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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    Evaluation of a field-deployable Nafion™-based air-drying system for collecting whole air samples and its application to stable isotope measurements of CO2
    Paul, Dipayan ; Scheeren, Hubertus A. ; Jansen, Henk G. ; Kers, Bert A.M. ; Miller, John B. ; Crotwell, Andrew M. ; Michel, Sylvia E. ; Gatti, Luciana V. ; Domingues, Lucas G. ; Correia, Caio S.C. ; Neves, Raiane A.L. ; Meijer, Harro A.J. ; Peters, Wouter - \ 2020
    Atmospheric Measurement Techniques 13 (2020)7. - ISSN 1867-1381 - p. 4051 - 4064.

    Atmospheric flask samples are either collected at atmospheric pressure by opening a valve of a pre-evacuated flask or pressurized with the help of a pump to a few bar above ambient pressure. Under humid conditions, there is a risk that water vapor in the sample leads to condensation on the walls of the flask, notably at higher than ambient sampling pressures. Liquid water in sample flasks is known to affect the CO2 mixing ratios and also alters the isotopic composition of oxygen (17O and 18O) in CO2 via isotopic equilibration. Hence, for accurate determination of CO2 mole fractions and its stable isotopic composition, it is vital to dry the air samples to a sufficiently low dew point before they are pressurized in flasks to avoid condensation. Moreover, the drying system itself should not influence the mixing ratio and the isotopic composition of CO2 or that of the other constituents under study. For the Airborne Stable Isotopes of Carbon from the Amazon (ASICA) project focusing on accurate measurements of CO2 and its singly substituted stable isotopologues over the Amazon, an air-drying system capable of removing water vapor from air sampled at a dew point lower than -2 °C, flow rates up to 12 L min-1 and without the need for electrical power was needed. Since to date no commercial air-drying device that meets these requirements has been available, we designed and built our own consumable-free, power-free and portable drying system based on multitube Nafion™ gas sample driers (Perma Pure, Lakewood, USA). The required dry purge air is provided by feeding the exhaust flow of the flask sampling system through a dry molecular sieve (type 3A) cartridge. In this study we describe the systematic evaluation of our Nafion™-based air sample dryer with emphasis on its performance concerning the measurements of atmospheric CO2 mole fractions and the three singly substituted isotopologues of CO2 (16O13C16O, 16O12C17O and 16O12C18O), as well as the trace gas species CH4, CO, N2O and SF6. Experimental results simulating extreme tropical conditions (saturated air at 33 °C) indicated that the response of the air dryer is almost instantaneous and that approximately 85 L of air, containing up to 4 % water vapor, can be processed staying below a -2 °C dew point temperature (at 275 kPa). We estimated that at least eight flasks can be sampled (at an overpressure of 275 kPa) with a water vapor content below -2 °C dew point temperature during a typical flight sampling up to 5 km altitude over the Amazon, whereas the remaining samples would stay well below 5 °C dew point temperature (at 275 kPa). The performance of the air dryer on measurements of CO2, CH4, CO, N2O, and SF6 and the CO2 isotopologues 16O13C16O and 16O12C18O was tested in the laboratory simulating real sampling conditions by compressing humidified air from a calibrated cylinder, after being dried by the air dryer, into sample flasks. We found that the mole fraction and the isotopic composition difference between the different test conditions (including the dryer) and the base condition (dry air, without dryer) remained well within or very close to, in the case of N2O, the World Meteorological Organization recommended compatibility goals for independent measurement programs, proving that the test condition induced no significant bias on the sample measurements.

    Corrigendum to costs and carbon benefits of mangrove conservation and restoration: a global analysis (Ecological Economics
    Jakovac, Catarina C. ; Latawiec, Agnieszka Ewa ; Lacerda, Eduardo ; Lucas, Isabella Leite ; Korys, Katarzyna Anna ; Iribarrem, Alvaro ; Malaguti, Gustavo Abreu ; Turner, Kerry ; Luisetti, Tiziana ; Strassburg, Bernardo Baeta Neves - \ 2020
    Ecological Economics 177 (2020). - ISSN 0921-8009

    The authors regret . The authors would like to apologise for any inconvenience caused.

    A new background method for greenhouse gases flux calculation based in back-trajectories over the Amazon
    Domingues, Lucas Gatti ; Gatti, Luciana Vanni ; Aquino, Afonso ; Sánchez, Alber ; Correia, Caio ; Gloor, Manuel ; Peters, Wouter ; Miller, John ; Turnbull, Jocelyn ; Santana, Ricardo ; Marani, Luciano ; Câmara, Gilberto ; Neves, Raiane ; Crispim, Stéphane - \ 2020
    Atmosphere 11 (2020)7. - ISSN 2073-4433
    Amazon - Background calculation - Greenhouse gases

    The large amount of carbon stored in trees and soils of the Amazon rain forest is under pressure from land use as well as climate change. Therefore, various efforts to monitor greenhouse gas exchange between the Amazon forest and the atmosphere are now ongoing, including regular vertical profile (surface to 4.5 km) greenhouse gas measurements across the Amazon. These profile measurements can be used to calculate fluxes to and from the rain forest to the atmosphere at large spatial scales by considering the enhancement or depletion relative to the mole fraction of air entering the Amazon basin from the Atlantic, providing an important diagnostic of the state, changes and sensitivities of the forests. Previous studies have estimated greenhouse gas mole fractions of incoming air ('background') as a weighted mean of mole fractions measured at two background sites, Barbados (Northern Hemisphere) and Ascension (Southern hemisphere) in the Tropical Atlantic, where the weights were based on sulphur hexafluoride (SF6) measured locally (in the Amazon vertical profiles) and at the two background sites. However, this method requires the accuracy and precision of SF6 measurements to be significantly better than 0.1 parts per trillion (picomole mole-1), which is near the limit for the best SF6 measurements and assumes that there are no SF6 sources in the Amazon basin. We therefore present here an alternative method. Instead of using SF6, we use the geographical position of each air-mass back-trajectory when it intersects the limit connecting these two sites to estimate contributions from Barbados versus Ascension. We furthermore extend the approach to include an observation site further south, Cape Point, South Africa. We evaluate our method using CO2 vertical profile measurements at a coastal site in Brazil comparing with values obtained using this method where we find a high correlation (r2 = 0.77). Similarly, we obtain good agreement for CO2 background when comparing our results with those based on SF6, for the period 2010-2011 when the SF6 measurements had excellent precision and accuracy. We also found high correspondence between the methods for background values of CO, N2O and CH4. Finally, flux estimates based on our new method agree well with the CO2 flux estimates for 2010 and 2011 estimated using the SF6-based method. Together, our findings suggest that our trajectory-based method is a robust new way to derive background air concentrations for the purpose of greenhouse gas flux estimation using vertical profile data.

    Costs and Carbon Benefits of Mangrove Conservation and Restoration : A Global Analysis
    Jakovac, Catarina C. ; Latawiec, Agnieszka Ewa ; Lacerda, Eduardo ; Leite Lucas, Isabella ; Korys, Katarzyna Anna ; Iribarrem, Alvaro ; Malaguti, Gustavo Abreu ; Turner, R.K. ; Luisetti, Tiziana ; Baeta Neves Strassburg, Bernardo - \ 2020
    Ecological Economics 176 (2020). - ISSN 0921-8009
    Break-even price - Deforestation - Global mangrove map - Land opportunity cost - Map of worlds - Payment for ecosystem services - REDD+

    Blue carbon in mangroves represents one of highest values of carbon stocks per hectare, and could play an important role in climate change mitigation. In this study we estimated the carbon prices needed to promote mangrove conservation and restoration under mechanisms of payment for ecosystem services (PES). We mapped the remaining and deforested mangroves across the globe in 2017, and crossed this information with carbon stocks in the biomass and soil and with land opportunity and restoration costs. In accordance with previous studies we found that Southeast Asia holds the largest opportunities for blue carbon programs to support conservation and restoration. Conserving remaining mangroves would avoid the release of up to 15.51 PgCO2 to the atmosphere, and could be achieved at carbon prices between 3.0 and 13.0 US$ per tCO2 for 90% of remaining mangroves. Restoring mangroves can sequester up to 0.32 PgCO2 globally. Carbon prices between 4.5 and 18.0 US$ per tCO2 could support the restoration of 90% of deforested mangroves. Such prices, however, may not apply to contexts of high-profit alternative land-uses. In such contexts, the valuation of co-benefits and the combination of carbon-based mechanisms and sustainable management may be a viable pathway.

    Genetics and genomics of uniformity and resilience in livestock and aquaculture species: A review
    Souza Lung, Laiza Helena de; Carvalheiro, Roberto ; Rezende Neves, Haroldo Henrique de; Mulder, Herman Arend - \ 2020
    Journal of Animal Breeding and Genetics 137 (2020)3. - ISSN 0931-2668 - p. 263 - 280.
    genetic control of residual variance - genetic heterogeneity of residual variance - micro-environmental sensitivity - resilience - uniformity

    Genetic control of residual variance offers opportunities to increase uniformity and resilience of livestock and aquaculture species. Improving uniformity and resilience of animals will improve health and welfare of animals and lead to more homogenous products. Our aims in this review were to summarize the current models and methods to study genetic control of residual variance, genetic parameters and genomic results for residual variance and discuss future research directions. Typically, the genetic coefficient of variation is high (median = 0.27; range 0–0.86) and the heritability of residual variance is low (median = 0.01; range 0–0.10). Higher heritabilities can be achieved when increasing the number of records per animal. Divergent selection experiments have supported the feasibility of selecting for high or low residual variance. Genomic studies have revealed associations in regions related to stress, including those from the heat shock protein family. Although the number of studies is growing, genetic control of residual variance is still poorly understood, but big data and genomics offer great opportunities.

    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

    ATLANTIC EPIPHYTES: a data set of vascular and non-vascular epiphyte plants and lichens from the Atlantic Forest
    Ramos, Flavio Nunes ; Mortara, Sara Ribeiro ; Monalisa-Francisco, Nathalia ; Elias, João Pedro Costa ; Neto, Luiz Menini ; Freitas, Leandro ; Kersten, Rodrigo ; Amorim, André Márcio ; Matos, Fernando Bittencourt ; Nunes-Freitas, André Felippe ; Alcantara, Suzana ; Alexandre, Marcia Helena Nagahama ; Almeida-Scabbia, Renata Jimenez de; Almeida, Odair José Garcia de; Alves, Fernanda Eliane ; Oliveira Alves, Rogério Marcos de; Alvim, Francine Seehaber ; Andrade, Antônio Carlos Silva de; Andrade, Simone de; Aona, Lidyanne Yuriko Saleme ; Araujo, Andréa Cardoso ; Araújo, Kelianne Carolina Targino de; Ariati, Vanessa ; Assis, Julia Camara ; Azevedo, Cecília Oliveira de; Barbosa, Bruno Ferreira ; Barbosa, Daniel Elias Ferreira ; Reis Barbosa, Fernando dos; Barros, Fabio de; Basilio, Geicilaine Alves ; Bataghin, Fernando Antonio ; Bered, Fernanda ; Bianchi, Juliana Santos ; Blum, Christopher Thomas ; Boelter, Carlos Renato ; Bonnet, Annete ; Brancalion, Pedro Henrique Santin ; Breier, Tiago Bӧer ; Toledo Brion, Caio de; Buzatto, Cristiano Roberto ; Cabral, Andressa ; Cadorin, Tiago João ; Caglioni, Eder ; Canêz, Luciana ; Cardoso, Pedro Henrique ; Carvalho, Fábia Silva de; Carvalho, Renan Gonçalves ; Catharino, Eduardo Luis Martins ; Ceballos, Sergio Javier ; Cerezini, Monise Terra ; César, Ricardo Gomes ; Cestari, Cesar ; Chaves, Cleber Juliano Neves ; Citadini-Zanette, Vanilde ; Coelho, Luiz Francisco Mello ; Coffani-Nunes, João Vicente ; Colares, Renato ; Colletta, Gabriel Dalla ; Medeiros Corrêa, Nadjara de; Ferreira da Costa, Andrea ; Costa, Grênivel Mota da; Costa, Laís Mara Santana ; Costa, Natália Gabriela Souza ; Couto, Dayvid Rodrigues ; Cristofolini, Caroline ; Rodrigues da Cruz, Ana Carolina ; Neri, Leopoldo Angelo Del; Pasquo, Mercedes di; Santos Dias, Aline dos; Carmo Dutra Dias, Letícia do; Dislich, Ricardo ; Duarte, Marília Cristina ; Fabricante, Juliano Ricardo ; Farache, Fernando H.A. ; Gelli de Faria, Ana Paula ; Faxina, Claudenice ; Terrola Martins Ferreira, Mariana ; Fischer, Erich ; Fonseca, Carlos Roberto ; Fontoura, Talita ; Francisco, Talitha Mayumi ; Furtado, Samyra Gomes ; Galetti, Mauro ; Garbin, Mário Luís ; Gasper, André Luís de; Goetze, Márcia ; Gomes-da-Silva, Janaína ; Gonçalves, Mateus Felipe Araujo ; Gonzaga, Diego Rafael ; Granero e Silva, Ana Carolina ; Camargo Guaraldo, André de; Souza Gomes Guarino, Ernestino de; Votri Guislon, Aline ; Bitencourt Hudson, Luigy ; Jardim, Jomar Gomes ; Jungbluth, Patricia ; Santos Kaeser, Selma dos; Musauer Kessous, Igor ; Mossmann Koch, Natália ; Kuniyoshi, Yoshiko Saito ; Labiak, Paulo Henrique ; Lapate, Maria Esther ; Laurenti Santos, Ana Carolina ; Barbosa Leal, Roberta Luísa ; Leite, Felipe Silveira ; Leitman, Paula ; Liboni, Ana Paula ; Liebsch, Dieter ; Lingner, Débora Vanessa ; Lombardi, Julio Antonio ; Lucas, Eve ; Reis Luzzi, Jhonny dos; Mai, Patricia ; Mania, Luiz Felipe ; Mantovani, Waldir ; Maragni, Angelica Guidoni ; Marques, Marcia Cristina Mendes ; Marquez, Gonzalo ; Martins, Cristiane ; Nascimento Martins, Laura do; Luiz Sanglard Silva Martins, Pedro ; Fregolente Faracco Mazziero, Frederico ; Aguiar Melo, Camila de; Fiuza de Melo, Maria Margarida ; Mendes, Alex Fernando ; Mesacasa, Letícia ; Cerdeira Morellato, Leonor Patricia ; Souza Moreno, Vanessa de; Muller, Adelcio ; Silva Murakami, Mariana Moreira da; Cecconello, Edinete ; Nardy, Camila ; Nervo, Michelle Helena ; Neves, Beatriz ; Guimarães Cardoso Nogueira, Matheus ; Nonato, Fabiana Regina ; Oliveira-Filho, Ary Teixeira de; Oliveira, César Pedro Lopes de; Overbeck, Gerhard Ernst ; Marcusso, Gabriel Mendes ; Paciencia, Mateus Luís Barradas ; Padilha, Patricia ; Padilha, Peterson Teodoro ; Pereira, Ana Clara Alves ; Pereira, Luciana Carvalho ; Pereira, Rodrigo Augusto Santinelo ; Pincheira-Ulbrich, Jimmy ; Pires, José Salatiel Rodrigues ; Pizo, Marco Aurélio ; Pôrto, Kátia Cavalcanti ; Rattis, Ludmila ; Rodrigues de Mendonça Reis, Joice ; Gonçalves dos Reis, Simone ; Rocha-Pessôa, Thereza Christina da; Rocha, Carlos Frederico Duarte ; Rocha, Fernando Souza ; Rodrigues, Alba Regina Pereira ; Rodrigues, Ricardo Ribeiro ; Rogalski, Juliana Marcia ; Rosanelli, Roberta Luiza ; Rossado, Andrés ; Rossatto, Davi Rodrigo ; Rother, Débora Cristina ; Ruiz-Miranda, Carlos Ramon ; Saiter, Felipe Zamborlini ; Sampaio, Mauricio Bonesso ; Santana, Lucas Deziderio ; Silveira dos Santos, Juliana ; Sartorello, Ricardo ; Sazima, Marlies ; Schmitt, Juliane Luzía ; Schneider, Geniane ; Schroeder, Bruna Grosch ; Sevegnani, Lucia ; Júnior, Vasconcelos Oliveira Silva ; Silva, Fernando Rodrigues da; Silva, Maria Juliana da; Silva, Mércia Patrícia Pereira ; Silva, Rafaela Guimarães ; Silva, Sandro Menezes ; Singer, Rodrigo Bustos ; Siqueira, Geovane ; Soares, Luis Eduardo ; Sousa, Hildeberto Caldas de; Spielmann, Adriano ; Tonetti, Vinicius Rodrigues ; Toniato, Maria Teresa Zugliani ; Ulguim, Paulo Sérgio Bordoni ; Berg, Cássio van den; Berg, Eduardo van den; Varassin, Isabela Galarda ; Silva, Izabela Bitencourt Veloso da; Vibrans, Alexander Christian ; Waechter, Jorge Luiz ; Weissenberg, Erick Willy ; Windisch, Paulo Günter ; Wolowski, Marina ; Yañez, Agustina ; Yoshikawa, Vania Nobuko ; Zandoná, Luciano Ramos ; Zanella, Camila Martini ; Zanin, Elisabete Maria ; Zappi, Daniela Cristina ; Zipparro, Valesca Bononi ; Zorzanelli, João Paulo Fernandes ; Ribeiro, Milton Cezar - \ 2019
    Ecology 100 (2019)2. - ISSN 0012-9658
    abundance - Atlantic Forest - biodiversity data set - biodiversity hotspot - epiphyte - phorophyte - presence/absence - tropical forest

    Epiphytes are hyper-diverse and one of the frequently undervalued life forms in plant surveys and biodiversity inventories. Epiphytes of the Atlantic Forest, one of the most endangered ecosystems in the world, have high endemism and radiated recently in the Pliocene. We aimed to (1) compile an extensive Atlantic Forest data set on vascular, non-vascular plants (including hemiepiphytes), and lichen epiphyte species occurrence and abundance; (2) describe the epiphyte distribution in the Atlantic Forest, in order to indicate future sampling efforts. Our work presents the first epiphyte data set with information on abundance and occurrence of epiphyte phorophyte species. All data compiled here come from three main sources provided by the authors: published sources (comprising peer-reviewed articles, books, and theses), unpublished data, and herbarium data. We compiled a data set composed of 2,095 species, from 89,270 holo/hemiepiphyte records, in the Atlantic Forest of Brazil, Argentina, Paraguay, and Uruguay, recorded from 1824 to early 2018. Most of the records were from qualitative data (occurrence only, 88%), well distributed throughout the Atlantic Forest. For quantitative records, the most common sampling method was individual trees (71%), followed by plot sampling (19%), and transect sampling (10%). Angiosperms (81%) were the most frequently registered group, and Bromeliaceae and Orchidaceae were the families with the greatest number of records (27,272 and 21,945, respectively). Ferns and Lycophytes presented fewer records than Angiosperms, and Polypodiaceae were the most recorded family, and more concentrated in the Southern and Southeastern regions. Data on non-vascular plants and lichens were scarce, with a few disjunct records concentrated in the Northeastern region of the Atlantic Forest. For all non-vascular plant records, Lejeuneaceae, a family of liverworts, was the most recorded family. We hope that our effort to organize scattered epiphyte data help advance the knowledge of epiphyte ecology, as well as our understanding of macroecological and biogeographical patterns in the Atlantic Forest. No copyright restrictions are associated with the data set. Please cite this Ecology Data Paper if the data are used in publication and teaching events.

    Optimal strategies for ecosystem services provision in Amazonian production forests
    Piponiot, Camille ; Rutishauser, Ervan ; Derroire, Géraldine ; Putz, Francis E. ; Sist, Plinio ; West, Thales A.P. ; Descroix, Laurent ; Guedes, Marcelino Carneiro ; Honorio Coronado, Eurídice N. ; Kanashiro, Milton ; Mazzei, Lucas ; Oliveira, Marcus Vinicio Neves D'; Pena Claros, Marielos ; Rodney, Ken ; Ruschel, Ademir R. ; Souza, Cintia Rodrigues De; Vidal, Edson ; Wortel, Verginia ; Hérault, Bruno - \ 2019
    Environmental Research Letters 14 (2019)12. - ISSN 1748-9318
    Amazonia - Biodiversity - Carbon - Ecosystem services - Multi-criteria optimisation - Selective logging - Timber production

    Although tropical forests harbour most of the terrestrial carbon and biological diversity on Earth they continue to be deforested or degraded at high rates. In Amazonia, the largest tropical forest on Earth, a sixth of the remaining natural forests is formally dedicated to timber extraction through selective logging. Reconciling timber extraction with the provision of other ecosystem services (ES) remains a major challenge for forest managers and policy-makers. This study applies a spatial optimisation of logging in Amazonian production forests to analyse potential trade-offs between timber extraction and recovery, carbon storage, and biodiversity conservation. Current logging regulations with unique cutting cycles result in sub-optimal ES-use efficiency. Long-term timber provision would require the adoption of a land-sharing strategy that involves extensive low-intensity logging, although high transport and road-building costs might make this approach economically unattractive. By contrast, retention of carbon and biodiversity would be enhanced by a land-sparing strategy restricting high-intensive logging to designated areas such as the outer fringes of the region. Depending on management goals and societal demands, either choice will substantially influence the future of Amazonian forests. Overall, our results highlight the need for revaluation of current logging regulations and regional cooperation among Amazonian countries to enhance coherent and trans-boundary forest management.

    Genetics and Breeding of Lupinus mutabilis: An Emerging Protein Crop
    Gulisano, Agata ; Alves, Sofia ; Martins, João Neves ; Trindade, Luisa M. - \ 2019
    Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
    breeding - genetics - lupin - Lupinus mutabilis - plant protein - protein crop

    Protein crops have gained increasing interest in recent years, as a transition towards plant-protein based diets appears pivotal to ensure global food security and preserve the environment. The Andean species Lupinus mutabilis emerges as an ideal protein crop with great potential for Europe and other regions with temperate climates. This species is characterized by oil and protein content similar to soybean and is highly valued for its adaptability to colder climates and low input agriculture on marginal land. However, its introduction outside the Andes has yet to take off. To date, L. mutabilis remains an under-studied crop, lacking high yield, early maturity and a consistent breeding history. This review paper identifies L. mutabilis limitations and potential uses, and suggests the main breeding targets for further improvement of this crop. It also highlights the potential of new molecular tools and available germplasm resources that can now be used to establish L. mutabilis as a viable protein crop.

    Evolutionary diversity is associated with wood productivity in Amazonian forests
    Coelho de Souza, Fernanda ; Dexter, Kyle G. ; Phillips, Oliver L. ; Pennington, Toby R. ; Neves, Danilo ; Sullivan, Martin J.P. ; Alvarez-Davila, Esteban ; Alves, Átila ; Amaral, Ieda ; Andrade, Ana ; Aragao, Luis E.O.C. ; Araujo-Murakami, Alejandro ; Arets, Eric J.M.M. ; Arroyo, Luzmilla ; Aymard C, Gerardo A. ; Bánki, Olaf ; Baraloto, Christopher ; Barroso, Jorcely G. ; Boot, Rene G.A. ; Brienen, Roel J.W. ; Brown, Foster ; Camargo, José Luís C. ; Castro, Wendeson ; Chave, Jerome ; Cogollo, Alvaro ; Comiskey, James A. ; Cornejo-Valverde, Fernando ; Costa, Antonio Lola da; Camargo, Plínio B. de; Fiore, Anthony Di; Feldpausch, Ted R. ; Galbraith, David R. ; Gloor, Emanuel ; Goodman, Rosa C. ; Gilpin, Martin ; Herrera, Rafael ; Higuchi, Niro ; Honorio Coronado, Eurídice N. ; Jimenez-Rojas, Eliana ; Killeen, Timothy J. ; Laurance, Susan ; Laurance, William F. ; Lopez-Gonzalez, Gabriela ; Lovejoy, Thomas E. ; Malhi, Yadvinder ; Marimon, Beatriz S. ; Marimon-Junior, Ben Hur ; Mendoza, Casimiro ; Monteagudo-Mendoza, Abel ; Neill, David A. ; Vargas, Percy Núñez ; Peñuela Mora, Maria C. ; Pickavance, Georgia C. ; Pipoly, John J. ; Pitman, Nigel C.A. ; Poorter, Lourens ; Prieto, Adriana ; Ramirez, Freddy ; Roopsind, Anand ; Rudas, Agustin ; Salomão, Rafael P. ; Silva, Natalino ; Silveira, Marcos ; Singh, James ; Stropp, Juliana ; Steege, Hans ter; Terborgh, John ; Thomas-Caesar, Raquel ; Umetsu, Ricardo K. ; Vasquez, Rodolfo V. ; Célia-Vieira, Ima ; Vieira, Simone A. ; Vos, Vincent A. ; Zagt, Roderick J. ; Baker, Timothy R. - \ 2019
    Nature Ecology & Evolution 3 (2019). - ISSN 2397-334X - p. 1754 - 1761.

    Higher levels of taxonomic and evolutionary diversity are expected to maximize ecosystem function, yet their relative importance in driving variation in ecosystem function at large scales in diverse forests is unknown. Using 90 inventory plots across intact, lowland, terra firme, Amazonian forests and a new phylogeny including 526 angiosperm genera, we investigated the association between taxonomic and evolutionary metrics of diversity and two key measures of ecosystem function: aboveground wood productivity and biomass storage. While taxonomic and phylogenetic diversity were not important predictors of variation in biomass, both emerged as independent predictors of wood productivity. Amazon forests that contain greater evolutionary diversity and a higher proportion of rare species have higher productivity. While climatic and edaphic variables are together the strongest predictors of productivity, our results show that the evolutionary diversity of tree species in diverse forest stands also influences productivity. As our models accounted for wood density and tree size, they also suggest that additional, unstudied, evolutionarily correlated traits have significant effects on ecosystem function in tropical forests. Overall, our pan-Amazonian analysis shows that greater phylogenetic diversity translates into higher levels of ecosystem function: tropical forest communities with more distantly related taxa have greater wood productivity.

    Can timber provision from Amazonian production forests be sustainable?
    Piponiot, Camille ; Rödig, Edna ; Putz, Francis E. ; Rutishauser, Ervan ; Sist, Plinio ; Ascarrunz, Nataly ; Blanc, Lilian ; Derroire, Géraldine ; Descroix, Laurent ; Guedes, Marcelino Carneiro ; Coronado, Euridice Honorio ; Huth, Andreas ; Kanashiro, Milton ; Licona, Juan Carlos ; Mazzei, Lucas ; Oliveira, Marcus Vinicio Neves D'; Peña-Claros, Marielos ; Rodney, Ken ; Shenkin, Alexander ; Souza, Cintia Rodrigues De; Vidal, Edson ; West, Thales A.P. ; Wortel, Verginia ; Hérault, Bruno - \ 2019
    Environmental Research Letters 14 (2019)6. - ISSN 1748-9318
    Amazonia - disturbance - ecosystem recovery - macroecology - Selective logging - tropical forestry

    Around 30 Mm3 of sawlogs are extracted annually by selective logging of natural production forests in Amazonia, Earth's most extensive tropical forest. Decisions concerning the management of these production forests will be of major importance for Amazonian forests' fate. To date, no regional assessment of selective logging sustainability supports decision-making. Based on data from 3500 ha of forest inventory plots, our modelling results show that the average periodic harvests of 20 m3 ha-1 will not recover by the end of a standard 30 year cutting cycle. Timber recovery within a cutting cycle is enhanced by commercial acceptance of more species and with the adoption of longer cutting cycles and lower logging intensities. Recovery rates are faster in Western Amazonia than on the Guiana Shield. Our simulations suggest that regardless of cutting cycle duration and logging intensities, selectively logged forests are unlikely to meet timber demands over the long term as timber stocks are predicted to steadily decline. There is thus an urgent need to develop an integrated forest resource management policy that combines active management of production forests with the restoration of degraded and secondary forests for timber production. Without better management, reduced timber harvests and continued timber production declines are unavoidable.

    Genomic regions underlying uniformity of yearling weight in Nellore cattle evaluated under different response variables
    Souza Iung, Laiza Helena de; Mulder, Herman ; Rezende Neves, Haroldo Henrique de; Carvalheiro, Roberto - \ 2018
    São Paulo State University
    beef cattle - DHGLM - genetic heterogeneity of residual variance - growth traits - GWAS - micro-environmental sensitivity
    Background In livestock, residual variance has been studied because of the interest to improve uniformity of production. Several studies have provided evidence that residual variance is partially under genetic control; however, few investigations have elucidated genes that control it. The aim of this study was to identify genomic regions associated with within-family residual variance of yearling weight (YW; N = 423) in Nellore bulls with high density SNP data, using different response variables. For this, solutions from double hierarchical generalized linear models (DHGLM) were used to provide the response variables, as follows: a DGHLM assuming non-null genetic correlation between mean and residual variance (rmv ≠ 0) to obtain deregressed EBV for mean (dEBVm) and residual variance (dEBVv); and a DHGLM assuming rmv = 0 to obtain two alternative response variables for residual variance, dEBVv_r0 and log-transformed variance of estimated residuals (ln_ σ e ̂ 2 $$ {\upsigma}_{\widehat{\mathrm{e}}}^2 $$ ). Results The dEBVm and dEBVv were highly correlated, resulting in common regions associated with mean and residual variance of YW. However, higher effects on variance than the mean showed that these regions had effects on the variance beyond scale effects. More independent association results between mean and residual variance were obtained when null rmv was assumed. While 13 and 4 single nucleotide polymorphisms (SNPs) showed a strong association (Bayes Factor > 20) with dEBVv and ln_ σ e ̂ 2 $$ {\upsigma}_{\widehat{\mathrm{e}}}^2 $$ , respectively, only suggestive signals were found for dEBVv_r0. All overlapping 1-Mb windows among top 20 between dEBVm and dEBVv were previously associated with growth traits. The potential candidate genes for uniformity are involved in metabolism, stress, inflammatory and immune responses, mineralization, neuronal activity and bone formation. Conclusions It is necessary to use a strategy like assuming null rmv to obtain genomic regions associated with uniformity that are not associated with the mean. Genes involved not only in metabolism, but also stress, inflammatory and immune responses, mineralization, neuronal activity and bone formation were the most promising biological candidates for uniformity of YW. Although no clear evidence of using a specific response variable was found, we recommend consider different response variables to study uniformity to increase evidence on candidate regions and biological mechanisms behind it.
    Genomic regions underlying uniformity of yearling weight in Nellore cattle evaluated under different response variables
    Souza Iung, Laiza Helena de; Mulder, Herman Arend ; Rezende Neves, Haroldo Henrique de; Carvalheiro, Roberto - \ 2018
    BMC Genomics 19 (2018). - ISSN 1471-2164
    Beef cattle - DHGLM - Genetic heterogeneity of residual variance - Growth traits - GWAS - Micro-environmental sensitivity

    Background: In livestock, residual variance has been studied because of the interest to improve uniformity of production. Several studies have provided evidence that residual variance is partially under genetic control; however, few investigations have elucidated genes that control it. The aim of this study was to identify genomic regions associated with within-family residual variance of yearling weight (YW; N=423) in Nellore bulls with high density SNP data, using different response variables. For this, solutions from double hierarchical generalized linear models (DHGLM) were used to provide the response variables, as follows: a DGHLM assuming non-null genetic correlation between mean and residual variance (rmv0) to obtain deregressed EBV for mean (dEBVm) and residual variance (dEBVv); and a DHGLM assuming rmv=0 to obtain two alternative response variables for residual variance, dEBVv_r0 and log-transformed variance of estimated residuals (ln_ σ ě 2 $$ (\upsigma)_(\widehat(\mathrm(e)))^2 $$ ). Results: The dEBVm and dEBVv were highly correlated, resulting in common regions associated with mean and residual variance of YW. However, higher effects on variance than the mean showed that these regions had effects on the variance beyond scale effects. More independent association results between mean and residual variance were obtained when null rmv was assumed. While 13 and 4 single nucleotide polymorphisms (SNPs) showed a strong association (Bayes Factor>20) with dEBVv and ln_ σ ě 2 $$ (\upsigma)_(\widehat(\mathrm(e)))^2 $$ , respectively, only suggestive signals were found for dEBVv_r0. All overlapping 1-Mb windows among top 20 between dEBVm and dEBVv were previously associated with growth traits. The potential candidate genes for uniformity are involved in metabolism, stress, inflammatory and immune responses, mineralization, neuronal activity and bone formation. Conclusions: It is necessary to use a strategy like assuming null rmv to obtain genomic regions associated with uniformity that are not associated with the mean. Genes involved not only in metabolism, but also stress, inflammatory and immune responses, mineralization, neuronal activity and bone formation were the most promising biological candidates for uniformity of YW. Although no clear evidence of using a specific response variable was found, we recommend consider different response variables to study uniformity to increase evidence on candidate regions and biological mechanisms behind it.

    Small-scale coastal fisheries in European Seas are not what they were: Ecological, social and economic changes
    Lloret, Josep ; Cowx, Ian G. ; Cabral, Henrique ; Castro, Margarida ; Font, Toni ; Gonçalves, Jorge M.S. ; Gordoa, Ana ; Hoefnagel, Ellen ; Matić-Skoko, Sanja ; Mikkelsen, Eirik ; Morales-Nin, Beatriz ; Moutopoulos, Dimitrios K. ; Muñoz, Marta ; Santos, Miguel Neves Dos; Pintassilgo, Pedro ; Pita, Cristina ; Stergiou, Konstantinos I. ; Ünal, Vahdet ; Veiga, Pedro ; Erzini, Karim - \ 2018
    Marine Policy 98 (2018). - ISSN 0308-597X - p. 176 - 186.
    Coastal, small-scale fisheries (SSF), whether artisanal (professional) or recreational, represent important socioeconomic activities across Europe that are currently undergoing a number of changes. This paper reviews and analyses the drivers of these changes, and makes recommendations for the future management of SSF. From the biological standpoint, the use of fishing gears that actively select certain species, sizes and sexes, the deployment of fishing gears on certain fragile habitats, the loss of fishing gears and the use of non-native species as bait are examples of how SSFs can threaten the sustainability of vulnerable coastal species and habitats. From a socioeconomic perspective, several factors are altering the traditional characteristics of coastal SSF. Among the most important is the growth of recreational fisheries in coastal waters and the disappearance of traditional low technology fisheries or their substitution by more mechanised, technical fisheries, which is leading to a loss of the traditional ecological knowledge held by artisanal fishers. On the other hand, the increasing competition between artisanal and recreational fisheries, and between them and commercial fishing operations, are also altering the classical features of coastal fisheries in some European countries. SSFs must adapt to the requirements of the new Common Fisheries Policy (CFP), namely management based on Maximum Sustainable Yield (MSY), multi-annual management plans and ecosystem based principles. It is concluded that it is necessary to integrate different assessment approaches (biological, social and economic), with active participation from stakeholders, governments and relevant research institutions, to better evaluate and manage coastal fisheries.
    Genetic control of uniformity of yearling weight in Nellore cattle
    Souza Iung, Laiza de; Mulder, H.A. ; Neves Haroldo, H.R. ; Carvalheiro, Roberto - \ 2017
    In: Final Abstract Booklet Zoology 2017
    In livestock breeding, genetic canalization is studied because of the interest to improve uniformity of production and to increase resilience. Several studies have confirmed the existence of genetic canalization characterized by genetic variation in the size of the environmental variance. In beef cattle, we have found evidence for genetic variation in environmental variance of body weight at 550 days of age, i.e. yearling weight (YW). However, a limited number of investigations have been done to elucidate genes controlling environmental variance. The aim of our study was identify genomic regions controlling environmental variance of YW through a genome-wide association study (GWAS). As response variable, we used the log-transformed variance of estimated residuals for each paternal half-sib family (n=423) from the mean model of YW of a double hierarchical generalized linear model (DHGLM). The GWAS was performed using a Bayesian variable selection method (BayesC) and 333,877 single nucleotide polymorphisms (SNP). In total, four SNPs on chromosomes 2, 5, 8 and 10 were strongly associated with environmental variance of YW (Bayes Factor > 20). Together, they explained less than 5% of the genetic variance, indicating that the environmental variance is a complex trait determined by several genes with small effects, like body weight itself. Within these regions, promising genes involved in metabolism (LPL, ATP6V1B2, OSBPL8, GLI2) and response to stress (SLC18A1, HIF1A, BBS10) were found. Our findings show that studying the genetics of environmental variance of body weight reveals not only metabolic genes, but also genes related to response to stress and adaptation.
    Genetic control of residual variance of yearling weight in nellore beef cattle
    Iung, L.H.S. ; Neves, H.H.R. ; Mulder, H.A. ; Carvalheiro, R. - \ 2017
    Journal of Animal Science 95 (2017)4. - ISSN 0021-8812 - p. 1425 - 1433.
    Beef cattle - Cross-validation - Double hierarchical generalized linear model - Genetic heterogeneity of residual variance - Uniformity of production - Yearling weight

    There is evidence for genetic variability in residual variance of livestock traits, which offers the potential for selection for increased uniformity of production. Different statistical approaches have been employed to study this topic; however, little is known about the concordance between them. The aim of our study was to investigate the genetic heterogeneity of residual variance on yearling weight (YW; 291.15 ± 46.67) in a Nellore beef cattle population; to compare the results of the statistical approaches, the two-step approach and the double hierarchical generalized linear model (DHGLM); and to evaluate the effectiveness of power transformation to accommodate scale differences. The comparison was based on genetic parameters, accuracy of EBV for residual variance, and cross-validation to assess predictive performance of both approaches. A total of 194,628 yearling weight records from 625 sires were used in the analysis. The results supported the hypothesis of genetic heterogeneity of residual variance on YW in Nellore beef cattle and the opportunity of selection, measured through the genetic coefficient of variation of residual variance (0.10 to 0.12 for the two-step approach and 0.17 for DHGLM, using an untransformed data set). However, low estimates of genetic variance associated with positive genetic correlations between mean and residual variance (about 0.20 for two-step and 0.76 for DHGLM for an untransformed data set) limit the genetic response to selection for uniformity of production while simultaneously increasing YW itself. Moreover, large sire families are needed to obtain accurate estimates of genetic merit for residual variance, as indicated by the low heritability estimates (<0.007). Box-Cox transformation was able to decrease the dependence of the variance on the mean and decreased the estimates of genetic parameters for residual variance. The transformation reduced but did not eliminate all the genetic heterogeneity of residual variance, highlighting its presence beyond the scale effect. The DHGLM showed higher predictive ability of EBV for residual variance and therefore should be preferred over the two-step approach.

    Soil quality after six years of paper mill industrial wastewater application
    Almeida, Ivan Carlos Carreiro ; Fernandes, Raphael Bragança Alves ; Neves, Júlio César Lima ; Ruiz, Hugo Alberto ; Lima, Túlio Luís Borges de; Hoogmoed, Willem - \ 2017
    Revista Brasileira de Ciência do Solo 41 (2017). - ISSN 0100-0683
    Clay dispersion - Industrial effluent - Salinity - Wastewater disposal - Water reuse

    The application of wastewater to irrigate soils may be an attractive option for paper mills, especially when the effluents can also provide nutrients to plants. Since there could be negative environmental effects, such activity must be preceded by a thorough evaluation of the consequences. The changes in soil quality of a Neossolo Flúvico Distrófico (Typic Udifluvent) were evaluated over a period of six years of irrigation with treated effluent from a wood pulp company. Although effluent application for six years did not affect soil resistance to penetration and soil hydraulic conductivity, it promoted a decrease in the mean size of aggregates and an increase in clay dispersion. Effluent application increased soil pH but did not change exchangeable Ca and Mg contents and organic carbon. After a full rotation of eucalyptus cultivation common in Brazil (six years), no negative effects in tree growth were found due to effluent irrigation. However, effluent addition caused higher values of Na adsorption ratio and intermediate electrical conductivity in the soil, which indicates a possible negative effect on soil quality if the application continues over a longer period. Therefore, a monitoring program should be carried out during subsequent crop rotations, and alternatives must be studied to obtain better effluent quality, such as adding Ca and Mg to the wastewater and using gypsum in the soil.

    Monitoring plastic ingestion in selected Azorean marine organisms
    Rodriguez, Yasmina ; Frias, Joao P.G.L. ; Carrico, Rita ; Neves, Veronica ; Bried, Joel ; Martins, Helen R. ; Vandeperre, Frederic ; Santos, Marco R. ; Franeker, J.A. van; Bolton, Alan B. ; Bjorndal, Karen A. ; Pham, Christopher K. - \ 2016
    Anaerobic co-digestion of cork based oil sorbent and cow manure or sludge
    Cavaleiro, A.J. ; Neves, T.M. ; Guedes, A.P. ; Alves, M.M. ; Pinto, P. ; Silva, S.P. ; Machado de Sousa, Diana - \ 2015
    In: Wastes: Solutions, Treatments and Opportunities - Selected Papers from the 3rd Edition of the International Conference on Wastes: Solutions, Treatments and Opportunities, 2015. - CRC Press/Balkema - ISBN 9781138028821 - p. 43 - 48.

    Cork, a material with great economic, social and environmental importance in Portugal, is also a good oil sorbent that can be used in the remediation of oil spills. The oil-impregnated cork can be easily removed, but requires further treatment. In the case of vegetable oil spills, anaerobic digestion may be a potential solution. This study aims to evaluate the effect of adding cork contaminated with sunflower oil as co-substrate in anaerobic digestion processes. Biodegradability assays were prepared with cow manure or sludge from a wastewater treatment plant, in the presence of five concentrations of oil-contaminated cork, between 200 and 1000 mg · L−1 as COD. Maxi-mum cumulative methane production increased with the amount of oily cork up to 41% and 101% in the assays with manure and sludge, respectively. Sporadic addition of cork contaminated with vegetable oil during anaerobic digestion of manure or sludge increases significantly the methane production of these processes.

    Response to comment by McMichael, piperno and bush
    Clement, Charles R. ; Denevan, William M. ; Heckenberger, Michael J. ; Junqueira, André Braga ; Neves, Eduardo G. ; Teixeira, Wenceslau G. ; Woods, William I. - \ 2015
    Proceedings of the Royal Society. B: Biological Sciences 282 (2015)1821. - ISSN 0962-8452 - 3 p.
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