature and Landscape Conservation, Genetic diversity, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], business.industry, biology.organism_classification, L10 - Génétique et amélioration des animaux, M12 - Production de l'aquaculture, business, human activities
Abstract: International audience; The fast development of aquaculture over the past decades has made it the main source of fish protein and led to its integration into the global food system. Mostly originating from inland production systems, aquaculture has emerged as strategy to decrease malnutrition in low-income countries. The Nile tilapia (Oreochromis niloticus) was introduced to Madagascar in the 1950s, and is now produced nationally at various scales. Aquaculture mostly relies on fry harvested from wild populations and grow-out in ponds for decades. It has recently been diversified by the introduction of several fast-growing strains. Little is known how local genetic diversity compares to recently introduced strains, although high and comparable levels of genetic diversity have previously been observed for both wild populations and local stocks. Our study compares DNA barcode genetic diversity among eight farms and several strains belonging to three species sampled. DNA-based lineage delimitation methods were applied and resulted in the detection of six well differentiated and highly divergent lineages. A comparison of DNA barcode records to sequences on the Barcode of Life Data System (BOLD) helped to trace the origin of several of them. Both haplotype and nucleotide diversity indices highlight high levels of mitochondrial genetic diversity, with several local strains displaying higher diversity than recently introduced strains. This allows for multiple options to maintain high levels of genetic diversity in broodstock and provides more options for selective breeding programs.
Published: 2021
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26. RADSex: A computational workflow to study sex determination using restriction site-associated DNA sequencing data

Author: Ørjan Karlsen, Susanne Kneitz, Rafael Henrique Nóbrega, Qiaowei Pan, Masatoshi Nakamoto, Elodie Jouanno, Thomas Desvignes, John H. Postlethwait, Ato Takanashi, Braedan M. McCluskey, Amaury Herpin, Matthias Stöck, Alvaro S. Roco, Boudjema Imarazene, Manfred Schartl, Zhongwei Wang, Mateus Contar Adolfi, Romain Feron, Catherine Wilson, Hugues Parrinello, Takashi Sakamoto, Ingo Braasch, Christophe Klopp, Marcos Antonio de Oliveira, Frederick W. Goetz, Harry William Detrich, Robert M. Waterhouse, Ming Wen, Yann Guiguen, Mari Kawaguchi, Angel Amores, Laurent Journot, Anna Wargelius, Verena A. Kottler, Kang Du, Jennifer L. Anderson, IINRAE, Univ Lausanne, Swiss Inst Bioinformat, Hunan Normal Univ, Uppsala Univ, Univ Montpellier, INRAE, Univ Wurzburg, Texas State Univ, Univ Oregon, NOAA, Sophia Univ, Northeastern Univ, Universidade Estadual Paulista (Unesp), Tokyo Univ Marine Sci & Technol, Inst Marine Res, Chinese Acad Sci, IGB, Michigan State Univ, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Ecology and Evolution, University of Lausanne, Université de Lausanne (UNIL), Swiss Institute of Bioinformatics [Lausanne] (SIB), State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan University [Changsha] (HNU), Department of Systematic Biology [Uppsala], Evolutionary Biology Centre (EBC), Uppsala University-Uppsala University, Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Physiological Chemistry, Biocenter, University of Würzburg = Universität Würzburg, The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, Institute of Neuroscience, University of Oregon, Eugene, University of Oregon [Eugene], Tokyo University of Marine Science and Technology (TUMSAT), Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), Sophia University, Tokyo, Faculty of Science and Technology, Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Institute of Marine Research [Bergen] (IMR), University of Bergen (UiB), Institute of Hydrobiology [Wuhan], Chinese Academy of Sciences [Beijing] (CAS), Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Integrative Biology, Michigan State University, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, This project was supported by funds from the 'Agence Nationale de la Recherche', the 'Deutsche Forschungsgemeinschaft' (ANR/DFG, PhyloSex project,2014-2016, SCHA 408/10-1, MS), the National Institutes of Health (USA) grant R01GM085318, JHP), and the National Science Foundation (USA) Office of Polar Programs (grants PLR-1247510 and PLR-1444167 to HWD and grant OPP-1543383 to JHP, TD, and HWD). The MGX core sequencing facility was supported by France Genomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09). RF was partially supported by Swiss National Science Foundation grant PP00P3_170664 to RMW., ANR-13-ISV7-0005,PhyloSex,Evolution des déterminants majeurs du sexe chez les poissons.(2013), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Department of Ecology and Evolution [Lausanne], Institute of Neuroscience, University of Oregon, Eugene, Oregon, Department of Materials and Life Sciences, Sophia University [Tokyo], Department of Structural and Functional Biology, Department of Aquatic Marine Biosciences, Developmental Biochemistry, Biocenter, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), and This project was supported by funds from the 'Agence Nationale de la Recherche', the 'Deutsche Forschungsgemeinschaft' (ANR/DFG, PhyloSex project, 2014-2016, SCHA 408/10-1, MS), the National Institutes of Health (USA) grants R01GM085318 and R35GM139635, JHP), and the National Science Foundation (USA) Office of Polar Programs (grants PLR-1247510 and PLR-1444167 to HWD and grant OPP-1543383 to JHP, TD, and HWD). The MGX core sequencing facility was supported by France Genomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09). RF was partially supported by Swiss National Science Foundation grant PP00P3_170664 to RMW.
Subjects: 0106 biological sciences, 0301 basic medicine, Male, Sex Determination Analysis, Computer science, [SDV]Life Sciences [q-bio], sex determination, Locus (genetics), Computational biology, Biology, Y chromosome, 010603 evolutionary biology, 01 natural sciences, Computational workflow, DNA sequencing, Article, Workflow, 03 medical and health sciences, Sex-determination system, Genetics, Animals, Sequencing, RAD&#8208, Computational Biology, DNA, Female, Fishes/genetics, Sequence Analysis, DNA, Sex Chromosomes, Software, RAD-Sequencing, computational workflow, fish, visualization, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Visualization, 0303 health sciences, Fishes, Japanese Medaka, Sex determination, Restriction site, 030104 developmental biology, Fish, Identification (biology), Biotechnology
Abstract: Made available in DSpace on 2021-06-25T11:54:14Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-03-09 National Institute of Health (USA) Deutsche Forschungsgemeinschaft National Science Foundation (USA) Office of Polar Programs Agence Nationale de la Recherche Schweizerischer Nationalfonds zur Forderung der Wissenschaftlichen Forschung The study of sex determination and sex chromosome organization in nonmodel species has long been technically challenging, but new sequencing methodologies now enable precise and high-throughput identification of sex-specific genomic sequences. In particular, restriction site-associated DNA sequencing (RAD-Seq) is being extensively applied to explore sex determination systems in many plant and animal species. However, software specifically designed to search for and visualize sex-biased markers using RAD-Seq data is lacking. Here, we present RADSex, a computational analysis workflow designed to study the genetic basis of sex determination using RAD-Seq data. RADSex is simple to use, requires few computational resources, makes no prior assumptions about the type of sex-determination system or structure of the sex locus, and offers convenient visualization through a dedicated R package. To demonstrate the functionality of RADSex, we re-analysed a published data set of Japanese medaka, Oryzias latipes, where we uncovered a previously unknown Y chromosome polymorphism. We then used RADSex to analyse new RAD-Seq data sets from 15 fish species spanning multiple taxonomic orders. We identified the sex determination system and sex-specific markers in six of these species, five of which had no known sex-markers prior to this study. We show that RADSex greatly facilitates the study of sex determination systems in nonmodel species thanks to its speed of analyses, low resource usage, ease of application and visualization options. Furthermore, our analysis of new data sets from 15 species provides new insights on sex determination in fish. IINRAE, LPGP, Rennes, France Univ Lausanne, Dept Ecol & Evolut, Lausanne, Switzerland Swiss Inst Bioinformat, Lausanne, Switzerland Hunan Normal Univ, Coll Life Sci, State Key Lab Dev Biol Freshwater Fish, Changsha, Peoples R China Uppsala Univ, Dept Organismal Biol, Systemat Biol, Uppsala, Sweden Univ Montpellier, Inst Genom Fonct, INSERM, IGF,CNRS, Montpellier, France INRAE, Math & Informat Appl Toulouse, SIGENAE, Castanet Tolosan, France Univ Wurzburg, Physiol Chem, Bioctr, Wurzburg, Germany Texas State Univ, Xiphophorus Genet Stock Ctr, Dept Chem & Biochem, San Marcos, TX USA Univ Wurzburg, Dev Biochem, Bioctr, Wurzburg, Germany Univ Oregon, Inst Neurosci, Eugene, OR USA NOAA, Environm & Fisheries Sci Div, Northwest Fisheries Sci Ctr, Natl Marine Fisheries Serv, Seattle, WA USA Sophia Univ, Fac Sci & Technol, Dept Mat & Life Sci, Tokyo, Japan Northeastern Univ, Ctr Marine Sci, Dept Marine & Environm Sci, Nahant, MA 01908 USA Sao Paulo State Univ, Inst Biosci, Dept Struct & Funct Biol, Reprod & Mol Biol Grp, Botucatu, SP, Brazil Tokyo Univ Marine Sci & Technol, Dept Aquat Marine Biosci, Tokyo, Japan Inst Marine Res, Bergen, Norway Chinese Acad Sci, Inst Hydrobiol, Beijing, Peoples R China IGB, Leibniz Inst Freshwater Ecol & Inland Fishe, Berlin, Germany Michigan State Univ, Dept Integrat Biol, Ecol Evolut & Behav Program, E Lansing, MI 48824 USA Sao Paulo State Univ, Inst Biosci, Dept Struct & Funct Biol, Reprod & Mol Biol Grp, Botucatu, SP, Brazil National Institute of Health (USA): R01GM085318 National Institute of Health (USA): R35GM139635 Deutsche Forschungsgemeinschaft: SCHA 408/10-1 National Science Foundation (USA) Office of Polar Programs: OPP-1543383 National Science Foundation (USA) Office of Polar Programs: PLR-1247510 National Science Foundation (USA) Office of Polar Programs: PLR-1444167 Agence Nationale de la Recherche: SCHA 408/10-1 Agence Nationale de la Recherche: ANR-10-INBS-09 Schweizerischer Nationalfonds zur Forderung der Wissenschaftlichen Forschung: PP00P3_170664
Published: 2021
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27. Epigenetics drive the evolution of sex chromosomes in animals and plants

Author: Aline Muyle, James M. A. Turner, Doris Bachtrog, Gabriel A. B. Marais, University of California [Irvine] (UCI), University of California, Department of Integrative Biology [Berkeley] (IB), University of California [Berkeley], University of California-University of California, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), The Francis Crick Institute [London], University of California [Irvine] (UC Irvine), University of California (UC), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), and ANR-20-CE20-0015,PlantGenomYX,Identifier les gènes du déterminisme du sexe chez la plante dioïque Silene latifolia(2020)
Subjects: Evolution of sexual reproduction, Heterochromatin, Biology, Y chromosome, General Biochemistry, Genetics and Molecular Biology, X-inactivation, Epigenesis, Genetic, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Meiosis, Dosage Compensation, Genetic, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, Epigenetics, Dosage compensation, X upregulation, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Sex Chromosomes, fungi, Chromosome, Articles, Plants, Y degeneration, Invertebrates, Y toxicity, meiotic sex chromosome inactivation, Evolutionary biology, Vertebrates, DNA Transposable Elements, imprinting, General Agricultural and Biological Sciences, X chromosome inactivation, 030217 neurology & neurosurgery
Abstract: We review how epigenetics affect sex chromosome evolution in animals and plants. In a few species, sex is determined epigenetically through the action of Y-encoded small RNAs. Epigenetics is also responsible for changing the sex of individuals through time, even in species that carry sex chromosomes, and could favour species adaptation through breeding system plasticity. The Y chromosome accumulates repeats that become epigenetically silenced which leads to an epigenetic conflict with the expression of Y genes and could accelerate Y degeneration. Y heterochromatin can be lost through ageing, which activates transposable elements and lowers male longevity. Y chromosome degeneration has led to the evolution of meiotic sex chromosome inactivation in eutherians (placentals) and marsupials, and dosage compensation mechanisms in animals and plants. X-inactivation convergently evolved in eutherians and marsupials via two independently evolved non-coding RNAs. In Drosophila , male X upregulation by the male specific lethal (MSL) complex can spread to neo-X chromosomes through the transposition of transposable elements that carry an MSL-binding motif. We discuss similarities and possible differences between plants and animals and suggest future directions for this dynamic field of research. This article is part of the theme issue ‘How does epigenetics influence the course of evolution?’
Published: 2021
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28. At each site its diversity: DNA barcoding reveals remarkable earthworm diversity in neotropical rainforests of French Guiana

Author: Christopher Baraloto, Heidy Schimann, Thibaud Decaëns, Karl Cottenie, Virginie Roy, Marie-Eugénie Maggia, Emmanuel Lapied, Lise Dupont, Jérôme Murienne, Dirk Steinke, Jérôme Orivel, Department of Integrative Biology (University of Guelph), University of Guelph, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-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 de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - 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 d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Range (biology), Rare species, Soil Science, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Rainforest, Biology, 01 natural sciences, DNA barcoding, Sampling methods, Tropical rainforest, Diversity level, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Ecology, Earthworm, 04 agricultural and veterinary sciences, biology.organism_classification, Agricultural and Biological Sciences (miscellaneous), DNA Barcoding, Community Ecology, Habitat, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Biological dispersal, Epiphyte, Species richness, 010606 plant biology & botany
Abstract: Despite their recognized essential role in soil, earthworms in tropical environments are still understudied. The aim of this study was to re-evaluate the diversity at the regional scale, as well as to investigate the environmental and spatial drivers of earthworm communities. We sampled earthworm communities across a range of habitats at six locations in French Guiana using three different sampling methods. We generated 1675 DNA barcodes and combined them with data from a previous study. Together, all sequences clustered into 119 MOTUs which were used as proxy to assess species richness. Only two MOTUs were common between the six locations and 20.2 % were singletons, showing very high regional species richness and a high number of rare species. A canonical redundancy analysis was used to identify key drivers of the earthworm community composition. The RDA results and beta-diversity calculations both show strong species turnover and a strong spatial effect, resulting from dispersal limitations that are responsible for the current community composition. Sampling in different microhabitats allowed the discovery of 23 MOTUs that are exclusively found in decaying trunks and epiphytes, highlighting hidden diversity of earthworms outside of soil.
Published: 2020
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29. Assessing the Potential for Mobilization of Old Soil Carbon After Permafrost Thaw: A Synthesis of 14 C Measurements From the Northern Permafrost Region

Author: Peter A. Raymond, Jocelyn Egan, Suzanne E. Tank, Iain P. Hartley, Claudia I. Czimczik, Jonathan A. O'Donnell, Massimo Lupascu, Susan M. Natali, Mark H. Garnett, Alison M. Hoyt, Edward A. G. Schuur, Benjamin W. Abbott, Andrew J. Tanentzap, Jeffrey P. Chanton, Laure Gandois, David Olefeldt, Katey M. Walter Anthony, Cristian Estop-Aragonés, Merritt R. Turetsky, Joshua F. Dean, Olefeldt, David, 1 Department of Renewable Resources University of Alberta Edmonton Canada, Abbott, Benjamin W., 3 Department of Plant and Wildlife Sciences Brigham Young University Provo UT USA, Chanton, Jeffrey P., 4 Department of Earth Ocean and Atmospheric Science Florida State University Tallahassee FL USA, Czimczik, Claudia I., 5 Department of Earth System Science University of California Irvine CA USA, Dean, Joshua F., 6 School of Environmental Sciences University of Liverpool Liverpool UK, Egan, Jocelyn E., 7 Department of Earth Sciences Dalhousie University Halifax Canada, Gandois, Laure, 8 Laboratoire Ecologie Fonctionnelle et Environnement Université de Toulouse, CNRS Toulouse France, Garnett, Mark H., 9 NEIF Radiocarbon Laboratory, Scottish Enterprise Technology Park, Rankine Avenue East Kilbride UK, Hartley, Iain P., 10 Geography, College of Life and Environmental Sciences University of Exeter Exeter UK, Hoyt, Alison, 11 Max Planck Institute for Biogeochemistry Jena Germany, Lupascu, Massimo, 12 Department of Geography National University of Singapore Singapore Singapore, Natali, Susan M., 13 Woodwell Climate Research Center Falmouth MA USA, O'Donnell, Jonathan A., 14 National Park Service, Arctic Network Anchorage AK USA, Raymond, Peter A., 15 Yale School of Forestry and Environmental Studies New Haven CT USA, Tanentzap, Andrew J., 16 Ecosystems and Global Change Group, Department of Plant Sciences University of Cambridge Cambridge UK, Tank, Suzanne E., 17 Department of Biological Sciences University of Alberta Edmonton Canada, Schuur, Edward A. G., 18 Department of Biological Sciences Northern Arizona University Flagstaff AZ USA, Turetsky, Merritt, 19 Department of Integrative Biology University of Guelph Guelph Canada, Anthony, Katey Walter, 20 Water and Environmental Research Center University of Alaska Fairbanks Fairbanks AK USA, Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées
Subjects: particulate organic carbon, 0106 biological sciences, Atmospheric Science, 551.9, Peat, 010504 meteorology & atmospheric sciences, permafrost thaw, [SDE.MCG]Environmental Sciences/Global Changes, Permafrost, 01 natural sciences, Thermokarst, Dissolved organic carbon, Environmental Chemistry, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, General Environmental Science, Global and Planetary Change, geography, geography.geographical_feature_category, methane, 010604 marine biology & hydrobiology, carbon dioxide, Soil carbon, 15. Life on land, dissolved organic carbon, Tundra, 13. Climate action, [SDE]Environmental Sciences, Soil water, radiocarbon, Erosion, Environmental science, Physical geography
Abstract: The magnitude of future emissions of greenhouse gases from the northern permafrost region depends crucially on the mineralization of soil organic carbon (SOC) that has accumulated over millennia in these perennially frozen soils. Many recent studies have used radiocarbon (14C) to quantify the release of this “old” SOC as CO2 or CH4 to the atmosphere or as dissolved and particulate organic carbon (DOC and POC) to surface waters. We compiled ~1,900 14C measurements from 51 sites in the northern permafrost region to assess the vulnerability of thawing SOC in tundra, forest, peatland, lake, and river ecosystems. We found that growing season soil 14C‐CO2 emissions generally had a modern (post‐1950s) signature, but that well‐drained, oxic soils had increased CO2 emissions derived from older sources following recent thaw. The age of CO2 and CH4 emitted from lakes depended primarily on the age and quantity of SOC in sediments and on the mode of emission, and indicated substantial losses of previously frozen SOC from actively expanding thermokarst lakes. Increased fluvial export of aged DOC and POC occurred from sites where permafrost thaw caused soil thermal erosion. There was limited evidence supporting release of previously frozen SOC as CO2, CH4, and DOC from thawing peatlands with anoxic soils. This synthesis thus suggests widespread but not universal release of permafrost SOC following thaw. We show that different definitions of “old” sources among studies hamper the comparison of vulnerability of permafrost SOC across ecosystems and disturbances. We also highlight opportunities for future 14C studies in the permafrost region., Key Points: We compiled ~1,900 14C measurements of CO2, CH4, DOC, and POC from the northern permafrost region. Old carbon release increases in thawed oxic soils (CO2), thermokarst lakes (CH4 and CO2), and headwaters with thermal erosion (DOC and POC). Simultaneous and year‐long 14C analyses of CO2, CH4, DOC, and POC are needed to assess the vulnerability of permafrost carbon across ecosystems., EC | H2020 | H2020 Priority Excellent Science | H2020 European Research Council (ERC) http://dx.doi.org/10.13039/100010663, Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC) http://dx.doi.org/10.13039/501100000038, National Science Foundation (NSF) http://dx.doi.org/10.13039/100000001
Published: 2020
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30. A simple framework for estimating potential distributions of amphibious marine species and implications for conservation

Author: Iulian Gherghel, Árpád S. Nyári, Monica Papeş, François Brischoux, Department of Integrative Biology [OK, USA] (Oklahoma State University), Oklahoma State University [Stillwater], Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and University of Tenessee [USA]
Subjects: 0106 biological sciences, Ecology (disciplines), Niche, Aquatic Science, 010603 evolutionary biology, 01 natural sciences, Laticauda, 14. Life underwater, Species distribution models, Life history, Ecological niche, geography, geography.geographical_feature_category, Ecology, 010604 marine biology & hydrobiology, Large scale, Coral reef, 15. Life on land, Ecological niche models, Natural resource, Environmental niche modelling, Taxon, 13. Climate action, Threatened species, [SDE]Environmental Sciences, Environmental science, Maxent
Abstract: International audience; Due to their complexity, coral reefs are difficult to study especially when considering the role that the interplay between the terrestrial and marine environments has in shaping distribution of marine, terrestrial, and amphibious species. Many organisms live in remote areas of the ocean and inhabit both terrestrial and marine environments. Such amphibious lifestyle poses analytical difficulties due to broad distribution and scale of coral reefs. Ecological niche modeling is a widely used technique that allows to estimate the environmental set of conditions (niche) in which organisms can survive and reproduce. Estimating the distributions of species with complex life histories (i.e., dependent on various natural resources) at broad geographic scales is crucial, as many of these taxa are threatened (i.e., amphibians, aquatic reptiles, birds, and mammals). However, distribution estimates of such species remain challenging; thus, here we propose an approach to account for marine and terrestrial environmental domains to estimate the distribution of amphibious species. We also test whether inclusion of both environments leads to improved estimates of these species’ distributions. First we calibrated ecological niche models for marine and terrestrial domains separately, and subsequently we outlined a method to combine the marine–terrestrial potential distributions by integrating estimates of the two ecological niches into a single predictive model. Our ecological niche models produced inaccurate distribution predictions of species with amphibious life histories when only one of the environments was used in model calibration. When both aquatic and terrestrial environments were included, our models predicted narrower and more accurate potential distributions. Accounting for the dual environments involved in shaping the niches of amphibious species and their distributions is essential for studying the ecology and proposing conservation management actions for the species studied here. Models that take into account only a subset of the environmental factors are prone to overestimating species’ distributions and should be interpreted with caution.
Published: 2020
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31. Organizing principles for vegetation dynamics

Author: Stephan A. Pietsch, Elena Rovenskaya, Ehud Meron, Guy F. Midgley, Josep Peñuelas, Peter M. van Bodegom, Karin T. Rebel, Ian J. Wright, Sandy P. Harrison, Philippe Ciais, Marcel van Oijen, Daniel S. Falster, I. Colin Prentice, Michel Loreau, Sönke Zaehle, Caroline E. Farrior, Oskar Franklin, Wolfgang Cramer, Stefano Manzoni, Florian Hofhansl, César Terrer, Nadejda A. Soudzilovskaia, Åke Brännström, Han Wang, Ulf Dieckmann, Roderick C. Dewar, Annikki Mäkelä, Benjamin D. Stocker, Stanislaus J. Schymanski, Global Ecohydrology and Sustainability, Environmental Sciences, International Institute for Applied Systems Analysis (IIASA), Ecosystems Services and Management, Schlossplatz 1, A-2361 Laxenburg, Austria, Department of Forest Ecology and Management, Swedish University of Agricultural Sciences (SLU), Department of Geography and Environmental Science, University of Reading, Plant Sciences Division, Research School of Biology, The Australian National University, Institute for Atmospheric and Earth System Research (INAR), University of Helsinki, Department of Integrative Biology, University of Texas at Austin, Department of Mathematics and Mathematical Statistics, Umeå University, Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies (Sokendai), Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Copernicus Institute of Sustainable Development, Environmental Sciences, Faculty of Geosciences, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Department of Physics, Ben-Gurion University of the Negev, Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Department of Environmental Systems Sciences [Zürich], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), CREAF CERDANYOLA DEL VALLES ESP, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Max Planck Institute for Biogeochemistry (MPI-BGC), Max-Planck-Gesellschaft, Department of Physical Geography, Stockholm University, Bolin Centre for Climate Research, Stockholm University, Centre for Ecology and Hydrology (CEH-Edinburgh), Department of Biological Sciences, Macquarie University, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), ICOS-ATC (ICOS-ATC), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Universiteit Leiden [Leiden], Global Ecology Unit CREAF-CEAB-CSIC, Universitat Autònoma de Barcelona (UAB), Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Stellenbosch University, ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Umeå University, Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Ben-Gurion University of the Negev (BGU), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Universiteit Leiden, AXA Research Fund, and Commission of the European Communities
Subjects: 0106 biological sciences, 0301 basic medicine, Stomatal conductance, Ecosystem ecology, 0607 Plant Biology, 0703 Crop and Pasture Production, Plant Development, Plant Science, Theoretical ecology, 01 natural sciences, 03 medical and health sciences, medicine, Temporal scales, Plant ecology, Biological sciences, Ecosystem, Plant Physiological Phenomena, Ecosytem ecology, Ecology, 15. Life on land, Plants, Vegetation dynamics, Biological Evolution, 030104 developmental biology, 13. Climate action, [SDE]Environmental Sciences, Environmental science, medicine.symptom, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Vegetation (pathology), 010606 plant biology & botany
Abstract: Plants and vegetation play a critical-but largely unpredictable-role in global environmental changes due to the multitude of contributing processes at widely different spatial and temporal scales. In this Perspective, we explore approaches to master this complexity and improve our ability to predict vegetation dynamics by explicitly taking account of principles that constrain plant and ecosystem behaviour: natural selection, self-organization and entropy maximization. These ideas are increasingly being used in vegetation models, but we argue that their full potential has yet to be realized. We demonstrate the power of natural selection-based optimality principles to predict photosynthetic and carbon allocation responses to multiple environmental drivers, as well as how individual plasticity leads to the predictable self-organization of forest canopies. We show how models of natural selection acting on a few key traits can generate realistic plant communities and how entropy maximization can identify the most probable outcomes of community dynamics in space- and time-varying environments. Finally, we present a roadmap indicating how these principles could be combined in a new generation of models with stronger theoretical foundations and an improved capacity to predict complex vegetation responses to environmental change.Integrating natural selection and other organizing principles into next-generation vegetation models could render them more theoretically sound and useful for earth system applications and modelling climate impacts.
Published: 2020
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32. Key questions for next-generation biomonitoring

Author: Andreas Makiola, Zacchaeus G. Compson, Donald J. Baird, Matthew A. Barnes, Sam P. Boerlijst, Agnès Bouchez, Georgina Brennan, Alex Bush, Elsa Canard, Tristan Cordier, Simon Creer, R. Allen Curry, Patrice David, Alex J. Dumbrell, Dominique Gravel, Mehrdad Hajibabaei, Brian Hayden, Berry van der Hoorn, Philippe Jarne, J. Iwan Jones, Battle Karimi, Francois Keck, Martyn Kelly, Ineke E. Knot, Louie Krol, Francois Massol, Wendy A. Monk, John Murphy, Jan Pawlowski, Timothée Poisot, Teresita M. Porter, Kate C. Randall, Emma Ransome, Virginie Ravigné, Alan Raybould, Stephane Robin, Maarten Schrama, Bertrand Schatz, Alireza Tamaddoni-Nezhad, Krijn B. Trimbos, Corinne Vacher, Valentin Vasselon, Susie Wood, Guy Woodward, David A. Bohan, Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Environment and Climate Change Canada, University of New Brunswick (UNB), Texas Tech University [Lubbock] (TTU), Naturalis Biodiversity Center [Leiden], Leiden University, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Bangor University, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, 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), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), 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]), Université de Sherbrooke (UdeS), Department of Integrative Biology & Biodiversity Institute of Ontario, University of Guelph, Simon Fraser University (SFU.ca), School of Biological and Chemical Sciences, Queen Mary University of London (QMUL), Bowburn Consultancy, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Google Inc., Department of genetics and evolution, University of Geneva [Switzerland], Université de Montréal (UdeM), Plymouth Marine Laboratory (PML), PML, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Syngenta, Institut National Agronomique Paris-Grignon (INA P-G), Department of Computing, Imperial College London, Bio-Protection Research Centre, Lincoln University, Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Biodiversité, Gènes et Communautés, Institut National de la Recherche Agronomique (INRA), Université de Sherbrooke [Sherbrooke], 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), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Université de Montréal [Montréal], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Universiteit Leiden, Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paul-Valéry - Montpellier 3 (UPVM)-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 de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Genève = University of Geneva (UNIGE), Natural Environment Research Council (NERC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), INRAE UMR IGEPP RENNES FRA, Partenaires IRSTEA, and Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)
Subjects: 0106 biological sciences, Computer science, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, DIVERSITY, 01 natural sciences, Field (computer science), TEXT, Biomonitoring, 0502 Environmental Science and Management, lcsh:Environmental sciences, ComputingMilieux_MISCELLANEOUS, General Environmental Science, lcsh:GE1-350, 0303 health sciences, Biodiversity assessment, Suite, SCIENCE, METRICS, artificial intelligence, NETWORKS, biodiversity assessment, PARADIGM, [SDE]Environmental Sciences, Évaluation des ressources, P01 - Conservation de la nature et ressources foncières, Biodiversité, Environmental risk management, Life Sciences & Biomedicine, Écosystème, INDEXES, Environmental Sciences & Ecology, 010603 evolutionary biology, Surveillance de l’environnement, 03 medical and health sciences, QH301, ecological networks, PLANT, QH426, 030304 developmental biology, Science & Technology, Frame (networking), [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, 15. Life on land, Data science, Ecological network, MICROBIOME, metabarcoding, Key (cryptography), eDNA, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ENVIRONMENTAL DNA, Environmental Sciences, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Classical biomonitoring techniques have focused primarily on measures linked to various biodiversity metrics and indicator species. Next-generation biomonitoring (NGB) describes a suite of tools and approaches that allow the examination of a broader spectrum of organizational levels-from genes to entire ecosystems. Here, we frame 10 key questions that we envisage will drive the field of NGB over the next decade. While not exhaustive, this list covers most of the key challenges facing NGB, and provides the basis of the next steps for research and implementation in this field. These questions have been grouped into current- and outlook-related categories, corresponding to the organization of this paper.
Published: 2020
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33. Key questions for next-generation of biomonitoring

Author: Makiola, Andreas, Compson, Zacchaeus G., Baird, Donald J, Barnes, Matthew, Boerlijst, Sam P, Bouchez, Agnes, Brennan, Georgina, Bush, Alex, Canard, Elsa, Cordier, Tristan, Creer, Simon, Curry, Allen, Dumbrell, Alex J, Gravel, Dominique, Hajibabaei, Mehrdad, van Der Hoorn, Berry, Jarne, Philippe, Jones, J.Iwan, Karimi, Battle, Keck, François, Kelly, Martyn, Knot, Ineke, Krol, Louie, Massol, François, Monk, Wendy A., Murphy, John, Pawlowski, Jan, Poisot, Timothée, M. Porter, Teresita, C. Randall, Kate, Ransome, Emma, Ravigné, Virginie, Raybould, Alan, Robin, Stephane, Schrama, Maarten, Schatz, Bertrand, Tamaddoni- Nezhad, Alireza, Trimbos, Krijn B., Vacher, Corinne, Vasselon, Valentin, Wood, Susie, Woodward, Guy, Bohan, David, Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Environment and Climate Change Canada @ Canadian Rivers Institute, Department of Biology, University of New Brunswick, NB, Canada, Centre for Environmental Genomics Applications, St. John’s, NL, Canada, Department of Natural Resources Management, Texas Tech University, Lubbock, TX, United States, Naturalis Biodiversity Center [Leiden], Institute of Environmental Sciences, Leiden University, Leiden, Netherlands, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), School of Natural Sciences, Bangor University, Bangor, United Kingdom, Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, 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), Université de Genève = University of Geneva (UNIGE), Canadian Rivers Institute, Biology, Forestry and Environmental Management, University of New Brunswick, Fredericton, NB, Canada, School of Biological Sciences, University of Essex, Colchester, United Kingdom, Département de Médecine Nucléaire et Radiobiologie - Université de Sherbrooke - Canada, Université de Sherbrooke (UdeS), Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, ON, Canada, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-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 de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom, Bowburn Consultancy, Durham, United Kingdom, Institute for Biodiversity and Ecosystem Dynamics, Department of Evolutionary and Population Biology, University of Amsterdam, Amsterdam The Netherlands, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB, Canada, Département de sciences biologiques, Université de Montréal, Montreal, QC, Canada, Great Lakes Forestry Centre, Canadian Forest Service, Natural Resources Canada, Sault Ste. Marie, ON, Canada, Imperial College London, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Syngenta Crop Protection AG, Basel, Switzerland, School of Social and Political Science, The University of Edinburgh, Edinburgh, United Kingdom, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Global Academy of Agriculture and Food Security, Edinburgh, United Kingdom, Mathématiques et Informatique Appliquées (MIA Paris-Saclay), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Surrey (UNIS), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agence Française pour la Biodiversité, Pôle R&D ECLA, Évian-les-Bains, France, Cawthron Institute, Nelson, New Zealand, Naturalis Biodiversity Center, Leiden, Netherlands, CARRTEL, USMB, INRA, Thonon-les-Bains, France, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Department of Genetics and Evolution, University of Geneva, Science III, Geneva, Switzerland, Université Paul-Valéry - Montpellier 3 (UPVM)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Department of Life Sciences, Silwood Park Campus, Imperial College London, London, United Kingdom, Mathématiques et Informatique Appliquées (MIA-Paris), and BIOGECO, INRA, Univ. Bordeaux, Pessac, France
Subjects: metabarcoding, ecological networkseDNA, ecological networks, eDNA, artificial intelligence, biodiversity assessment, [SHS]Humanities and Social Sciences
Abstract: International audience; Classical biomonitoring techniques have focused primarily on measures linked tovarious biodiversity metrics and indicator species. Next-generation biomonitoring (NGB)describes a suite of tools and approaches that allow the examination of a broaderspectrum of organizational levels—from genes to entire ecosystems. Here, we frame10 key questions that we envisage will drive the field of NGB over the next decade. Whilenot exhaustive, this list covers most of the key challenges facing NGB, and provides thebasis of the next steps for research and implementation in this field. These questionshave been grouped into current- and outlook-related categories, corresponding to theorganization of this paper.
Published: 2020
Full Text: View/download PDF

34. Long-term thermal sensitivity of Earth's tropical forests

Author: Bruno Herault, Peter J. Van Der Meer, Jean-François Bastin, Aurora Levesley, Michael D. Swaine, Rodolfo Vásquez Martínez, Martin Dančák, Matt Bradford, Frans Bongers, Stuart J. Davies, Reuben Nilus, Adriano José Nogueira Lima, Lip Khoon Kho, Edmar Almeida de Oliveira, Joey Talbot, Richard F. Preziosi, Jagoba Malumbres-Olarte, James A. Comiskey, Thalès de Haulleville, José Luís Camargo, Terese B. Hart, Juliana Schietti, Peter S. Ashton, Thomas E. Lovejoy, Ophelia Wang, Kanehiro Kitayama, Francis Q. Brearley, Peter van der Hout, Amy C. Bennett, Janvier Lisingo, Luis Valenzuela Gamarra, Lily Rodriguez Bayona, Zorayda Restrepo Correa, Jérôme Chave, Connie J. Clark, Christopher Baraloto, Gerardo Aymard, Serge K. Begne, Kofi Affum-Baffoe, Abel Monteagudo-Mendoza, Geertje M. F. van der Heijden, Fernanda Coelho de Souza, Timothy R. Baker, Rahayu Sukmaria Sukri, Julie Peacock, Hermann Taedoumg, Simon L. Lewis, Yahn Carlos Soto Shareva, Greta C. Dargie, Murielle Simo-Droissart, David Harris, Faizah Metali, Hans ter Steege, Richard Lowe, Géraldine Derroire, Benoit Burban, Camila Silva Valeria, Martin Svátek, Wannes Hubau, Sarah A. Batterman, Vincent A. Vos, Elizabeth Kearsley, Peter M. Umunay, Martin J. P. Sullivan, Flávia R. C. Costa, Hans Verbeeck, Maria Cristina Peñuela Mora, John R. Poulsen, Simon Willcock, Simone Aparecida Vieira, Jean-Louis Doucet, Foster Brown, Yadvinder Malhi, Luisa Fernanda Duque, Ronald Vernimmen, Miguel E. Leal, Alan Hamilton, Martin Gilpin, Colin R. Maycock, Carlos Cerón, Radim Hédl, Oliver L. Phillips, Walter Huaraca Huasco, Jon C. Lovett, Beatriz Schwantes Marimon, Roderick Zagt, Ted R. Feldpausch, Gabriela Lopez-Gonzalez, Ima Célia Guimarães Vieira, Pascal Boeckx, Roel J. W. Brienen, Marcelo F. Simon, Keith C. Hamer, Alberto Vicentini, Corneille E. N. Ewango, Clément Stahl, Javier Silva Espejo, Ana Andrade, Anand Roopsind, Erika Berenguer, Pieter A. Zuidema, Vianet Mihindou, Murray Collins, Simone Matias Reis, Emilio Vilanova Torre, Kathryn J. Jeffery, Marie Noël Kamdem Djuikouo, Terry Brncic, Percy Núñez Vargas, John Terborgh, Paulo S. Morandi, Bonaventure Sonké, Jan Bogaert, William E. Magnusson, Lilian Blanc, Terry L. Erwin, Ervan Rutishauser, Anthony Di Fiore, Isau Huamantupa-Chuquimaco, Edward T. A. Mitchard, Massiel Corrales Medina, Nicholas J. Berry, Juliana Stropp, Maureen Playfair, Luzmila Arroyo, Douglas Sheil, Armando Torres-Lezama, David A. Neill, Sean C. Thomas, Eric Arets, Ernest G. Foli, Lola da Costa, Ricardo Keichi Umetsu, Lan Qie, James Singh, Lise Zemagho, Agustín Rudas, Richard B. Primack, Jan Reitsma, Annette Hladik, Alexander K. Koch, Colin A. Pendry, Walter A. Palacios, Sabina Cerruto Ribeiro, Nicolas Labrière, Fernando Elias, Eric Chezeaux, William Milliken, Manuel Gloor, Romeo Ekoungoulou, Jefferson S. Hall, Henrique E. M. Nascimento, Susan G. Laurance, Axel Dalberg Poulsen, Marcos Silveira, Carolina V. Castilho, Plínio Barbosa de Camargo, Eurídice N. Honorio Coronado, Kamariah Abu Salim, Joeri A. Zwerts, Marcelo Brilhante de Medeiros, Jos Barlow, Georgia Pickavance, Joice Ferreira, Mark van Nieuwstadt, Jorcely Barroso, Andrew R. Marshall, Miguel Alexiades, Lindsay F. Banin, Terry Sunderland, Lourens Poorter, Alejandro Araujo-Murakami, Varun Swamy, Rafael Herrera, Hans Beeckman, Gerardo Flores Llampazo, Shin-ichiro Aiba, Adriane Esquivel-Muelbert, Michelle Kalamandeen, Adriana Prieto, Ben Hur Marimon, Casimiro Mendoza, Victor Chama Moscoso, Eliana Jimenez-Rojas, Hirma Ramírez-Angulo, Maxime Réjou-Méchain, Vincent Droissart, Nigel C. A. Pitman, Hannah L. Mossman, Everton Cristo de Almeida, Fernando Cornejo Valverde, Ângelo Gilberto Manzatto, Aurélie Dourdain, Luiz E. O. C. Aragão, Raquel Thomas, David W. Galbraith, Kenneth R. Young, Nallaret Davila Cardozo, Timothy J. Killeen, Rafael de Paiva Salomão, Bente B. Klitgaard, James Taplin, Damien Bonal, Karina Melgaço, William F. Laurance, Jason Vleminckx, Esteban Alvarez Dávila, Verginia Wortel, Richarlly da Costa Silva, Thaiane Rodrigues de Sousa, Sophie Fauset, Nadir Pallqui Camacho, Wendeson Castro, Toby R. Marthews, Fabricio Beggiato Baccaro, John T. Woods, David Taylor, Patricia Alvarez Loayza, Andrew Ford, Niro Higuchi, Aida Cuni Sanchez, Aline Pontes Lopes, Laszlo Nagy, John Pipoly, Lee J. T. White, Jhon del Aguila Pasquel, European Research Council, European Commission, Royal Society (UK), Leverhulme Trust, Gordon and Betty Moore Foundation, David and Lucile Packard Foundation, Fundação de Amparo à Pesquisa do Estado de São Paulo, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Agence Nationale de la Recherche (France), Missouri Botanical Garden, Smithsonian Institution, Wildlife Conservation Society, National Geographic Society, Centre for International Forestry Research, Agence Nationale Des Parcs Nationaux (Gabon), University of Leeds, Mensurat Unit, Forestry Research Institute of Ghana, Centro de Pesquisa Agroflorestal de Roraima, Brazilian Agricultural Research Corporation (Embrapa), Sch Geog, University of Nottingham, Department of Biology, Higher Teachers Training College (HTTC), Université deYaoundé I, School of Geography [Leeds], University of Edinburgh, School of Geography and the Environment, Environmental Change Institute, University of Oxford [Oxford], Grad Sch Sci & Engn, Kagoshima University, University of Kent [Canterbury], Universidade Federal do Mato Grosso (UFMT), Universidad Nacional de Colombia, Duke University [Durham], Instituto Nacional de Pesquisas da Amazônia (INPA), University of Campinas [Campinas] (UNICAMP), National Institute for Space Research [Sao José dos Campos] (INPE), Universidad Autonoma Gabriel René Moreno (UAGRM), Wageningen University and Research [Wageningen] (WUR), Dept Organism & Evolutionary Biol, Harvard University [Cambridge], Ecologie des forêts de Guyane (ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université des Antilles et de la Guyane (UAG)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Universidade de São Paulo (USP), Universidade Federal do Acre (UFAC), Research Unit of Landscape Ecology and Plant Production Systems, Université libre de Bruxelles (ULB), School of Engineering and Science, Jacobs University [Bremen], Lancaster Environment Centre, Lancaster University, Sch Geosci, Laboratory of Applied Physical Chemistry, Universiteit Gent = Ghent University [Belgium] (UGENT), Biodiversité et Paysage, Université de Liège - Gembloux, Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Forest Ecol & Forest Management Grp, CSIRO Land and Water, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Woods Hole Research Center, Partenaires INRAE, Herbario Alfredo Paredes, Universidad Agraria del Ecuador, Universidad Nacional de San Antonio Abad del Cusco (UNSAAC), Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Rougier Gabon, Andes to Amazon Biodiversity Program, Federal University of Para - Universidade Federal do Para [Belem - Brésil], Smithsonian Tropical Research Institute, Universidad Nacional de la Amazonía Peruana [Loreto, Perou] (UNAP), AgroParisTech, University of Texas at Austin [Austin], Université de Liège, Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des Milieux Désordonnés et Hétérogènes (LMDH), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Commonwealth Scientific & Industrial Research Organisation (CSIRO), Royal Botanic Gardens, Czech Academy of Sciences [Prague] (CAS), Commissariat général du Plan (CGP), Premier ministre, Instituto Nacional de Pequisas da Amazônia, Instituto National de Pequisas da Amazonia Brazil, Éco-Anthropologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Agence Nationale des Parcs Nationaux, Agence Nationale des Parcs Nationaux, BP 30 379 Libreville, Gabon, Malaysian Palm Oil Board, Kyoto University, Institute of Inorganic and Analytical Chemistry, Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], James Cook University (JCU), Laboratoire d'Etude de l'Apprentissage et du Développement [Dijon] (LEAD), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB), Coordenac Bao de Pesquisas em Ecologia, Universidade do Estado de Mato Grosso (UNEMAT), University of Mary Washington, Chercheur indépendant, Royal Botanic Garden , Kew, Department of Biochemistry and Molecular Biology, Medical and Health Science Center, Instituto Superior Técnico, Universidade Técnica de Lisboa (IST), Universidad Estatal Amazonica, Forest Research Centre (FRC), Forest Ecology and Forest Management Group, Natural History Museum [Oslo], University of Oslo (UiO), Bur Waarderburg, Iwokrama International Centre for Rainforest Conservation and Development, CarboForExpert, Museu Paraense Emílio Goeldi [Belém, Brésil] (MPEG), Center for International Forestry Research (CIFOR), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), University of Yaoundé [Cameroun], JRC Institute for Environment and Sustainability (IES), European Commission - Joint Research Centre [Ispra] (JRC), Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Plant Systemat & Ecol Lab, Université de Yaoundé I, Department of Neurology, Great Ormond Street Hospital for Children [London] (GOSH), Naturalis Biodiversity Center [Leiden], Division of Marine Science and Conservation, Nicholas School of the Environment, Instituto de Investigaciones para el Desarrollo Forestal, Universidad de los Andes [Bogota] (UNIANDES), University of Wisconsin - Milwaukee, Van der Hout Forestry Consulting, University Medical Center Groningen [Groningen] (UMCG), Computational & Applied Vegetation Ecology (CAVElab), Department of Integrative Biology [Berkeley] (IB), University of California [Berkeley], University of California-University of California, Sch Earth Sci & Environm Sustainabil, Northern Arizona University [Flagstaff], University of Stirling, Biol Sci, Liverpool John Moore University (ljmu), Biodiversity Department, Center for Agricultural Research in Suriname (CELOS), Sub Ecology and Biodiversity, Sub Animal Ecology, Ecology and Biodiversity, Animal Ecology, and Systems Ecology
Subjects: 0106 biological sciences, Tropical trees, Hot Temperature, 010504 meteorology & atmospheric sciences, Earth, Planet, Climate, Acclimatization, Tropical forest carbon stocks, Bos- en Landschapsecologie, Growth, Forests, Atmospheric sciences, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Trees, Tropical climate, SDG 13 - Climate Action, Forest and Landscape Ecology, Biomass, Photosynthesis, Hectare, Productivity, Biomass (ecology), Multidisciplinary, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, PE&RC, Wood, Productivity (ecology), Vegetatie, Bos- en Landschapsecologie, C180 Ecology, Tree, Leaf Respiration, Carbon-Cycle Feedbacks, Climate Change, Climate change and forestry, Climate change, 010603 evolutionary biology, Carbon cycle, Carbon Cycle, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Life Science, Bosecologie en Bosbeheer, Vegetatie, 0105 earth and related environmental sciences, Tropical Climate, Vegetation, Global warming, Tropics, 15. Life on land, Forest Ecology and Forest Management, Carbon, CO₂ Fertilization, 13. Climate action, Environmental science, Vegetation, Forest and Landscape Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Acclimation
Abstract: The sensitivity of tropical forest carbon to climate is a key uncertainty in predicting global climate change. Although short-term drying and warming are known to affect forests, it is unknown if such effects translate into long-term responses. Here, we analyze 590 permanent plots measured across the tropics to derive the equilibrium climate controls on forest carbon. Maximum temperature is the most important predictor of aboveground biomass (-9.1 megagrams of carbon per hectare per degree Celsius), primarily by reducing woody productivity, and has a greater impact per °C in the hottest forests (>32.2°C). Our results nevertheless reveal greater thermal resilience than observations of short-term variation imply. To realize the long-term climate adaptation potential of tropical forests requires both protecting them and stabilizing Earth's climate., Our plot monitoring networks havebeen supported by multiple grants from a large number of funding bodies: European Research Council; Natural Environment Research Council; European Union’s Fifth, Sixth, and Seventh Framework Programme; Royal Society, Leverhulme Trust; Gordon and Betty Moore Foundation; David and Lucile Packard Foundation; State of São Paulo Research Foundation (FAPESP); National Council for Science and Technology Development of Brazil (CNPq); Agence Nationale de la Recherche; Conservation International; Missouri Botanical Garden; Smithsonian Institution; Wildlife Conservation Society; National Geographic Society; Centre for International Forestry; and Gabon’s National Park Agency.
Published: 2020
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35. Reframing conservation physiology to be more inclusive, integrative, relevant and forward-looking: reflections and a horizon scan

Author: Cooke, Steven J., Madliger, Christine L., Cramp, Rebecca L., Beardall, John, Burness, Gary P., Chown, Steven L., Clark, Timothy D., Dantzer, Ben, Barrera, Erick de la, Fangue, Nann A., Franklin, Craig E., Fuller, Andrea, Hawkes, Lucy A., Hultine, Kevin R., Hunt, Kathleen E., Love, Oliver P., MacMillan, Heath A., Mandelman, John W., Mark, Felix C., Martin, Lynn B., Newman, Amy E. M., Nicotra, Adrienne B., Robinson, Sharon A., Ropert‐Coudert, Yan, Rummer, Jodie L., Seebacher, Frank, Todgham, Anne E., Cooke, Steven, Madliger, Christine, Cramp, Rebecca, Burness, Gary, Chown, Steven, Clark, Timothy, De La Barrera, Erick, Fangue, Nann, Fish Ecology and Conservation Physiology Laboratory, Carleton University, School of Biological Sciences [University of Queensland, Australia], University of Southern Queensland (USQ), School of Biological Sciences [Monash University, Australia], Monash University [Clayton], Department of Biology, Trent University [Canada], School of Life and Environmental Sciences, Deakin University, Victoria, Australia], Deakin University [Victoria, Australia], University of Michigan [Ann Arbor], University of Michigan System, Instituto de Investigaciones en Ecosistemas y Sustentabilidad (IIES), Universidad Nacional Autónoma de México (UNAM), Department of Wildlife, Fish & Conservation Biology [University of California, Davis, USA], University of California [Davis] (UC Davis), University of California-University of California, Brain Function Research Group, Faculty of Health Sciences, College of Life and Environmental Sciences, Hatherly Laboratories [Exeter, UK], University of Exeter, Desert Botanical Garden, Department of Biology, George Mason University, George Mason University, Department of Biological Sciences, University of Windsor [Ca], Department of Biology, University of Western Ontario, University of Western Ontario (UWO), Anderson Cabot Center for Ocean Life [New England Aquarium, USA], New England Aquarium, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research [Germany], Global Health and Infectious Disease Research [University of South Florida, USA], University of South Florida (USF), Department of Integrative Biology (University of Guelph), University of Guelph, Australian National University (ANU), School of Earth, Atmospheric and Life Sciences (SEALS) and Centre for Sustainable Ecosystem Solutions [Wollongong, Australia], University of Wollongong, Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR), ARC Centre of Excellence for Coral Reef Studies (CoralCoE), James Cook University (JCU), School of Life and Environmental Sciences A08 [Australia) (University of Sydney), The University of Sydney, Department of Animal Science [Davis, USA] (University of California Davis), Haddon, Lindsay, School of Biological Sciences [Brisbane], University of Queensland [Brisbane], Department of Integrative Ecophysiology, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), University of South Florida [Tampa] (USF), University of Wollongong [Australia], Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), School of Biological Sciences [Victoria, Australia] (Monash University), and Monash University [Victoria, Australia]
Subjects: 0106 biological sciences, Horizon scan, Life on Land, Physiology, conservation physiology, Sustainable Development Goals, Marine Biology, Management, Monitoring, Policy and Law, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, horizon scan, Restoration ecology, Biochemistry, Biophysics, and Structural Biology, Evidence, 030304 developmental biology, Nature and Landscape Conservation, Sustainable development, 0303 health sciences, evidence, End user, Ecological Modeling, Life Sciences, Conservation physiology, Biodiversity, Cognitive reframing, Biological Sciences, 15. Life on land, 13. Climate action, Perspective, [SDE]Environmental Sciences, Forward looking, Generic health relevance, Environmental Sciences
Abstract: Applying physiological tools, knowledge and concepts to understand conservation problems (i.e. conservation physiology) has become commonplace and confers an ability to understand mechanistic processes, develop predictive models and identify cause-and-effect relationships. Conservation physiology is making contributions to conservation solutions; the number of ‘success stories’ is growing, but there remain unexplored opportunities for which conservation physiology shows immense promise and has the potential to contribute to major advances in protecting and restoring biodiversity. Here, we consider how conservation physiology has evolved with a focus on reframing the discipline to be more inclusive and integrative. Using a ‘horizon scan’, we further explore ways in which conservation physiology can be more relevant to pressing conservation issues of today (e.g. addressing the Sustainable Development Goals; delivering science to support the UN Decade on Ecosystem Restoration), as well as more forward-looking to inform emerging issues and policies for tomorrow. Our horizon scan provides evidence that, as the discipline of conservation physiology continues to mature, it provides a wealth of opportunities to promote integration, inclusivity and forward-thinking goals that contribute to achieving conservation gains. To advance environmental management and ecosystem restoration, we need to ensure that the underlying science (such as that generated by conservation physiology) is relevant with accompanying messaging that is straightforward and accessible to end users.
Published: 2020
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36. Making sense of ultrahigh-resolution movement data: A new algorithm for inferring sites of interest

Author: Anne Loison, Rory P. Wilson, James Redcliffe, Jonathan R. Potts, Mathieu Garel, Rhys Munden, Luca Börger, Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Department of Integrative Biology, University of Guelph, Biosciences, Swansea University, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Computer science, Inference, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, biologging, Representation (mathematics), ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, Original Research, 030304 developmental biology, Nature and Landscape Conservation, 2. Zero hunger, 0303 health sciences, Ecology, Movement (music), Data stream mining, Schematic, 15. Life on land, Resolution (logic), animal movement, high‐resolution data, Color scheme, [SDE]Environmental Sciences, Path (graph theory), movement ecology, site fidelity, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Algorithm
Abstract: International audience; Decomposing the life track of an animal into behavioral segments is a fundamental challenge for movement ecology. The proliferation of high‐resolution data, often collected many times per second, offers much opportunity for understanding animal movement. However, the sheer size of modern data sets means there is an increasing need for rapid, novel computational techniques to make sense of these data. Most existing methods were designed with smaller data sets in mind and can thus be prohibitively slow. Here, we introduce a method for segmenting high‐resolution movement trajectories into sites of interest and transitions between these sites. This builds on a previous algorithm of Benhamou and Riotte‐Lambert (2012). Adapting it for use with high‐resolution data. The data’s resolution removed the need to interpolate between successive locations, allowing us to increase the algorithm’s speed by approximately two orders of magnitude with essentially no drop in accuracy. Furthermore, we incorporate a color scheme for testing the level of confidence in the algorithm's inference (high = green, medium = amber, low = red). We demonstrate the speed and accuracy of our algorithm with application to both simulated and real data (Alpine cattle at 1 Hz resolution). On simulated data, our algorithm correctly identified the sites of interest for 99% of “high confidence” paths. For the cattle data, the algorithm identified the two known sites of interest: a watering hole and a milking station. It also identified several other sites which can be related to hypothesized environmental drivers (e.g., food). Our algorithm gives an efficient method for turning a long, high‐resolution movement path into a schematic representation of broadscale decisions, allowing a direct link to existing point‐to‐point analysis techniques such as optimal foraging theory. It is encoded into an R package called SitesInterest, so should serve as a valuable tool for making sense of these increasingly large data streams.
Published: 2018
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37. Functional characterization of estrogen receptor subtypes, ER{alpha} and ER{beta}, mediating vitellogenin production in the liver of rainbow trout

Author: Kraak, Glen [Department of Integrative Biology, University of Guelph, Ontario, N1G 2W1 (Canada)]
Published: 2007
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38. More than the eye can see: Genomic insights into the drivers of genetic differentiation in Royal/Macaroni penguins across the Southern Ocean

Author: Phil Trathan, Pierre A. Pistorius, María José Frugone, Jonathan M. Waters, Cynthia Y Wang-Claypool, Gisele P. M. Dantas, Andrew D. Lowther, Andrea M. Polanowski, Theresa L. Cole, Maria Virginia Petry, María E. López, Rauri C. K. Bowie, Elie Poulin, Barbara Wienecke, Ke Bi, Francesco Bonadonna, Juliana A. Vianna, Nicolás I. Segovia, Instituto de Ecología y Biodiversidad (IEB), Department of Animal Ecology and Systematics, Justus-Liebig-Universität Gießen (JLU), National Research Foundation Centre of Excellence at the Percy FitzPatrick Institute, Pontifícia Universidade Católica de Minas Gerais (PUC Minas), Universidade do Vale do Rio dos Sinos (UNISINOS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), 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]), British Antarctic Survey (BAS), Natural Environment Research Council (NERC), Australian Antarctic Division (AAD), Australian Government, Department of the Environment and Energy, Department of Integrative Biology [Berkeley] (IB), University of California [Berkeley], University of California-University of California, Laboratorio de Ecología Molecular (LEM), Universidad de Santiago de Chile [Santiago] (USACH), 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), and Universidad de Santiago de Chile [Santiago] (USACH)-Instituto de Ecología y Biodiversidad (IEB)
Subjects: 0106 biological sciences, 0301 basic medicine, Systematics, Chrysolophus, Range (biology), Zoology, Antarctic Regions, 010603 evolutionary biology, 01 natural sciences, Polymorphism, Single Nucleotide, 03 medical and health sciences, Genetics, Animals, Cluster Analysis, 14. Life underwater, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Phylogeny, ComputingMilieux_MISCELLANEOUS, Isolation by distance, Eudyptes chrysolophus, Genome, biology, [SDV.NEU.PC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior, [SDV.BA]Life Sciences [q-bio]/Animal biology, Genetic Variation, biology.organism_classification, Spheniscidae, 030104 developmental biology, Natal homing, Biological dispersal, Royal penguin, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: The study of systematics in wide-ranging seabirds can be challenging due to the vast geographic scales involved, as well as the possible discordance between molecular, morphological and behavioral data. In the Southern Ocean, macaroni penguins (Eudyptes chrysolophus) are distributed over a circumpolar range including populations in Antarctic and sub-Antarctic areas. Macquarie Island, in its relative isolation, is home to a closely related endemic taxon — the royal penguin (Eudyptes schlegeli), which is distinguishable from E. chrysolophus mainly by facial coloration. Although these sister taxa are widely accepted as representing distinct species based on morphological grounds, the extent of their genome-wide differentiation remains uncertain. In this study, we use genome-wide Single Nucleotide Polymorphisms to test genetic differentiation between these geographically isolated taxa and evaluate the main drivers of population structure among breeding colonies of macaroni/royal penguins. Genetic similarity observed between macaroni and royal penguins suggests they constitute a single evolutionary unit. Nevertheless, royal penguins exhibited a tendency to cluster only with macaroni individuals from Kerguelen Island, suggesting that dispersal occurs mainly between these neighboring colonies. A stepping stone model of differentiation of macaroni/royal populations was further supported by a strong pattern of isolation by distance detected across its whole distribution range, possibly driven by large geographic distances between colonies as well as natal philopatry. However, we also detected intraspecific genomic differentiation between Antarctic and sub-Antarctic populations of macaroni penguins, highlighting the role of environmental factors together with geographic distance in the processes of genetic differentiation between Antarctic and sub-Antarctic waters.
Published: 2019
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39. Science policies: How should science funding be allocated? An evolutionary biologists’ perspective

Author: Kayla C. King, Hanna Kokko, Astrid T. Groot, Stephanie Meirmans, Roger K. Butlin, Anne Charmantier, Jane M. Reid, Maurine Neiman, Jan Engelstädter, Department of Animal and Plant Sciences [Sheffield], University of Sheffield [Sheffield], Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Department of Integrative Biology [Zurich], Institute for Biodiversity and Ecosystem Dynamics (IBED), Centre of Excellence in Biological Interactions, Australian National University (ANU), 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), 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), Evolutionary and Population Biology (IBED, FNWI), University of Zurich, and Meirmans, Stephanie
Subjects: 0106 biological sciences, 0301 basic medicine, funding rate, Evolution, Ecology (disciplines), Science, Distribution (economics), Public Policy, Biology, 010603 evolutionary biology, 01 natural sciences, Constructive, Capital Financing, 10127 Institute of Evolutionary Biology and Environmental Studies, 03 medical and health sciences, Behavior and Systematics, Research Support as Topic, Relevance (information retrieval), grant proposal, scientific quality, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Ecology, business.industry, Forum, funding, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Individual mobility, Public relations, Biological Evolution, United States, science policy, 1105 Ecology, Evolution, Behavior and Systematics, 030104 developmental biology, Incentive, 570 Life sciences, biology, 590 Animals (Zoology), Science policy, business, Diversity (business)
Abstract: In an ideal world, funding agencies could identify the best scientists and projects and provide them with the resources to undertake these projects. Most scientists would agree that in practice, how funding for scientific research is allocated is far from ideal and likely compromises research quality. We, nine evolutionary biologists from different countries and career stages, provide a comparative summary of our impressions on funding strategies for evolutionary biology across eleven different funding agencies. We also assess whether and how funding effectiveness might be improved. We focused this assessment on 14 elements within four broad categories: (a) topical shaping of science, (b) distribution of funds, (c) application and review procedures, and (d) incentives for mobility and diversity. These comparisons revealed striking among‐country variation in those elements, including wide variation in funding rates, the effort and burden required for grant applications, and the extent of emphasis on societal relevance and individual mobility. We use these observations to provide constructive suggestions for the future and urge the need to further gather informed considerations from scientists on the effects of funding policies on science across countries and research fields.
Published: 2019
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40. The three Rs of river ecosystem resilience: Resources, recruitment, and refugia

Author: Van Looy, K., Tonkin, J.D., Floury, M., Leigh, C., Soininen, J., Larsen, S., Heino, J., Le Roy Poff, N., Delong, M., Jahnig, S.C., Datry, T., Bonada, N., Tison-Rosebery, Juliette, Jamoneau, Aurélien, Ormerod, S.J., Collier, K.J., Wolter, C., Institute of Bio- and Geosciences [Jülich] (IBG), Forschungszentrum Jülich GmbH, Department of River Ecology and Conservation, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Griffith University [Brisbane], University of Helsinki, Natural Environment Centre [Oulu], Finnish Environment Institute (SYKE), Milieux aquatiques, écologie et pollutions (UR MALY), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Grup de Recerca 'Freshwater Biology and Management' (FEM), Universitat de Barcelona (UB), Unité Dynamiques des Systèmes Anthropisés, Université de Picardie Jules Verne (UPJV), School of Biosciences [Cardiff], Cardiff University, Leibniz Institute of Freshwater Ecology & Inland Fisheries, IRSTEA Lyon, DEPARTMENT OF INTEGRATIVE BIOLOGY OREGON STATE UNIVERSITY CORVALLIS OREGON USA, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), School of biological Sciences [Christchurch], University of Canterbury [Christchurch], Queensland University of Technology [Brisbane] (QUT), Australian Rivers Institute, German Ctr Integrat Biodivers Res iDiv, Leipzig, Germany, Partenaires INRAE, DEPARTMENT OF BIOLOGY COLORADO STATE UNIVERSITY FORT COLLINS COLORADO USA, Colorado State University [Fort Collins] (CSU), University of Canberra, DEPARTMENT OF BIOLOGY WINONA STATE UNIVERSITY WINONA MINNESOTA USA, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), IRSTEA Bordeaux, Univ Waikato, Sch Sci, Environm Res Inst, Hamilton, New Zealand, Federal Ministry of Education & Research (BMBF) 1 LN1320A, H2020 Science with and for Society 642317, European Project: 642317,H2020,H2020-SC5-2014-two-stage,AQUACROSS(2015), INSTITUTE OF BIO AND GEOSCIENCESJULICH DEU, RiverLy (UR Riverly), SCIENCE AND ENGINEERING FACULTY QUEENSLAND UNIVERSITY OF TECHNOLOGY BRISBANE AUS, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, German Centre for Integrative Biodiversity Research (iDiv), FINNISH ENVIRONMENT INSTITUTE OULU FIN, INSTITUTE FOR APPLIED ECOLOGY UNIVERSITY OF CANBERRA AUS, LEIBNIZ INSTITUTE OF FRESHWATER ECOLOGY AND INLAND FISHERIES BERLIN DEU, GRUP DE RECERCA FRESHWATER ECOLOGY AND MANAGEMENT DEPARTMENT DE BIOLOGIA EVOLUTIVA ECOLOGIA I CIENCIES AMBIENTALS FACULTAT DE BIOLOGIA INSTITUT DE RECERCA DE LA BIODIVERSITAT UNIVERSITAT DE BARCELONA ESP, Ecosystèmes aquatiques et changements globaux (UR EABX), Water Research Institute [Cardiff], ENVIRONMENTAL RESEARCH INSTITUTE THE UNIVERSITY OF WAIKATO HAMILTON NZL, SCHOOL OF BIOLOGICAL SCIENCES UNIVERSITY OF CANTERBURY CHRISTCHURCH NZL, and IDIV GERMAN CENTRE OF INTEGRATIVE BIODIVERSITY RESEARCH LEIPZIG DEU
Subjects: disturbance, resilience trait, recruitment, [SDE]Environmental Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, resource partitioning, functional redundancy, ComputingMilieux_MISCELLANEOUS
Abstract: [Departement_IRSTEA]Eaux [TR1_IRSTEA]QUASARE [ADD1_IRSTEA]Systèmes aquatiques soumis à des pressions multiples [Departement_IRSTEA]Eaux [TR1_IRSTEA]QUASARE [ADD1_IRSTEA]Systèmes aquatiques soumis à des pressions multiples; International audience; Resilience in river ecosystems requires that organisms must persist in the face of highly dynamic hydrological and geomorphological variations. Disturbance events such as floods and droughts are postulated to shape life history traits that support resilience, but river management and conservation would benefit from greater understanding of the emergent effects in communities of river organisms. We unify current knowledge of taxonomic‐, phylogenetic‐, and trait‐based aspects of river communities that might aid the identification and quantification of resilience mechanisms. Temporal variations in river productivity, physical connectivity, and environmental heterogeneity resulting from floods and droughts are highlighted as key characteristics that promote resilience in these dynamic ecosystems. Three community‐wide mechanisms that underlie resilience are (a) partitioning (competition/facilitation) of dynamically varying resources, (b) dispersal, recolonization, and recruitment promoted by connectivity, and (c) functional redundancy in communities promoted by resource heterogeneity and refugia. Along with taxonomic and phylogenetic identity, biological traits related to feeding specialization, dispersal ability, and habitat specialization mediate organism responses to disturbance. Measures of these factors might also enable assessment of the relative contributions of different mechanisms to community resilience. Interactions between abiotic drivers and biotic aspects of resource use, dispersal, and persistence have clear implications for river conservation and management. To support these management needs, we propose a set of taxonomic, phylogenetic, and life‐history trait metrics that might be used to measure resilience mechanisms. By identifying such indicators, our proposed framework can enable targeted management strategies to adapt river ecosystems to global change.
Published: 2019
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41. Examining variation in hydraulic and resource acquisition traits along climatic gradients tests our understanding of plant form and function

Author: Robert P. Skelton, Laurent J. Lamarque, Leander D. L. Anderegg, Department of Integrative Biology, University of California, Stanford University, Biodiversité, Gènes & Communautés (BioGeCo), and Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)
Subjects: 0106 biological sciences, Physiology, Ecology, Comparative physiology, [SDV]Life Sciences [q-bio], Water, Plant Science, 15. Life on land, Biology, Plants, plant functional types, resource acquisition traits, comparative physiology, 010603 evolutionary biology, 01 natural sciences, trait-environment and trait-trait relationships, Plant Leaves, within- and between-species variation, Variation (linguistics), Form and function, Resource Acquisition Is Initialization, hydraulic traits, functional tradeoffs, 010606 plant biology & botany
Abstract: International audience; A goal of comparative physiology is to understand underlying causes of the tremendous diversity of land plant form and function. The hope is that functional diversity of land plants can be distilled to a few traits that together capture the essence of plant form and function (Díaz et al., 2016), thereby simplifying plant diversity into a tractable number of fundamental ecophysiological ‘strategies’ (or plant functional types). However, there has been disagreement and uncertainty as to (1) which traits should make the shortlist – that is what the key dimensions of trait covariation are, and (2) whether broad‐scale trait patterns and the inferred functional tradeoffs hold at smaller scales relevant to predicting species responses to global change (e.g. whether between species trait patterns hold within individual species). In this issue of New Phytologist, the article by Rosas et al. (pp. 632–646) is a thought‐provoking article that investigates within‐ and among‐species variation in key plant traits along a water availability gradient in two major plant families from a European forest.
Published: 2019
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42. Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance

Author: Daniel Ebert, Marco Todesco, John M. Burke, Lexuan Gao, Loren H. Rieseberg, Irina Ćalić, Brook T. Moyers, Timo Kubach, Nicolas B. Langlade, Nolan C. Kane, Emanuel Ziegler, Natalia Bercovich, Katherine L. Ostevik, Jens Odenheimer, Sariel Hübner, Christopher J. Grassa, Dirk Z H Swanevelder, Joon S. Lee, Stéphane Muños, Gregory L. Owens, Sarah B. Yakimowski, Gregory J. Baute, Rishi R. Masalia, Jennifer R. Mandel, John E. Bowers, Galilee Research Institute (Migal), Department of Botany and Biodiversity Research Centre, University of British Columbia (UBC), Department of Biotechnology, Tel-Hai College, Department of Biological Sciences, The Open University [Milton Keynes] (OU), SAP, Department of Integrative Biology, University of California, Herbaria, Harvard University [Cambridge], University of New England (UNE), Department of Biology, Duke University, Colorado State University [Fort Collins] (CSU), Department of Plant Biology, Miller Plant Sciences, University of Georgia [USA], Department of Ecology and Evolutionary Biology (Faculty of Biology), University of Science-Vietnam National Universities, Agricultural Research Council (ARC), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Genome Canada, Genome BC : LSARP2014-223SUN, NSF Plant Genome Program : DBI-0820451, DBI-1444522, and International Consortium for Sunflower Genomic Resources
Subjects: 0106 biological sciences, 0301 basic medicine, Crops, Agricultural, Introgression, Plant Science, Plant disease resistance, Biology, Genes, Plant, 01 natural sciences, 03 medical and health sciences, Genetic variation, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Selection, Genetic, Domestication, Gene, Disease Resistance, Plant Diseases, 2. Zero hunger, Genetics, Recombination, Genetic, Genetic diversity, Pan-genome, Genetic Variation, Sunflower, 030104 developmental biology, Gene Ontology, Helianthus, Hybridization, Genetic, Genome, Plant, 010606 plant biology & botany
Abstract: International audience; Domesticated plants and animals often display dramatic responses to selection, but the origins of the genetic diversity underlying these responses remain poorly understood. Despite domestication and improvement bottlenecks, the cultivated sunflower remains highly variable genetically, possibly due to hybridization with wild relatives. To characterize genetic diversity in the sunflower and to quantify contributions from wild relatives, we sequenced 287 cultivated lines, 17 Native American landraces and 189 wild accessions representing 11 compatible wild species. Cultivar sequences failing to map to the sunflower reference were assembled de novo for each genotype to determine the gene repertoire, or 'pan-genome', of the cultivated sunflower. Assembled genes were then compared to the wild species to estimate origins. Results indicate that the cultivated sunflower pan-genome comprises 61,205 genes, of which 27% vary across genotypes. Approximately 10% of the cultivated sunflower pan-genome is derived through introgression from wild sunflower species, and 1.5% of genes originated solely through introgression. Gene ontology functional analyses further indicate that genes associated with biotic resistance are over-represented among introgressed regions, an observation consistent with breeding records. Analyses of allelic variation associated with downy mildew resistance provide an example in which such introgressions have contributed to resistance to a globally challenging disease.
Published: 2019
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43. Zebra diel migrations reduce encounter risk with lions at night

Author: Simon Chamaillé-Jammes, Nicolas Courbin, Andrew J. Loveridge, Hervé Fritz, Rémi Patin, David W. Macdonald, Marion Valeix, 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), Ecologie quantitative et évolutive des communautés, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre d'études biologiques de Chizé (CEBC), Centre National de la Recherche Scientifique (CNRS), Department of Integrative Biology [Canada], University of Guelph, 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]), 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), and ANR-16-CE02-0001,LANDTHIRST,Les paysages de la soif: changement climatique et ajustements comportementaux face au manque d'eau(2016)
Subjects: 0106 biological sciences, Lions, Zimbabwe, Forage (honey bee), 010603 evolutionary biology, 01 natural sciences, Predation, biology.animal, Animals, 14. Life underwater, Diel vertical migration, Predator, Ecology, Evolution, Behavior and Systematics, Ecosystem, ComputingMilieux_MISCELLANEOUS, biology, National park, Ecology, 010604 marine biology & hydrobiology, Equidae, 15. Life on land, biology.organism_classification, Equus, Geography, Predatory Behavior, [SDE]Environmental Sciences, Animal Science and Zoology, Terrestrial ecosystem, Panthera
Abstract: 1. Diel migrations (DM; back and forth diel movements along an ecological gradient) undertaken by prey to avoid predators during the day have been demonstrated in many taxa in aquatic ecosystems. In terrestrial ecosystems, prey often shift between various vegetation types whose cover determine their vulnerability (i.e. likelihood of being killed when attacked). 2. We conceptualized that in terrestrial ecosystems DM could also occur, and that the contribution of DM and shifts in vegetation cover use in reducing predation risk should depend upon the predator behaviour and the correlation between encounter risk and vulnerability across vegetation types. We further hypothesized that when the predator distribution is predictable, terrestrial prey could have evolved DM strategies taking them away from the predator when it is active or efficient. 3. We investigated whether plains zebras Equus quagga perform DM in Hwange National Park (Zimbabwe). There, zebras can forage in large patches of open grasslands located near waterholes where they can also easily detect predators. However, they are there at high risk of encountering their main predator, lions Panthera leo, especially at night. 4. We found out that zebras employ a DM anti-predator strategy. Zebras forage near waterholes during the day but move away from them at sunset, when lions become active. We demonstrated that this DM, occurring over a few kilometres, dramatically reduces their nighttime risk of encountering lions, which generally remain close to waterholes. Zebra changes in nighttime selection for vegetation cover types reduced their risk of encountering lions much less. This may arise from a trade-off between encounter risk and vulnerability across vegetation types, with zebras favouring low vulnerability once DM has reduced encounter risk. 5. In summary, here we (1) quantify, in a terrestrial system, the effect of a predator-induced DM on the likelihood of encountering a predator, and (2) distinguish the effects of the DM on encounter risk from those related to day/night changes in selection for vegetation types. We discuss how prey partition their risk between encounter risk and habitat-driven vulnerability and why it is likely critical to understand the emergence of anti-predator behavioural strategies.
Published: 2019
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44. The Forest Observation System, building a global reference dataset for remote sensing of forest biomass

Author: Cintia Rodrigues de Souza, Ivan Lakyda, Ulrik Ilstedt, Luzmila Arroyo, Jean Claude Konan Koffi, Dennis Del Castillo Torres, Klaus Scipal, Bruno Hérault, Olga V. Trefilova, Krzysztof Stereńczak, Rodolfo Vásquez Martínez, Pulchérie Bissiengou, John T. Woods, Petro Lakyda, Andrii Bilous, Olga V. Moroziuk, Sergey Vasiliev, Casimiro Mendoza, C. Dresel, Jason Vleminckx, José Antonio Manzanera, Thales A.P. West, Ted R. Feldpausch, Hervé Memiaghe, Estella F. Vedrova, Maria Shchepashchenko, Linda See, Hans ter Steege, Samsudin Musa, Nicolas Labrière, Eurídice N. Honorio Coronado, Maxime Réjou-Méchain, Christoph Perger, Terry L. Erwin, Alexei Aleinikov, Ervan Rutishauser, Hannsjorg Woell, Irie Casimir Zo-Bi, Simon L. Lewis, Marcus Vinicio Neves d'Oliveira, Mikhail A. Kuznetsov, N. V. Lukina, Nataly Ascarrunz, Justyna Szatniewska, Lucas Mazzei, Dilshad M. Danilina, Wannes Hubau, V.N. Karminov, Alejandro Araujo-Murakami, Toshinori Okuda, Steffen Fritz, Vladimir G. Radchenko, Edson Vidal, Raisa K. Matyashuk, Martin J. P. Sullivan, Bonaventure Sonké, Toshihiro Yamada, Maksym Matsala, Viktor V. Ivanov, Timothy J. Killeen, Mikhail D. Evdokimenko, John R. Poulsen, Hermann Taedoumg, David F. R. P. Burslem, Zamah Shari Nur Hajar, K. S. Bobkova, Nicholas J. Berry, C. Amani, Eleneide Doff Sotta, Sergey V. Verhovets, Caroline Bedeau, Celso Paulo de Azevedo, Yadvinder Malhi, Ernest Gothard-Bassébé, Verginia Wortel, Kenneth Rodney, N. E. Shevchenko, Antonio García-Abril, Milton Kanashiro, Marcelino Carneiro Guedes, Timothy R. Baker, Maureen Playfair, Leonid Krivobokov, Laurent Descroix, Elena B. Tikhonova, Ernest G. Foli, Sylvie Gourlet-Fleury, Kofi Affum-Baffoe, Keith C. Hamer, Anatoly Shvidenko, Dmitry Schepaschenko, Alfonso Alonso, Olga Martynenko, M. E. Konovalova, Svitlana Bilous, Jan Krejza, Florian Hofhansl, Jan Falck, Luis Valenzuela Gamarra, Abel Monteagudo Mendoza, Stuart J. Davies, John Armston, Vincent A. Vos, Roel J. W. Brienen, Oliver L. Phillips, Andrey Osipov, Wolfgang Wanek, Farida Herry Susanty, Jérôme Chave, Robin B. Foster, Richard Condit, Anders Karlsson, Lilian Blanc, Juan Carlos Licona, Niro Higuchi, Ademir Roberto Ruschel, Stephen P. Hubbell, Stephan A. Pietsch, Radomir Bałazy, Marisol Toledo, Ben Hur Marimon Junior, Ruben Valbuena, Richard Lucas, Luís Cláudio de Oliveira, P. V. Ontikov, Nadezhda A. Vladimirova, Daniel Lussetti, Florian Kraxner, Aida Cuni-Sanchez, Andes Hamuraby Rozak, Foma K. Vozmitel, Maria Gornova, Marcos Silveira, Plinio Sist, A. V. Gornov, Tatyana Braslavskaya, Haruni Krisnawati, Leonid Stonozhenko, D. I. Nazimova, James Singh, Géraldine Derroire, Liudmila Mukhortova, Beatriz Schwantes Marimon, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Smithsonian Tropical Research Institute, 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]), Forêts et Sociétés (Cirad-Es-UPR 105 Forêts et Sociétés), Département Environnements et Sociétés (Cirad-ES), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), European Space Research and Technology Centre (ESTEC), European Space Agency (ESA), Commissariat général du Plan (CGP), Premier ministre, AgroParisTech, Mensurat Unit, Forestry Research Institute of Ghana, Smithsonian Conservation Biology Institute, Universidad Autonoma Gabriel René Moreno (UAGRM), University of Maryland [College Park], University of Maryland System, Missouri Botanical Garden (USA), Instituto Boliviano de Investigacion Forestal (IBIF), Universidade Federal do Espírito Santo (UFES), ONF - Direction régionale de la Guyane [Cayenne], Office National des Forêts (ONF), Centre national de la recherche scientifique et technologique (CENAREST), CENAREST, School of Geography [Leeds], University of Leeds, Dept Geog, University College of London [London] (UCL), Brazilian Agricultural Research Corporation (Embrapa), International Institute for Applied Systems Analysis [Laxenburg] (IIASA), Embrapa Amapa, Forestry Research and Development Agency (FORDA), Instituto Nacional de Pequisas da Amazônia, Instituto National de Pequisas da Amazonia Brazil, Royal Museum for Central Africa [Tervuren] (RMCA), Department of Forest Ecology and Management, Swedish University of Agricultural Sciences (SLU), Laboratoire de Mathématiques de Neuchâtel, Fond National Suisse, International Institute for Applied Systems Analysis (IIASA), Moscow Institute of Physics and Technology [Moscow] (MIPT), Department of Geography and Earth Sciences (DGES), Aberystwyth University, Environmental Change Institute, University of Oxford [Oxford], Universidade Federal do Mato Grosso (UFMT), Instituto de Manejo Forestal, Institute of Silviculture, Department of Forest and Soil Sciences, Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), Institute for Evolutionary Ecology (IEE), National Academy of Sciences of Ukraine (NASU), CarboForExpert, Universidade Federal do Acre (UFAC), Université Libre de Bruxelles [Bruxelles] (ULB), University of Yaoundé [Cameroun], Naturalis Biodiversity Center [Leiden], Escola Superior de Agricultura Luiz de Queiroz, University of São Paulo, Department of Integrative Biology [Berkeley] (IB), University of California [Berkeley], University of California-University of California, Biodiversity Department, Center for Agricultural Research in Suriname (CELOS), Graduate School of Integrated Arts and Sciences, Hiroshima University, DMITRY SCHEPASCHENKO, SAMSUDIN MUSA, DINA I. NAZIMOVA, TOSHINORI OKUDA, PETR V. ONTIKOV, ANDREY F. OSIPOV, STEPHAN PIETSCH, MAUREEN PLAYFAIR, JOHN POULSEN, VLADIMIR G. RADCHENKO, KENNETH RODNEY, ANDES H. ROZAK, ERVAN RUTISHAUSER, LINDA SEE, MARIA SHCHEPASHCHENKO, RAISA K. MATYASHUK, MAKSYM MATSALA, OLGA V. MARTYNENKO, RODOLFO VASQUEZ MARTINEZ, BEN HUR MARIMON JUNIOR, BEATRIZ MARIMON, JOSÉ ANTONIO MANZANERA, FLORIAN HOFHANSL, MARCELINO CARNEIRO GUEDES, CPAF-AP, LUCAS JOSE MAZZEI DE FREITAS, CPATU, PETRO I. LAKYDA, JUAN CARLOS LICONA, JÉRÔME CHAVE, OLIVER L. PHILLIPS, SIMON L. LEWIS, STUART J. DAVIES, MAXIME RÉJOU-MÉCHAIN, PLINIO SIST, KLAUS SCIPAL, CHRISTOPH PERGER, BRUNO HERAULT, NICOLAS LABRIÈRE, KOFI AFFUM-BAFFOE, ALEXEI ALEINIKOV, ALFONSO ALONSO, CHRISTIAN AMANI, ALEJANDRO ARAUJO-MURAKAMI, JOHN ARMSTON, LUZMILA ARROYO, NATALY ASCARRUNZ, CELSO PAULO DE AZEVEDO, CPAA, TIMOTHY BAKER, RADOMIR BALAZY, CAROLINE BEDEAU, NICHOLAS BERRY, ANDRII M. BILOUS, SVITLANA YU. BILOUS, PULCHÉRIE BISSIENGOU, LILIAN BLANC, KAPITOLINA S. BOBKOVA, TATYANA BRASLAVSKAYA, ROEL BRIENEN, DAVID F. R. P. BURSLEM, RICHARD CONDIT, AIDA CUNI-SANCHEZ, DILSHAD DANILINA, DENNIS DEL CASTILLO TORRES, GÉRALDINE DERROIRE, LAURENT DESCROIX, ELENEIDE DOFF SOTTA, MARCUS VINICIO NEVES D OLIVEIRA, CPAF-AC, CHRISTOPHER DRESEL, TERRY ERWIN, MIKHAIL D. EVDOKIMENKO, JAN FALCK, TED R. FELDPAUSCH, ERNEST G. FOLI, ROBIN FOSTER, STEFFEN FRITZ, ANTONIO DAMIAN GARCIA-ABRIL, ALEKSEY GORNOV, MARIA GORNOVA, ERNEST GOTHARD-BASSÉBÉ, SYLVIE GOURLET-FLEURY, KEITH C. HAMER, FARIDA HERRY SUSANTY, NIRO HIGUCHI, EURÍDICE N. HONORIO CORONADO, WANNES HUBAU, STEPHEN HUBBELL, ULRIK ILSTEDT, VIKTOR V. IVANOV, MILTON KANASHIRO, CPATU, ANDERS KARLSSON, VIKTOR N. KARMINOV, TIMOTHY KILLEEN, JEAN-CLAUDE KONAN KOFFI, MARIA KONOVALOVA, FLORIAN KRAXNER, JAN KREJZA, HARUNI KRISNAWATI, LEONID V. KRIVOBOKOV, MIKHAIL A. KUZNETSOV, IVAN LAKYDA, RICHARD M. LUCAS, NATALIA LUKINA, DANIEL LUSSETTI, YADVINDER MALHI, NIKOLAY SHEVCHENKO, ANATOLY SHVIDENKO, MARCOS SILVEIRA, JAMES SINGH, BONAVENTURE SONKÉ, CINTIA RODRIGUES DE SOUZA, CPAA, KRZYSZTOF STERENCZAK, LEONID STONOZHENKO, MARTIN J. P. SULLIVAN, JUSTYNA SZATNIEWSKA, HERMANN TAEDOUMG, HANS TER STEEGE, ELENA TIKHONOVA, MARISOL TOLEDO, OLGA V. TREFILOVA, RUBEN VALBUENA, LUIS VALENZUELA GAMARRA, SERGEY VASILIEV, ESTELLA F. VEDROVA, SERGEY V. VERHOVETS, EDSON VIDAL, NADEZHDA A. VLADIMIROVA, JASON VLEMINCKX, VINCENT A. VOS, FOMA K. VOZMITEL, WOLFGANG WANEK, THALES A. P. WEST, HANNSJORG WOELL, JOHN T. WOODS, VERGINIA WORTEL, TOSHIHIRO YAMADA, ZAMAH SHARI NUR HAJAR, IRIÉ CASIMIR ZO-BI., LUIS CLAUDIO DE OLIVEIRA, CPAF-AC, HERVÉ MEMIAGHE, ADEMIR ROBERTO RUSCHEL, CPATU, CASIMIRO MENDOZA, ABEL MONTEAGUDO MENDOZA, OLGA V. MOROZIUK, LIUDMILA MUKHORTOVA, Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, 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]), Forêts et Sociétés (UPR Forêts et Sociétés), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Missouri Botanical Garden, Universidade Federal do Espirito Santo (UFES), Université libre de Bruxelles (ULB), Systems Ecology, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Agence Spatiale Européenne = European Space Agency (ESA), Office national des forêts (ONF), University of Oxford, Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), Universidade de São Paulo = University of São Paulo (USP), University of California [Berkeley] (UC Berkeley), and University of California (UC)-University of California (UC)
Subjects: DYNAMICS, 0106 biological sciences, Canopy, Monitoreo de bosques, Data Descriptor, 010504 meteorology & atmospheric sciences, DIVERSITY, Biomasa, Biomassa, Forests, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 7. Clean energy, 01 natural sciences, biomasse aérienne des arbres, Forest Observation System (FOS), CARBON STORAGE, K01 - Foresterie - Considérations générales, Teledetección, Biomass, NETWORK, Greenhouse gas accounting, lcsh:Science, SDG 15 - Life on Land, Biomass (ecology), Evaluación de los recursos forestales, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Renewable energy, Computer Science Applications, aaaaaaaaaaaaaaaaaaaaa, Biogeography, Manejo Florestal, Forêt, P01 - Conservation de la nature et ressources foncières, SENSITIVITY, Statistics, Probability and Uncertainty, Banque de données, Environmental Monitoring, Sensoriamento Remoto, ABOVEGROUND BIOMASS, Information Systems, Statistics and Probability, Conservation of Natural Resources, Forest biomass, P40 - Météorologie et climatologie, Télédétection, Ecologia Florestal, Library and Information Sciences, 010603 evolutionary biology, Education, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Forest ecology, Ecosystem, RATES, atténuation des effets du changement climatique, 0105 earth and related environmental sciences, business.industry, bbbbbbbbbbbbbbbbb, 15. Life on land, cartographie des fonctions de la forêt, Climate change mitigation, Bosque tropical, 13. Climate action, Earth and Environmental Sciences, DENSITY, Remote Sensing Technology, PATTERNS, Environmental science, lcsh:Q, Physical geography, U30 - Méthodes de recherche, Réchauffement global, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Scale (map), business, ccccccccccccccccccccc
Abstract: Forest biomass is an essential indicator for monitoring the Earth’s ecosystems and climate. It is a critical input to greenhouse gas accounting, estimation of carbon losses and forest degradation, assessment of renewable energy potential, and for developing climate change mitigation policies such as REDD+, among others. Wall-to-wall mapping of aboveground biomass (AGB) is now possible with satellite remote sensing (RS). However, RS methods require extant, up-to-date, reliable, representative and comparable in situ data for calibration and validation. Here, we present the Forest Observation System (FOS) initiative, an international cooperation to establish and maintain a global in situ forest biomass database. AGB and canopy height estimates with their associated uncertainties are derived at a 0.25 ha scale from field measurements made in permanent research plots across the world’s forests. All plot estimates are geolocated and have a size that allows for direct comparison with many RS measurements. The FOS offers the potential to improve the accuracy of RS-based biomass products while developing new synergies between the RS and ground-based ecosystem research communities., Measurement(s)above-ground biomass • organic materialTechnology Type(s)tree species census • measurement methodFactor Type(s)geographic location • tree speciesSample Characteristic - Environmentforest biomeSample Characteristic - LocationEarth (planet) Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.9850571
Published: 2019
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45. MicroRNAs facilitate skeletal muscle maintenance and metabolic suppression in hibernating brown bears

Author: Kenneth B. Storey, Blandine Chazarin, Sylvain Giroud, Guillemette Gauquelin-Koch, Bryan E. Luu, Jon M. Arnemo, Fabrice Bertile, Etienne Lefai, Jon E. Swenson, Alina L. Evans, Biology, SAMS, MCGill University, Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Department of Integrative Biology and Evolution, Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Norwegian University of Life Sciences, Faculty of Environmental Sciences and Natural Resource Management (NMBU), Norvegian Institute for Nature Research, Centre National d’Études Spatiales [Paris] (CNES), Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Forestry & Wildlife Management, Inland Norway University of Applied Sciences - Høgskolen i Innlandet, Wildlife Fish and Environment Studies, Swedish University of Agricultural Sciences (SLU), McGill University = Université McGill [Montréal, Canada], Unité de Nutrition Humaine (UNH), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Department of Wildlife, Fish and Environmental Studies, Centre National D'etudes Spatiales874Natural Sciences and Engineering Research Council of Canada6793Universite de Strasbourg Center National de la Recherche Scientifique Miljodirektoratet Naturvardsverket Svenska Jagareforbundet Austrian Science Fund (FWF) Centre National D'etudes Spatiales, and Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Hibernation, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Physiology, Glucose uptake, Clinical Biochemistry, Inflammation, ubiquitin ligase, noncoding RNA, 03 medical and health sciences, 0302 clinical medicine, Atrophy, Downregulation and upregulation, atrophy, medicine, [SDV.MHEP.PHY]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Animals, RNA, Messenger, Muscle, Skeletal, biology, Skeletal muscle, myomiR, Cell Biology, medicine.disease, Muscle atrophy, Mef2a, Cell biology, Ubiquitin ligase, Ursus arctos, MicroRNAs, Muscular Atrophy, 030104 developmental biology, medicine.anatomical_structure, 030220 oncology & carcinogenesis, biology.protein, medicine.symptom, Ursidae, Signal Transduction
Abstract: Early ViewOnline Version of Record before inclusion in an issue; Hibernating brown bears, Ursus arctos, undergo extended periods of inactivity and yet these large hibernators are resilient to muscle disuse atrophy. Physiological characteristics associated with atrophy resistance in bear muscle have been examined (e.g., muscle mechanics, neural activity) but roles for molecular signaling/regulatory mechanisms in the resistance to muscle wasting in bears still require investigation. Using quantitative reverse transcription PCR (RT-qPCR), the present study characterized the responses of 36 microRNAs linked with development, metabolism, and regeneration of skeletal muscle, in the vastus lateralis of brown bears comparing winter hibernating and summer active animals. Relative levels of mRNA of selected genes (mef2a, pax7, id2, prkaa1, and mstn) implicated upstream and downstream of the microRNAs were examined. Results indicated that hibernation elicited a myogenic microRNA, or "myomiR", response via MEF2A-mediated signaling. Upregulation of MEF2A-controlled miR-1 and miR-206 and respective downregulation of pax7 and id2 mRNA are suggestive of responses that promote skeletal muscle maintenance. Increased levels of metabolic microRNAs, such as miR-27, miR-29, and miR-33, may facilitate metabolic suppression during hibernation via mechanisms that decrease glucose uptake and fatty acid oxidation. This study identified myomiR-mediated mechanisms for the promotion of muscle regeneration, suppression of ubiquitin ligases, and resistance to muscle atrophy during hibernation mediated by observed increases in miR-206, miR-221, miR-31, miR-23a, and miR-29b. This was further supported by the downregulation of myomiRs associated with a muscle injury and inflammation (miR-199a and miR-223) during hibernation. The present study provides evidence of myomiR-mediated signaling pathways that are activated during hibernation to maintain skeletal muscle functionality in brown bears.
Published: 2019
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46. Large birds travel farther in homogeneous environments

Author: Holger Schulz, Steffen Oppel, Marlee A. Tucker, Pascual López-López, Mitra Shariati, Dana G. Schabo, Carlos Carrapato, Vicente Urios, Alan D. Maccarone, John N. Brzorad, Roland Kays, Roi Harel, Nina Farwig, Alastair Franke, Ran Nathan, Adam Shreading, Scott H. Newman, Anne E. Lacy, Adam Kane, Rubén Limiñana, Martin Wikelski, Erik Kleyheeg, Robert Domenech, Keith L. Bildstein, Yan Ropert-Coudert, Chloe Bracis, Javier Vidal-Mateo, William F. Fagan, André Chiaradia, John Y. Takekawa, Elizabeth K. Mojica, Richard O. Bierregaard, Orr Spiegel, Lisa C. Davenport, Henrik Skov, Christopher R. DeSorbo, Wolfgang Fiedler, Mark Prostor, Katrin Böhning-Gaese, Olga Alexandrou, Sarah C. Davidson, Sascha Rösner, Michael J. Noonan, Larry Griffin, Christen H. Fleming, Evan R. Buechley, Scott D. LaPoint, Bryan D. Watts, Mariëlle Liduine van Toor, Justin M. Calabrese, Ugo Mellone, Mark Desholm, Clara García-Ripollés, Kerri Wolter, Matthias Schmidt, Peter Enggist, Eileen C. Rees, Qiang Wang, David Cabot, John M. Fryxell, David Grémillet, João P. Silva, Ramūnas Žydelis, Claire S. Teitelbaum, Nir Sapir, Thomas Mueller, Senckenberg Biodiversity and Climate Research Centre [Germany], Senckenberg Gesellschaft für Naturforschung, Department of Biological Sciences [Germany], Goethe University [Germany], Society for the Protection of Prespa, Biology Department [North Carolina], University of North Carolina [Charlotte] (UNC), University of North Carolina System (UNC)-University of North Carolina System (UNC), Hawk Mountain Sanctuary [Pennsylvania], Acopian Center for Conservation Learning, Reese Institute for Conservation of Natural Resources [North Carolina, Lenoir‐Rhyne University, HawkWatch International [USA], Biodiversity and Conservation Ecology Laboratory [USA], University of Utah, School of Biological, Earth and Environmental Sciences [Cork] (BEES), University College Cork (UCC), Smithsonian Conservation Biology Institute, Department of Biology [USA], University of Maryland [College Park], University of Maryland System-University of Maryland System, Instituto da Conservação da Natureza e das Florestas [Portugal], Phillip Island Nature Parks, School of Biological Sciences [Australia], Monash University [Australia], Florida Museum of Natural History, University of Florida [Gainesville], Department of Biology and Florida Museum of Natural History [USA], College of Science and Engineering [Australia], James Cook University (JCU), Department of Civil, Environmental and Geodetic Engineering [Ohio, UISA], Ohio State University [Columbus] (OSU), Department of Migration and Immuno-ecology, Max Planck Institute for Ornithology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, BirdLife Denmark [Denmark], Biodiversity Research Institute, Raptor View Research Institute, Storch Schweiz [Switzerland], Department of Ecology-Conservation Ecology, Faculty of Biology, Phillips Universität (Marburg), Department of Biology [Kintanz, Germany], University of Konstanz, Arctic Raptors Project [Canada], Department of Biological Science [Canada], University of Alberta [Canada], Department of Integrative Biology [Canada], University of Guelph, Vertebrates Zoology Research Group [Spain], University of Alicante [Spain], Environment Science and Solutions SL [Spain], DST-NRF Centre of Excellence at the Percy FitzPatrick Institute, University of Cape Town, 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), Caerlaverock Wetland Centre [UK], Wildfowl & Wetlands Trust [UK], Movement Ecology Laboratory [ISRAEL], The Hebrew University of Jerusalem (HUJ), School of Biology and Environmental Science and Earth Institute [Ireland], University College Dublin [Dublin] (UCD), North Carolina Museum of Natural Sciences, Department of Forestry and Environmental Resources (FER), North Carolina State University [Raleigh] (NC State), Ecology & Biodiversity Group - Institute of Environmental Biology [The Netherlands], Utrecht University [Utrecht], International Crane Foundation [USA], Lamont-Doherty Earth Observatory (LDEO), Columbia University [New York], Grupo de Investigación Zoología de Vertebrados, CIBIO, Universidad de Alicante, Cavanilles Institute of Biodiversity and Evolutionary Biology, Terrestrial Vertebrates Group, University of Valencia, Biology Department [Kansas, USA], Friends University [Kansas, USA], Center for Conservation Biology (Virginia USA), College of William and Mary [Williamsburg] (WM), Food and Agricultural Organization of the United Nations (FAO), United Nations Organization, Royal Society for the Protection of Birds, National Insitute of Polar Research, National Institute of Polar Research [Tokyo] (NiPR), Conservation Ecology - Faculty of Biology (Germany], Philipps University Marburg [Germany], Institute of Evolution and Department of Evolutionary and Environmental Biology, University of Haifa [Haifa], BirdLife Österreich [Austria], Schulz Wildlife Consulting [Germany], Faculty of Geo-Information Science and Earth Observation (ITC), University of Twente [Netherlands], DHI, National Environmental Research Institute, School of Zoology, Faculty of Life Sciences [Israel], Tel Aviv University [Tel Aviv], U.S. Geological Survey, Western Ecological Research Center, Department of Infectious Diseases [Athens, GA, USA] (Odum School of Ecology), University of Georgia [USA]-College of Veterinary Medicine [Athens, GA, USA], Departamento de Didáctica General y Didácticas Específicas [Spain], Key Laboratory of Wetland Ecology and Environment, Chinese Academy of Sciences [Changchun Branch] (CAS)-Northeast Institute of Geography and Agroecology, VulPro NP [South Africa], Ornitela UAB [Lithuania], Universidad de Alicante. Departamento de Ciencias Ambientales y Recursos Naturales, Universidad de Alicante. Departamento de Didáctica General y Didácticas Específicas, Zoología de Vertebrados, Didáctica de las Ciencias y la Tecnología, Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association-Leibniz Association, Florida Museum of Natural History [Gainesville], University of Florida [Gainesville] (UF), 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]), Department of Forestry and Environmental Resources [Raleigh] (FER), Food and Agriculture Organization of the United Nations [Rome, Italie] (FAO), Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), and Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, productivity, Enhanced vegetation index, Population, Foraging, enhanced vegetation index, landscape complementation, movement ecology, productivity, spatial behaviour, terrestrial birds, waterbirds, spatial behaviour, 010603 evolutionary biology, 01 natural sciences, Movement ecology, ddc:570, landscape complementation, Waterbirds, Zoología, education, Spatial analysis, Ecology, Evolution, Behavior and Systematics, Productivity, terrestrial birds, 2. Zero hunger, Global and Planetary Change, education.field_of_study, Ecology, 010604 marine biology & hydrobiology, waterbirds, 15. Life on land, Landscape complementation, Spatial behaviour, enhanced vegetation index, Taxon, Geography, Habitat, 13. Climate action, Homogeneous, Terrestrial birds, Complementarity (molecular biology), [SDE]Environmental Sciences, movement ecology
Abstract: Aim: Animal movement is an important determinant of individual survival, population dynamics and ecosystem structure and function. Nonetheless, it is still unclear how local movements are related to resource availability and the spatial arrangement of resources. Using resident bird species and migratory bird species outside the migratory period, we examined how the distribution of resources affects the movement patterns of both large terrestrial birds (e.g., raptors, bustards and hornbills) and waterbirds (e.g., cranes, storks, ducks, geese and flamingos). Location: Global. Time period: 2003–2015. Major taxa studied: Birds. Methods: We compiled GPS tracking data for 386 individuals across 36 bird species. We calculated the straight‐line distance between GPS locations of each individual at the 1‐hr and 10‐day time‐scales. For each individual and time‐scale, we calculated the median and 0.95 quantile of displacement. We used linear mixed‐effects models to examine the effect of the spatial arrangement of resources, measured as enhanced vegetation index homogeneity, on avian movements, while accounting for mean resource availability, body mass, diet, flight type, migratory status and taxonomy and spatial autocorrelation. Results: We found a significant effect of resource spatial arrangement at the 1‐hr and 10‐day time‐scales. On average, individual movements were seven times longer in environments with homogeneously distributed resources compared with areas of low resource homogeneity. Contrary to previous work, we found no significant effect of resource availability, diet, flight type, migratory status or body mass on the non‐migratory movements of birds. Main conclusions: We suggest that longer movements in homogeneous environments might reflect the need for different habitat types associated with foraging and reproduction. This highlights the importance of landscape complementarity, where habitat patches within a landscape include a range of different, yet complementary resources. As habitat homogenization increases, it might force birds to travel increasingly longer distances to meet their diverse needs. National Trust for Scotland; Penguin Foundation; The U.S. Department of Energy, Grant/Award Number: DE-EE0005362; Australian Research Council; NASA's Arctic Boreal Vulnerability Experiment (ABoVE), Grant/Award Number: NNX15AV92A; Netherlands Organization for Scientific Research, Grant/Award Number: VIDI 864.10.006; BCC; NSF Award, Grant/Award Number: ABI-1458748; U.K. Department for Energy and Climate Change; ‘Juan de la Cierva ‐ Incorporación’ postdoctoral grant; Irish Research Council, Grant/Award Number: GOIPD/2015/81 ; DECC; Goethe International Postdoctoral Programme, People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007‐2013/ under REA grant agreement no [291776]; German Aerospace Center Award, Grant/Award Number: 50JR1601; Scottish Natural Heritage; Solway Coast AONB Sustainable Development Fund; COWRIE Ltd.; Heritage Lottery Fund; Robert Bosch Stiftung; NSF Division of Biological Infrastructure Award, Grant/Award Number: 1564380; Spanish Ministry of Economy and Competitiveness, Grant/Award Number: IJCI-2014-19190; Energinet.dk; NASA Award, Grant/Award Number: NNX15AV92A; MAVA Foundation; Fundação para a Ciência e Tecnologia, Grant/Award Number: SFRH/BPD/118635/2016; National Key R&D Program of China, Grant/Award Number: 2016YFC0500406; Green Fund of the Greek Ministry of Environment
Published: 2019
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47. Intracellular Ca 2+ Dynamics in Astrocytes: Modeling the Underlying Spatiotemporal Diversity

Author: Denizot, Audrey, Berry, Hugues, Venugopal, Sharmila, Artificial Evolution and Computational Biology (BEAGLE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2), Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria), Department of Integrative Biology and Physiology, University of California [Los Angeles] (UCLA), University of California-University of California, Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), and University of California (UC)-University of California (UC)
Subjects: [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019

48. Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana

Author: Cheng-Ruei Lee, Janny L. Peters, Paul Fransz, Saulo Alves Aflitos, Christopher Toomajian, Gabriella Linc, Hoda B.M Ali, Ingo Schubert, Hans de Jong, Peter M. van Dam, Thomas E. Juenger, Vincent Colot, M.E. Schranz, Korbinian Schneeberger, Maarten Koornneef, Robert A. Martienssen, Mateusz Kuzak, Tom Gerats, Jesse R. Lasky, Xianwen Ji, Magnus Nordborg, Systems Biology, Plant Development & (Epi)Genetics (SILS, FNWI), Molecular Plant Pathology (SILS, FNWI), RNA Biology & Applied Bioinformatics (SILS, FNWI), Department of Plant Development and (Epi)Genetics - Swammerdam Institute for Life Sciences, University of Amsterdam [Amsterdam] (UvA), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA), Gregor Mendel Institute (GMI) - Vienna Biocenter (VBC), Austrian Academy of Sciences (OeAW), Biosystematics Group, Wageningen University and Research [Wageningen] (WUR), Department of Biology, Northern Arizona University [Flagstaff], Pennsylvania State University (Penn State), Penn State System, Department of Plant Pathology, Cornell University [New York], Department of Cytogenetics and Genome Analysis, Leibniz Institute of Plant Genetics and Crop Plant Research, Section Plant Genetics - Institute for Wetland and Water Research Faculty of Science, Radboud University Nijmegen, Department of Molecular Plant Pathology, 7Section Plant Genetics,Institute for Wetland and Water Research Faculty of Science, Laboratory of Genetics, MAD - Dutch Genomics Service & Support Provider - Swammerdam Institute for Life Sciences, Max Planck Institute for Plant Breeding Research (MPIPZ), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Cold Spring Harbor Laboratory, Department of Integrative Biology [Berkeley] (IB), University of California [Berkeley], University of California-University of California, Marie Curie Individual Fellowship [OTKA K 108555], EMBO Long-Term Fellowship, National Science Foundation [DEB-0618347], University of Amsterdam, Wageningen University and Research Centre [Wageningen] (WUR), Cornell University, Unité de recherche en génomique végétale (URGV), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Fransz, Paul, Schranz, Michael E., Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of California [Berkeley] (UC Berkeley), and University of California (UC)-University of California (UC)
Subjects: 0106 biological sciences, 0301 basic medicine, Linkage disequilibrium, Arabidopsis thaliana, transposon, Introgression, [SDV]Life Sciences [q-bio], Molecular Plant Physiology, introgression, Arabidopsis, Plant Science, Chromosomal rearrangement, Biology, 01 natural sciences, Chromosomes, Plant, Linkage Disequilibrium, Phylogenetic relationship, Evolution, Molecular, 03 medical and health sciences, BIOS Applied Bioinformatics, Phylogenetics, chromosome rearrangement, haplotype pattern, Genetics, Groep Koornneef, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), Transposon, Pericentric heterochromatin, Phylogeny, Chromosomal inversion, Chromosome rearrangement, Phylogenetic tree, Arabidopsis Proteins, phylogenetic relationship, Haplotype, Cell Biology, Haplotype pattern, Featured Article, Biosystematiek, 030104 developmental biology, Haplotypes, Biosystematics, Original Article, EPS, 010606 plant biology & botany, SNP array
Abstract: Summary Chromosomal inversions can provide windows onto the cytogenetic, molecular, evolutionary and demographic histories of a species. Here we investigate a paracentric 1.17‐Mb inversion on chromosome 4 of Arabidopsis thaliana with nucleotide precision of its borders. The inversion is created by Vandal transposon activity, splitting an F‐box and relocating a pericentric heterochromatin segment in juxtaposition with euchromatin without affecting the epigenetic landscape. Examination of the RegMap panel and the 1001 Arabidopsis genomes revealed more than 170 inversion accessions in Europe and North America. The SNP patterns revealed historical recombinations from which we infer diverse haplotype patterns, ancient introgression events and phylogenetic relationships. We find a robust association between the inversion and fecundity under drought. We also find linkage disequilibrium between the inverted region and the early flowering Col‐FRIGIDA allele. Finally, SNP analysis elucidates the origin of the inversion to South‐Eastern Europe approximately 5000 years ago and the FRI‐Col allele to North‐West Europe, and reveals the spreading of a single haplotype to North America during the 17th to 19th century. The ‘American haplotype’ was identified from several European localities, potentially due to return migration., Significance Statement Structural rearrangements redefine chromosomes, shape genome diversity and can have profound effects on selection, adaptation and spread. Here we elucidate the history of a paracentric inversion in Arabidopsis thaliana, including its origin a few thousand years ago, its maintenance under certain environmental conditions and its migration patterns, from Europe to North America and back.
Published: 2016
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49. Maternal High-Protein and Low-Protein Diets Perturb Hypothalamus and Liver Transcriptome and Metabolic Homeostasis in Adult Mouse Offspring

Author: Lisa J. Martin, Qingying Meng, Montgomery Blencowe, Sandrine Lagarrigue, Sheila Xiao, Calvin Pan, Julian Wier, William C. Temple, Sherin U. Devaskar, Aldons J. Lusis, Xia Yang, David Geffen School of Medicine [Los Angeles], University of California [Los Angeles] (UCLA), University of California-University of California, Department of Integrative Biology and Physiology, University of California [San Diego] (UC San Diego), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, 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), and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, Low protein, tolérance au glucose, medicine.medical_treatment, Reproductive health and childbirth, souris, Transcriptome, high protein, 0302 clinical medicine, Lactation, taux de protéine, maternal diet, désordre métabolique, hypothalamus, low protein, Genetics (clinical), Original Research, Pediatric, Animal biology, 2. Zero hunger, alimentation maternelle, Metabolic dysfunction, [SDV.BA]Life Sciences [q-bio]/Animal biology, Diabetes, foie, Hedgehog signaling pathway, medicine.anatomical_structure, Liver, Molecular Medicine, animal feeding, expression des gènes, medicine.medical_specialty, mice, lcsh:QH426-470, High protein, alimentation animale, Offspring, Clinical Sciences, Weanling, Biology, liver, 03 medical and health sciences, Internal medicine, Biologie animale, Genetics, medicine, Maternal diet, Circadian rhythm, Glucose intolerance, Metabolic and endocrine, Nutrition, metabolic dysfunction, Prevention, Insulin, Perinatal Period - Conditions Originating in Perinatal Period, Gene expression, Hypothalamus, lcsh:Genetics, 030104 developmental biology, Endocrinology, glucose intolerance, gene expression, liver function tests, Law, 030217 neurology & neurosurgery
Abstract: Early life nutritional imbalances are risk factors for metabolic dysfunctions in adulthood, but the long term effects of perinatal exposure to high versus low protein diets are not completely understood. We exposed C57BL/6J offspring to a high protein/low carbohydrate (HP/LC) or low protein/high carbohydrate (LP/HC) diet during gestation and lactation, and measured metabolic phenotypes between birth and 10 months of age in male offspring. Perinatal HP/LC and LP/HC exposures resulted in a decreased ability to clear glucose in the offspring, with reduced baseline insulin and glucose concentrations in the LP/HC group and a reduced insulin response post-glucose challenge in the HP/LC group. The LP/HC diet group also showed reduced birth and weanling weights, whereas the HP/LC offspring displayed increased weanling weight with increased adiposity beyond 5 months of age. Gene expression profiling of hypothalamus and liver revealed alterations in diverse molecular pathways by both diets. Specifically, hypothalamic transcriptome and pathway analyses demonstrated perturbations of MAPK and hedgehog signaling, processes associated with neural restructuring and transmission, and phosphate metabolism by perinatal protein imbalances. Liver transcriptomics revealed changes in purine and phosphate metabolism, hedgehog signaling, and circadian rhythm pathways. Our results indicate maternal protein imbalances perturbing molecular pathways in central and peripheral metabolic tissues, thereby predisposing the male offspring to metabolic dysfunctions.
Published: 2018
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50. Disentangling good from bad practices in the selection of spatial or phylogenetic eigenvectors

Author: Stéphane Dray, Thomas Drouet, David Bauman, Jason Vleminckx, Université libre de Bruxelles (ULB), Ecologie quantitative et évolutive des communautés, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Department of Integrative Biology [Berkeley] (IB), University of California [Berkeley], University of California-University of California, University of California [Berkeley] (UC Berkeley), and University of California (UC)-University of California (UC)
Subjects: 0106 biological sciences, Ecology, 010604 marine biology & hydrobiology, Autocorrelation, 010603 evolutionary biology, 01 natural sciences, Statistical power, Phylogenetic Pattern, Statistics, Spatial ecology, Fraction (mathematics), Akaike information criterion, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [STAT.ME]Statistics [stat]/Methodology [stat.ME], Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), ComputingMilieux_MISCELLANEOUS, Type I and type II errors, Mathematics
Abstract: Eigenvector mapping techniques are widely used by ecologists and evolutionary biologists to describe and control for spatial and/or phylogenetic patterns in their data. The selection of an appropriate subset of eigenvectors is a critical step (misspecification can lead to highly biased results and interpretations), and there is no consensus yet on how to proceed. We conducted a ten‐year review of the practices of eigenvector selection and highlighted three main procedures: selecting the subset of descriptors minimising the Akaike information criterion (AIC), using a forward selection with double stopping criterion after testing the global model significance (FWD), and selecting the subset minimising the autocorrelation in the model residuals (MIR). We compared the type I error rates, statistical power, and R² estimation accuracy of these methods using simulated data. Finally, a real dataset was analysed using variation partitioning analysis to illustrate to what extent the different selection approaches affected the ecological interpretation of the results. We show that, while the FWD and MIR approaches presented a correct type I error rate and were accurate, the AIC approach displayed extreme type I error rates (100%), and strongly overestimated the R². Moreover, the AIC approach resulted in wrong ecological interpretations, as it overestimated the pure spatial fraction (and the joint spatial‐environmental fraction to a lesser extent) of the variation partitioning. Both the FWD and MIR methods performed well at broad and medium scales but had a very low power to detect fine‐scale patterns. The FWD approach selected more eigenvectors than the MIR approach but also returned more accurate R² estimates. Hence, we discourage any future use of the AIC approach, and advocate choosing between the MIR and FWD approaches depending on the objective of the study: controlling for spatial or phylogenetic autocorrelation (MIR) or describing the patterns as accurately as possible (FWD).
Published: 2018
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