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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Model inter-comparison design for large-scale water quality models
Vliet, Michelle T.H. van; Flörke, Martina ; Harrison, John A. ; Hofstra, Nynke ; Keller, Virginie ; Ludwig, Fulco ; Spanier, J.E. ; Strokal, Maryna ; Wada, Yoshihide ; Wen, Yingrong ; Williams, Richard J. - \ 2019
Current Opinion in Environmental Sustainability 36 (2019). - ISSN 1877-3435 - p. 59 - 67.

Several model inter-comparison projects (MIPs) have been carried out recently by the climate, hydrological, agricultural and other modelling communities to quantify modelling uncertainties and improve modelling systems. Here we focus on MIP design for large-scale water quality models. Water quality MIPs can be useful to improve our understanding of pollution problems and facilitate the development of harmonized estimates of current and future water quality. This can provide new opportunities for assessing robustness in estimates of water quality hotspots and trends, improve understanding of processes, pollution sources, water quality model uncertainties, and to identify priorities for water quality data collection and monitoring. Water quality MIP design should harmonize relevant model input datasets, use consistent spatial/temporal domains and resolutions, and similar output variables to improve understanding of water quality modelling uncertainties and provide harmonized water quality data that suit the needs of decision makers and other users.

Models for assessing engineered nanomaterial fate and behaviour in the aquatic environment
Williams, Richard J. ; Harrison, Samuel ; Keller, Virginie ; Kuenen, Jeroen ; Lofts, Stephen ; Praetorius, Antonia ; Svendsen, Claus ; Vermeulen, Lucie C. ; Wijnen, Jikke van - \ 2019
Current Opinion in Environmental Sustainability 36 (2019). - ISSN 1877-3435 - p. 105 - 115.

Engineered nanomaterials (ENMs, material containing particles with at least one dimension less than 100 nm) are present in a range of consumer products and could be released into the environment from these products during their production, use or end-of-life. The high surface to volume ratio of nanomaterials imparts a high reactivity, which is of interest for novel applications but may raise concern for the environment. In the absence of measurement methods, there is a need for modelling to assess likely concentrations and fate arising from current and future releases. To assess the capability that exists to do such modelling, progress in modelling ENM fate since 2011 is reviewed. ENM-specific processes represented in models are mainly limited to aggregation and, in some instances, dissolution. Transformation processes (e.g. sulphidation), the role of the manufactured coatings, particle size distribution and particle form and state are still usually excluded. Progress is also being made in modelling ENMs at larger scales. Currently, models can give a reasonable assessment of the fate of ENMs in the environment, but a full understanding will likely require fuller inclusion of these ENM-specific processes.

Global multi-pollutant modelling of water quality: scientific challenges and future directions
Strokal, M. ; Spanier, Emiel ; Kroeze, C. ; Koelmans, A.A. ; Florke, Martina ; Franssen, W.H.P. ; Hofstra, N. ; Langan, Simon ; Ting, Tang ; Vliet, M.T.H. van; Wada, Yoshihide ; Wang, M. ; Wijnen, Jikke van; Williams, R. - \ 2019
Current Opinion in Environmental Sustainability 36 (2019). - ISSN 1877-3435 - p. 116 - 125.
Assessing global water quality issues requires a multi-pollutant modelling approach. We discuss scientific challenges and future directions for such modeling. Multi-pollutant river models need to integrate information on sources of pollutants such as plastic debris, nutrients, chemicals, pathogens, their effects and possible solutions. In this paper, we first explain what we consider multi-pollutant modelling. Second, we discuss scientific challenges in multi-pollutant modelling relating to consistent model inputs, modelling approaches and model evaluation. Next, we illustrate the potential of global multi-pollutant modelling for hotspot analyses. We show hotspots of river pollution with microplastics, nutrients, triclosan and Cryptosporidium in many sub-basins of Europe, North America and South Asia. Finally, we reflect on future directions for multi-pollutant modelling, and for linking model results to policy-making.
The pastoral farming system: Balancing between tradition and transition
Leeuw, J. de; Osano, P. ; Said, M. ; Ayantunde, A.A. ; Dube, S. ; Neely, C. ; Vrieling, A. ; Thornton, P. ; Ericksen, P. - \ 2019
In: Farming Systems and Food Security in Africa / Dixon, J., Garrity, D.P., Boffa, J.M., Williams, T.O., Amede, T., Auricht, C., Lott, R., Mburathi, G., Routledge, Taylor & Francis Group (Earthsan food and agriculture ) - ISBN 9781138963351
Farming and food systems potentials
Dixon, J. ; Boffa, J.M. ; Williams, T.O. ; Leeuw, J. de; Fischer, G. ; Velthuizen, H. van - \ 2019
In: Farming Systems and Food Security in Africa / Dixon, J., Garrity, D., Boffa, J.M., Williams, T.O., Amede, T., Auricht, C., Lott, R., Mburathi, G., Routledge, Taylor & Francis Group (Earthscan food and agriculture ) - ISBN 9781138963351
First records of Hyalomma rufipes and Ixodes neitzi (Acari : Ixodidae) found on large carnivores in South Africa
Baauw, Anna H. ; Heyne, Heloise ; Williams, Kathryn S. ; Hill, Russell A. ; Heitkönig, Ignas M.A. ; Williams, Samual T. - \ 2019
Ticks and Tick-borne Diseases 10 (2019)1. - ISSN 1877-959X - p. 128 - 131.
Brown hyena - Hyalomma rufipes - Ixodes neitzi - Leopard

Ixodid ticks (Acari: Ixodidae) are important disease vectors for large carnivores, but the composition of the tick communities that parasitize carnivores is poorly understood. We collected ticks from leopards (Panthera pardus) and brown hyenas (Hyaena brunnea) in the Soutpansberg Mountains, South Africa, to determine which species feed on these carnivores. We identified a total of eight tick species belonging to six genera, and recorded Ixodes neitzi and Hyalomma rufipes on P. pardus for the first time.

SerpinA3N is a novel hypothalamic gene upregulated by a high-fat diet and leptin in mice
Sergi, Domenico ; Campbell, Fiona M. ; Grant, Christine ; Morris, Amanda C. ; Bachmair, Eva Maria ; Koch, Christiane ; McLean, Fiona H. ; Muller, Aifric ; Hoggard, Nigel ; Roos, Baukje de; Porteiro, Begona ; Boekschoten, Mark V. ; McGillicuddy, Fiona C. ; Kahn, Darcy ; Nicol, Phyllis ; Benzler, Jonas ; Mayer, Claus Dieter ; Drew, Janice E. ; Roche, Helen M. ; Muller, Michael ; Nogueiras, Ruben ; Dieguez, Carlos ; Tups, Alexander ; Williams, Lynda M. - \ 2018
Genes & Nutrition 13 (2018). - ISSN 1555-8932
High-fat diet - Hypothalamus - Leptin - SerpinA3N

Background: Energy homeostasis is regulated by the hypothalamus but fails when animals are fed a high-fat diet (HFD), and leptin insensitivity and obesity develops. To elucidate the possible mechanisms underlying these effects, a microarray-based transcriptomics approach was used to identify novel genes regulated by HFD and leptin in the mouse hypothalamus. Results: Mouse global array data identified serpinA3N as a novel gene highly upregulated by both a HFD and leptin challenge. In situ hybridisation showed serpinA3N expression upregulation by HFD and leptin in all major hypothalamic nuclei in agreement with transcriptomic gene expression data. Immunohistochemistry and studies in the hypothalamic clonal neuronal cell line, mHypoE-N42 (N42), confirmed that alpha 1-antichymotrypsin (α1AC), the protein encoded by serpinA3, is localised to neurons and revealed that it is secreted into the media. SerpinA3N expression in N42 neurons is upregulated by palmitic acid and by leptin, together with IL-6 and TNFα, and all three genes are downregulated by the anti-inflammatory monounsaturated fat, oleic acid. Additionally, palmitate upregulation of serpinA3 in N42 neurons is blocked by the NFκB inhibitor, BAY11, and the upregulation of serpinA3N expression in the hypothalamus by HFD is blunted in IL-1 receptor 1 knockout (IL-1R1 -/- ) mice. Conclusions: These data demonstrate that serpinA3 expression is implicated in nutritionally mediated hypothalamic inflammation.

State of the world's raptors : Distributions, threats, and conservation recommendations
McClure, Christopher J.W. ; Westrip, James R.S. ; Johnson, Jeff A. ; Schulwitz, Sarah E. ; Virani, Munir Z. ; Davies, Robert ; Symes, Andrew ; Wheatley, Hannah ; Thorstrom, Russell ; Amar, Arjun ; Buij, Ralph ; Jones, Victoria R. ; Williams, Nick P. ; Buechley, Evan R. ; Butchart, Stuart H.M. - \ 2018
Biological Conservation 227 (2018). - ISSN 0006-3207 - p. 390 - 402.
Bird of prey - Important Bird and Biodiversity Areas - IUCN Red List - Ornithology - Raptors MoU - United Nations Convention on the Conservation of Migratory Species of Wild Animals

Raptors provide critical ecosystem services, yet there is currently no systematic, global synthesis of their conservation status or threats. We review the International Union for the Conservation of Nature's Red List to examine the conservation status, distributions, threats, and conservation recommendations for all 557 raptor species. We further assess the significance of Important Bird and Biodiversity Areas (IBAs) for raptor conservation. We also determine which countries contain the most species listed under the Memorandum of Understanding on the Conservation of Migratory Birds of Prey in Africa and Eurasia (Raptors MoU). Raptors, especially Old World vultures, are more threatened than birds in general. Eighteen percent of raptors are threatened with extinction and 52% of raptors have declining global populations. South and Southeast Asia have the highest richness and the largest number of threatened raptor species. By country, Indonesia has the highest richness of raptor species (119) and most declining species (63). China and Russia contain the most Raptors MoU species, although they are not yet signatories to the agreement. Raptor species that require forest are more likely to be threatened and declining than those that do not. Agriculture and logging are the most frequently identified threats, although poisoning is especially detrimental to Old World vultures. Of the 10 most important IBAs for raptors, six are in Nepal. Highest priority conservation actions to protect raptors include preventing mortality and conserving key sites and priority habitats. Improved long-term monitoring would allow for conservation to be appropriately targeted and effectiveness of interventions to be assessed.

Top-down NOx emissions of european cities based on the downwind plume of modelled and space-borne tropospheric NO2 columns
Verstraeten, Willem W. ; Boersma, Klaas Folkert ; Douros, John ; Williams, Jason E. ; Eskes, Henk ; Liu, Fei ; Beirle, Steffen ; Delcloo, Andy - \ 2018
Sensors 18 (2018)9. - ISSN 1424-8220
LOTOS-EUROS CTM - OMI data - Surface NO emissions - Tropospheric NO column

Top-down estimates of surface NOX emissions were derived for 23 European cities based on the downwind plume decay of tropospheric nitrogen dioxide (NO2) columns from the LOTOS-EUROS (Long Term Ozone Simulation-European Ozone Simulation) chemistry transport model (CTM) and from Ozone Monitoring Instrument (OMI) satellite retrievals, averaged for the summertime period (April–September) during 2013. Here we show that the top-down NOX emissions derived from LOTOS-EUROS for European urban areas agree well with the bottom-up NOX emissions from the MACC-III inventory data (R2 = 0.88) driving the CTM demonstrating the potential of this method. OMI top-down NOX emissions over the 23 European cities are generally lower compared with the MACC-III emissions and their correlation is slightly lower (R2 = 0.79). The uncertainty on the derived NO2 lifetimes and NOX emissions are on average ~55% for OMI and ~63% for LOTOS-EUROS data. The downwind NO2 plume method applied on both LOTOS-EUROS and OMI tropospheric NO2 columns allows to estimate NOX emissions from urban areas, demonstrating that this is a useful method for real-time updates of urban NOX emissions with reasonable accuracy.

Designing Vulnerable Zones of Nitrogen and Phosphorus Transfers to Control Water Pollution in China
Bai, Zhaohai ; Lu, Jie ; Zhao, Hao ; Velthof, Gerard L. ; Oenema, Oene ; Chadwick, Dave ; Williams, John R. ; Jin, Shuqin ; Liu, Hongbin ; Wang, Mengru ; Strokal, Maryna ; Kroeze, Carolien ; Hu, Chunsheng ; Ma, Lin - \ 2018
Environmental Science and Technology 52 (2018)16. - ISSN 0013-936X - p. 8987 - 8988.
Arabidopsis phospholipase C3 is involved in lateral root initiation and ABA responses in seed germination and stomatal closure
Zhang, Qianqian ; Wijk, Ringo van; Shahbaz, Muhammad ; Roels, Wendy ; Schooten, Bas Van; Vermeer, Joop E.M. ; Zarza, Xavier ; Guardia, Aisha ; Scuffi, Denise ; García-Mata, Carlos ; Laha, Debabrata ; Williams, Phoebe ; Willems, Leo A.J. ; Ligterink, Wilco ; Hoffmann-Benning, Susanne ; Gillaspy, Glenda ; Schaaf, Gabriel ; Haring, Michel A. ; Laxalt, Ana M. ; Munnik, Teun - \ 2018
Plant and Cell Physiology 59 (2018)3. - ISSN 0032-0781 - p. 469 - 486.
ABA - Arabidopsis - Drought tolerance - Lateral root formation - Seed germination - Stomatal closure

Phospholipase C (PLC) is well known for its role in animal signaling, where it generates the second messengers, inositol 1,4,5-trisphosphate (IP3) and diacylglycerol (DAG), by hydrolyzing the minor phospholipid, phosphatidylinositol 4,5-bisphosphate (PIP2), upon receptor stimulation. In plants, PLC's role is still unclear, especially because the primary targets of both second messengers are lacking, i.e. the ligand-gated Ca2+ channel and protein kinase C, and because PIP2 levels are extremely low. Nonetheless, the Arabidopsis genome encodes nine PLCs. We used a reversed-genetic approach to explore PLC's function in Arabidopsis, and report here that PLC3 is required for proper root development, seed germination and stomatal opening. Two independent knock-down mutants, plc3-2 and plc3-3, were found to exhibit reduced lateral root densities by 10-20%. Mutant seeds germinated more slowly but were less sensitive to ABA to prevent germination. Guard cells of plc3 were also compromised in ABA-dependent stomatal closure. Promoter-b-glucuronidase (GUS) analyses confirmed PLC3 expression in guard cells and germinating seeds, and revealed that the majority is expressed in vascular tissue, most probably phloem companion cells, in roots, leaves and flowers. In vivo 32Pi labeling revealed that ABA stimulated the formation of PIP2 in germinating seeds and guard cell-enriched leaf peels, which was significantly reduced in plc3 mutants. Overexpression of PLC3 had no effect on root system architecture or seed germination, but increased the plant's tolerance to drought. Our results provide genetic evidence for PLC's involvement in plant development and ABA signaling, and confirm earlier observations that overexpression increases drought tolerance. Potential molecular mechanisms for the above observations are discussed.

Problemshed or watershed? Participatory modeling towards IWRM in North Ghana
Daré, Williams ; Venot, Jean Philippe ; Page, Christophe Le ; Aduna, Aaron - \ 2018
Water 10 (2018)6. - ISSN 2073-4441
Agent-based model - Companion modeling - Role-playing game - Sub-Saharan Africa - Water resources

This paper is a reflexive analysis of a three-year participatory water research project conducted in the Upper East Region (UER) of Ghana, whose explicit objective was to initiate a multi-level dialogue to support the national Integrated Water Resources Management (IWRM) policy framework. The transdisciplinary team adopted the Companion Modeling approach (ComMod), using role-playing games and a computerized agent-based model to support the identification of a problemshed centered on issues of river bank cultivation, erosion, and flooding, and initiate a multi-level dialogue on ways that this problemshed could be tackled. On the basis of this experience, we identify three key criteria for transdisciplinary research to support innovative water governance: (1) the iterative adaptation of tools and facilitation techniques based on feedback from participants; (2) a common understanding of the objectives pursued and the approach used among researchers, who need to explicit their posture, and crucially; (3) the co-identification of a problemshed that diverse stakeholders are interested in tackling. Finally, we argue that the context in which research is funded and conducted in the development sector constitutes a challenge for researchers to be "participants like any other" in the projects they coordinate, which constitutes a barrier to true transdisciplinarity.

Ten essentials for action-oriented and second order energy transitions, transformations and climate change research
Fazey, Ioan ; Schäpke, Niko ; Caniglia, Guido ; Patterson, James ; Hultman, Johan ; Mierlo, Barbara Van; Säwe, Filippa ; Wiek, Arnim ; Wittmayer, Julia ; Aldunce, Paulina ; Waer, Husam Al; Battacharya, Nandini ; Bradbury, Hilary ; Carmen, Esther ; Colvin, John ; Cvitanovic, Christopher ; D’Souza, Marcella ; Gopel, Maja ; Goldstein, Bruce ; Hämäläinen, Timo ; Harper, Gavin ; Henfry, Tom ; Hodgson, Anthony ; Howden, Mark S. ; Kerr, Andy ; Klaes, Matthias ; Lyon, Christopher ; Midgley, Gerald ; Moser, Susanne ; Mukherjee, Nandan ; Müller, Karl ; O’brien, Karen ; O’Connell, Deborah A. ; Olsson, Per ; Page, Glenn ; Reed, Mark S. ; Searle, Beverley ; Silvestri, Giorgia ; Spaiser, Viktoria ; Strasser, Tim ; Tschakert, Petra ; Uribe-Calvo, Natalia ; Waddell, Steve ; Rao-Williams, Jennifer ; Wise, Russel ; Wolstenholme, Ruth ; Woods, Mel ; Wyborn, Carina - \ 2018
Energy Research & Social Science 40 (2018). - ISSN 2214-6296 - p. 54 - 70.
The most critical question for climate research is no longer about the problem, but about how to facilitate the transformative changes necessary to avoid catastrophic climate-induced change. Addressing this question, however, will require massive upscaling of research that can rapidly enhance learning about transformations. Ten essentials for guiding action-oriented transformation and energy research are therefore presented, framed in relation to second-order science. They include: (1) Focus on transformations to low-carbon, resilient living; (2) Focus on solution processes; (3) Focus on ‘how to’ practical knowledge; (4) Approach research as occurring from within the system being intervened; (5) Work with normative aspects; (6) Seek to transcend current thinking; (7) Take a multi-faceted approach to understand and shape change; (8) Acknowledge the value of alternative roles of researchers; (9) Encourage second-order experimentation; and (10) Be reflexive. Joint application of the essentials would create highly adaptive, reflexive, collaborative and impact-oriented research able to enhance capacity to respond to the climate challenge. At present, however, the practice of such approaches is limited and constrained by dominance of other approaches. For wider transformations to low carbon living and energy systems to occur, transformations will therefore also be needed in the way in which knowledge is produced and used.
Reviewing research priorities in weed ecology, evolution and management: a horizon scan
Neve, P. ; Barney, J.N. ; Buckley, Y. ; Cousens, R.D. ; Graham, S. ; Jordan, N.R. ; Lawton-Rauh, A. ; Liebman, M. ; Mesgaran, M.B. ; Shaw, J. ; Storkey, J. ; Baraibar, B. ; Baucom, R.S. ; Chalak, M. ; Childs, D.Z. ; Christensen, S. ; Eizenberg, H. ; Fernández-Quintanilla, C. ; French, K. ; Harsch, M. ; Heijting, S. ; Harrison, L. ; Loddo, D. ; Macel, M. ; Maczey, N. ; Merotto, A. ; Mortensen, D. ; Necajeva, J. ; Peltzer, D.A. ; Recasens, J. ; Renton, M. ; Riemens, M. ; Sønderskov, M. ; Williams, M. ; Rew, Lisa - \ 2018
Weed Research 58 (2018)4. - ISSN 0043-1737 - p. 250 - 258.
Weedy plants pose a major threat to food security, biodiversity, ecosystem services and consequently to human health and wellbeing. However, many currently used weed management approaches are increasingly unsustainable. To address this knowledge and practice gap, in June 2014, 35 weed and invasion ecologists, weed scientists, evolutionary biologists and social scientists convened a workshop to explore current and future perspectives and approaches in weed ecology and management. A horizon scanning exercise ranked a list of 124 pre‐submitted questions to identify a priority list of 30 questions. These questions are discussed under seven themed headings that represent areas for renewed and emerging focus for the disciplines of weed research and practice. The themed areas considered the need for transdisciplinarity, increased adoption of integrated weed management and agroecological approaches, better understanding of weed evolution, climate change, weed invasiveness and finally, disciplinary challenges for weed science. Almost all the challenges identified rested on the need for continued efforts to diversify and integrate agroecological, socio‐economic and technological approaches in weed management. These challenges are not newly conceived, though their continued prominence as research priorities highlights an ongoing intransigence that must be addressed through a more system‐oriented and transdisciplinary research agenda that seeks an embedded integration of public and private research approaches. This horizon scanning exercise thus set out the building blocks needed for future weed management research and practice; however, the challenge ahead is to identify effective ways in which sufficient research and implementation efforts can be directed towards these needs.
Monoterpene chemical speciation in a tropical rainforest : variation with season, height, and time of dayat the Amazon Tall Tower Observatory (ATTO)
Maria Yanez-Serrano, Ana ; Christine Nölscher, Anke ; Bourtsoukidis, Efstratios ; Gomes Alves, Eliane ; Ganzeveld, Laurens ; Bonn, Boris ; Wolff, Stefan ; Sa, Marta ; Yamasoe, Marcia ; Williams, Jonathan ; Andreae, Meinrat O. - \ 2018
Atmospheric Chemistry and Physics 18 (2018)5. - ISSN 1680-7316 - p. 3403 - 3418.
Speciated monoterpene measurements in rainforest air are scarce, but they are essential for understanding the contribution of these compounds to the overall reactivity of volatile organic compound (VOC) emissions towards the main atmospheric oxidants, such as hydroxyl radicals (OH), ozone (O3) and nitrate radicals (NO3). In this study, we present the chemical speciation of gas-phase monoterpenes measured in the tropical rainforest at the Amazon Tall Tower Observatory (ATTO, Amazonas, Brazil). Samples of VOCs were collected by two automated sampling systems positioned on a tower at 12 and 24ĝ€-m height and analysed using gas chromatography-flame ionization detection. The samples were collected in October 2015, representing the dry season, and compared with previous wet and dry season studies at the site. In addition, vertical profile measurements (at 12 and 24ĝ€-m) of total monoterpene mixing ratios were made using proton-transfer-reaction mass spectrometry. The results showed a distinctly different chemical speciation between day and night. For instance, α-pinene was more abundant during the day, whereas limonene was more abundant at night. Reactivity calculations showed that higher abundance does not generally imply higher reactivity. Furthermore, inter- and intra-annual results demonstrate similar chemodiversity during the dry seasons analysed. Simulations with a canopy exchange modelling system show simulated monoterpene mixing ratios that compare relatively well with the observed mixing ratios but also indicate the necessity of more experiments to enhance our understanding of in-canopy sinks of these compounds.
Phylogenetic classification of the world's tropical forests
Slik, J.W.F. ; Franklin, Janet ; Arroyo-Rodríguez, Víctor ; Field, Richard ; Aguilar, Salomon ; Aguirre, Nikolay ; Ahumada, Jorge ; Aiba, Shin Ichiro ; Alves, Luciana F. ; Anitha, K. ; Avella, Andres ; Mora, Francisco ; Aymard, Gerardo A.C. ; Báez, Selene ; Balvanera, Patricia ; Bastian, Meredith L. ; Bastin, Jean François ; Bellingham, Peter J. ; Berg, Eduardo Van Den; Conceição Bispo, Polyanna Da; Boeckx, Pascal ; Boehning-Gaese, Katrin ; Bongers, Frans ; Boyle, Brad ; Brambach, Fabian ; Brearley, Francis Q. ; Brown, Sandra ; Chai, Shauna Lee ; Chazdon, Robin L. ; Chen, Shengbin ; Chhang, Phourin ; Chuyong, George ; Ewango, Corneille ; Coronado, Indiana M. ; Cristóbal-Azkarate, Jurgi ; Culmsee, Heike ; Damas, Kipiro ; Dattaraja, H.S. ; Davidar, Priya ; DeWalt, Saara J. ; Din, Hazimah ; Drake, Donald R. ; Duque, Alvaro ; Durigan, Giselda ; Eichhorn, Karl ; Eler, Eduardo Schmidt ; Enoki, Tsutomu ; Ensslin, Andreas ; Fandohan, Adandé Belarmain ; Farwig, Nina ; Feeley, Kenneth J. ; Fischer, Markus ; Forshed, Olle ; Garcia, Queila Souza ; Garkoti, Satish Chandra ; Gillespie, Thomas W. ; Gillet, Jean Francois ; Gonmadje, Christelle ; Granzow-De La Cerda, Iñigo ; Griffith, Daniel M. ; Grogan, James ; Hakeem, Khalid Rehman ; Harris, David J. ; Harrison, Rhett D. ; Hector, Andy ; Hemp, Andreas ; Homeier, Jürgen ; Hussain, M.S. ; Ibarra-Manríquez, Guillermo ; Hanum, I.F. ; Imai, Nobuo ; Jansen, Patrick A. ; Joly, Carlos Alfredo ; Joseph, Shijo ; Kartawinata, Kuswata ; Kearsley, Elizabeth ; Kelly, Daniel L. ; Kessler, Michael ; Killeen, Timothy J. ; Kooyman, Robert M. ; Laumonier, Yves ; Laurance, Susan G. ; Laurance, William F. ; Lawes, Michael J. ; Letcher, Susan G. ; Lindsell, Jeremy ; Lovett, Jon ; Lozada, Jose ; Lu, Xinghui ; Lykke, Anne Mette ; Mahmud, Khairil Bin; Mahayani, Ni Putu Diana ; Mansor, Asyraf ; Marshall, Andrew R. ; Martin, Emanuel H. ; Matos, Darley Calderado Leal ; Meave, Jorge A. ; Melo, Felipe P.L. ; Mendoza, Zhofre Huberto Aguirre ; Metali, Faizah ; Medjibe, Vincent P. ; Metzger, Jean Paul ; Metzker, Thiago ; Mohandass, D. ; Munguía-Rosas, Miguel A. ; Muñoz, Rodrigo ; Nurtjahy, Eddy ; Oliveira, Eddie Lenza De; Onrizal, ; Parolin, Pia ; Parren, Marc ; Parthasarathy, N. ; Paudel, Ekananda ; Perez, Rolando ; Pérez-García, Eduardo A. ; Pommer, Ulf ; Poorter, Lourens ; Qi, Lan ; Piedade, Maria Teresa F. ; Pinto, José Roberto Rodrigues ; Poulsen, Axel Dalberg ; Poulsen, John R. ; Powers, Jennifer S. ; Prasad, Rama Chandra ; Puyravaud, Jean Philippe ; Rangel, Orlando ; Reitsma, Jan ; Rocha, Diogo S.B. ; Rolim, Samir ; Rovero, Francesco ; Rozak, Andes ; Ruokolainen, Kalle ; Rutishauser, Ervan ; Rutten, Gemma ; Mohd Said, Mohd Nizam ; Saiter, Felipe Z. ; Saner, Philippe ; Santos, Braulio ; Santos, João Roberto Dos; Sarker, Swapan Kumar ; Schmitt, Christine B. ; Schoengart, Jochen ; Schulze, Mark ; Sheil, Douglas ; Sist, Plinio ; Souza, Alexandre F. ; Spironello, Wilson Roberto ; Sposito, Tereza ; Steinmetz, Robert ; Stevart, Tariq ; Suganuma, Marcio Seiji ; Sukri, Rahayu ; Sultana, Aisha ; Sukumar, Raman ; Sunderland, Terry ; Supriyadi, S. ; Suresh, H.S. ; Suzuki, Eizi ; Tabarelli, Marcelo ; Tang, Jianwei ; Tanner, Ed V.J. ; Targhetta, Natalia ; Theilade, Ida ; Thomas, Duncan ; Timberlake, Jonathan ; Morisson Valeriano, Márcio De; Valkenburg, Johan Van; Do, Tran Van; Sam, Hoang Van; Vandermeer, John H. ; Verbeeck, Hans ; Vetaas, Ole Reidar ; Adekunle, Victor ; Vieira, Simone A. ; Webb, Campbell O. ; Webb, Edward L. ; Whitfeld, Timothy ; Wich, Serge ; Williams, John ; Wiser, Susan ; Wittmann, Florian ; Yang, Xiaobo ; Yao, C.Y.A. ; Yap, Sandra L. ; Zahawi, Rakan A. ; Zakaria, Rahmad ; Zang, Runguo - \ 2018
Proceedings of the National Academy of Sciences of the United States of America 115 (2018)8. - ISSN 0027-8424 - p. 1837 - 1842.
Biogeographic legacies - Forest classification - Forest functional similarity - Phylogenetic community distance - Tropical forests

Knowledge about the biogeographic affinities of the world's tropical forests helps to better understand regional differences in forest structure, diversity, composition, and dynamics. Such understanding will enable anticipation of region-specific responses to global environmental change. Modern phylogenies, in combination with broad coverage of species inventory data, now allow for global biogeographic analyses that take species evolutionary distance into account. Here we present a classification of the world's tropical forests based on their phylogenetic similarity. We identify five principal floristic regions and their floristic relationships: (i) Indo-Pacific, (ii) Subtropical, (iii) African, (iv) American, and (v) Dry forests. Our results do not support the traditional neo- versus paleotropical forest division but instead separate the combined American and African forests from their Indo-Pacific counterparts. We also find indications for the existence of a global dry forest region, with representatives in America, Africa, Madagascar, and India. Additionally, a northern-hemisphere Subtropical forest region was identified with representatives in Asia and America, providing support for a link between Asian and American northernhemisphere forests.

Rapid evolution of phenology during range expansion with recent climate change
Lustenhouwer, Nicky ; Wilschut, Rutger A. ; Williams, Jennifer L. ; Putten, Wim H. van der; Levine, Jonathan M. - \ 2018
Global Change Biology 24 (2018)2. - ISSN 1354-1013 - p. e534 - e544.
Although climate warming is expected to make habitat beyond species’ current cold range edge suitable for future colonization, this new habitat may present an array of biotic or abiotic conditions not experienced within the current range. Species’ ability to shift their range with climate change may therefore depend on how populations evolve in response to such novel environmental conditions. However, due to the recent nature of thus far observed range expansions, the role of rapid adaptation during climate change migration is only beginning to be understood. Here, we evaluated evolution during the recent native range expansion of the annual plant Dittrichia graveolens, which is spreading northward in Europe from the Mediterranean region. We examined genetically based differentiation between core and edge populations in their phenology, a trait that is likely under selection with shorter growing seasons and greater seasonality at northern latitudes. In parallel common garden experiments at range edges in Switzerland and the Netherlands, we grew plants from Dutch, Swiss, and central and southern French populations. Population genetic analysis following RAD-sequencing of these populations supported the hypothesized central France origins of the Swiss and Dutch range edge populations. We found that in both common gardens, northern plants flowered up to 4 weeks earlier than southern plants. This differentiation in phenology extended from the core of the range to the Netherlands, a region only reached from central France over approximately the last 50 years. Fitness decreased as plants flowered later, supporting the hypothesized benefits of earlier flowering at the range edge. Our results suggest that native range expanding populations can rapidly adapt to novel environmental conditions in the expanded range, potentially promoting their ability to spread.
The ALFAM2 database on ammonia emission from field-applied manure : Description and illustrative analysis
Hafner, Sasha D. ; Pacholski, Andreas ; Bittman, Shabtai ; Burchill, William ; Bussink, Wim ; Chantigny, Martin ; Carozzi, Marco ; Génermont, Sophie ; Häni, Christoph ; Hansen, Martin N. ; Huijsmans, Jan ; Hunt, Derek ; Kupper, Thomas ; Lanigan, Gary ; Loubet, Benjamin ; Misselbrook, Tom ; Meisinger, John J. ; Neftel, Albrecht ; Nyord, Tavs ; Pedersen, Simon V. ; Sintermann, Jörg ; Thompson, Rodney B. ; Vermeulen, Bert ; Voylokov, Polina ; Williams, John R. ; Sommer, Sven G. - \ 2018
Agricultural and Forest Meteorology 258 (2018). - ISSN 0168-1923 - p. 66 - 79.
Ammonia - Cattle - Emission - Manure - Pig - Slurry
Ammonia (NH3) emission from animal manure contributes to air pollution and ecosystem degradation, and the loss of reactive nitrogen (N) from agricultural systems. Estimates of NH3 emission are necessary for national inventories and nutrient management, and NH3 emission from field-applied manure has been measured in many studies over the past few decades. In this work, we facilitate the use of these data by collecting and organizing them in the ALFAM2 database. In this paper we describe the development of the database and summarise its contents, quantify effects of application methods and other variables on emission using a data subset, and discuss challenges for data analysis and model development. The database contains measurements of emission, manure and soil properties, weather, application technique, and other variables for 1895 plots from 22 research institutes in 12 countries. Data on five manure types (cattle, pig, mink, poultry, mixed, as well as sludge and "other") applied to three types of crops (grass, small grains, maize, as well as stubble and bare soil) are included. Application methods represented in the database include broadcast, trailing hose, trailing shoe (narrow band application), and open slot injection. Cattle manure application to grassland was the most common combination, and analysis of this subset (with dry matter (DM) limited to <15%) was carried out using mixed- and fixed-effects models in order to quantify effects of management and environment on ammonia emission, and to highlight challenges for use of the database. Measured emission in this subset ranged from <1% to 130% of applied ammonia after 48 h. Results showed clear, albeit variable, reductions in NH3 emission due to trailing hose, trailing shoe, and open slot injection of slurry compared to broadcast application. There was evidence of positive effects of air temperature and wind speed on NH3 emission, and limited evidence of effects of slurry DM. However, random-effects coefficients for differences among research institutes were among the largest model coefficients, and showed a deviation from the mean response by more than 100% in some cases. The source of these institute differences could not be determined with certainty, but there is some evidence that they are related to differences in soils, or differences in application or measurement methods. The ALFAM2 database should be useful for development and evaluation of both emission factors and emission models, but users need to recognize the limitations caused by confounding variables, imbalance in the dataset, and dependence among observations from the same institute. Variation among measurements and in reported variables highlights the importance of international agreement on how NH3 emission should be measured, along with necessary types of supporting data and standard protocols for their measurement. Both are needed in order to produce more accurate and useful ammonia emission measurements. Expansion of the ALFAM2 database will continue, and readers are invited to contact the corresponding author for information on data submission. The latest version of the database is available at http://www.alfam.dk.
Non-Chemical Weed Management
Melander, Bo ; Liebman, Matt ; Davis, Adam S. ; Gallandt, Eric R. ; Bàrberi, Paolo ; Moonen, Anna Camilla ; Rasmussen, Jesper ; Weide, Rommie van der; Vidotto, Francesco - \ 2017
In: Weed Research / Hatcher, Paul E., Froud-Williams, Robert J., Wiley - ISBN 9781119969143 - p. 245 - 270.
Crop competition - Cultural methods - European weed research - Non-chemical weed management - North America - Organic crop production - Weed control methods - Weed germination

Non-chemical weed management covers all management practices that influence weeds except herbicides. This chapter summarises the major achievements in European research, as well as work undertaken in North America. Research groups from both continents have interacted strongly on the topic over the years and shared common interests on the development of non-chemical tactics. The chapter encompasses preventive, cultural and direct weed control methods, explaining the basic principles and the integration of these tactics in weed management strategies for agricultural and horticultural crops and in some cases amenity areas as well. Preventive methods reduce weed germination, cultural methods improve crop competition and direct physical weed control reduces weed survival. Non-chemical weed management is mainly adopted in organic crop production, as conventional growers still perceive it as more costly and less reliable than herbicide-based weed control programmes.

Dataset supplementing Lichtenberg et al. (2017) A global synthesis of the effects of diversified farming systems on arthropod diversity within fields and across agricultural landscapes. Global Change Biology
Lichtenberg, Elinor M. ; Kennedy, Christina M. ; Kremen, Claire ; Batáry, Péter ; Berendse, F. ; Bommarco, Riccardo ; Bosque-Pérez, Nilsa A. ; Carvalheiro, Luísa G. ; Snyder, William E. ; Williams, Neal M. - \ 2017
agricultural management schemes - arthropod diversity - functional groups - landscape complexity - meta-analysis - evenness - biodiversity - organic farming - plant diversity
This dataset contains data and scripts that supplement the publication
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