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.

    We have a manual that explains all the features 

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    Transforming knowledge systems for life on Earth: Visions of future systems and how to get there
    Fazey, Ioan ; Schäpke, Niko ; Caniglia, Guido ; Hodgson, Anthony ; Kendrick, Ian ; Lyon, Christopher ; Page, Glenn ; Patterson, James ; Riedy, Chris ; Strasser, Tim ; Verveen, Stephan ; Adams, David ; Goldstein, Bruce ; Klaes, Matthias ; Leicester, Graham ; Linyard, Alison ; McCurdy, Adrienne ; Ryan, Paul ; Sharpe, Bill ; Silvestri, Giorgia ; Abdurrahim, Ali Yansyah ; Abson, David ; Adetunji, Olufemi Samson ; Aldunce, Paulina ; Alvarez-Pereira, Carlos ; Amparo, Jennifer Marie ; Amundsen, Helene ; Anderson, Lakin ; Andersson, Lotta ; Asquith, Michael ; Augenstein, Karoline ; Barrie, Jack ; Bent, David ; Bentz, Julia ; Bergsten, Arvid ; Berzonsky, Carol ; Bina, Olivia ; Blackstock, Kirsty ; Boehnert, Joanna ; Bradbury, Hilary ; Brand, Christine ; Böhme (born Sangmeister), Jessica ; Bøjer, Marianne Mille ; Carmen, Esther ; Charli-Joseph, Lakshmi ; Choudhury, Sarah ; Chunhachoti-ananta, Supot ; Cockburn, Jessica ; Colvin, John ; Connon, Irena L.C. ; Cornforth, Rosalind ; Cox, Robin S. ; Cradock-Henry, Nicholas ; Cramer, Laura ; Cremaschi, Almendra ; Dannevig, Halvor ; Day, Catherine T. ; Lima Hutchison, Cathel de; Vrieze, Anke de; Desai, Vikas ; Dolley, Jonathan ; Duckett, Dominic ; Durrant, Rachael Amy ; Egermann, Markus ; Elsner (Adams), Emily ; Fremantle, Chris ; Fullwood-Thomas, Jessica ; Galafassi, Diego ; Gobby, Jen ; Golland, Ami ; González-Padrón, Shiara Kirana ; Gram-Hanssen, Irmelin ; Grandin, Jakob ; Grenni, Sara ; Lauren Gunnell, Jade ; Gusmao, Felipe ; Hamann, Maike ; Harding, Brian ; Harper, Gavin ; Hesselgren, Mia ; Hestad, Dina ; Heykoop, Cheryl Anne ; Holmén, Johan ; Holstead, Kirsty ; Hoolohan, Claire ; Horcea-Milcu, Andra Ioana ; Horlings, Lummina Geertruida ; Howden, Stuart Mark ; Howell, Rachel Angharad ; Huque, Sarah Insia ; Inturias Canedo, Mirna Liz ; Iro, Chidinma Yvonne ; Ives, Christopher D. ; John, Beatrice ; Joshi, Rajiv ; Juarez-Bourke, Sadhbh ; Juma, Dauglas Wafula ; Karlsen, Bea Cecilie ; Kliem, Lea ; Kläy, Andreas ; Kuenkel, Petra ; Kunze, Iris ; Lam, David Patrick Michael ; Lang, Daniel J. ; Larkin, Alice ; Light, Ann ; Luederitz, Christopher ; Luthe, Tobias ; Maguire, Cathy ; Mahecha-Groot, Ana Maria ; Malcolm, Jackie ; Marshall, Fiona ; Maru, Yiheyis ; McLachlan, Carly ; Mmbando, Peter ; Mohapatra, Subhakanta ; Moore, Michele Lee ; Moriggi, Angela ; Morley-Fletcher, Mark ; Moser, Susanne ; Mueller, Konstanze Marion ; Mukute, Mutizwa ; Mühlemeier, Susan ; Naess, Lars Otto ; Nieto-Romero, Marta ; Novo, Paula ; ÓBrien, Karen ; O'Connell, Deborah Anne ; O'Donnell, Kathleen ; Olsson, Per ; Pearson, Kelli Rose ; Pereira, Laura ; Petridis, Panos ; Peukert, Daniela ; Phear, Nicky ; Pisters, Siri Renée ; Polsky, Matt ; Pound, Diana ; Preiser, Rika ; Rahman, Md Sajidur ; Reed, Mark S. ; Revell, Philip ; Rodriguez, Iokiñe ; Rogers, Briony Cathryn ; Rohr, Jascha ; Nordbø Rosenberg, Milda ; Ross, Helen ; Russell, Shona ; Ryan, Melanie ; Saha, Probal ; Schleicher, Katharina ; Schneider, Flurina ; Scoville-Simonds, Morgan ; Searle, Beverley ; Sebhatu, Samuel Petros ; Sesana, Elena ; Silverman, Howard ; Singh, Chandni ; Sterling, Eleanor ; Stewart, Sarah Jane ; Tàbara, J.D. ; Taylor, Douglas ; Thornton, Philip ; Tribaldos, Theresa Margarete ; Tschakert, Petra ; Uribe-Calvo, Natalia ; Waddell, Steve ; Waddock, Sandra ; Merwe, Liza van der; Mierlo, Barbara van; Zwanenberg, Patrick van; Velarde, Sandra Judith ; Washbourne, Carla Leanne ; Waylen, Kerry ; Weiser, Annika ; Wight, Ian ; Williams, Stephen ; Woods, Mel ; Wolstenholme, Ruth ; Wright, Ness ; Wunder, Stefanie ; Wyllie, Alastair ; Young, Hannah R. - \ 2020
    Energy Research & Social Science 70 (2020). - ISSN 2214-6296
    Climate and energy research - Epistemology - Knowledge - Social-technical transitions - Sustainability science - Transformation

    Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innovations, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent.

    Characterizing the structure of aerobic granular sludge using ultra-high field magnetic resonance
    Kirkland, Catherine M. ; Krug, Julia R. ; Vergeldt, Frank J. ; Berg, Lenno van den; Velders, Aldrik H. ; Seymour, Joseph D. ; Codd, Sarah L. ; As, Henk Van; Kreuk, Merle K. de - \ 2020
    Water Science and Technology 82 (2020)4. - ISSN 0273-1223 - p. 627 - 639.
    Despite aerobic granular sludge wastewater treatment plants operating around the world, our understanding of internal granule structure and its relation to treatment efficiency remains limited. This can be attributed in part to the drawbacks of time-consuming, labor-intensive, and invasive microscopy protocols which effectively restrict samples sizes and may introduce artefacts. Time-domain nuclear magnetic resonance (NMR) allows non-invasive measurements which describe internal structural features of opaque, complex materials like biofilms. NMR was used to image aerobic granules collected from five full-scale wastewater treatment plants in the Netherlands and United States, as well as laboratory granules and control beads. T1 and T2 relaxation-weighted images reveal heterogeneous structures that include high- and low-density biofilm regions, water-like voids, and solid-like inclusions. Channels larger than approximately 50 μm and connected to the bulk fluid were not visible. Both cluster and ring-like structures were observed with each granule source having a characteristic structural type. These structures, and their NMR relaxation behavior, were stable over several months of storage. These observations reveal the complex structures within aerobic granules from a range of sources and highlight the need for non-invasive characterization methods like NMR to be applied in the ongoing effort to correlate structure and function.
    Evolution of nitrogen-fixing root nodules : Analysis of conserved signalling modules in legumes and Parasponia
    Rutten, Lukas Johannes Joseph - \ 2020
    Wageningen University. Promotor(en): A.H.J. Bisseling, co-promotor(en): R. Geurts. - Wageningen : Wageningen University - ISBN 9789463953504 - 233
    Global root traits (GRooT) database
    Guerrero-Ramírez, Nathaly R. ; Mommer, Liesje ; Freschet, Grégoire T. ; Iversen, Colleen M. ; McCormack, M.L. ; Kattge, Jens ; Poorter, Hendrik ; Plas, Fons van der; Bergmann, Joana ; Kuyper, Thom W. ; York, Larry M. ; Bruelheide, Helge ; Laughlin, Daniel C. ; Meier, Ina C. ; Roumet, Catherine ; Semchenko, Marina ; Sweeney, Christopher J. ; Ruijven, Jasper van; Valverde-Barrantes, Oscar J. ; Aubin, Isabelle ; Catford, Jane A. ; Manning, Peter ; Martin, Adam ; Milla, Rubén ; Minden, Vanessa ; Pausas, Juli G. ; Smith, Stuart W. ; Soudzilovskaia, Nadejda A. ; Ammer, Christian ; Butterfield, Bradley ; Craine, Joseph ; Cornelissen, Johannes H.C. ; Vries, Franciska T. de; Isaac, Marney E. ; Kramer, Koen ; König, Christian ; Lamb, Eric G. ; Onipchenko, Vladimir G. ; Peñuelas, Josep ; Reich, Peter B. ; Rillig, Matthias C. ; Sack, Lawren ; Shipley, Bill ; Tedersoo, Leho ; Valladares, Fernando ; Bodegom, Peter van; Weigelt, Patrick ; Wright, Justin P. ; Weigelt, Alexandra - \ 2020
    Global Ecology and Biogeography (2020). - ISSN 1466-822X
    Belowground ecology - functional biogeography - macroecological studies - plant form and function - publicly-available database - root traits

    Motivation: Trait data are fundamental to the quantitative description of plant form and function. Although root traits capture key dimensions related to plant responses to changing environmental conditions and effects on ecosystem processes, they have rarely been included in large-scale comparative studies and global models. For instance, root traits remain absent from nearly all studies that define the global spectrum of plant form and function. Thus, to overcome conceptual and methodological roadblocks preventing a widespread integration of root trait data into large-scale analyses we created the Global Root Trait (GRooT) Database. GRooT provides ready-to-use data by combining the expertise of root ecologists with data mobilization and curation. Specifically, we (a) determined a set of core root traits relevant to the description of plant form and function based on an assessment by experts, (b) maximized species coverage through data standardization within and among traits, and (c) implemented data quality checks. Main types of variables contained: GRooT contains 114,222 trait records on 38 continuous root traits. Spatial location and grain: Global coverage with data from arid, continental, polar, temperate and tropical biomes. Data on root traits were derived from experimental studies and field studies. Time period and grain: Data were recorded between 1911 and 2019. Major taxa and level of measurement: GRooT includes root trait data for which taxonomic information is available. Trait records vary in their taxonomic resolution, with subspecies or varieties being the highest and genera the lowest taxonomic resolution available. It contains information for 184 subspecies or varieties, 6,214 species, 1,967 genera and 254 families. Owing to variation in data sources, trait records in the database include both individual observations and mean values. Software format: GRooT includes two csv files. A GitHub repository contains the csv files and a script in R to query the database.

    Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age
    Merid, Simon Kebede ; Novoloaca, Alexei ; Sharp, Gemma C. ; Küpers, Leanne K. ; Kho, Alvin T. ; Roy, Ritu ; Gao, Lu ; Annesi-Maesano, Isabella ; Jain, Pooja ; Plusquin, Michelle ; Kogevinas, Manolis ; Allard, Catherine ; Vehmeijer, Florianne O. ; Kazmi, Nabila ; Salas, Lucas A. ; Rezwan, Faisal I. ; Zhang, Hongmei ; Sebert, Sylvain ; Czamara, Darina ; Rifas-Shiman, Sheryl L. ; Melton, Phillip E. ; Lawlor, Debbie A. ; Pershagen, Göran ; Breton, Carrie V. ; Huen, Karen ; Baiz, Nour ; Gagliardi, Luigi ; Nawrot, Tim S. ; Corpeleijn, Eva ; Perron, Patrice ; Duijts, Liesbeth ; Nohr, Ellen Aagaard ; Bustamante, Mariona ; Ewart, Susan L. ; Karmaus, Wilfried ; Zhao, Shanshan ; Page, Christian M. ; Herceg, Zdenko ; Jarvelin, Marjo Riitta ; Lahti, Jari ; Baccarelli, Andrea A. ; Anderson, Denise ; Kachroo, Priyadarshini ; Relton, Caroline L. ; Bergström, Anna ; Eskenazi, Brenda ; Soomro, Munawar Hussain ; Vineis, Paolo ; Snieder, Harold ; Bouchard, Luigi ; Jaddoe, Vincent W. ; Sørensen, Thorkild I.A. ; Vrijheid, Martine ; Arshad, S.H. ; Holloway, John W. ; Håberg, Siri E. ; Magnus, Per ; Dwyer, Terence ; Binder, Elisabeth B. ; Demeo, Dawn L. ; Vonk, Judith M. ; Newnham, John ; Tantisira, Kelan G. ; Kull, Inger ; Wiemels, Joseph L. ; Heude, Barbara ; Sunyer, Jordi ; Nystad, Wenche ; Munthe-Kaas, Monica C. ; Raïkkönen, Katri ; Oken, Emily ; Huang, Rae Chi ; Weiss, Scott T. ; Antó, Josep Maria ; Bousquet, Jean ; Kumar, Ashish ; Söderhäll, Cilla ; Almqvist, Catarina ; Cardenas, Andres ; Gruzieva, Olena ; Xu, Cheng Jian ; Reese, Sarah E. ; Kere, Juha ; Brodin, Petter ; Solomon, Olivia ; Wielscher, Matthias ; Holland, Nina ; Ghantous, Akram ; Hivert, Marie France ; Felix, Janine F. ; Koppelman, Gerard H. ; London, Stephanie J. ; Melén, Erik - \ 2020
    Karolinska Institute
    Development - Epigenetics - Gestational age - Preterm birth - Transcriptomics
    Background Preterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated associations between gestational age and blood DNA methylation in children. Methods We performed meta-analysis of Illumina’s HumanMethylation450-array associations between gestational age and cord blood DNA methylation in 3648 newborns from 17 cohorts without common pregnancy complications, induced delivery or caesarean section. We also explored associations of gestational age with DNA methylation measured at 4–18 years in additional pediatric cohorts. Follow-up analyses of DNA methylation and gene expression correlations were performed in cord blood. DNA methylation profiles were also explored in tissues relevant for gestational age health effects: fetal brain and lung. Results We identified 8899 CpGs in cord blood that were associated with gestational age (range 27–42 weeks), at Bonferroni significance, P
    Correction to: Microbiome definition re-visited: old concepts and new challenges
    Berg, Gabriele ; Rybakova, Daria ; Fischer, Doreen ; Cernava, Tomislav ; Vergès, Marie Christine Champomier ; Charles, Trevor ; Chen, Xiaoyulong ; Cocolin, Luca ; Eversole, Kellye ; Corral, Gema Herrero ; Kazou, Maria ; Kinkel, Linda ; Lange, Lene ; Lima, Nelson ; Loy, Alexander ; Macklin, James A. ; Maguin, Emmanuelle ; Mauchline, Tim ; McClure, Ryan ; Mitter, Birgit ; Ryan, Matthew ; Sarand, Inga ; Smidt, Hauke ; Schelkle, Bettina ; Roume, Hugo ; Kiran, G.S. ; Selvin, Joseph ; Souza, Rafael Soares Correa de; Overbeek, Leo van; Singh, Brajesh K. ; Wagner, Michael ; Walsh, Aaron ; Sessitsch, Angela ; Schloter, Michael - \ 2020
    Microbiome 8 (2020)1. - ISSN 2049-2618 - 1 p.
    Detection of peanut allergens in serum : circumventing the inhibitory effect of immunoglobulins
    Koppelman, Stef J. ; Witteveen, Michel ; JanssenDuijghuijsen, Lonneke ; Baumert, Joseph L. ; Witkamp, Renger F. ; Norren, Klaske van - \ 2020
    Allergy 75 (2020)7. - ISSN 0105-4538 - p. 1835 - 1836.
    allergens - food allergy - IgE - IgG4 - peanut
    The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data
    Pastorello, Gilberto ; Trotta, Carlo ; Canfora, Eleonora ; Chu, Housen ; Christianson, Danielle ; Cheah, You Wei ; Poindexter, Cristina ; Chen, Jiquan ; Elbashandy, Abdelrahman ; Humphrey, Marty ; Isaac, Peter ; Polidori, Diego ; Ribeca, Alessio ; Ingen, Catharine van; Zhang, Leiming ; Amiro, Brian ; Ammann, Christof ; Arain, M.A. ; Ardö, Jonas ; Arkebauer, Timothy ; Arndt, Stefan K. ; Arriga, Nicola ; Aubinet, Marc ; Aurela, Mika ; Baldocchi, Dennis ; Barr, Alan ; Beamesderfer, Eric ; Marchesini, Luca Belelli ; Bergeron, Onil ; Beringer, Jason ; Bernhofer, Christian ; Berveiller, Daniel ; Billesbach, Dave ; Black, Thomas Andrew ; Blanken, Peter D. ; Bohrer, Gil ; Boike, Julia ; Bolstad, Paul V. ; Bonal, Damien ; Bonnefond, Jean Marc ; Bowling, David R. ; Bracho, Rosvel ; Brodeur, Jason ; Brümmer, Christian ; Buchmann, Nina ; Burban, Benoit ; Burns, Sean P. ; Buysse, Pauline ; Cale, Peter ; Cavagna, Mauro ; Cellier, Pierre ; Chen, Shiping ; Chini, Isaac ; Christensen, Torben R. ; Cleverly, James ; Collalti, Alessio ; Consalvo, Claudia ; Cook, Bruce D. ; Cook, David ; Coursolle, Carole ; Cremonese, Edoardo ; Curtis, Peter S. ; Andrea, Ettore D'; Rocha, Humberto da; Dai, Xiaoqin ; Davis, Kenneth J. ; Cinti, Bruno De; Grandcourt, Agnes de; Ligne, Anne De; Oliveira, Raimundo C. De; Delpierre, Nicolas ; Desai, Ankur R. ; Bella, Carlos Marcelo Di; Tommasi, Paul di; Dolman, Han ; Domingo, Francisco ; Dong, Gang ; Dore, Sabina ; Duce, Pierpaolo ; Dufrêne, Eric ; Dunn, Allison ; Dušek, Jiří ; Eamus, Derek ; Eichelmann, Uwe ; ElKhidir, Hatim Abdalla M. ; Eugster, Werner ; Ewenz, Cacilia M. ; Ewers, Brent ; Famulari, Daniela ; Fares, Silvano ; Feigenwinter, Iris ; Feitz, Andrew ; Fensholt, Rasmus ; Filippa, Gianluca ; Fischer, Marc ; Frank, John ; Galvagno, Marta ; Gharun, Mana ; Gianelle, Damiano ; Gielen, Bert ; Gioli, Beniamino ; Gitelson, Anatoly ; Goded, Ignacio ; Goeckede, Mathias ; Goldstein, Allen H. ; Gough, Christopher M. ; Goulden, Michael L. ; Graf, Alexander ; Griebel, Anne ; Gruening, Carsten ; Grünwald, Thomas ; Hammerle, Albin ; Han, Shijie ; Han, Xingguo ; Hansen, Birger Ulf ; Hanson, Chad ; Hatakka, Juha ; He, Yongtao ; Hehn, Markus ; Heinesch, Bernard ; Hinko-Najera, Nina ; Hörtnagl, Lukas ; Hutley, Lindsay ; Ibrom, Andreas ; Ikawa, Hiroki ; Jackowicz-Korczynski, Marcin ; Janouš, Dalibor ; Jans, Wilma ; Jassal, Rachhpal ; Jiang, Shicheng ; Kato, Tomomichi ; Khomik, Myroslava ; Klatt, Janina ; Knohl, Alexander ; Knox, Sara ; Kobayashi, Hideki ; Koerber, Georgia ; Kolle, Olaf ; Kosugi, Yoshiko ; Kotani, Ayumi ; Kowalski, Andrew ; Kruijt, Bart ; Kurbatova, Julia ; Kutsch, Werner L. ; Kwon, Hyojung ; Launiainen, Samuli ; Laurila, Tuomas ; Law, Bev ; Leuning, Ray ; Li, Yingnian ; Liddell, Michael ; Limousin, Jean Marc ; Lion, Marryanna ; Liska, Adam J. ; Lohila, Annalea ; López-Ballesteros, Ana ; López-Blanco, Efrén ; Loubet, Benjamin ; Loustau, Denis ; Lucas-Moffat, Antje ; Lüers, Johannes ; Ma, Siyan ; Macfarlane, Craig ; Magliulo, Vincenzo ; Maier, Regine ; Mammarella, Ivan ; Manca, Giovanni ; Marcolla, Barbara ; Margolis, Hank A. ; Marras, Serena ; Massman, William ; Mastepanov, Mikhail ; Matamala, Roser ; Matthes, Jaclyn Hatala ; Mazzenga, Francesco ; McCaughey, Harry ; McHugh, Ian ; McMillan, Andrew M.S. ; Merbold, Lutz ; Meyer, Wayne ; Meyers, Tilden ; Miller, Scott D. ; Minerbi, Stefano ; Moderow, Uta ; Monson, Russell K. ; Montagnani, Leonardo ; Moore, Caitlin E. ; Moors, Eddy ; Moreaux, Virginie ; Moureaux, Christine ; Munger, J.W. ; Nakai, Taro ; Neirynck, Johan ; Nesic, Zoran ; Nicolini, Giacomo ; Noormets, Asko ; Northwood, Matthew ; Nosetto, Marcelo ; Nouvellon, Yann ; Novick, Kimberly ; Oechel, Walter ; Olesen, Jørgen Eivind ; Ourcival, Jean Marc ; Papuga, Shirley A. ; Parmentier, Frans Jan ; Paul-Limoges, Eugenie ; Pavelka, Marian ; Peichl, Matthias ; Pendall, Elise ; Phillips, Richard P. ; Pilegaard, Kim ; Pirk, Norbert ; Posse, Gabriela ; Powell, Thomas ; Prasse, Heiko ; Prober, Suzanne M. ; Rambal, Serge ; Rannik, Üllar ; Raz-Yaseef, Naama ; Reed, David ; Dios, Victor Resco de; Restrepo-Coupe, Natalia ; Reverter, Borja R. ; Roland, Marilyn ; Sabbatini, Simone ; Sachs, Torsten ; Saleska, Scott R. ; Sánchez-Cañete, Enrique P. ; Sanchez-Mejia, Zulia M. ; Schmid, Hans Peter ; Schmidt, Marius ; Schneider, Karl ; Schrader, Frederik ; Schroder, Ivan ; Scott, Russell L. ; Sedlák, Pavel ; Serrano-Ortíz, Penélope ; Shao, Changliang ; Shi, Peili ; Shironya, Ivan ; Siebicke, Lukas ; Šigut, Ladislav ; Silberstein, Richard ; Sirca, Costantino ; Spano, Donatella ; Steinbrecher, Rainer ; Stevens, Robert M. ; Sturtevant, Cove ; Suyker, Andy ; Tagesson, Torbern ; Takanashi, Satoru ; Tang, Yanhong ; Tapper, Nigel ; Thom, Jonathan ; Tiedemann, Frank ; Tomassucci, Michele ; Tuovinen, Juha Pekka ; Urbanski, Shawn ; Valentini, Riccardo ; Molen, Michiel van der; Gorsel, Eva van; Huissteden, Ko van; Varlagin, Andrej ; Verfaillie, Joseph ; Vesala, Timo ; Vincke, Caroline ; Vitale, Domenico ; Vygodskaya, Natalia ; Walker, Jeffrey P. ; Walter-Shea, Elizabeth ; Wang, Huimin ; Weber, Robin ; Westermann, Sebastian ; Wille, Christian ; Wofsy, Steven ; Wohlfahrt, Georg ; Wolf, Sebastian ; Woodgate, William ; Li, Yuelin ; Zampedri, Roberto ; Zhang, Junhui ; Zhou, Guoyi ; Zona, Donatella ; Agarwal, Deb ; Biraud, Sebastien ; Torn, Margaret ; Papale, Dario - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463 - 1 p.

    The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.

    The global abundance of tree palms
    Muscarella, Robert ; Emilio, Thaise ; Phillips, Oliver L. ; Lewis, Simon L. ; Slik, Ferry ; Baker, William J. ; Couvreur, Thomas L.P. ; Eiserhardt, Wolf L. ; Svenning, Jens Christian ; Affum-Baffoe, Kofi ; Aiba, Shin Ichiro ; Almeida, Everton C. de; Almeida, Samuel S. de; Oliveira, Edmar Almeida de; Álvarez-Dávila, Esteban ; Alves, Luciana F. ; Alvez-Valles, Carlos Mariano ; Carvalho, Fabrício Alvim ; Guarin, Fernando Alzate ; Andrade, Ana ; Aragão, Luis E.O.C. ; Murakami, Alejandro Araujo ; Arroyo, Luzmila ; Ashton, Peter S. ; Corredor, Gerardo A.A. ; Baker, Timothy R. ; Camargo, Plinio Barbosa de; Barlow, Jos ; Bastin, Jean François ; Bengone, Natacha Nssi ; Berenguer, Erika ; Berry, Nicholas ; Blanc, Lilian ; Böhning-Gaese, Katrin ; Bonal, Damien ; Bongers, Frans ; Bradford, Matt ; Brambach, Fabian ; Brearley, Francis Q. ; Brewer, Steven W. ; Camargo, Jose L.C. ; Campbell, David G. ; Castilho, Carolina V. ; Castro, Wendeson ; Catchpole, Damien ; Cerón Martínez, Carlos E. ; Chen, Shengbin ; Chhang, Phourin ; Cho, Percival ; Chutipong, Wanlop ; Clark, Connie ; Collins, Murray ; Comiskey, James A. ; Medina, Massiel Nataly Corrales ; Costa, Flávia R.C. ; Culmsee, Heike ; David-Higuita, Heriberto ; Davidar, Priya ; Aguila-Pasquel, Jhon del; Derroire, Géraldine ; Fiore, Anthony Di; Do, Tran Van; Doucet, Jean Louis ; Dourdain, Aurélie ; Drake, Donald R. ; Ensslin, Andreas ; Erwin, Terry ; Ewango, Corneille E.N. ; Ewers, Robert M. ; Fauset, Sophie ; Feldpausch, Ted R. ; Ferreira, Joice ; Ferreira, Leandro Valle ; Fischer, Markus ; Franklin, Janet ; Fredriksson, Gabriella M. ; Gillespie, Thomas W. ; Gilpin, Martin ; Gonmadje, Christelle ; Gunatilleke, Arachchige Upali Nimal ; Hakeem, Khalid Rehman ; Hall, Jefferson S. ; Hamer, Keith C. ; Harris, David J. ; Harrison, Rhett D. ; Hector, Andrew ; Hemp, Andreas ; Herault, Bruno ; Pizango, Carlos Gabriel Hidalgo ; Honorio Coronado, Eurídice N. ; Hubau, Wannes ; Hussain, Mohammad Shah ; Ibrahim, Faridah Hanum ; Imai, Nobuo ; Joly, Carlos A. ; Joseph, Shijo ; Anitha, K. ; Kartawinata, Kuswata ; Kassi, Justin ; Killeen, Timothy J. ; Kitayama, Kanehiro ; Klitgård, Bente Bang ; Kooyman, Robert ; Labrière, Nicolas ; Larney, Eileen ; Laumonier, Yves ; Laurance, Susan G. ; Laurance, William F. ; Lawes, Michael J. ; Levesley, Aurora ; Lisingo, Janvier ; Lovejoy, Thomas ; Lovett, Jon C. ; Lu, Xinghui ; Lykke, Anne Mette ; Magnusson, William E. ; Mahayani, Ni Putu Diana ; Malhi, Yadvinder ; Mansor, Asyraf ; Peña, Jose Luis Marcelo ; Marimon-Junior, Ben H. ; Marshall, Andrew R. ; Melgaco, Karina ; Bautista, Casimiro Mendoza ; Mihindou, Vianet ; Millet, Jérôme ; Milliken, William ; Mohandass, D. ; Mendoza, Abel Lorenzo Monteagudo ; Mugerwa, Badru ; Nagamasu, Hidetoshi ; Nagy, Laszlo ; Seuaturien, Naret ; Nascimento, Marcelo T. ; Neill, David A. ; Neto, Luiz Menini ; Nilus, Rueben ; Vargas, Mario Percy Núñez ; Nurtjahya, Eddy ; Araújo, R.N.O. de; Onrizal, Onrizal ; Palacios, Walter A. ; Palacios-Ramos, Sonia ; Parren, Marc ; Paudel, Ekananda ; Morandi, Paulo S. ; Pennington, R.T. ; Pickavance, Georgia ; Pipoly, John J. ; Pitman, Nigel C.A. ; Poedjirahajoe, Erny ; Poorter, Lourens ; Poulsen, John R. ; Prasad, P.R.C. ; Prieto, Adriana ; Puyravaud, Jean Philippe ; Qie, Lan ; Quesada, Carlos A. ; Ramírez-Angulo, Hirma ; Razafimahaimodison, Jean Claude ; Reitsma, Jan Meindert ; Requena-Rojas, Edilson J. ; Correa, Zorayda Restrepo ; Rodriguez, Carlos Reynel ; Roopsind, Anand ; Rovero, Francesco ; Rozak, Andes ; Lleras, Agustín Rudas ; Rutishauser, Ervan ; Rutten, Gemma ; Punchi-Manage, Ruwan ; Salomão, Rafael P. ; Sam, Hoang Van; Sarker, Swapan Kumar ; Satdichanh, Manichanh ; Schietti, Juliana ; Schmitt, Christine B. ; Marimon, Beatriz Schwantes ; Senbeta, Feyera ; Nath Sharma, Lila ; Sheil, Douglas ; Sierra, Rodrigo ; Silva-Espejo, Javier E. ; Silveira, Marcos ; Sonké, Bonaventure ; Steininger, Marc K. ; Steinmetz, Robert ; Stévart, Tariq ; Sukumar, Raman ; Sultana, Aisha ; Sunderland, Terry C.H. ; Suresh, Hebbalalu Satyanarayana ; Tang, Jianwei ; Tanner, Edmund ; Steege, Hans ter; Terborgh, John W. ; Theilade, Ida ; Timberlake, Jonathan ; Torres-Lezama, Armando ; Umunay, Peter ; Uriarte, María ; Gamarra, Luis Valenzuela ; Bult, Martin van de; Hout, Peter van der; Martinez, Rodolfo Vasquez ; Vieira, Ima Célia Guimarães ; Vieira, Simone A. ; Vilanova, Emilio ; Cayo, Jeanneth Villalobos ; Wang, Ophelia ; Webb, Campbell O. ; Webb, Edward L. ; White, Lee ; Whitfeld, Timothy J.S. ; Wich, Serge ; Willcock, Simon ; Wiser, Susan K. ; Young, Kenneth R. ; Zakaria, Rahmad ; Zang, Runguo ; Zartman, Charles E. ; Zo-Bi, Irié Casimir ; Balslev, Henrik - \ 2020
    Global Ecology and Biogeography 29 (2020)9. - ISSN 1466-822X - p. 1495 - 1514.
    above-ground biomass - abundance patterns - Arecaceae - local abiotic conditions - Neotropics - pantropical biogeography - tropical rainforest - wood density

    Aim: Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and in terms of responses to climate change. We quantified global patterns of tree palm relative abundance to help improve understanding of tropical forests and reduce uncertainty about these ecosystems under climate change. Location: Tropical and subtropical moist forests. Time period: Current. Major taxa studied: Palms (Arecaceae). Methods: We assembled a pantropical dataset of 2,548 forest plots (covering 1,191 ha) and quantified tree palm (i.e., ≥10 cm diameter at breast height) abundance relative to co-occurring non-palm trees. We compared the relative abundance of tree palms across biogeographical realms and tested for associations with palaeoclimate stability, current climate, edaphic conditions and metrics of forest structure. Results: On average, the relative abundance of tree palms was more than five times larger between Neotropical locations and other biogeographical realms. Tree palms were absent in most locations outside the Neotropics but present in >80% of Neotropical locations. The relative abundance of tree palms was more strongly associated with local conditions (e.g., higher mean annual precipitation, lower soil fertility, shallower water table and lower plot mean wood density) than metrics of long-term climate stability. Life-form diversity also influenced the patterns; palm assemblages outside the Neotropics comprise many non-tree (e.g., climbing) palms. Finally, we show that tree palms can influence estimates of above-ground biomass, but the magnitude and direction of the effect require additional work. Conclusions: Tree palms are not only quintessentially tropical, but they are also overwhelmingly Neotropical. Future work to understand the contributions of tree palms to biomass estimates and carbon cycling will be particularly crucial in Neotropical forests.

    Snellere en efficiëntere diagnose met behulp van camerasystemen. Op zoek naar slimme detectietechnieken
    Peller, Joseph ; Hernandez Olesinki, Estuardo - \ 2020
    An empirical evaluation of camera trap study design : How many, how long and when?
    Kays, Roland ; Arbogast, Brian S. ; Baker-Whatton, Megan ; Beirne, Chris ; Boone, Hailey M. ; Bowler, Mark ; Burneo, Santiago F. ; Cove, Michael V. ; Ding, Ping ; Espinosa, Santiago ; Gonçalves, André Luis Sousa ; Hansen, Christopher P. ; Jansen, Patrick A. ; Kolowski, Joseph M. ; Knowles, Travis W. ; Lima, Marcela Guimarães Moreira ; Millspaugh, Joshua ; McShea, William J. ; Pacifici, Krishna ; Parsons, Arielle W. ; Pease, Brent S. ; Rovero, Francesco ; Santos, Fernanda ; Schuttler, Stephanie G. ; Sheil, Douglas ; Si, Xingfeng ; Snider, Matt ; Spironello, Wilson R. - \ 2020
    Methods in Ecology and Evolution 11 (2020)6. - ISSN 2041-210X - p. 700 - 713.
    camera traps - community ecology - detectability - mammals - relative abundance - species richness - study design - wildlife surveys

    Camera traps deployed in grids or stratified random designs are a well-established survey tool for wildlife but there has been little evaluation of study design parameters. We used an empirical subsampling approach involving 2,225 camera deployments run at 41 study areas around the world to evaluate three aspects of camera trap study design (number of sites, duration and season of sampling) and their influence on the estimation of three ecological metrics (species richness, occupancy and detection rate) for mammals. We found that 25–35 camera sites were needed for precise estimates of species richness, depending on scale of the study. The precision of species-level estimates of occupancy (ψ) was highly sensitive to occupancy level, with <20 camera sites needed for precise estimates of common (ψ > 0.75) species, but more than 150 camera sites likely needed for rare (ψ < 0.25) species. Species detection rates were more difficult to estimate precisely at the grid level due to spatial heterogeneity, presumably driven by unaccounted habitat variability factors within the study area. Running a camera at a site for 2 weeks was most efficient for detecting new species, but 3–4 weeks were needed for precise estimates of local detection rate, with no gains in precision observed after 1 month. Metrics for all mammal communities were sensitive to seasonality, with 37%–50% of the species at the sites we examined fluctuating significantly in their occupancy or detection rates over the year. This effect was more pronounced in temperate sites, where seasonally sensitive species varied in relative abundance by an average factor of 4–5, and some species were completely absent in one season due to hibernation or migration. We recommend the following guidelines to efficiently obtain precise estimates of species richness, occupancy and detection rates with camera trap arrays: run each camera for 3–5 weeks across 40–60 sites per array. We recommend comparisons of detection rates be model based and include local covariates to help account for small-scale variation. Furthermore, comparisons across study areas or times must account for seasonality, which could have strong impacts on mammal communities in both tropical and temperate sites.

    ENIGMA and global neuroscience : A decade of large-scale studies of the brain in health and disease across more than 40 countries
    Thompson, Paul M. ; Jahanshad, Neda ; Ching, Christopher R.K. ; Salminen, Lauren E. ; Thomopoulos, Sophia I. ; Bright, Joanna ; Baune, Bernhard T. ; Bertolín, Sara ; Bralten, Janita ; Bruin, Willem B. ; Bülow, Robin ; Chen, Jian ; Chye, Yann ; Dannlowski, Udo ; Kovel, Carolien G.F. de; Donohoe, Gary ; Eyler, Lisa T. ; Faraone, Stephen V. ; Favre, Pauline ; Filippi, Courtney A. ; Frodl, Thomas ; Garijo, Daniel ; Gil, Yolanda ; Grabe, Hans J. ; Grasby, Katrina L. ; Hajek, Tomas ; Han, Laura K.M. ; Hatton, Sean N. ; Hilbert, Kevin ; Ho, Tiffany C. ; Holleran, Laurena ; Homuth, Georg ; Hosten, Norbert ; Houenou, Josselin ; Ivanov, Iliyan ; Jia, Tianye ; Kelly, Sinead ; Klein, Marieke ; Kwon, Jun Soo ; Laansma, Max A. ; Leerssen, Jeanne ; Lueken, Ulrike ; Nunes, Abraham ; Neill, Joseph O. ; Opel, Nils ; Piras, Fabrizio ; Piras, Federica ; Postema, Merel C. ; Pozzi, Elena ; Wang, Lei - \ 2020
    Translational Psychiatry 10 (2020)1. - ISSN 2158-3188 - 1 p.

    This review summarizes the last decade of work by the ENIGMA (Enhancing NeuroImaging Genetics through Meta Analysis) Consortium, a global alliance of over 1400 scientists across 43 countries, studying the human brain in health and disease. Building on large-scale genetic studies that discovered the first robustly replicated genetic loci associated with brain metrics, ENIGMA has diversified into over 50 working groups (WGs), pooling worldwide data and expertise to answer fundamental questions in neuroscience, psychiatry, neurology, and genetics. Most ENIGMA WGs focus on specific psychiatric and neurological conditions, other WGs study normal variation due to sex and gender differences, or development and aging; still other WGs develop methodological pipelines and tools to facilitate harmonized analyses of "big data" (i.e., genetic and epigenetic data, multimodal MRI, and electroencephalography data). These international efforts have yielded the largest neuroimaging studies to date in schizophrenia, bipolar disorder, major depressive disorder, post-traumatic stress disorder, substance use disorders, obsessive-compulsive disorder, attention-deficit/hyperactivity disorder, autism spectrum disorders, epilepsy, and 22q11.2 deletion syndrome. More recent ENIGMA WGs have formed to study anxiety disorders, suicidal thoughts and behavior, sleep and insomnia, eating disorders, irritability, brain injury, antisocial personality and conduct disorder, and dissociative identity disorder. Here, we summarize the first decade of ENIGMA's activities and ongoing projects, and describe the successes and challenges encountered along the way. We highlight the advantages of collaborative large-scale coordinated data analyses for testing reproducibility and robustness of findings, offering the opportunity to identify brain systems involved in clinical syndromes across diverse samples and associated genetic, environmental, demographic, cognitive, and psychosocial factors.

    Critical transitions in Chinese dunes during the past 12,000 years
    Xu, Zhiwei ; Mason, Joseph A. ; Xu, Chi ; Yi, Shuangwen ; Bathiany, Sebastian ; Yizhaq, Hezi ; Zhou, Yali ; Cheng, Jun ; Holmgren, Milena ; Lu, Huayu - \ 2020
    Science Advances 6 (2020)9. - ISSN 2375-2548 - p. eaay8020 - eaay8020.

    Dune systems can have alternative stable states that coexist under certain environmental conditions: a vegetated, stabilized state and a bare active state. This behavior implies the possibility of abrupt transitions from one state to another in response to gradual environmental change. Here, we synthesize stratigraphic records covering 12,000 years of dynamics of this system at 144 localities across three dune fields in northern China. We find side-by-side coexistence of active and stabilized states, and occasional sharp shifts in time between those contrasting states. Those shifts occur asynchronously despite the fact that the entire landscape has been subject to the same gradual changes in monsoon rainfall and other conditions. At larger scale, the spatial heterogeneity in dune dynamics averages out to produce relatively smooth change. However, our results do show different paths of recovery and collapse of vegetation at system-wide scales, implying that hysteretic behavior occurs in spatially extended systems.

    Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age
    Merid, Simon Kebede ; Novoloaca, Alexei ; Sharp, Gemma C. ; Küpers, Leanne K. ; Kho, Alvin T. ; Roy, Ritu ; Gao, Lu ; Annesi-Maesano, Isabella ; Jain, Pooja ; Plusquin, Michelle ; Kogevinas, Manolis ; Allard, Catherine ; Vehmeijer, Florianne O. ; Kazmi, Nabila ; Salas, Lucas A. ; Rezwan, Faisal I. ; Zhang, Hongmei ; Sebert, Sylvain ; Czamara, Darina ; Rifas-Shiman, Sheryl L. ; Melton, Phillip E. ; Lawlor, Debbie A. ; Pershagen, Göran ; Breton, Carrie V. ; Huen, Karen ; Baiz, Nour ; Gagliardi, Luigi ; Nawrot, Tim S. ; Corpeleijn, Eva ; Perron, Patrice ; Duijts, Liesbeth ; Nohr, Ellen Aagaard ; Bustamante, Mariona ; Ewart, Susan L. ; Karmaus, Wilfried ; Zhao, Shanshan ; Page, Christian M. ; Herceg, Zdenko ; Jarvelin, Marjo Riitta ; Lahti, Jari ; Baccarelli, Andrea A. ; Anderson, Denise ; Kachroo, Priyadarshini ; Relton, Caroline L. ; Bergström, Anna ; Eskenazi, Brenda ; Soomro, Munawar Hussain ; Vineis, Paolo ; Snieder, Harold ; Bouchard, Luigi ; Jaddoe, Vincent W. ; Sørensen, Thorkild I.A. ; Vrijheid, Martine ; Arshad, S.H. ; Holloway, John W. ; Håberg, Siri E. ; Magnus, Per ; Dwyer, Terence ; Binder, Elisabeth B. ; Demeo, Dawn L. ; Vonk, Judith M. ; Newnham, John ; Tantisira, Kelan G. ; Kull, Inger ; Wiemels, Joseph L. ; Heude, Barbara ; Sunyer, Jordi ; Nystad, Wenche ; Munthe-Kaas, Monica C. ; Raïkkönen, Katri ; Oken, Emily ; Huang, Rae Chi ; Weiss, Scott T. ; Antó, Josep Maria ; Bousquet, Jean ; Kumar, Ashish ; Söderhäll, Cilla ; Almqvist, Catarina ; Cardenas, Andres ; Gruzieva, Olena ; Xu, Cheng Jian ; Reese, Sarah E. ; Kere, Juha ; Brodin, Petter ; Solomon, Olivia ; Wielscher, Matthias ; Holland, Nina ; Ghantous, Akram ; Hivert, Marie France ; Felix, Janine F. ; Koppelman, Gerard H. ; London, Stephanie J. ; Melén, Erik - \ 2020
    Genome Medicine 12 (2020)1. - ISSN 1756-994X
    Development - Epigenetics - Gestational age - Preterm birth - Transcriptomics

    Background: Preterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated associations between gestational age and blood DNA methylation in children. Methods: We performed meta-analysis of Illumina's HumanMethylation450-array associations between gestational age and cord blood DNA methylation in 3648 newborns from 17 cohorts without common pregnancy complications, induced delivery or caesarean section. We also explored associations of gestational age with DNA methylation measured at 4-18 years in additional pediatric cohorts. Follow-up analyses of DNA methylation and gene expression correlations were performed in cord blood. DNA methylation profiles were also explored in tissues relevant for gestational age health effects: Fetal brain and lung. Results: We identified 8899 CpGs in cord blood that were associated with gestational age (range 27-42 weeks), at Bonferroni significance, P < 1.06 × 10-7, of which 3343 were novel. These were annotated to 4966 genes. After restricting findings to at least three significant adjacent CpGs, we identified 1276 CpGs annotated to 325 genes. Results were generally consistent when analyses were restricted to term births. Cord blood findings tended not to persist into childhood and adolescence. Pathway analyses identified enrichment for biological processes critical to embryonic development. Follow-up of identified genes showed correlations between gestational age and DNA methylation levels in fetal brain and lung tissue, as well as correlation with expression levels. Conclusions: We identified numerous CpGs differentially methylated in relation to gestational age at birth that appear to reflect fetal developmental processes across tissues. These findings may contribute to understanding mechanisms linking gestational age to health effects.

    TRY plant trait database – enhanced coverage and open access
    Kattge, Jens ; Bönisch, Gerhard ; Díaz, Sandra ; Lavorel, Sandra ; Prentice, Iain Colin ; Leadley, Paul ; Tautenhahn, Susanne ; Werner, Gijsbert D.A. ; Aakala, Tuomas ; Abedi, Mehdi ; Acosta, Alicia T.R. ; Adamidis, George C. ; Adamson, Kairi ; Aiba, Masahiro ; Albert, Cécile H. ; Alcántara, Julio M. ; Alcázar C, Carolina ; Aleixo, Izabela ; Ali, Hamada ; Amiaud, Bernard ; Ammer, Christian ; Amoroso, Mariano M. ; Anand, Madhur ; Anderson, Carolyn ; Anten, Niels ; Antos, Joseph ; Apgaua, Deborah Mattos Guimarães ; Ashman, Tia Lynn ; Asmara, Degi Harja ; Asner, Gregory P. ; Aspinwall, Michael ; Atkin, Owen ; Aubin, Isabelle ; Baastrup-Spohr, Lars ; Bahalkeh, Khadijeh ; Bahn, Michael ; Bekker, Renee ; Cromsigt, Joris P.G.M. ; Finegan, Bryan ; Kramer, Koen ; Lohbeck, Madelon ; Onoda, Yusuke ; Ozinga, Wim A. ; Prinzing, Andreas ; Robroek, Bjorn ; Slot, Martijn ; Sterck, Frank ; Beest, Mariska te; Bodegom, Peter M. van; Sande, Masha T. van der - \ 2020
    Global Change Biology 26 (2020)1. - ISSN 1354-1013 - p. 119 - 188.
    data coverage - data integration - data representativeness - functional diversity - plant traits - TRY plant trait database

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

    CLASS4GL
    Wouters, Hendrik ; Petrova, Irina Y. ; Heerwaarden, Chiel C. Van; Vilà-Guerau de Arellano, Jordi ; Teuling, Adriaan J. ; Meulenberg, Vicky ; Santanello, Joseph A. ; Miralles, Diego G. - \ 2019
    The framework CLASS4GL is designed to facilitate the investigation of the atmospheric boundary layer evolution in response to different land and atmospheric conditions observed around the world. The core of the platform is the model CLASS that is used to simulate the evolution of the atmospheric boundary layer. Instruction video about the boundary layer processes and how they are considered in the CLASS model can be found as on the CLASS model website. Observational data from balloons, satellites and reanalysis, are used to constrain and initialize the model. CLASS4GL uses 2 million global balloon soundings from the integrated global radio sounding archive and satellite data from the last 40 years.
    ATLANTIC BIRD TRAITS: a data set of bird morphological traits from the Atlantic forests of South America
    Rodrigues, Rodolpho Credo ; Hasui, Érica ; Assis, Julia Camara ; Pena, João Carlos Castro ; Muylaert, Renata L. ; Tonetti, Vinicius Rodrigues ; Martello, Felipe ; Regolin, André Luis ; Vernaschi Vieira da Costa, Thiago ; Pichorim, Mauro ; Carrano, Eduardo ; Lopes, Leonardo Esteves ; Vasconcelos, Marcelo Ferreira de; Fontana, Carla Suertegaray ; Roos, Andrei Langeloh ; Gonçalves, Fernando ; Banks-Leite, Cristina ; Cavarzere, Vagner ; Efe, Marcio Amorim ; Alves, Maria Alice S. ; Uezu, Alexandre ; Metzger, Jean Paul ; Tarso Zuquim de Antas, Paulo de; Paschoaletto Micchi de Barros Ferraz, Katia Maria de; Calsavara, Larissa Corsini ; Bispo, Arthur Angelo ; Araujo, Helder F.P. ; Duca, Charles ; Piratelli, Augusto João ; Naka, Luciano N. ; Dias, Rafael Antunes ; Gatto, Cassiano A.F.R. ; Villegas Vallejos, Marcelo Alejandro ; Reis Menezes, Gregório dos; Bugoni, Leandro ; Rajão, Henrique ; Zocche, Jairo José ; Willrich, Guilherme ; Silva, Elsimar Silveira da; Manica, Lilian Tonelli ; Camargo Guaraldo, André de; Althmann, Giulyana ; Serafini, Patricia Pereira ; Francisco, Mercival Roberto ; Lugarini, Camile ; Machado, Caio Graco ; Marques-Santos, Fernando ; Bobato, Rafaela ; Souza, Elivan Arantes de; Donatelli, Reginaldo José ; Ferreira, Carolina Demetrio ; Morante-Filho, José Carlos ; Paes-Macarrão, Natalia Dantas ; Macarrão, Arthur ; Lima, Marcos Robalinho ; Jacoboski, Lucilene Inês ; Candia-Gallardo, Carlos ; Alegre, Vanesa Bejarano ; Jahn, Alex E. ; Camargo Barbosa, Karlla Vanessa de; Cestari, Cesar ; Silva, José Nilton da; Silveira, Natalia Stefanini da; Vara Crestani, Ana Cristina ; Petronetto, Adeliane Peterle ; Abreu Bovo, Alex Augusto ; Viana, Anderson Durão ; Araujo, Andrea Cardoso ; Santos, Andressa Hartuiq dos; Araújo do Amaral, Andreza Clarinda ; Ferreira, Ariane ; Vieira-Filho, Arnaldo Honorato ; Ribeiro, Bianca Costa ; Missagia, Caio C.C. ; Bosenbecker, Camila ; Bronzato Medolago, Cesar Augusto ; Rodriguez Espínola, Cid Rodrigo ; Faxina, Claudenice ; Campodonio Nunes, Cristiane Estrela ; Prates, Cristine ; Apolinario da Luz, Daniela Tomasio ; Moreno, Daniele Janina ; Mariz, Daniele ; Faria, Deborah ; Meyer, Douglas ; Doná, Eder Afonso ; Alexandrino, Eduardo Roberto ; Fischer, Erich ; Girardi, Fabiane ; Giese, Felipe Borba ; Santos Shibuya, Felipe Leonardo ; Faria, Fernando Azevedo ; Bittencourt de Farias, Fernando ; Lima Favaro, Fernando de; Ferneda Freitas, Fernando José ; Chaves, Flávia G. ; Guedes Las-Casas, Flor Maria ; Rosa, Gabriel L.M. ; Massaccesi de laTorre, Gabriel ; Bochio, Gabriela Menezes ; Bonetti, Giselle Evelise ; Kohler, Glauco ; Toledo-Lima, Guilherme Santos ; Plucenio, Gustavo Piletti ; Menezes, Ícaro ; Denóbile Torres, Ingrid Maria ; Carvalho Provinciato, Ivan Celso ; Viana, Ivan Réus ; Roper, James Joseph ; Persegona, Jaqueline Evelyn ; Barcik, Jean Júnior ; Martins-Silva, Jimi ; Gava Just, João Paulo ; Tavares-Damasceno, João Paulo ; Almeida Ferreira, João Ricardo de; Rodrigues Rosoni, Jonas Rafael ; Teixeira Falcon, José Eduardo ; Schaedler, Laura Maria ; Mathias, Leonardo Brioschi ; Deconto, Leonardo Rafael ; Cruz Rodrigues, Licléia da; Meyer, Marcela Afonso P. ; Repenning, Márcio ; Melo, Marcos Antônio ; Santos de Carvalho, Maria Amélia ; Rodrigues, Marcos ; Conti Nunes, Maria Flavia ; Ogrzewalska, Maria Halina ; Lopes Gonçalves, Mariana ; Vecchi, Maurício B. ; Bettio, Maurício ; Matta Baptista, Michelle Noronha da; Arantes, Murilo Sérgio ; Ruiz, Nicolás Luciano ; Bisetto de Andrade, Paulo Guilherme ; Lima Ribeiro, Pedro Henrique ; Galetti Junior, Pedro Manoel ; Macario, Phoeve ; Oliveira Fratoni, Rafael de; Meurer, Rafael ; Saint-Clair, Rafael S. ; Romagna, Rafael Spilere ; Alves Lacerda, Raquel Caroline ; Serpa Cerboncini, Ricardo Augusto ; Lyra, Ricardo Brioschi ; Lau, Ricardo ; Rodrigues, Roberta Costa ; Faria, Rogério Rodrigues ; Laps, Rudi Ricardo ; Althoff, Sérgio Luiz ; Jesus, Shayana de; Namba, Sumiko ; Braga, Talita Vieira ; Molin, Tamara ; França Câmara, Thanyria P. ; Enedino, Thayz Rodrigues ; Wischhoff, Uschi ; Oliveira, Vanessa Cristina de; Leandro-Silva, Victor ; Araújo-Lima, Vitor ; Oliveira Lunardi, Vitor de; Gusmão, Reginaldo Farias de; Souza Correia, Jozélia Maria de; Gaspar, Lucas P. ; Batista Fonseca, Renata Cristina ; Fonseca Pires Neto, Paulo Affonso ; Medeiros Morato de Aquino, Ana Carla ; Camargo, Bruna Betagni de; Cezila, Beatriz Azevedo ; Costa, Leonardo Marques ; Paolino, Roberta Montanheiro ; Kanda, Claudia Zukeran ; Monteiro, Erison C.S. ; Oshima, Júlia Emi F. ; Alves-Eigenheer, Milene ; Pizo, Marco Aurelio ; Silveira, Luís F. ; Galetti, Mauro ; Ribeiro, Milton Cezar - \ 2019
    Ecology 100 (2019)6. - ISSN 0012-9658
    body size - functional diversity - individual variation - interspecific variation - phenotypic plasticity - phylogenetic diversity - rapid evolution - tropical forest

    Scientists have long been trying to understand why the Neotropical region holds the highest diversity of birds on Earth. Recently, there has been increased interest in morphological variation between and within species, and in how climate, topography, and anthropogenic pressures may explain and affect phenotypic variation. Because morphological data are not always available for many species at the local or regional scale, we are limited in our understanding of intra- and interspecies spatial morphological variation. Here, we present the ATLANTIC BIRD TRAITS, a data set that includes measurements of up to 44 morphological traits in 67,197 bird records from 2,790 populations distributed throughout the Atlantic forests of South America. This data set comprises information, compiled over two centuries (1820–2018), for 711 bird species, which represent 80% of all known bird diversity in the Atlantic Forest. Among the most commonly reported traits are sex (n = 65,717), age (n = 63,852), body mass (n = 58,768), flight molt presence (n = 44,941), molt presence (n = 44,847), body molt presence (n = 44,606), tail length (n = 43,005), reproductive stage (n = 42,588), bill length (n = 37,409), body length (n = 28,394), right wing length (n = 21,950), tarsus length (n = 20,342), and wing length (n = 18,071). The most frequently recorded species are Chiroxiphia caudata (n = 1,837), Turdus albicollis (n = 1,658), Trichothraupis melanops (n = 1,468), Turdus leucomelas (n = 1,436), and Basileuterus culicivorus (n = 1,384). The species recorded in the greatest number of sampling localities are Basileuterus culicivorus (n = 243), Trichothraupis melanops (n = 242), Chiroxiphia caudata (n = 210), Platyrinchus mystaceus (n = 208), and Turdus rufiventris (n = 191). ATLANTIC BIRD TRAITS (ABT) is the most comprehensive data set on measurements of bird morphological traits found in a biodiversity hotspot; it provides data for basic and applied research at multiple scales, from individual to community, and from the local to the macroecological perspectives. No copyright or proprietary restrictions are associated with the use of this data set. Please cite this data paper when the data are used in publications or teaching and educational activities.

    Whole genome sequencing of Heterandria formosa reveals information about the evolution of the placenta in the livebearing fish family Poeciliidae
    Kruistum, Henri van; Heuvel, Joost van den; Travis, Joseph ; Kraaijeveld, Ken ; Zwaan, Bas ; Groenen, Martien ; Megens, Hendrik-Jan ; Pollux, Bart - \ 2019
    Wageningen University
    PRJEB28818 - ERP111075 - Heterandria formosa - Comparative genomics - Poeciliidae
    Background: The evolution of complex organs is thought to occur via a stepwise process, each subsequent step increasing the organ’s complexity by a tiny amount. Studying this process requires closely related species that vary in the complexity of their organs. This is the case for the placenta in the livebearing fish family Poeciliidae, as members of this family vary markedly in their placental complexity. Here, we look for the genomic basis underlying this phenotypic variation in the genome of Heterandria formosa, a poeciliid fish with a highly complex placenta. We compare this genome to three published reference genomes of non-placental poeciliid fish to gain insight in which genes play a role in the evolution of the placenta in the Poeciliidae. Results: We sequenced the genome of H. formosa, providing the first whole genome sequence information of a placental poeciliid. We looked for signatures of adaptive evolution by comparing its gene sequences to those of three non-placental live-bearing relatives. We found 18 positively selected genes exclusive to H. formosa, as well as 5 gene duplications. Eight of the genes evolving under positive selection in H. formosa have a placental function in mammals, most notably endometrial tissue remodelling or endometrial cell proliferation. Conclusions: Our results show that a substantial portion of positively selected genes have a function that correlates well with the morphological changes that form the placenta of H. formosa, compared to the corresponding tissue in non-placental poeciliids. These functions are mainly endometrial tissue remodelling and endometrial cell proliferation. Therefore, we hypothesize that natural selection acting on genes involved in these functions plays a key role in the evolution of the placenta in H. formosa.
    Health effects of dietary risks in 195 countries, 1990–2017: a systematic analysis for the Global Burden of Disease Study 2017
    Afshin, Ashkan ; Sur, Patrick John ; Fay, Kairsten A. ; Cornaby, Leslie ; Ferrara, Giannina ; Salama, Joseph S. ; Mullany, Erin C. ; Abate, Kalkidan Hassen ; Abbafati, Cristiana ; Abebe, Zegeye ; Afarideh, Mohsen ; Aggarwal, Anju ; Agrawal, Sutapa ; Akinyemiju, Tomi ; Alahdab, Fares ; Bacha, Umar ; Bachman, Victoria F. ; Badali, Hamid ; Badawi, Alaa ; Bensenor, Isabela M. ; Bernabe, Eduardo ; Biadgilign, Sibhatu Kassa K. ; Biryukov, Stan H. ; Cahill, Leah E. ; Carrero, Juan J. ; Cercy, Kelly M. ; Dandona, Lalit ; Dandona, Rakhi ; Dang, Anh Kim ; Degefa, Meaza Girma ; Sayed Zaki, Maysaa El; Esteghamati, Alireza ; Esteghamati, Sadaf ; Fanzo, Jessica ; Sá Farinha, Carla Sofia e; Farvid, Maryam S. ; Farzadfar, Farshad ; Feigin, Valery L. ; Fernandes, Joao C. ; Flor, Luisa Sorio ; Foigt, Nataliya A. ; Forouzanfar, Mohammad H. ; Ganji, Morsaleh ; Geleijnse, Johanna M. ; Gillum, Richard F. ; Goulart, Alessandra C. ; Grosso, Giuseppe ; Guessous, Idris ; Hamidi, Samer ; Nguyen, Cuong Tat - \ 2019
    The Lancet 393 (2019)10184. - ISSN 0140-6736 - p. 1958 - 1972.

    Background: Suboptimal diet is an important preventable risk factor for non-communicable diseases (NCDs); however, its impact on the burden of NCDs has not been systematically evaluated. This study aimed to evaluate the consumption of major foods and nutrients across 195 countries and to quantify the impact of their suboptimal intake on NCD mortality and morbidity. Methods: By use of a comparative risk assessment approach, we estimated the proportion of disease-specific burden attributable to each dietary risk factor (also referred to as population attributable fraction)among adults aged 25 years or older. The main inputs to this analysis included the intake of each dietary factor, the effect size of the dietary factor on disease endpoint, and the level of intake associated with the lowest risk of mortality. Then, by use of disease-specific population attributable fractions, mortality, and disability-adjusted life-years (DALYs), we calculated the number of deaths and DALYs attributable to diet for each disease outcome. Findings: In 2017, 11 million (95% uncertainty interval [UI]10–12)deaths and 255 million (234–274)DALYs were attributable to dietary risk factors. High intake of sodium (3 million [1–5]deaths and 70 million [34–118]DALYs), low intake of whole grains (3 million [2–4]deaths and 82 million [59–109]DALYs), and low intake of fruits (2 million [1–4]deaths and 65 million [41–92]DALYs)were the leading dietary risk factors for deaths and DALYs globally and in many countries. Dietary data were from mixed sources and were not available for all countries, increasing the statistical uncertainty of our estimates. Interpretation: This study provides a comprehensive picture of the potential impact of suboptimal diet on NCD mortality and morbidity, highlighting the need for improving diet across nations. Our findings will inform implementation of evidence-based dietary interventions and provide a platform for evaluation of their impact on human health annually. Funding: Bill & Melinda Gates Foundation.

    Global patterns and drivers of ecosystem functioning in rivers and riparian zones
    Tiegs, Scott D. ; Costello, David M. ; Isken, Mark W. ; Woodward, Guy ; McIntyre, Peter B. ; Gessner, Mark O. ; Chauvet, Eric ; Griffiths, Natalie A. ; Flecker, Alex S. ; Acuña, Vicenç ; Albariño, Ricardo ; Allen, Daniel C. ; Alonso, Cecilia ; Andino, Patricio ; Arango, Clay ; Aroviita, Jukka ; Barbosa, Marcus V.M. ; Barmuta, Leon A. ; Baxter, Colden V. ; Bell, Thomas D.C. ; Bellinger, Brent ; Boyero, Luz ; Brown, Lee E. ; Bruder, Andreas ; Bruesewitz, Denise A. ; Burdon, Francis J. ; Callisto, Marcos ; Canhoto, Cristina ; Capps, Krista A. ; Castillo, María M. ; Clapcott, Joanne ; Colas, Fanny ; Colón-Gaud, Checo ; Cornut, Julien ; Crespo-Pérez, Verónica ; Cross, Wyatt F. ; Culp, Joseph M. ; Danger, Michael ; Dangles, Olivier ; Eyto, Elvira De; Derry, Alison M. ; Villanueva, Veronica Díaz ; Douglas, Michael M. ; Elosegi, Arturo ; Encalada, Andrea C. ; Entrekin, Sally ; Espinosa, Rodrigo ; Ethaiya, Diana ; Ferreira, Verónica ; Ferriol, Carmen ; Flanagan, Kyla M. ; Fleituch, Tadeusz ; Follstad Shah, Jennifer J. ; Barbosa, André Frainer ; Friberg, Nikolai ; Frost, Paul C. ; Garcia, Erica A. ; Lago, Liliana García ; Soto, Pavel Ernesto García ; Ghate, Sudeep ; Giling, Darren P. ; Gilmer, Alan ; Gonçalves, José Francisco ; Gonzales, Rosario Karina ; Graça, Manuel A.S. ; Grace, Mike ; Grossart, Hans Peter ; Guérold, François ; Gulis, Vlad ; Hepp, Luiz U. ; Higgins, Scott ; Hishi, Takuo ; Huddart, Joseph ; Hudson, John ; Imberger, Samantha ; Iñiguez-Armijos, Carlos ; Iwata, Tomoya ; Janetski, David J. ; Jennings, Eleanor ; Kirkwood, Andrea E. ; Koning, Aaron A. ; Kosten, Sarian ; Kuehn, Kevin A. ; Laudon, Hjalmar ; Leavitt, Peter R. ; Lemes Da Silva, Aurea L. ; Leroux, Shawn J. ; LeRoy, Carri J. ; Lisi, Peter J. ; MacKenzie, Richard ; Marcarelli, Amy M. ; Masese, Frank O. ; McKie, Brendan G. ; Medeiros, Adriana Oliveira ; Meissner, Kristian ; Miliša, Marko ; Mishra, Shailendra ; Miyake, Yo ; Moerke, Ashley ; Mombrikotb, Shorok ; Mooney, Rob ; Moulton, Tim ; Muotka, Timo ; Negishi, Junjiro N. ; Neres-Lima, Vinicius ; Nieminen, Mika L. ; Nimptsch, Jorge ; Ondruch, Jakub ; Paavola, Riku ; Pardo, Isabel ; Patrick, Christopher J. ; Peeters, Edwin T.H.M. ; Pozo, Jesus ; Pringle, Catherine ; Prussian, Aaron ; Quenta, Estefania ; Quesada, Antonio ; Reid, Brian ; Richardson, John S. ; Rigosi, Anna ; Rincón, José ; Rîşnoveanu, Geta ; Robinson, Christopher T. ; Rodríguez-Gallego, Lorena ; Royer, Todd V. ; Rusak, James A. ; Santamans, Anna C. ; Selmeczy, Géza B. ; Simiyu, Gelas ; Skuja, Agnija ; Smykla, Jerzy ; Sridhar, Kandikere R. ; Sponseller, Ryan ; Stoler, Aaron ; Swan, Christopher M. ; Szlag, David ; Teixeira-De Mello, Franco ; Tonkin, Jonathan D. ; Uusheimo, Sari ; Veach, Allison M. ; Vilbaste, Sirje ; Vought, Lena B.M. ; Wang, Chiao Ping ; Webster, Jackson R. ; Wilson, Paul B. ; Woelfl, Stefan ; Xenopoulos, Marguerite A. ; Yates, Adam G. ; Yoshimura, Chihiro ; Yule, Catherine M. ; Zhang, Yixin X. ; Zwart, Jacob A. - \ 2019
    Science Advances 5 (2019)1. - ISSN 2375-2548 - p. 14966 - 14973.

    River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth's biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints toward the poles and greater roles for other environmental drivers (e.g., nutrient loading) toward the equator. These results and data set the stage for unprecedented "next-generation biomonitoring" by establishing baselines to help quantify environmental impacts to the functioning of ecosystems at a global scale.

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