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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    An integrated physical and cost-benefit approach to assess groins as a coastal erosion mitigation strategy
    Lima, M. ; Coelho, C. ; Veloso-Gomes, F. ; Roebeling, P. - \ 2020
    Coastal Engineering 156 (2020). - ISSN 0378-3839
    Coastal defense interventions - Coastal structural design - Cost-benefit analysis - Numerical modelling - Shoreline evolution

    Future investments required for the construction and maintenance of coastal defense interventions are expected to increase, due to increasing coastal erosion issues along social, environmental and economically valuable coastal areas. The high costs related with coastal defense interventions require improved knowledge on their performance, considering impacts, costs and benefits. Despite the existence of several cost-benefit approaches applied to coastal zones, in this study a well-defined, sequential and integrated methodology supported by already existent numerical models is developed and applied to assess the effectiveness (shoreline evolution impacts), costs and benefits of different coastal defense interventions. This methodology encompasses three integrated modules, including a shoreline evolution module (to estimate areas of territory maintained, gained or lost over time), a coastal structure pre-design module (to estimate material volumes of coastal works) and a cost-benefit evaluation module (to assess cost-benefit evaluation criteria). The approach allows for the physical and economic comparison of different coastal defense intervention scenarios, helping coastal management and planning entities to define strategies. In this study, the proposed methodology was applied to evaluate the performance of different groin scenarios, based on a hypothetical case study. The case study allowed highlighting the importance of the physical and economic analysis of different scenarios. Results show that the definition of coastal defense interventions is complex where, on the one hand, best physical solutions are sometimes related to very high costs and, on the other hand, best economic scenarios lead to high territory losses. Thus, the innovative approach presented in this study shows that an integrated analysis of shoreline evolution, coastal intervention design and subsequent costs and benefits allows to improve the physical and economic performances of coastal defense interventions.

    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.

    Modelling and mapping soil organic carbon stocks in Brazil
    Gomes, Lucas Carvalho ; Faria, Raiza Moniz ; Souza, Eliana de; Veloso, Gustavo Vieira ; Schaefer, Carlos Ernesto G.R. ; Filho, Elpídio Inácio Fernandes - \ 2019
    Geoderma 340 (2019). - ISSN 0016-7061 - p. 337 - 350.
    Machine learning - Protected areas - Random Forests - Soil carbon stock - Spatial prediction

    Brazil has extensive forests and savannas on deep weathered soils and plays a key role in the discussions about carbon sequestration, but the distribution of soil organic carbon (SOC) stocks up to 1 m depth has not been investigated in Brazil using machine learning techniques. In this study, we applied a methodological framework to optimize the prediction of SOC stocks for the entire Brazilian territory and determine how the environmental heterogeneity of Brazil influences the SOC stocks distribution. We used a legacy dataset of 8227 soil profiles which consisted of 37,693 samples. For each profile, the vertical distribution of SOC and bulk density were interpolated to standard depths (0–5, 5–15, 15–30, 30–60 and 60–100 cm) using mass preserving equal-area quadratic splines. The covariates database was composed of 74 variables including bioclimatic (temperature and precipitation) data, soil and biome maps, vegetation indexes and morphometric maps derived from a digital elevation model, with a 1 km spatial resolution. To obtain the best prediction performance, we tested four machine learning algorithms: Random Forests, Cubist, Generalized Linear Model Boosting and Support Vector Machines. Random Forests showed the best performance in predicting SOC stocks for all depths, with the highest performance at 30–60 cm for training (R 2 = 0.32) and validation (R 2 = 0.33); hence, it was selected for the spatial prediction of SOC stocks. The most important covariates selected by Random Forests using the recursive feature elimination were: soil class, sum of monthly mean temperature (SAMT), precipitation, slope height and vegetation indexes (NDVI, GPP). In total, Brazilian soils store approximately 71.3 PgC within the top 100 cm, where the first 0–30 cm contains almost 36 PgC. Approximately 31% of the total SOC stocks (22.2 PgC) occurs in protected areas (2.6 million km 2 ), which are not subjected to land use pressure and carbon losses. Although the Amazon biome has the highest amount of stored SOC (36.1 PgC), its soils do not represent a good potential for carbon accumulation. Among soil classes, the Luvisols showed the lowest SOC density (6.45 kg m −2 ) and the Histosols presented the highest values (14.87 kg m −2 ). More than 57% of the total SOC was found in nutrient-poor, deep-weathered Ferralsols and Acrisols, which are the dominant soils in Brazil. The presented methodological framework covers all steps of prediction process, building maps with known accuracy and has great potential to be used in future soil carbon inventories at large scales. Concerning conservation issues, the results highlight the importance of nature reserves for protecting SOC in the long-term.

    Wet and dry tropical forests show opposite successional pathways in wood density but converge over time
    Poorter, Lourens ; Rozendaal, Danaë M.A. ; Bongers, Frans ; Almeida-Cortez, Jarcilene S. de; Almeyda Zambrano, Angélica María ; Álvarez, Francisco S. ; Andrade, José Luís ; Villa, Luis Felipe Arreola ; Balvanera, Patricia ; Becknell, Justin M. ; Bentos, Tony V. ; Bhaskar, Radika ; Boukili, Vanessa ; Brancalion, Pedro H.S. ; Broadbent, Eben N. ; César, Ricardo G. ; Chave, Jerome ; Chazdon, Robin L. ; Colletta, Gabriel Dalla ; Craven, Dylan ; Jong, Ben H.J. de; Denslow, Julie S. ; Dent, Daisy H. ; DeWalt, Saara J. ; García, Elisa Díaz ; Dupuy, Juan Manuel ; Durán, Sandra M. ; Espírito Santo, Mário M. ; Fandiño, María C. ; Fernandes, Geraldo Wilson ; Finegan, Bryan ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Jakovac, Catarina C. ; Junqueira, André B. ; Kennard, Deborah ; Lebrija-Trejos, Edwin ; Letcher, Susan G. ; Lohbeck, Madelon ; Lopez, Omar R. ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Martins, Sebastião V. ; Massoca, Paulo E.S. ; Meave, Jorge A. ; Mesquita, Rita ; Mora, Francisco ; Souza Moreno, Vanessa de; Müller, Sandra C. ; Muñoz, Rodrigo ; Muscarella, Robert ; Oliveira Neto, Silvio Nolasco de; Nunes, Yule R.F. ; Ochoa-Gaona, Susana ; Paz, Horacio ; Peña-Claros, Marielos ; Piotto, Daniel ; Ruíz, Jorge ; Sanaphre-Villanueva, Lucía ; Sanchez-Azofeifa, Arturo ; Schwartz, Naomi B. ; Steininger, Marc K. ; Thomas, William Wayt ; Toledo, Marisol ; Uriarte, Maria ; Utrera, Luis P. ; Breugel, Michiel van; Sande, Masha T. van der; Wal, Hans van der; Veloso, Maria D.M. ; Vester, Hans F.M. ; Vieira, Ima C.G. ; Villa, Pedro Manuel ; Williamson, G.B. ; Wright, S.J. ; Zanini, Kátia J. ; Zimmerman, Jess K. ; Westoby, Mark - \ 2019
    Nature Ecology & Evolution 3 (2019). - ISSN 2397-334X - p. 928 - 934.

    Tropical forests are converted at an alarming rate for agricultural use and pastureland, but also regrow naturally through secondary succession. For successful forest restoration, it is essential to understand the mechanisms of secondary succession. These mechanisms may vary across forest types, but analyses across broad spatial scales are lacking. Here, we analyse forest recovery using 1,403 plots that differ in age since agricultural abandonment from 50 sites across the Neotropics. We analyse changes in community composition using species-specific stem wood density (WD), which is a key trait for plant growth, survival and forest carbon storage. In wet forest, succession proceeds from low towards high community WD (acquisitive towards conservative trait values), in line with standard successional theory. However, in dry forest, succession proceeds from high towards low community WD (conservative towards acquisitive trait values), probably because high WD reflects drought tolerance in harsh early successional environments. Dry season intensity drives WD recovery by influencing the start and trajectory of succession, resulting in convergence of the community WD over time as vegetation cover builds up. These ecological insights can be used to improve species selection for reforestation. Reforestation species selected to establish a first protective canopy layer should, among other criteria, ideally have a similar WD to the early successional communities that dominate under the prevailing macroclimatic conditions.

    Comparative genomics of plant pathogenic Botrytis species with distinct host specificity
    Valero-Jiménez, Claudio A. ; Veloso, Javier ; Staats, Martijn ; Kan, Jan A.L. van - \ 2019
    BMC Genomics 20 (2019)1. - ISSN 1471-2164
    Effector - Grey mould - Necrotroph - Secondary metabolite - Secretome

    Background: Fungi of the genus Botrytis (presently containing ~ 35 species) are able to infect more than 1400 different plant species and cause losses in a wide range of crops of economic importance. The best studied species is B. cinerea, which has a broad host range and is one of the best studied necrotrophic plant pathogenic fungi. Most other Botrytis spp. have a narrow host range and have been studied in less detail. To characterize genomic variation among different representatives of Botrytis spp., we sequenced and annotated the draft genomes of nine Botrytis species: B. calthae, B. convoluta, B. elliptica, B. galanthina, B. hyacinthi, B. narcissicola, B. paeoniae, B. porri and B. tulipae. Results: Bioinformatics and comparative genomics tools were applied to determine a core of 7668 shared protein families in all Botrytis species, which grouped them in two distinct phylogenetic clades. The secretome of all nine Botrytis spp. was similar in number (ranging from 716 to 784 predicted proteins). A detailed analysis of the molecular functions of the secretome revealed that shared activities were highly similar. Orthologs to effectors functionally studied in B. cinerea were also present in the other Botrytis species. A complex pattern of presence/absence of secondary metabolite biosynthetic key enzymes was observed. Conclusions: Comparative genomics of Botrytis show that overall, species share the main signatures and protein families in the secreted proteins, and of known effectors. Our study provides leads to study host range determinants in the genus Botrytis and provides a stepping stone to elucidate the roles of effector candidates in the infection process of these species.

    Biodiversity recovery of Neotropical secondary forests
    Rozendaal, Danaë M.A. ; Bongers, Frans ; Aide, T.M. ; Alvarez-Dávila, Esteban ; Ascarrunz, Nataly ; Balvanera, Patricia ; Becknell, Justin M. ; Bentos, Tony V. ; Brancalion, Pedro H.S. ; Cabral, George A.L. ; Calvo-Rodriguez, Sofia ; Chave, Jerome ; César, Ricardo G. ; Chazdon, Robin L. ; Condit, Richard ; Dallinga, Jorn S. ; Almeida-Cortez, Jarcilene S. De; Jong, Ben de; Oliveira, Alexandre De; Denslow, Julie S. ; Dent, Daisy H. ; Dewalt, Saara J. ; Dupuy, Juan Manuel ; Durán, Sandra M. ; Dutrieux, Loïc P. ; Espírito-Santo, Mario M. ; Fandino, María C. ; Fernandes, G.W. ; Finegan, Bryan ; García, Hernando ; Gonzalez, Noel ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Hubbell, Stephen ; Jakovac, Catarina C. ; Hernández, Alma Johanna ; Junqueira, André B. ; Kennard, Deborah ; Larpin, Denis ; Letcher, Susan G. ; Licona, Juan-Carlos ; Lebrija-trejos, Edwin ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Massoca, Paulo E.S. ; Meave, Jorge A. ; Mesquita, Rita C.G. ; Mora, Francisco ; Müller, Sandra C. ; Muñoz, Rodrigo ; Oliveira Neto, Silvio Nolasco De; Norden, Natalia ; Nunes, Yule R.F. ; Ochoa-Gaona, Susana ; Ortiz-Malavassi, Edgar ; Ostertag, Rebecca ; Peña-Caros, Marielos ; Pérez-García, Eduardo A. ; Piotto, Daniel ; Powers, Jennifer S. ; Aguilar-Cano, José ; Rodriguez-Buritica, Susana ; Rodríguez-Velázquez, Jorge ; Romero-Romero, Marco Antonio ; Ruíz, Jorge ; Sanchez-Azofeifa, Arturo ; Almeida, Arlete Silva De; Silver, Whendee L. ; Schwartz, Naomi B. ; Thomas, William Wayt ; Toledo, Marisol ; Uriarte, Maria ; Sá Sampaio, Everardo Valadares De; Breugel, Michiel van; Wal, Hans van der; Martins, Sebastião Venâncio ; Veloso, Maria D.M. ; Vester, Hans F.M. ; Vicentini, Alberto ; Vieira, Ima C.G. ; Villa, Pedro ; Williamson, G.B. ; Zanini, Kátia J. ; Zimmerman, Jess ; Poorter, Lourens - \ 2019
    Science Advances 5 (2019)3. - ISSN 2375-2548 - 10 p.
    Old-growth tropical forests harbor an immense diversity of tree species but are rapidly being cleared, while secondary forests that regrow on abandoned agricultural lands increase in extent. We assess how tree species richness and composition recover during secondary succession across gradients in environmental conditions and anthropogenic disturbance in an unprecedented multisite analysis for the Neotropics. Secondary forests recover remarkably fast in species richness but slowly in species composition. Secondary forests take a median time of five decades to recover the species richness of old-growth forest (80% recovery after 20 years) based on rarefaction analysis. Full recovery of species composition takes centuries (only 34% recovery after 20 years). A dual strategy that maintains both old-growth forests and species-rich secondary forests is therefore crucial for biodiversity conservation in human-modified tropical landscapes.
    BRAZIL ROAD-KILL: a data set of wildlife terrestrial vertebrate road-kills
    Grilo, Clara ; Coimbra, Michely R. ; Cerqueira, Rafaela C. ; Barbosa, Priscilla ; Dornas, Rubem A.P. ; Gonçalves, Larissa O. ; Teixeira, Fernanda Z. ; Coelho, Igor Pfeifer ; Schmidt, Brenda R. ; Pacheco, Diana L.K. ; Schuck, Gabriela ; Esperando, Isadora B. ; Anza, Juan A. ; Beduschi, Júlia ; Oliveira, Nicole R. ; Pinheiro, Paula F. ; Bager, Alex ; Secco, Helio ; Guerreiro, Marcello ; Carvalho, Carine F. ; Veloso, Aline C. ; Custódio, Ana E.I. ; Marçal, Oswaldo ; Ciocheti, Giordano ; Assis, Julia ; Ribeiro, Milton Cezar ; Francisco, Beatriz S.S. ; Cherem, Jorge J. ; Trigo, Tatiane C. ; Jardim, Márcia M.A. ; Franceschi, Ingridi C. ; Espinosa, Caroline ; Tirelli, Flávia P. ; Rocha, Vlamir J. ; Sekiama, Margareth L. ; Barbosa, Gedimar P. ; Rossi, Helen R. ; Moreira, Tainah C. ; Cervini, Marcelo ; Rosa, Clarissa Alves ; Silva, Lucas Gonçalves ; Ferreira, Claudia M.M. ; César, Augusto ; Casella, Janaina ; Mendes, Sérgio L. ; Zina, Juliana ; Bastos, Deivson F.O. ; Souza, Ricardo A.T. ; Hartmann, Paulo A. ; Deffaci, Angela C.G. ; Mulinari, Jéssica ; Luzzi, Siane C. ; Rezzadori, Tiago ; Kolcenti, Cassiane ; Reis, Tiago Xavier ; Fonseca, Vanessa S.C. ; Giorgi, Camilo F. ; Migliorini, Raissa P. ; Kasper, Carlos Benhur ; Bueno, Cecília ; Sobanski, Marcela ; Pereira, Ana P.F.G. ; Andrade, Fernanda A.G. ; Fernandes, Marcus E.B. ; Corrêa, Luiz L.C. ; Nepomuceno, Adriana ; Banhos, Aureo ; Hannibal, Wellington ; Fonseca, Rogério ; Costa, Lizit A. ; Medici, Emilia P. ; Croce, Aline ; Werther, Karin ; Oliveira, Juliana P. ; Ribeiro, Julia M. ; Santi, Mariele de; Kawanami, Aline E. ; Perles, Livia ; Couto, Caroline do; Figueiró, Daniela S. ; Eizirik, Eduardo ; Correia, Antonio A. ; Corrêa, Fabio M. ; Queirolo, Diego ; Quagliatto, André L. ; Saranholi, Bruno H. ; Galetti, Pedro M. ; Rodriguez-Castro, Karen G. ; Braz, Vivian S. ; França, Frederico G.R. ; Buss, Gerson ; Rezini, Josias A. ; Lion, Marília B. ; Cheida, Carolina C. ; Lacerda, Ana C.R. ; Freitas, Carlos Henrique ; Venâncio, Fernando ; Adania, Cristina H. ; Batisteli, Augusto F. ; Hegel, Carla G.Z. ; Mantovani, José A. ; Rodrigues, Flávio H.G. ; Bagatini, Tathiana ; Curi, Nelson H.A. ; Emmert, Luciano ; Erdmann, Renato H. ; Costa, Raoni R.G.F. ; Martinelli, Agustín ; Santos, Clarice V.F. ; Kindel, Andreas - \ 2018
    Ecology 99 (2018)11. - ISSN 0012-9658 - 1 p.
    1988–2017 - amphibians - birds - Brazil - mammals - reptiles - road effects - road mortality - road survey - species occurrence - wildlife-vehicle collisions

    Mortality from collision with vehicles is the most visible impact of road traffic on wildlife. Mortality due to roads (hereafter road-kill) can affect the dynamic of populations of many species and can, therefore, increase the risk of local decline or extinction. This is especially true in Brazil, where plans for road network upgrading and expansion overlaps biodiversity hotspot areas, which are of high importance for global conservation. Researchers, conservationists and road planners face the challenge to define a national strategy for road mitigation and wildlife conservation. The main goal of this dataset is a compilation of geo-referenced road-kill data from published and unpublished road surveys. This is the first Data Paper in the BRAZIL series (see ATLANTIC, NEOTROPICAL, and BRAZIL collections of Data Papers published in Ecology), which aims make public road-kill data for species in the Brazilian Regions. The dataset encompasses road-kill records from 45 personal communications and 26 studies published in peer-reviewed journals, theses and reports. The road-kill dataset comprises 21,512 records, 83% of which are identified to the species level (n = 450 species). The dataset includes records of 31 amphibian species, 90 reptile species, 229 bird species, and 99 mammal species. One species is classified as Endangered, eight as Vulnerable and twelve as Near Threatened. The species with the highest number of records are: Didelphis albiventris (n = 1,549), Volatinia jacarina (n = 1,238), Cerdocyon thous (n = 1,135), Helicops infrataeniatus (n = 802), and Rhinella icterica (n = 692). Most of the records came from southern Brazil. However, observations of the road-kill incidence for non-Least Concern species are more spread across the country. This dataset can be used to identify which taxa seems to be vulnerable to traffic, analyze temporal and spatial patterns of road-kill at local, regional and national scales and also used to understand the effects of road-kill on population persistence. It may also contribute to studies that aims to understand the influence of landscape and environmental influences on road-kills, improve our knowledge on road-related strategies on biodiversity conservation and be used as complementary information on large-scale and macroecological studies. No copyright or proprietary restrictions are associated with the use of this data set other than citation of this Data Paper.

    Many Shades of Grey in Botrytis–Host Plant Interactions
    Veloso, Javier ; Kan, Jan A.L. van - \ 2018
    Trends in Plant Science 23 (2018)7. - ISSN 1360-1385 - p. 613 - 622.
    cross-kingdom gene silencing - endophyte - grey mould - programmed cell death

    The grey mould Botrytis cinerea causes disease in more than 1000 plant species, including important crops. The interaction between Botrytis and its (potential) hosts is determined by quantitative susceptibility and virulence traits in both interacting partners, resulting in a greyscale of disease outcomes. Fungal infection was long thought to rely mainly on its capacity to kill the host plant and degrade plant tissue. Recent research has revealed that Botrytis exploits two crucial biological processes in host plants for its own success. We highlight recent findings that illustrate that the interactions between Botrytis and its host plants are subtle and we discuss the molecular and cellular mechanisms controlling the many shades of grey during these interactions.

    Legume abundance along successional and rainfall gradients in Neotropical forests
    Gei, Maga ; Rozendaal, Danaë M.A. ; Poorter, Lourens ; Bongers, Frans ; Sprent, Janet I. ; Garner, Mira D. ; Aide, T.M. ; Andrade, José Luis ; Balvanera, Patricia ; Becknell, Justin M. ; Brancalion, Pedro H.S. ; Cabral, George A.L. ; César, Ricardo Gomes ; Chazdon, Robin L. ; Cole, Rebecca J. ; Colletta, Gabriel Dalla ; Jong, Ben De; Denslow, Julie S. ; Dent, Daisy H. ; Dewalt, Saara J. ; Dupuy, Juan Manuel ; Durán, Sandra M. ; Espírito Santo, Mário Marcos Do; Fernandes, G.W. ; Nunes, Yule Roberta Ferreira ; Finegan, Bryan ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Junqueira, André B. ; Kennard, Deborah ; Lebrija-Trejos, Edwin ; Letcher, Susan G. ; Lohbeck, Madelon ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Meave, Jorge A. ; Menge, Duncan N.L. ; Mora, Francisco ; Muñoz, Rodrigo ; Muscarella, Robert ; Ochoa-Gaona, Susana ; Orihuela-Belmonte, Edith ; Ostertag, Rebecca ; Peña-Claros, Marielos ; Pérez-García, Eduardo A. ; Piotto, Daniel ; Reich, Peter B. ; Reyes-García, Casandra ; Rodríguez-Velázquez, Jorge ; Romero-Pérez, I.E. ; Sanaphre-Villanueva, Lucía ; Sanchez-Azofeifa, Arturo ; Schwartz, Naomi B. ; Almeida, Arlete Silva De; Almeida-Cortez, Jarcilene S. ; Silver, Whendee ; Souza Moreno, Vanessa De; Sullivan, Benjamin W. ; Swenson, Nathan G. ; Uriarte, Maria ; Breugel, Michiel Van; Wal, Hans Van Der; Veloso, Maria Das Dores Magalhães ; Vester, Hans F.M. ; Vieira, Ima Célia Guimarães ; Zimmerman, Jess K. ; Powers, Jennifer S. - \ 2018
    Nature Ecology & Evolution 2 (2018)7. - ISSN 2397-334X - p. 1104 - 1111.
    The nutrient demands of regrowing tropical forests are partly satisfied by nitrogen-fixing legume trees, but our understanding of the abundance of those species is biased towards wet tropical regions. Here we show how the abundance of Leguminosae is affected by both recovery from disturbance and large-scale rainfall gradients through a synthesis of forest inventory plots from a network of 42 Neotropical forest chronosequences. During the first three decades of natural forest regeneration, legume basal area is twice as high in dry compared with wet secondary forests. The tremendous ecological success of legumes in recently disturbed, water-limited forests is likely to be related to both their reduced leaflet size and ability to fix N2, which together enhance legume drought tolerance and water-use efficiency. Earth system models should incorporate these large-scale successional and climatic patterns of legume dominance to provide more accurate estimates of the maximum potential for natural nitrogen fixation across tropical forests.
    Functional analysis of mating type genes and transcriptome analysis during fruiting body development of botrytis cinerea
    Rodenburg, Sander Y.A. ; Terhem, Razak B. ; Veloso, Javier ; Stassen, Joost H.M. ; Kan, Jan A.L. van - \ 2018
    mBio 9 (2018)1. - ISSN 2161-2129
    Ascospore - Epigenetic regulation - Plant disease - Sexual reproduction - Transcriptome
    Botrytis cinerea is a plant-pathogenic fungus producing apothecia as sexual fruiting bodies. To study the function of mating type (MAT) genes, single-gene deletion mutants were generated in both genes of the MAT1-1 locus and both genes of the MAT1-2 locus. Deletion mutants in two MAT genes were entirely sterile, while mutants in the other two MAT genes were able to develop stipes but never formed an apothecial disk. Little was known about the reprogramming of gene expression during apothecium development. We analyzed transcriptomes of sclerotia, three stages of apothecium development (primordia, stipes, and apothecial disks), and ascospores by RNA sequencing. Ten secondary metabolite gene clusters were upregulated at the onset of sexual development and downregulated in ascospores released from apothecia. Notably, more than 3,900 genes were differentially expressed in ascospores compared to mature apothecial disks. Among the genes that were upregulated in ascospores were numerous genes encoding virulence factors, which reveals that ascospores are transcriptionally primed for infection prior to their arrival on a host plant. Strikingly, the massive transcriptional changes at the initiation and completion of the sexual cycle often affected clusters of genes, rather than randomly dispersed genes. Thirty-five clusters of genes were jointly upregulated during the onset of sexual reproduction, while 99 clusters of genes (com-prising >900 genes) were jointly downregulated in ascospores. These transcriptional changes coincided with changes in expression of genes encoding enzymes participating in chromatin organization, hinting at the occurrence of massive epigenetic regulation of gene expression during sexual reproduction. IMPORTANCE Fungal fruiting bodies are formed by sexual reproduction. We studied the development of fruiting bodies (“apothecia”) of the ubiquitous plant-pathogenic ascomycete Botrytis cinerea. The role of mating type genes in apothecium development was investigated by targeted mutation. Two genes are essential for the initiation of sexual development; mutants in these genes are sterile. Two other genes were not essential for development of stipes; however, they were essential for stipes to develop a disk and produce sexual ascospores. We examined gene expression profiles during apothecium development, as well as in ascospores sampled from apothecia. We provide the first study ever of the transcriptome of pure ascospores in a filamentous fungus. The expression of numerous genes involved in plant infection was induced in the ascospores, implying that ascospores are developmentally primed for infection before their release from apothecia.
    Draft genomes of nine plant pathogenic Botrytis species
    Valero Jimenez, Claudio ; Veloso, Javier ; Staats, Martijn ; Kan, Jan van - \ 2017
    Wageningen University
    PRJNA401386 - Botrytis
    The aim of the project is to compare the genomes of nine species of plant pathogens in the genus Botrytis with distinct host specificity, in order to identify genes involved in host range determination. Six of the nine fungal species infect ornamental bulb flower crops.
    Chemical composition and anti-inflammatory activity of the leaves of Byrsonima verbascifolia
    Saldanha, Aline Aparecida ; Carmo, Lucas Fernandes Do; Nascimento, Sara Batista Do; Matos, Natália Alves de; Carvalho Veloso, Clarice de; Castro, Ana Hortência Fonsêca ; Vos, Ric C.H. de; Klein, André ; Siqueira, João Máximo de; Carollo, Carlos Alexandre ; Nascimento, Thalita Vieira Do; Toffoli-Kadri, Mônica Cristina ; Soares, Adriana Cristina - \ 2016
    Journal of Natural Medicines 70 (2016)4. - ISSN 1340-3443 - p. 760 - 768.
    Anti-inflammation - Byrsonima verbascifolia leaves - Flavonoids - Mass spectrometry - Nitric oxide

    An ethnopharmacological survey indicates that the genus Byrsonima has some medicinal species that are commonly found in the Brazilian Cerrado and has been used as an anti-inflammatory and for gastroduodenal disorders. The aim of this study was to evaluate the anti-inflammatory and antioxidant activity along with qualitative chemical characterization of the methanolic extract of the leaves of Byrsonima verbascifolia (BvME) obtained by exhaustive percolation. The data from the chemical analyses by liquid chromatography–mass spectrometry led to tentative identification of 42 compounds belonging to proanthocyanidins, galloyl quinic acid derivatives, flavonoids, and triterpene glycoside derivatives. BvME contain flavonoids and show an antioxidative activity. The methanolic extract administered intraperitoneally at doses of 50, 100, or 300 mg/kg showed a significant reduction in paw edema and modulated the neutrophil influx in a mouse model. Furthermore, the anti-edematogenic activity of the extract provided in smaller doses (12.5 and 25 mg/kg) was also demonstrated in a mouse paw edema model. The extract inhibited NO production by macrophages induced by lipopolysaccharide. We presume that the anti-inflammatory effects of BvME are due to a combination of compounds present in B. verbascifolia, including catechins (procyanidins), flavonoids, and triterpene glycosides and that these anti-inflammatory actions should be mediated, at least partly, through the inhibition of NO production. This study supports and validates the ethnopharmacological uses of B. verbascifolia as an anti-inflammatory.

    Report on adaptation and mitigation options in the showcase farms : Deliverable 10.5
    Stienezen, M.W.J. ; Sillebak Kristensen, Ib ; Olesen, J.E. ; Hutchings, N. ; Mogensen, Lisbeth ; Barioni, Luis ; Veloso, Rui - \ 2015
    Seventh Framework Programme (Animal Change : SEVENTH FRAMEWORK PROGRAMME : THEME 2: FOOD, AGRICULTURE AND FISHERIES, AND BIOTECHNOLOGIES Grant agreement number: FP7- 266018) - 72 p.
    This deliverable collates the information on simulated effects of mitigation and adaptation options at the farm scale in the non-European study regions from AnimalChange, primarily using the FarmAC model for the mitigation options, and applying semi quantitative modelling for the adaptation options
    New Phytophthora populations: A shift from indirect to direct sporangial germination?
    Kessel, G.J.T. ; Veloso, S. ; Forch, M.G. ; Latorse, M.P. - \ 2009
    In: Proceedings of the Eleventh EuroBlight Workshop, Hamar, Norway, 28-31 October 2008. - Lelystad, The Netherlands : Applied Plant Research, AGV Research Unit - p. 171 - 176.
    Phytophthora infestans, the causal agent of potato- and tomato late blight, remains a serious threat for (commercial) potato and tomato production. In North Western Europe, frequent fungicide applications, mostly aimed to prevent infection, form the back bone of potato late blight control. Modern protectants such as Shirlan (a.i. fluazinam) are highly effective against (germinating) P. infestans sporangia and zoospores. Zoospores in particular are so sensitive to low concentrations that the many applications over the past two decades may well have exerted sufficient selection to pressure against the formation of zoospores. Thus, over the years the balance between direct and indirect germination may have shifted towards direct germination. This hypothesis was investigated at Bayer Crop Science and Plant Research International
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