Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Study of improvement for the analysis and exploitation of observers' reports EU fisheries from NW African waters : Final report
    Garcia-Isarch, E. ; Clark, J.M. ; Fernandez-Peralta, L. ; Gonzalez-Lorenza, J.G. ; Duque-Nogal, V. ; Corten, A.A.H.M. ; Rey, J. ; Young, C. ; Perales-Raya, C. ; Cervantes, A. ; Verver, S.W. - \ 2020
    Luxembourg : European Commission (Specific Contract No. 12 of the Framework Contract EASME/EMFF/2016/008 12) - 190 p.
    The availability of detailed information on fishing activities and the biology of exploited species is an essential element for fishery resource assessment. Given the diversity of the fleets operating in the Atlantic waters of West Africa, obtaining this information is a challenge. The protocols for mixed Sustainable Fisheries Partnership Agreements (SFPAs) in West Africa (Morocco, Mauritania,
    Senegal and Guinea-Bissau) include provisions for observers from these countries to join EU vessels. Member States (MS) must also provide biological information from the exploited resources, under the EU Multi-Annual Programme (EU MAP) for the Data Collection Framework (DCF). For vessels that operate and unload their catches outside EU waters, this information can only be obtained from scientific observers. Although such observer data is analysed, there is considerable scope for further analysis to maximise information obtained. It is therefore necessary to ensure the observer schemes obtain complementary information to provide the data necessary to formulate relevant fisheries management advice in the region. The main objective of this Specific Contract is twofold: a) to scrutinise and deeply analyse the available information in DG MARE and MS in order to maximise its use; b) to critically analyse the content of these reports to identify strengths and weaknesses in data coverage, with a view to establish a standardised manual for the use of the observers.
    Biased-corrected richness estimates for the Amazonian tree flora
    Steege, Hans ter; Prado, Paulo I. ; Lima, Renato A.F. de; Pos, Edwin ; Souza Coelho, Luiz de; Andrade Lima Filho, Diogenes de; Salomão, Rafael P. ; Amaral, Iêda Leão ; Almeida Matos, Francisca Dionízia de; Castilho, Carolina V. ; Phillips, Oliver L. ; Guevara, Juan Ernesto ; Jesus Veiga Carim, Marcelo de; Cárdenas López, Dairon ; Magnusson, William E. ; Wittmann, Florian ; Martins, Maria Pires ; Sabatier, Daniel ; Irume, Mariana Victória ; Silva Guimarães, José Renan da; Molino, Jean François ; Bánki, Olaf S. ; Piedade, Maria Teresa Fernandez ; Pitman, Nigel C.A. ; Ramos, José Ferreira ; Monteagudo Mendoza, Abel ; Venticinque, Eduardo Martins ; Luize, Bruno Garcia ; Núñez Vargas, Percy ; Silva, Thiago Sanna Freire ; Leão Novo, Evlyn Márcia Moraes de; Reis, Neidiane Farias Costa ; Terborgh, John ; Manzatto, Angelo Gilberto ; Casula, Katia Regina ; Honorio Coronado, Euridice N. ; Montero, Juan Carlos ; Duque, Alvaro ; Costa, Flávia R.C. ; Castaño Arboleda, Nicolás ; Schöngart, Jochen ; Zartman, Charles Eugene ; Killeen, Timothy J. ; Marimon, Beatriz S. ; Marimon-Junior, Ben Hur ; Vasquez, Rodolfo ; Mostacedo, Bonifacio ; Demarchi, Layon O. ; Feldpausch, Ted R. ; Engel, Julien ; Petronelli, Pascal ; Baraloto, Chris ; Assis, Rafael L. ; Castellanos, Hernán ; Simon, Marcelo Fragomeni ; Medeiros, Marcelo Brilhante de; Quaresma, Adriano ; Laurance, Susan G.W. ; Rincón, Lorena M. ; Andrade, Ana ; Sousa, Thaiane R. ; Camargo, José Luís ; Schietti, Juliana ; Laurance, William F. ; Queiroz, Helder Lima de; Nascimento, Henrique Eduardo Mendonça ; Lopes, Maria Aparecida ; Sousa Farias, Emanuelle de; Magalhães, José Leonardo Lima ; Brienen, Roel ; Aymard C, Gerardo A. ; Revilla, Juan David Cardenas ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Stevenson, Pablo R. ; Feitosa, Yuri Oliveira ; Duivenvoorden, Joost F. ; Mogollón, Hugo F. ; Araujo-Murakami, Alejandro ; Ferreira, Leandro Valle ; Lozada, José Rafael ; Comiskey, James A. ; Toledo, José Julio de; Damasco, Gabriel ; Dávila, Nállarett ; Lopes, Aline ; García-Villacorta, Roosevelt ; Draper, Freddie ; Vicentini, Alberto ; Cornejo Valverde, Fernando ; Lloyd, Jon ; Gomes, Vitor H.F. ; Neill, David ; Alonso, Alfonso ; Dallmeier, Francisco ; Souza, Fernanda Coelho de; Maas, Paul ; Baker, Tim R. ; Andel, Tinde R. van; Noronha, Janaína Costa ; Barbosa, Edelcilio Marques ; Malhi, Yadvinder ; Tirado, Milton ; Wang, Ophelia ; Nascimento, Marcelo Trindade ; Flores, Bernardo Monteiro - \ 2020
    Scientific Reports 10 (2020)1. - ISSN 2045-2322

    Amazonian forests are extraordinarily diverse, but the estimated species richness is very much debated. Here, we apply an ensemble of parametric estimators and a novel technique that includes conspecific spatial aggregation to an extended database of forest plots with up-to-date taxonomy. We show that the species abundance distribution of Amazonia is best approximated by a logseries with aggregated individuals, where aggregation increases with rarity. By averaging several methods to estimate total richness, we confirm that over 15,000 tree species are expected to occur in Amazonia. We also show that using ten times the number of plots would result in an increase to just ~50% of those 15,000 estimated species. To get a more complete sample of all tree species, rigorous field campaigns may be needed but the number of trees in Amazonia will remain an estimate for years to come.

    A schematic sampling protocol for contaminant monitoring in raptors
    Espín, Silvia ; Andevski, Jovan ; Duke, Guy ; Eulaers, Igor ; Gómez-Ramírez, Pilar ; Hallgrimsson, Gunnar Thor ; Helander, Björn ; Herzke, Dorte ; Jaspers, Veerle L.B. ; Krone, Oliver ; Lourenço, Rui ; María-Mojica, Pedro ; Martínez-López, Emma ; Mateo, Rafael ; Movalli, Paola ; Sánchez-Virosta, Pablo ; Shore, Richard F. ; Sonne, Christian ; Brink, Nico W. van den; Hattum, Bert van; Vrezec, Al ; Wernham, Chris ; García-Fernández, Antonio J. - \ 2020
    Ambio (2020). - ISSN 0044-7447
    Best practices - Birds of prey - Falcons - Large-scale biomonitoring - Owls - Pan-European network

    Birds of prey, owls and falcons are widely used as sentinel species in raptor biomonitoring programmes. A major current challenge is to facilitate large-scale biomonitoring by coordinating contaminant monitoring activities and by building capacity across countries. This requires sharing, dissemination and adoption of best practices addressed by the Networking Programme Research and Monitoring for and with Raptors in Europe (EURAPMON) and now being advanced by the ongoing international COST Action European Raptor Biomonitoring Facility. The present perspective introduces a schematic sampling protocol for contaminant monitoring in raptors. We provide guidance on sample collection with a view to increasing sampling capacity across countries, ensuring appropriate quality of samples and facilitating harmonization of procedures to maximize the reliability, comparability and interoperability of data. The here presented protocol can be used by professionals and volunteers as a standard guide to ensure harmonised sampling methods for contaminant monitoring in raptors.

    Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts
    Li, Fay Wei ; Nishiyama, Tomoaki ; Waller, Manuel ; Frangedakis, Eftychios ; Keller, Jean ; Li, Zheng ; Fernandez-Pozo, Noe ; Barker, Michael S. ; Bennett, Tom ; Blázquez, Miguel A. ; Cheng, Shifeng ; Cuming, Andrew C. ; Vries, Jan de; Vries, Sophie de; Delaux, Pierre Marc ; Diop, Issa S. ; Harrison, Jill C. ; Hauser, Duncan ; Hernández-García, Jorge ; Kirbis, Alexander ; Meeks, John C. ; Monte, Isabel ; Mutte, Sumanth K. ; Neubauer, Anna ; Quandt, Dietmar ; Robison, Tanner ; Shimamura, Masaki ; Rensing, Stefan A. ; Villarreal, Juan Carlos ; Weijers, Dolf ; Wicke, Susann ; Wong, Gane K.S. ; Sakakibara, Keiko ; Szövényi, Péter - \ 2020
    Nature Plants 6 (2020)3. - ISSN 2055-026X - p. 259 - 272.

    Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants.

    Impact of genotype, body weight and sex on the prenatal muscle transcriptome of Iberian pigs
    García-Contreras, Consolación ; Madsen, Ole ; Groenen, Martien A.M. ; López-García, Adrián ; Vázquez-Gómez, Marta ; Astiz, Susana ; Núñez, Yolanda ; Benítez, Rita ; Fernández, Almudena ; Isabel, Beatriz ; Rey, Ana Isabel ; González-Bulnes, Antonio ; Óvilo, Cristina - \ 2020
    PLoS ONE 15 (2020)1. - ISSN 1932-6203

    Growth is dependent on genotype and diet, even at early developmental stages. In this study, we investigated the effects of genotype, sex, and body weight on the fetal muscle transcriptome of purebred Iberian and crossbred Iberian x Large White pigs sharing the same uterine environment. RNA sequencing was performed on 16 purebred and crossbred fetuses with high body weight (340±14g and 415±14g, respectively) and 16 with low body weight (246±14g and 311±14g, respectively), on gestational day 77. Genotype had the greatest effect on gene expression, with 645 genes identified as differentially expressed (DE) between purebred and crossbred animals. Functional analysis showed differential regulation of pathways involved in energy and lipid metabolism, muscle development, and tissue disorders. In purebred animals, fetal body weight was associated with 35 DE genes involved in development, lipid metabolism and adipogenesis. In crossbred animals, fetal body weight was associated with 60 DE genes involved in muscle development, viability, and immunity. Interestingly, the results suggested an interaction genotype∗weight for some DE genes. Fetal sex had only a modest effect on gene expression. This study allowed the identification of genes, metabolic pathways, biological functions and regulators related to fetal genotype, weight and sex, in animals sharing the same uterine environment. Our findings contribute to a better understanding of the molecular events that influence prenatal muscle development and highlight the complex interactions affecting transcriptional regulation during development.

    NEOTROPICAL XENARTHRANS: a data set of occurrence of xenarthran species in the Neotropics
    Santos, Paloma Marques ; Bocchiglieri, Adriana ; Chiarello, Adriano Garcia ; Paglia, Adriano Pereira ; Moreira, Adryelle ; Souza, Agnis Cristiane de; Abba, Agustin Manuel ; Paviolo, Agustin ; Gatica, Ailin ; Medeiro, Akyllan Zoppi ; Costa, Alan Nilo ; Gallina, Alberto Gonzalez ; Yanosky, Alberto A. ; Jesus, Alejandro ; Bertassoni, Alessandra ; Rocha, Alessandro ; Bovo, Alex Augusto Abreu ; Bager, Alex ; Mol, Alexandra Cravino ; Martensen, Alexandre Camargo ; Faustino, Alexandre Casagrande ; Lopes, Alexandre Martins Costa ; Percequillo, Alexandre Reis ; Vogliotti, Alexandre ; Keuroghlian, Alexine ; Colina, María Alicia de la; Devlin, Allison L. ; García-Olaechea, Alvaro ; Sánchez, Amadeo ; Srbek-Araujo, Ana Carolina ; Ochoa, Ana Cecilia ; Oliveira, Ana Cristina Mendes ; Lacerda, Ana Cristyna Reis ; Campelo, Ana Kellen Nogueira ; Oliveira Paschoal, Ana Maria de; Costa, Ana Raíssa Cunha ; Meiga, Ana Yoko Ykeuti ; Jesus, Anamélia Souza ; Feijó, Anderson ; Hirsch, André ; Silva, André Luiz Ferreira da; Botelho, André Luis Moura ; Regolin, André Luis ; Lanna, André Monnerat ; Nunes, André Valle ; Kindel, Andreas ; Moraes, Andreia Magro ; Gatti, Andressa ; Noss, Andrew J. ; Nobre, Andrezza Bellotto ; Montanarin, Anelise ; Deffaci, Ângela Camila ; Albuquerque, Anna Carolina Figueiredo de; Oliveira, Anne Karoline de; Mangione, Antonio Marcelo ; Pontes, Antonio Rossano Mendes ; Bertoldi, Ariane Teixeira ; Calouro, Armando Muniz ; Desbiez, Arnaud L.J. ; Fernandes, Arthur ; Ferreguetti, Atilla Colombo ; Silva, Maria Augusta Andrade da; Zimbres, Barbara ; Luciano, Beatriz Fernandes Lima ; Thoisy, Benoit de; Niebuhr, Bernardo Brandão S. ; Papi, Bernardo ; Gómez-Valencia, Bibiana ; Santos, Bráulio A. ; Lima, Breno Campelo ; Oliveira, Bruna Gomes ; Santos, Bruna Silva ; Campos, Bruno Augusto Torres Parahyba ; Leles, Bruno ; Albuquerque França, Bruno Rodrigo de; Lim, Burton ; Oliveira, Caetano Troncoso ; Cantagallo, Camila ; Lara, Camila Clozato ; Lima, Camila Silveira ; Gestich, Carla Cristina ; Melo-Soares, Carla Danielle de; Peres, Carlos A. ; Kasper, Carlos Benhur ; Candia-Gallardo, Carlos ; Angelo, Carlos De; Fragoso, Carlos Eduardo ; Freitas, Carlos Henrique de; Salvador, Carlos Henrique ; Brocardo, Carlos R. ; Melo, Carolina Depolito ; Leuchtenberger, Caroline ; Braga, Caryne ; Sánchez-Lalinde, Catalina ; Bueno, Cecília ; Luna, Cecília Licarião ; Rojano, Cesar ; Hurtado, Cindy Meliza ; Santos, Cinthya Chiva dos; Tellaeche, Cintia ; Rosa, Clarissa ; Campos, Claudia Bueno de; Silva, Cláudia Regina ; Kanda, Claudia Zukeran ; Jenkins, Clinton N. ; McDonough, Colleen ; Trinca, Cristiano Trapé ; Cunha, Cristina Jaques da; Widmer, Cynthia Elisa ; Santos, Cyntia ; Buscariol, Daiane ; Carreira, Daiane Cristina ; Carvalho, Danianderson Rodrigues ; Silva Ferraz, Daniel da; Casali, Daniel ; Thornton, Daniel ; Vasconcellos, Daniela Rodrigues ; Barcelos, Daniele ; Brown, Danielle ; Ramos, Daniella Leal ; Moreira, Danielle Oliveira ; Yogui, Débora Regina ; Faria, Deborah ; Sana, Denis Alessio ; Mattia, Denise Lidoro de; Henz, Denison José ; Friedeberg, Diana B. ; Carvalho, Diana Letícia Kruger Pacheco ; Astúa, Diego ; Queirolo, Diego ; Varela, Diego M. ; Eaton, Donald P. ; Dias, Douglas Matos ; Rivadeneira, Edgar Federico ; Rocha, Ednaldo Cândido ; Abreu-Júnior, Edson Fiedler de; Carrano, Eduardo ; Santos, Eduardo Marques ; Setz, Eleonore Zulnara Freire ; Carvalho, Elildo Alves Ribeiro ; Almeida Chiquito, Elisandra de; Matos Cardoso, Elizandra de; Mendonça, Eloisa Neves ; Bastiani, Elvira D'; Vieira, Emerson M. ; Ramalho, Emiliano Esterci ; Guijosa-Guadarrama, Emiliano ; González, Enrique ; Maggiorini, Erica Vanessa ; Fischer, Erich ; Aguiar, Erick Francisco ; Castro, Érika Paula ; Peña-Cuéllar, Erika de la; Viveiros de Castro, Ernesto B. ; Brítez, Evelyn Beatriz ; Vanderhoeven, Ezequiel Andres ; Pedó, Ezequiel ; Rocha, Fabiana Lopes ; Girardi, Fabiane ; Oliveira Roque, Fabio de; Mazim, Fábio Dias ; Barros, Fabio Monteiro de; Martello, Felipe ; Fantacini, Felipe Moreli ; Pedrosa, Felipe ; Peters, Felipe Bortolotto ; Abra, Fernanda Delborgo ; Azevedo, Fernanda Cavalcanti de; Silva Santos, Fernanda da; Silva, Fernanda Guedes da; Teixeira, Fernanda Zimmermann ; Perini, Fernando Araujo ; Passos, Fernando C. ; Carvalho, Fernando ; Azevedo, Fernando Cesar Cascelli de; Pinho, Fernando Ferreira de; Gonçalves, Fernando ; Lima, Fernando ; Contreras-Moreno, Fernando M. ; Pedroni, Fernando ; Tortato, Fernando Rodrigo ; Santos, Filipe Pereira Rego ; Caruso, Flavia ; Tirelli, Flávia Pereira ; Miranda, Flávia Regina ; Rodrigues, Flávio Henrique Guimarães ; Ubaid, Flávio Kulaif ; Palmeira, Francesca Belem Lopes ; Silva, Franciane Almeida da; Grotta-Neto, Francisco ; Souza, Franco Leandro de; Costa, Francys Emanuelle ; Pérez-Garduza, Freddy ; Delsuc, Frédéric ; Lemos, Frederico ; Pinto, Fredy Ramirez ; Boaglio, Gabriel Ivan ; Massocato, Gabriel Fávero ; Preuss, Gabriel ; Hofmann, Gabriel Selbach ; Aguiar, Gabriel Lima ; Oliveira, Gabriela Schuck ; Duarte, Gabriela Teixeira ; Beca, Gabrielle ; Giné, Gastón Andrés Fernandez ; Batista, Graziele Oliveira ; Gil, Guillermo Eduardo ; Gonsioroski, Gustavo ; Secco, Helio ; Medeiros, Hugo Reis ; Coelho, Igor Pfeifer ; Franceschi, Ingridi Camboim ; Bernardi, Itiberê ; Torre, Antonio de la; Zocche, Jairo José ; Seibert, Jardel Brandão ; Faria Falcão, Jéssica Caroline de; Dias, Jéssica Helena Mangueira ; Nodari, Joana Zorzal ; Oliveira, João Alves ; Giovanelli, João Gabriel Ribeiro ; Favoretti, João Paulo Pandini ; Polisar, John ; Sponchiado, Jonas ; Cherem, Jorge José ; Ramírez, José Fernando Moreira ; Toledo, José Julio de; Duarte, José Maurício Barbanti ; Matos, Jose Roberto de; Arrabal, Juan Pablo ; Faria Oshima, Júlia Emi de; Ribeiro, Juliana Fernandes ; Bogoni, Juliano André ; Pacheco, Julio Javier Chacón ; Schuchmann, Karl L. ; Ferraz, Katia M.P.M.B. ; Santos Everton, Laís dos; Bailey, Larissa L. ; Gonçalves, Larissa Oliveira ; Cullen, Laury ; Andrade, Layla Reis de; Trevelin, Leonardo Carreira ; Bonjorne, Lilian ; Almeida Rodrigues, Livia de; Leuzinger, Lucas ; Perillo, Lucas Neves ; Araújo, Luciana Souza ; Hufnagel, Ludmila ; Ribeiro, Ludmilla Oliveira ; Bernardo, Luis Renato Rezende ; Oliveira-Santos, Luiz Gustavo Rodrigues ; Varzinczak, Luiz Henrique ; Borges, Luiz Henrique Medeiros ; Guimarães, Luiza Neves ; Möcklinghoff, Lydia ; Oliveira, Marcela Alvares ; Magioli, Marcelo ; Assis Jardim, Márcia Maria de; Oliveira, Márcio Leite de; Tortato, Marcos Adriano ; Dums, Marcos ; Iezzi, Maria Eugenia ; Pereira, Maria João Ramos ; Jorge, Maria Luísa ; Castro Morini, Maria Santina de; Landis, Mariana Bueno ; Xavier, Mariana Sampaio ; Barros, Marília A.S. ; Silva, Marina Lima da; Rivero, Marina ; Zanin, Marina ; Marques, Marinêz Isaac ; Alves, Mario Henrique ; Bitetti, Mario S. Di; Alvarez, Martín R. ; Graipel, Maurício Eduardo ; Godoi, Mauricio Neves ; Benedetti, Maximiliano Augusto ; Beltrão, Mayara Guimarães ; Monteiro, Miguel Coutinho Moretta ; Paula, Milton José de; Perilli, Miriam Lucia Lages ; Silva, Murillo Prado da; Villar, Nacho ; Albuquerque, Natasha Moraes De; Canassa, Nathália F. ; Filho, Newton Mota ; Rosa Oliveira, Nicole da; Pasqualotto, Nielson ; Cáceres, Nilton Carlos ; Attias, Nina ; Favarini, Marina Ochoa ; Ribeiro, Otávio Santi ; Gonçalves, Pablo Rodrigues ; Rocha, Patrício Adriano da; Condé, Paula Alves ; Akkawi, Paula ; Cruz, Paula ; Lira, Paula Koeler ; Ferreira, Paula Modenesi ; Arroyo-Gerala, Paulina ; Hartmann, Paulo Afonso ; Tarso Zuquim Antas, Paulo de; Marinho, Paulo Henrique ; Faria Peres, Pedro Henrique de; Peña-Mondragón, Juan Luis ; Lombardi, Pryscilla Moura ; Souza Laurindo, Rafael de; Alves, Rafael Souza Cruz ; Grangeiro, Raissa Danielle Praxedes ; Silva, Ramon Lima ; Beltrão-Mendes, Raone ; Bonikowski, Renata Twardowsky Ramalho ; Reppucci, Juan ; Arrais, Ricardo Corassa ; Sampaio, Ricardo ; Sartorello, Ricardo ; Bovendorp, Ricardo Siqueira ; McNab, Roan ; Hack, Robson Odeli Espíndola ; Magalhães, Rodolfo Assis ; Araújo, Rodrigo Costa ; Almeida Nobre, Rodrigo de; Pérez, Rodrigo Raúl León ; Massara, Rodrigo Lima ; Paula, Rogério Cunha de; Anleu, Rony García ; Marques, Rosane Vieira ; Dornas, Rubem ; Rolim, Samir Gonçalves ; Cavalcanti, Sandra M.C. ; Lima, Saulo Ramos ; Ballari, Sebastián A. ; Santamaría, Silvia Benito ; Silva, Sofia Marques ; Age, Stefani Gabrieli ; Godim, Tayana ; Sobral-Souza, Thadeu ; Maccarini, Thiago Bernardes ; Rodrigues, Thiago Ferreira ; Piovezan, Ubiratan ; Cunha Tavares, Valéria da; Quiroga, Verónica Andrea ; Krepschi, Victor Gasperotto ; Filho, Vilmar Picinatto ; Galvão Bastazini, Vinícius Augusto ; Oliveira Gasparotto, Vinicius Peron de; Orsini, Vinicius Santana ; Guedes Layme, Viviane Maria ; Hannibal, Wellington ; Dáttilo, Wesley ; Carvalho, William Douglas de; Loughry, William James ; Blanco, Yamil Edgardo Di; Núñez-Regueiro, Mauricio M. ; Giubbina, Marina Furlan ; Passamani, Marcelo ; Alagão Querido, Luciano Carramaschi de; Costa Toledo, Gustavo Alvez da; Ribeiro, Igor Kintopp ; Quintilham, Lucas ; Bustos, Soledad de; Maza, Javier de la; Lima Neto, Jorge Ferreira ; Kossel de Andrade Silva, Katyucha Von; Sartorello, Leonardo ; Rampim, Lilian Elaine ; Marás, Gustavo A. ; Camino, Micaela ; Freitas-Junior, Mozart ; Perovic, Pablo Gaston ; Paolino, Roberta Montanheiro ; Ferreira, Scarlat Dalva ; Towns, Valeria ; Esperandio, Isadora Beraldi ; Aximoff, Izar ; Beduschi, Júlia ; Guenther, Mariana ; Cassia Bianchi, Rita de; Keuroghlian-Eaton, Sean ; Mendes, Sérgio Lucena ; Fatima Cunha, Lerrane de; Cirignoli, Sebastián ; Ciocheti, Giordano ; Prado, Helena Alves do; Fernandes-Ferreira, Hugo ; Mendes de Sena, Liana Mara ; Yamane, Marcelo Hideki ; Brennand, Pamella G.G. ; Silva, Rayana Diniz da; Escobar, Santiago ; Endo, Whaldener ; Hurtado, Rafael Reyna ; Gontijo, Nila Rássia Costa ; Marsh, Laura K. ; Severo, Magnus Machado ; Pardo, Julia Martinez ; Costa, Sebastián Andrés ; Melo, Geruza Leal ; Santana, Gindomar Gomes ; Miranda Mourão, Guilherme de; Gaspari, Gustavo Gabirele ; Duarte, Herbert ; Cabral, Hugo ; Silva, Leonardo Henrique da; Mendonça, Luana ; Barbosa, Lucas Lobo ; Santos, Manuela Vieira dos; Moraes, Marcela Figuerêdo Duarte ; Gordo, Marcelo ; Versiani, Natalia Fraguas ; Cantero, Nicolás ; Pays, Olivier ; Guedes, Patrícia Gonçalves ; Colas-Rosas, Paul François ; Ribeiro, Paulo ; Renaud, Pierre Cyril ; Hoogesteijn, Rafael Jan ; Ayala, Rodrigo ; Cunha, Rogério Grassetto Teixeira da; Schaub, Roxane ; Laurito, Sabrina ; Betkowski, Samuel Eurich ; Cortez, Sara ; Silva, Shirley Seixas Pereira ; Oliveira, Tadeu Gomes de; Spironello, Wilson Roberto ; Gengler, Nicholas ; Hidalgo, Mircea Mihart ; Juárez, Rugieri ; Iglesias, Jesús A. ; Anacleto, Teresa Cristina ; Souza Fialho, Marcos de; Cavicchioli, Guilherme ; Beccato, Maria Angélica Barbosa ; Silva, Marcelo da; Neto, Omar Correia ; Lopes, Karine Galisteo Diemer ; Godoy, Leandro Perez ; Luiz, Micheli Ribeiro ; Rojas Bonzi, Viviana B. ; Ferreira, Guilherme Braga ; Oliveira, Marcelo Juliano Rabelo ; Hinojosa, Javier ; Oliveira, Luiz Flamarion Barbosa de; Nagy-Reis, Mariana Baldy ; Ramirez, Sixto Fernández ; Concone, Henrique Villas Boas ; Mourthe, Italo ; Martínez-Lanfranco, Juan A. ; Zanoni, Juliani Bruna ; Moreira, Tainah Cruz ; Guarderas, Zoila Vega ; Bazilio, Sérgio ; Cervini, Marcelo ; Pinheiro, Marcell Soares ; Morato, Ronaldo Gonçalves ; Peroni, Nivaldo ; Trigo, Tatiane Campos ; Machado, Ricardo Bomfim ; Gaspari, Fernando ; Koenemann, Joceleia G. ; Rudolf, Juan Carlos ; Benchimol, Maíra ; Vieira, Marcus Vinícius ; Retta, Lucía Martínez ; Santiago, Pablo Gerardo Fernández ; Ciccia, Paula Gonzalez ; Estrela, Pedro Cordeiro ; Carvalho, Santiago ; Esbérard, Carlos Eduardo Lustosa ; Cruz, Yaribeth Bravata de la; Castro-Prieto, Jessica ; Braga, Ricardo Miranda ; Cartes, Jose Luis ; Andrade-Núñez, María José ; Denkiewicz, Natalia Mariana ; Falconi, Nereyda ; Pezzuti, Juarez Carlos Brito ; Castillo Cordero, Hugo Fernando del; Sousa, Luziene Conceição de; Gaspari Júnior, Roque Lázaro de; Santos-Filho, Manoel ; Almeida, Josué Santos ; Thompson, Jeffrey J. ; Santos, Juliana Silveira dos; Pereira-Ribeiro, Juliane ; Burs, Kathrin ; Silva, Kena Ferrari Moreira da; Velilla, Marianela ; Silva, Marina Xavier da; Sancha, Noé U. de la; Pinheiro, Paula Fabiana ; Castilho, Pedro Volkmer de; Bercê, William ; Assis, Julia Camara ; Tonetti, Vinicius Rodrigues ; Alves-Eigenheer, Milene ; Chinem, Simonne ; Honda, Laura K. ; Godoy Bergallo, Helena de; Alberici, Vinicius ; Wallace, Robert ; Campos Krauer, Juan Manuel ; Ribeiro, Milton Cezar ; Galetti, Mauro - \ 2019
    Ecology 100 (2019)7. - ISSN 0012-9658
    biodiversity hotspot - cingulata - forest fragmentation - habitat loss - neotropical mammals - neotropical region - pilosa - xenarthra

    Xenarthrans—anteaters, sloths, and armadillos—have essential functions for ecosystem maintenance, such as insect control and nutrient cycling, playing key roles as ecosystem engineers. Because of habitat loss and fragmentation, hunting pressure, and conflicts with domestic dogs, these species have been threatened locally, regionally, or even across their full distribution ranges. The Neotropics harbor 21 species of armadillos, 10 anteaters, and 6 sloths. Our data set includes the families Chlamyphoridae (13), Dasypodidae (7), Myrmecophagidae (3), Bradypodidae (4), and Megalonychidae (2). We have no occurrence data on Dasypus pilosus (Dasypodidae). Regarding Cyclopedidae, until recently, only one species was recognized, but new genetic studies have revealed that the group is represented by seven species. In this data paper, we compiled a total of 42,528 records of 31 species, represented by occurrence and quantitative data, totaling 24,847 unique georeferenced records. The geographic range is from the southern United States, Mexico, and Caribbean countries at the northern portion of the Neotropics, to the austral distribution in Argentina, Paraguay, Chile, and Uruguay. Regarding anteaters, Myrmecophaga tridactyla has the most records (n = 5,941), and Cyclopes sp. have the fewest (n = 240). The armadillo species with the most data is Dasypus novemcinctus (n = 11,588), and the fewest data are recorded for Calyptophractus retusus (n = 33). With regard to sloth species, Bradypus variegatus has the most records (n = 962), and Bradypus pygmaeus has the fewest (n = 12). Our main objective with Neotropical Xenarthrans is to make occurrence and quantitative data available to facilitate more ecological research, particularly if we integrate the xenarthran data with other data sets of Neotropical Series that will become available very soon (i.e., Neotropical Carnivores, Neotropical Invasive Mammals, and Neotropical Hunters and Dogs). Therefore, studies on trophic cascades, hunting pressure, habitat loss, fragmentation effects, species invasion, and climate change effects will be possible with the Neotropical Xenarthrans data set. Please cite this data paper when using its data in publications. We also request that researchers and teachers inform us of how they are using these data

    Fetal genotype effects on morphomics, fatty acids composition and transcriptomics in swine
    Garcia Contreras, Consolacion ; Vazquez-Gomez, M. ; Madsen, O. ; Groenen, M. ; Astiz, S. ; Nunez, Y. ; Benitez, R. ; Heras-Molina, A. ; Fernandez, A. ; Isabel, B. ; Rey, A.I. ; Gonzalez-Bulnes, A. ; Ovilo, C. - \ 2019
    In: ISAG 2019 Abstract Book. - - p. 148 - 149.
    Iberian pigs are more prone to obesity and metabolic alterations than other lean swine breeds, due to leptin resistance and thrifty genotype, which makes the breed susceptible to changes in amount and composition of diet. This is especially manifested during prenatal development, where nutritional deficiencies in the diet of the mother may modify offspring’s gene expression to cope with postnatal challenging conditions. This work aimed to assess the role of the genotype in the metabolic and transcriptomic changes of pig fetuses derived from undernourished pregnant sows. Pure Iberian sows were inseminated with heterospermic semen from Iberian and Large White boars to obtain IBxIB and IBxLW genotypes. The pregnancy was challenged by diminishingmaternal intake to 50% of requirements during the last 2 thirds of pregnancy. Fifty-one fetuses were obtained at Day 77 of pregnancy and 32 of them (16 from each genotype) were selected at random. Assessment of body traits showed that IBxLW fetuses were heavier and more corpulent than their IBxIB littermates (P < 0.05). Analysis of liver fatty acids (FA) showed that IBxIB had higher level of saturated FA and monounsaturated FA and lower levels of polyunsaturated FA than IBxLW fetuses (P < 0.0001). Liver transcriptome analysis resulted in 249 genes differentially expressed (DE) between the 2 genotypes (q < 0.05 and FC >1.3). Functional annotation of the DE genes revealed a downregulation of biological functions related to growth and development (e.g.: Cell survival, Cell movement, Quantity of connective tissue or Survival of organism) in IBxIB fetuses. Potential transcription factors were assessed with IPA software, which allow the prediction of upstream regulators that may explain the molecular mechanisms responsible of transcriptome differences between genetic types. We highlighted 955 potential upstream regulators, some of them being involvedin growth and development (e.g.: IGF1) and downregulated in IBxIB fetuses. Hence, our results indicate differential regulation of relevant functions and pathways involved in growth and development, which may explain the phenotypic differences among the fatty and lean swine genotypes.
    Non-invasive continuous real-time in vivo analysis of microbial hydrogen production shows adaptation to fermentable carbohydrates in mice
    Schothorst, E.M. van; Fernández Calleja, J.M.S. ; Konstanti, Prokopis ; Swarts, J.J.M. ; Bouwman, L.M.S. ; Garcia-Campayo, Vicenta ; Billecke, Nils ; Oosting, Annemarie ; Smidt, H. - \ 2019
    Rarity of monodominance in hyperdiverse Amazonian forests
    Steege, Hans Ter; Henkel, Terry W. ; Helal, Nora ; Marimon, Beatriz S. ; Marimon-Junior, Ben Hur ; Huth, Andreas ; Groeneveld, Jürgen ; Sabatier, Daniel ; Souza Coelho, Luiz de; Andrade Lima Filho, Diogenes de; Salomão, Rafael P. ; Amaral, Iêda Leão ; Almeida Matos, Francisca Dionízia de; Castilho, Carolina V. ; Phillips, Oliver L. ; Guevara, Juan Ernesto ; Jesus Veiga Carim, Marcelo de; Cárdenas López, Dairon ; Magnusson, William E. ; Wittmann, Florian ; Irume, Mariana Victória ; Martins, Maria Pires ; Silva Guimarães, José Renan da; Molino, Jean François ; Bánki, Olaf S. ; Piedade, Maria Teresa Fernandez ; Pitman, Nigel C.A. ; Mendoza, Abel Monteagudo ; Ramos, José Ferreira ; Luize, Bruno Garcia ; Moraes de Leão Novo, Evlyn Márcia ; Núñez Vargas, Percy ; Silva, Thiago Sanna Freire ; Venticinque, Eduardo Martins ; Manzatto, Angelo Gilberto ; Reis, Neidiane Farias Costa ; Terborgh, John ; Casula, Katia Regina ; Honorio Coronado, Euridice N. ; Montero, Juan Carlos ; Feldpausch, Ted R. ; Duque, Alvaro ; Costa, Flávia R.C. ; Arboleda, Nicolás Castaño ; Schöngart, Jochen ; Killeen, Timothy J. ; Vasquez, Rodolfo ; Mostacedo, Bonifacio ; Demarchi, Layon O. ; Assis, Rafael L. ; Baraloto, Chris ; Engel, Julien ; Petronelli, Pascal ; Castellanos, Hernán ; Medeiros, Marcelo Brilhante de; Quaresma, Adriano ; Simon, Marcelo Fragomeni ; Andrade, Ana ; Camargo, José Luís ; Laurance, Susan G.W. ; Laurance, William F. ; Rincón, Lorena M. ; Schietti, Juliana ; Sousa, Thaiane R. ; Sousa Farias, Emanuelle de; Lopes, Maria Aparecida ; Magalhães, José Leonardo Lima ; Mendonça Nascimento, Henrique Eduardo ; Lima de Queiroz, Helder ; Aymard C, Gerardo A. ; Brienen, Roel ; Revilla, Juan David Cardenas ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Stevenson, Pablo R. ; Feitosa, Yuri Oliveira ; Duivenvoorden, Joost F. ; Mogollón, Hugo F. ; Araujo-Murakami, Alejandro ; Ferreira, Leandro Valle ; Lozada, José Rafael ; Comiskey, James A. ; Toledo, José Julio de; Damasco, Gabriel ; Dávila, Nállarett ; Draper, Freddie ; García-Villacorta, Roosevelt ; Lopes, Aline ; Vicentini, Alberto ; Alonso, Alfonso ; Dallmeier, Francisco ; Gomes, Vitor H.F. ; Lloyd, Jon ; Neill, David ; Aguiar, Daniel Praia Portela de; Arroyo, Luzmila ; Carvalho, Fernanda Antunes ; Souza, Fernanda Coelho de; Amaral, Dário Dantas do; Feeley, Kenneth J. ; Gribel, Rogerio ; Pansonato, Marcelo Petratti ; Barlow, Jos ; Berenguer, Erika ; Ferreira, Joice ; Fine, Paul V.A. ; Guedes, Marcelino Carneiro ; Jimenez, Eliana M. ; Licona, Juan Carlos ; Peñuela Mora, Maria Cristina ; Villa, Boris ; Cerón, Carlos ; Maas, Paul ; Silveira, Marcos ; Stropp, Juliana ; Thomas, Raquel ; Baker, Tim R. ; Daly, Doug ; Dexter, Kyle G. ; Huamantupa-Chuquimaco, Isau ; Milliken, William ; Pennington, Toby ; Ríos Paredes, Marcos ; Fuentes, Alfredo ; Klitgaard, Bente ; Pena, José Luis Marcelo ; Peres, Carlos A. ; Silman, Miles R. ; Tello, J.S. ; Chave, Jerome ; Cornejo Valverde, Fernando ; Fiore, Anthony Di; Hilário, Renato Richard ; Phillips, Juan Fernando ; Rivas-Torres, Gonzalo ; Andel, Tinde R. van; Hildebrand, Patricio von; Noronha, Janaína Costa ; Barbosa, Edelcilio Marques ; Barbosa, Flávia Rodrigues ; Matos Bonates, Luiz Carlos de; Sá Carpanedo, Rainiellen de; Dávila Doza, Hilda Paulette ; Fonty, Émile ; GómeZárate Z, Ricardo ; Gonzales, Therany ; Gallardo Gonzales, George Pepe ; Hoffman, Bruce ; Junqueira, André Braga ; Malhi, Yadvinder ; Andrade Miranda, Ires Paula de; Pinto, Linder Felipe Mozombite ; Prieto, Adriana ; Jesus Rodrigues, Domingos de; Rudas, Agustín ; Ruschel, Ademir R. ; Silva, Natalino ; Vela, César I.A. ; Vos, Vincent Antoine ; Zent, Egleé L. ; Zent, Stanford ; Weiss Albuquerque, Bianca ; Cano, Angela ; Carrero Márquez, Yrma Andreina ; Correa, Diego F. ; Costa, Janaina Barbosa Pedrosa ; Flores, Bernardo Monteiro ; Galbraith, David ; Holmgren, Milena ; Kalamandeen, Michelle ; Nascimento, Marcelo Trindade ; Oliveira, Alexandre A. ; Ramirez-Angulo, Hirma ; Rocha, Maira ; Scudeller, Veridiana Vizoni ; Sierra, Rodrigo ; Tirado, Milton ; Umaña Medina, Maria Natalia ; Heijden, Geertje van der; Vilanova Torre, Emilio ; Vriesendorp, Corine ; Wang, Ophelia ; Young, Kenneth R. ; 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 N. ; Oliveira, Edmar Almeida de; Garcia-Cabrera, Karina ; Hernandez, Lionel ; Palacios Cuenca, Walter ; Pansini, Susamar ; Pauletto, Daniela ; Ramirez Arevalo, Freddy ; Sampaio, Adeilza Felipe ; Valderrama Sandoval, Elvis H. ; Valenzuela Gamarra, Luis ; Levesley, Aurora ; Pickavance, Georgia ; Melgaço, Karina - \ 2019
    Scientific Reports 9 (2019). - ISSN 2045-2322

    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.

    Semi-supervised multivariate statistical network monitoring for learning security threats
    Camacho, Jose ; Macia-Fernandez, Gabriel ; Fuentes-Garcia, Noemi Marta ; Saccenti, Edoardo - \ 2019
    IEEE Transactions on Information Forensics and Security 14 (2019)8. - ISSN 1556-6013 - p. 2179 - 2189.
    anomaly detection - intrusion detection - Multivariate statistical network monitoring - partial least squares regression - principal components analysis - semi-supervised learning

    This paper presents a semi-supervised approach for intrusion detection. The method extends the unsupervised multivariate statistical network monitoring approach based on the principal component analysis by introducing a supervised optimization technique to learn the optimum scaling in the input data. It inherits the advantages of the unsupervised strategy, capable of uncovering new threats, with that of supervised strategies, capable of learning the pattern of a targeted threat. The supervised learning is based on an extension of the gradient descent method based on partial least squares (PLS). Moreover, we enhance this method by using sparse PLS variants. The practical application of the system is demonstrated on a recently published real case study, showing relevant improvements in detection performance and in the interpretation of the attacks.

    Corrigendum to “Opinion paper about organic trace pollutants in wastewater: Toxicity assessment in a European perspective"
    Pedrazzani, Roberta ; Bertanza, Giorgio ; Brnardić, Ivan ; Cetecioglu, Zeynep ; Dries, Jan ; Dvarionienė, Jolanta ; García-Fernández, Antonio J. ; Langenhoff, Alette ; Libralato, Giovanni ; Lofrano, Giusy ; Škrbić, Biljana ; Martínez-López, Emma ; Meriç, Süreyya ; Mutavdžić Pavlović, Dragana ; Papa, Matteo ; Schröder, Peter ; Tsagarakis, Konstantinos P. ; Vogelsang, Christian - \ 2019
    Science of the Total Environment 669 (2019). - ISSN 0048-9697 - p. 1062 - 1062.

    The authors regret that, despite thoroughly reviewing the manuscript, the content of a paragraph has been duplicated and has to be ignored .

    Opinion paper about organic trace pollutants in wastewater : Toxicity assessment in a European perspective
    Pedrazzani, Roberta ; Bertanza, Giorgio ; Brnardić, Ivan ; Cetecioglu, Zeynep ; Dries, Jan ; Dvarionienė, Jolanta ; García-Fernández, Antonio J. ; Langenhoff, Alette ; Libralato, Giovanni ; Lofrano, Giusy ; Škrbić, Biljana ; Martínez-López, Emma ; Meriç, Süreyya ; Pavlović, Dragana Mutavdžić ; Papa, Matteo ; Schröder, Peter ; Tsagarakis, Konstantinos P. ; Vogelsang, Christian - \ 2019
    Science of the Total Environment 651 (2019). - ISSN 0048-9697 - p. 3202 - 3221.
    Aquatic ecosystem - Bioassays - Ecotoxicity - Micro-pollutants - Risk assessment - Wastewater treatment

    This opinion paper focuses on the role of eco-toxicological tools in the assessment of possible impacts of emerging contaminants on the aquatic ecosystem, hence, on human health. Indeed, organic trace pollutants present in raw and treated wastewater are the pivot targets: a multidisciplinary approach allows defining the basic principles for managing this issue, from setting a proper monitoring campaign up to evaluating the optimal process treatment. Giving hints on trace pollutants fate and behaviour, attention is focused on the choice of the bioassay(s), by analysing the meaning of possible biological answers. Data interpretation and exploitation are detailed with the final goal of providing criteria in order to be able to select the best targeted treatment options. The manuscript deals with conventional and innovative analytical approaches for assessing toxicity, by reviewing laboratory and field assays; illustrative real scale and laboratory applications integrate and exemplify the proposed approach.

    Non-invasive continuous real-time in vivo analysis of microbial hydrogen production shows adaptation to fermentable carbohydrates in mice
    Fernández Calleja, J.M.S. ; Konstanti, Prokopis ; Swarts, J.J.M. ; Bouwman, L.M.S. ; Garcia-Campayo, Vicenta ; Billecke, Nils ; Oosting, Annemarie ; Smidt, H. ; Keijer, J. ; Schothorst, E.M. van - \ 2018
    Wageningen University
    PRJEB23475 - PRJEB23475 - ERP105229
    The gut microbiome interacts continuously with the host and its diet. Studying these interactions and their evolution in vivo as soon as they happen have been impossible. Here we develop a method to study microbiota-host-diet interactions continuously, non-invasively, and in real time, by measuring hydrogen (H2) and methane (CH4) production in mice housed in indirect calorimetry chambers.
    Non-invasive continuous real-time in vivo analysis of microbial hydrogen production shows adaptation to fermentable carbohydrates in mice
    Fernández-Calleja, José M.S. ; Konstanti, Prokopis ; Swarts, Hans J.M. ; Bouwman, Lianne M.S. ; Garcia-Campayo, Vicenta ; Billecke, Nils ; Oosting, Annemarie ; Smidt, Hauke ; Keijer, Jaap ; Schothorst, Evert M. van - \ 2018
    Scientific Reports 8 (2018)1. - ISSN 2045-2322 - 16 p.

    Real time in vivo methods are needed to better understand the interplay between diet and the gastrointestinal microbiota. Therefore, a rodent indirect calorimetry system was equipped with hydrogen (H2) and methane (CH4) sensors. H2 production was readily detected in C57BL/6J mice and followed a circadian rhythm. H2 production was increased within 12 hours after first exposure to a lowly-digestible starch diet (LDD) compared to a highly-digestible starch diet (HDD). Marked differences were observed in the faecal microbiota of animals fed the LDD and HDD diets. H2 was identified as a key variable explaining the variation in microbial communities, with specific taxa (including Bacteroides and Parasutterella) correlating with H2 production upon LDD-feeding. CH4 production was undetectable which was in line with absence of CH4 producers in the gut. We conclude that real-time in vivo monitoring of gases provides a non-invasive time-resolved system to explore the interplay between nutrition and gut microbes in a mouse model, and demonstrates potential for translation to other animal models and human studies.

    Species Distribution Modelling: Contrasting presence-only models with plot abundance data
    Gomes, Vitor H.F. ; Ijff, Stéphanie D. ; Raes, Niels ; Amaral, Iêda Leão ; Salomão, Rafael P. ; Coelho, Luiz De Souza ; Matos, Francisca Dionízia De Almeida ; Castilho, Carolina V. ; Filho, Diogenes De Andrade Lima ; López, Dairon Cárdenas ; Guevara, Juan Ernesto ; Magnusson, William E. ; Phillips, Oliver L. ; Wittmann, Florian ; Carim, Marcelo De Jesus Veiga ; Martins, Maria Pires ; Irume, Mariana Victória ; Sabatier, Daniel ; Molino, Jean François ; Bánki, Olaf S. ; Guimarães, José Renan Da Silva ; Pitman, Nigel C.A. ; Piedade, Maria Teresa Fernandez ; Mendoza, Abel Monteagudo ; Luize, Bruno Garcia ; Venticinque, Eduardo Martins ; de Leão Novo, E.M.M. ; Vargas, Percy Núñez ; Silva, Thiago Sanna Freire ; Manzatto, Angelo Gilberto ; Terborgh, John ; Reis, Neidiane Farias Costa ; Montero, Juan Carlos ; Montero, Juan Carlos ; Casula, Katia Regina ; Marimon, Beatriz S. ; Marimon, Ben Hur ; Honorio Coronado, Euridice N. ; Feldpausch, Ted R. ; Duque, Alvaro ; Zartman, Charles Eugene ; Arboleda, Nicolás Castaño ; Killeen, Timothy J. ; Mostacedo, Bonifacio ; Vasquez, Rodolfo ; Schöngart, Jochen ; Assis, Rafael L. ; Medeiros, Marcelo Brilhante ; Simon, Marcelo Fragomeni ; Andrade, Ana ; Laurance, William F. ; Camargo, José Luís ; Demarchi, Layon O. ; Laurance, Susan G.W. ; Farias, Emanuelle De Sousa ; Nascimento, Henrique Eduardo Mendonça ; Revilla, Juan David Cardenas ; Quaresma, Adriano ; Costa, Flavia R.C. ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Cintra, Bruno Barçante Ladvocat ; Castellanos, Hernán ; Brienen, Roel ; Stevenson, Pablo R. ; Feitosa, Yuri ; Duivenvoorden, Joost F. ; Aymard, Gerardo A.C. ; Mogollón, Hugo F. ; Targhetta, Natalia ; Comiskey, James A. ; Vicentini, Alberto ; Lopes, Aline ; Damasco, Gabriel ; Dávila, Nállarett ; García-Villacorta, Roosevelt ; Levis, Carolina ; Schietti, Juliana ; Souza, Priscila ; Emilio, Thaise ; Alonso, Alfonso ; Neill, David ; Dallmeier, Francisco ; Ferreira, Leandro Valle ; Araujo-Murakami, Alejandro ; Praia, Daniel ; Amaral, Dário Dantas Do; Carvalho, Fernanda Antunes ; Souza, Fernanda Coelho De - \ 2018
    Scientific Reports 8 (2018)1. - ISSN 2045-2322
    Species distribution models (SDMs) are widely used in ecology and conservation. Presence-only SDMs such as MaxEnt frequently use natural history collections (NHCs) as occurrence data, given their huge numbers and accessibility. NHCs are often spatially biased which may generate inaccuracies in SDMs. Here, we test how the distribution of NHCs and MaxEnt predictions relates to a spatial abundance model, based on a large plot dataset for Amazonian tree species, using inverse distance weighting (IDW). We also propose a new pipeline to deal with inconsistencies in NHCs and to limit the area of occupancy of the species. We found a significant but weak positive relationship between the distribution of NHCs and IDW for 66% of the species. The relationship between SDMs and IDW was also significant but weakly positive for 95% of the species, and sensitivity for both analyses was high. Furthermore, the pipeline removed half of the NHCs records. Presence-only SDM applications should consider this limitation, especially for large biodiversity assessments projects, when they are automatically generated without subsequent checking. Our pipeline provides a conservative estimate of a species' area of occupancy, within an area slightly larger than its extent of occurrence, compatible to e.g. IUCN red list assessments.
    Alien plant invasions in European woodlands
    Wagner, Viktoria ; Chytrý, Milan ; Jiménez-Alfaro, Borja ; Pergl, Jan ; Hennekens, Stephan ; Biurrun, Idoia ; Knollová, Ilona ; Berg, Christian ; Vassilev, Kiril ; Rodwell, John S. ; Škvorc, Željko ; Jandt, Ute ; Ewald, Jörg ; Jansen, Florian ; Tsiripidis, Ioannis ; Botta-Dukát, Zoltán ; Casella, Laura ; Attorre, Fabio ; Rašomavičius, Valerijus ; Ćušterevska, Renata ; Schaminée, Joop H.J. ; Brunet, Jörg ; Lenoir, Jonathan ; Svenning, Jens Christian ; Kącki, Zygmunt ; Petrášová-Šibíková, Mária ; Šilc, Urban ; García-Mijangos, Itziar ; Campos, Juan Antonio ; Fernández-González, Federico ; Wohlgemuth, Thomas ; Onyshchenko, Viktor ; Pyšek, Petr - \ 2017
    Diversity and Distributions 23 (2017)9. - ISSN 1366-9516 - p. 969 - 981.
    EUNIS - exotic - forest - invasive plants - life-form - neophyte - non-native - origin - tree
    Aim: Woodlands make up a third of European territory and carry out important ecosystem functions, yet a comprehensive overview of their invasion by alien plants has never been undertaken across this continent. Location: Europe. Methods: We extracted data from 251,740 vegetation plots stored in the recently compiled European Vegetation Archive. After filtering (resulting in 83,396 plots; 39 regions; 1970–2015 time period), we analysed the species pool and frequency of alien vascular plants with respect to geographic origin and life-forms, and the levels of invasion across the European Nature Information System (EUNIS) woodland habitats. Results: We found a total of 386 alien plant species (comprising 7% of all recorded vascular plants). Aliens originating from outside of and from within Europe were almost equally represented in the species pool (192 vs. 181 species) but relative frequency was skewed towards the former group (77% vs. 22%) due, to some extent, to the frequent occurrence of Impatiens parviflora (21% frequency among alien plants). Phanerophytes were the most species-rich life-form (148 species) and had the highest representation in terms of relative frequency (39%) among aliens in the dataset. Apart from Europe (181 species), North America was the most important source of alien plants (109 species). At the local scale, temperate and boreal softwood riparian woodland (5%) and mire and mountain coniferous woodland (<1%) had the highest and lowest mean relative alien species richness (percentage of alien species per plot), respectively. Main conclusions: Our results indicate that European woodlands are prone to alien plant invasions especially when exposed to disturbance, fragmentation, alien propagule pressure and high soil nutrient levels. Given the persistence of these factors in the landscape, competitive alien plant species with a broad niche, including alien trees and shrubs, are likely to persist and spread further into European woodlands.
    Fishing in the Amazonian Forest: A Gendered Social Network Puzzle
    Díaz-Reviriego, I. ; Fernández-Llamazares, ; Howard, P.L. ; Molina, J.L. ; Reyes-García, V. - \ 2017
    Society & Natural Resources 30 (2017)6. - ISSN 0894-1920 - p. 690 - 706.
    Fishing expertise - gender relations - perceptions - social network analysis - social status - Tsimane’ Amerindians
    LLCWe employ social network analysis (SNA) to describe the structure of subsistence fishing social networks and to explore the relation between fishers’ emic perceptions of fishing expertise and their position in networks. Participant observation and quantitative methods were employed among the Tsimane’ Amerindians of the Bolivian Amazon. A multiple-regression quadratic assignment procedure was used to explore the extent to which gender, kinship, and age homophilies influence the formation of fishing networks. Logistic regressions were performed to determine the association between fishers’ expertise, their sociodemographic identities, and network centrality. We found that fishing networks are gendered and that there is a positive association between fishers’ expertise and centrality in networks, an association that is more striking for women than for men. We propose that a social network perspective broadens understanding of the relations that shape the intracultural distribution of fishing expertise, as well as natural resource access and use.
    Gendered medicinal plant knowledge contributions to adaptive capacity and health sovereignty in Amazonia
    Díaz-Reviriego, Isabel ; Fernández-Llamazares, Álvaro ; Salpeteur, Matthieu ; Howard, Patricia L. ; Reyes-García, Victoria - \ 2016
    Ambio 45 (2016). - ISSN 0044-7447 - p. 263 - 275.
    Gendered knowledge - Knowledge diversity - Knowledge redundancy - Local knowledge systems - Local medical systems - Tsimane’

    Local medical systems are key elements of social-ecological systems as they provide culturally appropriate and locally accessible health care options, especially for populations with scarce access to biomedicine. The adaptive capacity of local medical systems generally rests on two pillars: species diversity and a robust local knowledge system, both threatened by local and global environmental change. We first present a conceptual framework to guide the assessment of knowledge diversity and redundancy in local medicinal knowledge systems through a gender lens. Then, we apply this conceptual framework to our research on the local medicinal plant knowledge of the Tsimane’ Amerindians. Our results suggest that Tsimane’ medicinal plant knowledge is gendered and that the frequency of reported ailments and the redundancy of knowledge used to treat them are positively associated. We discuss the implications of knowledge diversity and redundancy for local knowledge systems’ adaptive capacity, resilience, and health sovereignty.

    Social organization influences the exchange and species richness of medicinal plants in amazonian homegardens
    Díaz-Reviriego, Isabel ; González-Segura, Lara ; Fernández-Llamazares, Álvaro ; Howard, Patricia L. ; Molina, José Luis ; Reyes-García, Victoria - \ 2016
    Ecology and Society 21 (2016)1. - ISSN 1708-3087
    Exchange networks - Gender - Plant diversity - Social networks analysis - Tropical homegardens - Tsimane’

    Medicinal plants provide indigenous and peasant communities worldwide with means to meet their healthcare needs. Homegardens often act as medicine cabinets, providing easily accessible medicinal plants for household needs. Social structure and social exchanges have been proposed as factors influencing the species diversity that people maintain in their homegardens. Here, we assess the association between the exchange of medicinal knowledge and plant material and medicinal plant richness in homegardens. Using Tsimane’ Amazonian homegardens as a case study, we explore whether social organization shapes exchanges of medicinal plant knowledge and medicinal plant material. We also use network centrality measures to evaluate people’s location and performance in medicinal plant knowledge and plant material exchange networks. Our results suggest that social organization, specifically kinship and gender relations, influences medicinal plant exchange patterns significantly. Homegardens total and medicinal plant species richness are related to gardeners’ centrality in the networks, whereby people with greater centralitymaintain greater plant richness. Thus, together with agroecological conditions, social relations among gardeners and the culturally specific social structure seem to be important determinants of plant richness in homegardens. Understanding which factors pattern general species diversity in tropical homegardens, and medicinal plant diversity in particular, can help policy makers, health providers, and local communities to understand better how to promote and preserve medicinal plants in situ. Biocultural approaches that are also gender sensitive offer a culturally appropriate means to reduce the global and local loss of both biological and cultural diversity.

    Tracking pan-continental trends in environmental contamination using sentinel raptors—what types of samples should we use?
    Espín, S. ; García-Fernández, A.J. ; Herzke, D. ; Shore, R.F. ; Hattum, B. van; Martínez-López, E. ; Coeurdassier, M. ; Eulaers, I. ; Fritsch, C. ; Gómez-Ramírez, P. ; Jaspers, V.L.B. ; Krone, O. ; Duke, G. ; Helander, B. ; Mateo, R. ; Movalli, P. ; Sonne, C. ; Den Brink, N.W. van - \ 2016
    Ecotoxicology (2016). - ISSN 0963-9292 - p. 777 - 801.
    Bird of prey - Contaminant - Matrix - Monitoring - Sample type

    Biomonitoring using birds of prey as sentinel species has been mooted as a way to evaluate the success of European Union directives that are designed to protect people and the environment across Europe from industrial contaminants and pesticides. No such pan-European evaluation currently exists. Coordination of such large scale monitoring would require harmonisation across multiple countries of the types of samples collected and analysed-matrices vary in the ease with which they can be collected and the information they provide. We report the first ever pan-European assessment of which raptor samples are collected across Europe and review their suitability for biomonitoring. Currently, some 182 monitoring programmes across 33 European countries collect a variety of raptor samples, and we discuss the relative merits of each for monitoring current priority and emerging compounds. Of the matrices collected, blood and liver are used most extensively for quantifying trends in recent and longer-term contaminant exposure, respectively. These matrices are potentially the most effective for pan-European biomonitoring but are not so widely and frequently collected as others. We found that failed eggs and feathers are the most widely collected samples. Because of this ubiquity, they may provide the best opportunities for widescale biomonitoring, although neither is suitable for all compounds. We advocate piloting pan-European monitoring of selected priority compounds using these matrices and developing read-across approaches to accommodate any effects that trophic pathway and species differences in accumulation may have on our ability to track environmental trends in contaminants.

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