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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    Author Correction: Global status and conservation potential of reef sharks
    MacNeil, M.A. ; Chapman, Demian D. ; Heupel, Michelle ; Simpfendorfer, Colin A. ; Heithaus, Michael ; Meekan, Mark ; Harvey, Euan ; Goetze, Jordan ; Kiszka, Jeremy ; Bond, Mark E. ; Currey-Randall, Leanne M. ; Speed, Conrad W. ; Sherman, C.S. ; Rees, Matthew J. ; Udyawer, Vinay ; Flowers, Kathryn I. ; Clementi, Gina ; Valentin-Albanese, Jasmine ; Gorham, Taylor ; Adam, M.S. ; Ali, Khadeeja ; Pina-Amargós, Fabián ; Angulo-Valdés, Jorge A. ; Asher, Jacob ; Barcia, Laura García ; Beaufort, Océane ; Benjamin, Cecilie ; Bernard, Anthony T.F. ; Berumen, Michael L. ; Bierwagen, Stacy ; Bonnema, Erika ; Bown, Rosalind M.K. ; Bradley, Darcy ; Brooks, Edd ; Brown, J.J. ; Buddo, Dayne ; Burke, Patrick ; Cáceres, Camila ; Cardeñosa, Diego ; Carrier, Jeffrey C. ; Caselle, Jennifer E. ; Charloo, Venkatesh ; Claverie, Thomas ; Clua, Eric ; Cochran, Jesse E.M. ; Cook, Neil ; Cramp, Jessica ; D’Alberto, Brooke ; Graaf, Martin de; Dornhege, Mareike ; Estep, Andy ; Fanovich, Lanya ; Farabaugh, Naomi F. ; Fernando, Daniel ; Flam, Anna L. ; Floros, Camilla ; Fourqurean, Virginia ; Garla, Ricardo ; Gastrich, Kirk ; George, Lachlan ; Graham, Rory ; Guttridge, Tristan ; Hardenstine, Royale S. ; Heck, Stephen ; Henderson, Aaron C. ; Hertler, Heidi ; Hueter, Robert ; Johnson, Mohini ; Jupiter, Stacy ; Kasana, Devanshi ; Kessel, Steven T. ; Kiilu, Benedict ; Kirata, Taratu ; Kuguru, Baraka ; Kyne, Fabian ; Langlois, Tim ; Lédée, Elodie J.I. ; Lindfield, Steve ; Luna-Acosta, Andrea ; Maggs, Jade ; Manjaji-Matsumoto, B.M. ; Marshall, Andrea ; Matich, Philip ; McCombs, Erin ; McLean, Dianne ; Meggs, Llewelyn ; Moore, Stephen ; Mukherji, Sushmita ; Murray, Ryan ; Kaimuddin, Muslimin ; Newman, Stephen J. ; Nogués, Josep ; Obota, Clay ; O’Shea, Owen ; Osuka, Kennedy ; Papastamatiou, Yannis P. ; Perera, Nishan ; Peterson, Bradley ; Ponzo, Alessandro ; Prasetyo, Andhika ; Sjamsul Quamar, L.M. ; Quinlan, Jessica ; Ruiz-Abierno, Alexei ; Sala, Enric ; Samoilys, Melita ; Schärer-Umpierre, Michelle ; Schlaff, Audrey ; Simpson, Nikola ; Smith, Adam N.H. ; Sparks, Lauren ; Tanna, Akshay ; Torres, Rubén ; Travers, Michael J. ; Zinnicq Bergmann, Maurits van; Vigliola, Laurent ; Ward, Juney ; Watts, Alexandra M. ; Wen, Colin ; Whitman, Elizabeth ; Wirsing, Aaron J. ; Wothke, Aljoscha ; Zarza-Gonzâlez, Esteban ; Cinner, Joshua E. - \ 2020
    Nature (2020). - ISSN 0028-0836

    An Amendment to this paper has been published and can be accessed via a link at the top of the paper.

    Global status and conservation potential of reef sharks
    MacNeil, Aaron ; Chapman, Demian D. ; Heupel, Michelle ; Simpfendorfer, Colin A. ; Heithaus, Michael ; Meekan, Mark ; Harvey, Euan ; Goetze, Jordan ; Kiszka, Jeremy ; Bond, Mark E. ; Currey-Randall, Leanne M. ; Speed, Conrad W. ; Sherman, Samantha ; Rees, Matthew J. ; Udyawer, Vinay ; Flowers, Kathryn I. ; Clementi, Gina ; Valentin-Albanese, Jasmine ; Gorham, Taylor ; Adam, Shiham ; Khadeeja, Ali ; Pina-Amargós, Fabián ; Angulo-Valdés, Jorge A. ; Asher, Jacob ; García Barcia, Laura ; Beaufort, Océane ; Benjamin, Cecilie ; Bernard, Anthony T.F. ; Berumen, Michael L. ; Bierwagen, Stacy ; Bonnema, Erika ; Bown, Rosalind M.K. ; Bradley, Darcey ; Brooks, Edd ; Brown, Jed ; Buddo, Dayne ; Burke, Patrick ; Cáceres, Camila ; Cardeñosa, Diego ; Carrier, Jeffrey C. ; Caselle, Jennifer E. ; Charloo, Venkatesh ; Claverie, Thomas ; Clua, Eric ; Cochran, Jesse E.M. ; Cook, Neil ; Cramp, Jessica ; D’Alberto, Brooke ; Graaf, Martin de; Dornhege, Mareike ; Estep, Andy ; Fanovich, Lanya ; Farabough, Naomi F. ; Fernando, Daniel ; Flam, Anna L. ; Floros, Camilla ; Fourqurean, Virginia ; Garla, Ricardo ; Gastrich, Kirk ; George, Lachlan ; Graham, Rory ; Guttridge, Tristan ; Hardenstine, Royale S. ; Heck, Stephen ; Henderson, Aaron C. ; Hertler, Heidi ; Hueter, Robert ; Johnson, Mohini ; Jupiter, Stacy ; Kasana, Devanshi ; Kessel, Steven T. ; Kiilu, Benedict ; Kirata, Taratu ; Kuguru, Baraka ; Kyne, Fabian ; Langlois, Tim ; Lédée, Elodie J.I. ; Lindfield, Steve ; Luna-Acosta, Andrea ; Maggs, Jade ; Manjaji-Matsumoto, Mabel ; Marshall, Andrea ; Matich, Philip ; McCombs, Erin ; McLean, Dianne ; Meggs, Llewelyn ; Moore, Stephen ; Mukherji, Sushmita ; Murray, Ryan ; Kaimuddin, Muslimin ; Newman, Stephen J. ; Nogués, Josep ; Obota, Clay ; O’Shea, Owen ; Osuka, Kennedy ; Papastamatiou, Yannis P. ; Perera, Nishan ; Peterson, Bradley ; Ponzo, Alessandro ; Prasetyo, Andhika ; Quamar, Sjamsul ; Quinlan, Jessica ; Ruiz-Abierno, Alexei ; Sala, Enric ; Samoilys, Melita ; Schärer-Umpierre, Michelle ; Schlaff, Audrey ; Simpson, Nikola ; Smith, Adam N.H. ; Sparks, Lauren ; Tanna, Akshay ; Torres, Rubén ; Travers, Michael J. ; Zinnicq Bergmann, Maurits van; Vigliola, Laurent ; Ward, Juney ; Watts, Alexandra M. ; Wen, Colin ; Whitman, Elizabeth ; Wirsing, Aaron J. ; Wothke, Aljoscha ; Zarza-Gonzâlez, Esteban ; Cinner, Joshua E. - \ 2020
    Nature 583 (2020). - ISSN 0028-0836 - p. 801 - 806.

    Decades of overexploitation have devastated shark populations, leaving considerable doubt as to their ecological status1,2. Yet much of what is known about sharks has been inferred from catch records in industrial fisheries, whereas far less information is available about sharks that live in coastal habitats3. Here we address this knowledge gap using data from more than 15,000 standardized baited remote underwater video stations that were deployed on 371 reefs in 58 nations to estimate the conservation status of reef sharks globally. Our results reveal the profound impact that fishing has had on reef shark populations: we observed no sharks on almost 20% of the surveyed reefs. Reef sharks were almost completely absent from reefs in several nations, and shark depletion was strongly related to socio-economic conditions such as the size and proximity of the nearest market, poor governance and the density of the human population. However, opportunities for the conservation of reef sharks remain: shark sanctuaries, closed areas, catch limits and an absence of gillnets and longlines were associated with a substantially higher relative abundance of reef sharks. These results reveal several policy pathways for the restoration and management of reef shark populations, from direct top-down management of fishing to indirect improvement of governance conditions. Reef shark populations will only have a high chance of recovery by engaging key socio-economic aspects of tropical fisheries.

    OESO, internationaal platform voor kennisuitwisseling
    Poppe, Krijn - \ 2019

    Krijn Poppe, onderzoeker bij Wageningen Economic Research, en Jonathan Brooks, hoofd van de divisie voedselmarkten en internationale handel bij de OESO, vertellen hoe zij aankijken tegen kennisuitwisseling tussen de OESO en Nederland.

    Birds, mammals drove camouflage adaptations of stick, leaf insects
    Simon, S. - \ 2019
    Toward sustainable environmental quality : Priority research questions for Europe
    Brink, Paul J. Van den; Boxall, Alistair B.A. ; Maltby, Lorraine ; Brooks, Bryan W. ; Rudd, Murray A. ; Backhaus, Thomas ; Spurgeon, David ; Verougstraete, Violaine ; Ajao, Charmaine ; Ankley, Gerald T. ; Apitz, Sabine E. ; Arnold, Kathryn ; Brodin, Tomas ; Cañedo-Argüelles, Miguel ; Chapman, Jennifer ; Corrales, Jone ; Coutellec, Marie Agnès ; Fernandes, Teresa F. ; Fick, Jerker ; Ford, Alex T. ; Giménez Papiol, Gemma ; Groh, Ksenia J. ; Hutchinson, Thomas H. ; Kruger, Hank ; Kukkonen, Jussi V.K. ; Loutseti, Stefania ; Marshall, Stuart ; Muir, Derek ; Ortiz-Santaliestra, Manuel E. ; Paul, Kai B. ; Rico, Andreu ; Rodea-Palomares, Ismael ; Römbke, Jörg ; Rydberg, Tomas ; Segner, Helmut ; Smit, Mathijs ; Gestel, Cornelis A.M. van; Vighi, Marco ; Werner, Inge ; Zimmer, Elke I. ; Wensem, Joke van - \ 2018
    Environmental Toxicology and Chemistry 37 (2018)9. - ISSN 0730-7268 - p. 2281 - 2295.
    Chemical management - Environmental risk assessment - Global megatrends - Key questions exercise - Sustainability

    The United Nations' Sustainable Development Goals have been established to end poverty, protect the planet, and ensure prosperity for all. Delivery of the Sustainable Development Goals will require a healthy and productive environment. An understanding of the impacts of chemicals which can negatively impact environmental health is therefore essential to the delivery of the Sustainable Development Goals. However, current research on and regulation of chemicals in the environment tend to take a simplistic view and do not account for the complexity of the real world, which inhibits the way we manage chemicals. There is therefore an urgent need for a step change in the way we study and communicate the impacts and control of chemicals in the natural environment. To do this requires the major research questions to be identified so that resources are focused on questions that really matter. We present the findings of a horizon-scanning exercise to identify research priorities of the European environmental science community around chemicals in the environment. Using the key questions approach, we identified 22 questions of priority. These questions covered overarching questions about which chemicals we should be most concerned about and where, impacts of global megatrends, protection goals, and sustainability of chemicals; the development and parameterization of assessment and management frameworks; and mechanisms to maximize the impact of the research. The research questions identified provide a first-step in the path forward for the research, regulatory, and business communities to better assess and manage chemicals in the natural environment.

    An overview of the diurnal cycle of the atmospheric boundary layer during the West African monsoon season : Results from the 2016 observational campaign
    Kalthoff, Norbert ; Lohou, Fabienne ; Brooks, Barbara ; Jegede, Gbenga ; Adler, Bianca ; Babić, Karmen ; DIone, Cheikh ; Ajao, Adewale ; Amekudzi, Leonard K. ; Aryee, Jeffrey N.A. ; Ayoola, Muritala ; Bessardon, Geoffrey ; Danuor, Sylvester K. ; Handwerker, Jan ; Kohler, Martin ; Lothon, Marie ; Pedruzo-Bagazgoitia, Xabier ; Smith, Victoria ; Sunmonu, Lukman ; Wieser, Andreas ; Fink, Andreas H. ; Knippertz, Peter - \ 2018
    Atmospheric Chemistry and Physics 18 (2018)4. - ISSN 1680-7316 - p. 2913 - 2928.
    A ground-based field campaign was conducted in southern West Africa from mid-June to the end of July 2016 within the framework of the Dynamics-Aerosol-Chemistry-Cloud Interactions in West Africa (DACCIWA) project. It aimed to provide a high-quality comprehensive data set for process studies, in particular of interactions between low-level clouds (LLCs) and boundary-layer conditions. In this region missing observations are still a major issue. During the campaign, extensive remote sensing and in situ measurements were conducted at three supersites: Kumasi (Ghana), Savè (Benin) and Ile-Ife (Nigeria). Daily radiosoundings were performed at 06:00 UTC, and 15 intensive observation periods (IOPs) were performed during which additional radiosondes were launched, and remotely piloted aerial systems were operated. Extended stratiform LLCs form frequently in southern West Africa during the nighttime and persist long into the following day. They affect the radiation budget and hence the evolution of the atmospheric boundary layer and regional climate. The relevant parameters and processes governing the formation and dissolution of the LLCs are still not fully understood. This paper gives an overview of the diurnal cycles of the energy-balance components, near-surface temperature, humidity, wind speed and direction as well as of the conditions (LLCs, low-level jet) in the boundary layer at the supersites and relates them to synoptic-scale conditions (monsoon layer, harmattan layer, African easterly jet, tropospheric stratification) in the DACCIWA operational area. The characteristics of LLCs vary considerably from day to day, including a few almost cloud-free nights. During cloudy nights we found large differences in the LLCs' formation and dissolution times as well as in the cloud-base height. The differences exist at individual sites and also between the sites. The synoptic conditions are characterized by a monsoon layer with south-westerly winds, on average about 1.9 km deep, and easterly winds above; the depth and strength of the monsoon flow show great day-to-day variability. Within the monsoon layer, a nocturnal low-level jet forms in approximately the same layer as the LLC. Its strength and duration is highly variable from night to night. This unique data set will allow us to test some new hypotheses about the processes involved in the development of LLCs and their interaction with the boundary layer and can also be used for model evaluation.
    Practical steps toward integrating economic, social and institutional elements in fisheries policy and management
    Stephenson, Robert L. ; Benson, Ashleen J. ; Brooks, Kate ; Charles, Anthony ; Degnbol, Poul ; Dichmont, Catherine M. ; Kraan, Marloes ; Pascoe, Sean ; Paul, Stacey D. ; Rindorf, Anna ; Wiber, Melanie - \ 2017
    ICES Journal of Marine Science 74 (2017)7. - ISSN 1054-3139 - p. 1981 - 1989.
    ecosystem approach - fisheries sustainability - integrated management - integrating social and economic aspects - social-ecological system
    While international agreements and legislation call for incorporation of four pillars of sustainability, the social (including cultural), economic and institutional aspects (the ‘human dimension’) have been relatively neglected to date. Three key impediments have been identified: a relative lack of explicit social, economic and institutional objectives; a general lack of process (frameworks, governance) for routine integration of all four pillars of sustainability; and a bias towards biological considerations. Practical integration requires a ‘systems’ approach with explicit consideration of strategic and operational aspects of management; multidisciplinary or transdisciplinary evaluations; practical objectives for the four pillars of sustainability; appropriate participation; and a governance system that is able to integrate these diverse considerations in management. We challenge all involved in fisheries to immediately take five practical steps toward integrating ecological, economic, social and institutional aspects: (1) Adopt the perspective of the fishery as a ‘system’ with interacting natural, human and management elements; (2) Be aware of both strategic and operational aspects of fisheries assessment and management; (3) Articulate overarching objectives that incorporate all four pillars of sustainability; (4) Encourage appropriate (and diverse) disciplinary participation in all aspects of research, evaluation and management; and (5) Encourage development of (or emulate) participatory governance.
    Chobe district integrated land use plan
    Sluis, Theo van der; Cassidy, Lin ; Brooks, Chris ; Wolski, Piotr ; VanderPost, Cornelis ; Wit, Piet ; Henkens, Rene ; Eupen, Michiel van; Mosepele, K. ; Maruapula, O. ; Veenendaal, Elmar - \ 2017
    Wageningen : Wageningen Environmental Research (Wageningen Environmental Research rapport 2813) - 181
    land use - sustainability - tourism - ecosystems - savannas - botswana - landgebruik - duurzaamheid (sustainability) - toerisme - ecosystemen - savannen - botswana
    Supplementary data Chobe district land use plan
    Sluis, T. van der; Cassidy, L. ; Brooks, C. ; Wolski, P. ; Vanderpost, C. ; Wit, P. de; Henkes, R. ; Eupen, M. van; Mosepele, K. ; Maruapula, O. ; Veenendaal, E.M. - \ 2017
    Wageningen Environmental Research
    Implications and application of the Raats superclass of soils equations
    Heinen, Marius ; Bakker, Gerben - \ 2016
    Vadose Zone Journal 15 (2016)8. - ISSN 1539-1663 - 12 p.

    According to the Richards equation, the capacity of a soil to hold and conduct water is determined by the water retention and hydraulic conductivity characteristics. Many mathematical relationships have been proposed in the literature to describe these characteristics. Raats introduced a general functional relationship with only four parameters that included as special cases four pre-1990 models found in the literature, including the well-known relationships by Mualem-van Genuchten and Brooks and Corey. The aims of this study were (i) to discuss this general functional relationship and its four special cases, (ii) to present expressions for the differential moisture capacity, water diffusivity, and matric flux potential corresponding to the general functional relationship and its special cases, (iii) to discuss methods for determining the parameter elasticity and sensitivity, and (iv) to apply the Raats model to experimental data. Soil water retention and hydraulic conductivity data for 11 soils were used to optimize the values of the four major parameters in the Raats model. In none of the cases did the optimized coefficients indicate that the Raats model approached one of the four submodels that it includes.

    Practical steps toward integrating economic, social and institutional objectives and indicators in fisheries management
    Stephenson, R.G. ; Benson, Ashleen ; Brooks, K. ; Kraan, M.L. - \ 2016
    - 1 p.
    Identifying groundwater recharge connections in the Moscow (USA) sub-basin using isotopic tracers and a soil moisture routing model
    Candel, J.H.J. ; Brooks, Erin ; Sanchez-Murillo, Ricardo ; Grader, George ; Dijksma, R. - \ 2016
    Hydrogeology Journal 24 (2016)7. - ISSN 1431-2174 - p. 1739 - 1751.
    Globally, aquifers are suffering from large abstractions resulting in groundwater level declines. These declines can be caused by excessive abstraction for drinking water, irrigation purposes or industrial use. Basaltic aquifers also face these conflicts. A large flood basalt area (1.1 × 105 km2) can be found in the Northwest of the USA. This Columbia River Basalt Group (CRBG) consists of a thick series of basalt flows of Miocene age. The two major hydrogeological units (Wanapum and Grand Ronde formations) are widely used for water abstraction. The mean decline over recent decades has been 0.6 m year−1. At present day, abstraction wells are drying up, and base flow of rivers is reduced. At the eastern part of CRBG, the Moscow sub-basin on the Idaho/Washington State border can be found. Although a thick poorly permeable clay layer exists on top of the basalt aquifer, groundwater level dynamics suggest that groundwater recharge occurs at certain locations. A set of wells and springs has been monitored bi-weekly for 9 months for δ18O and δ2H. Large isotopic fluctuations and d-excess values close to the meteoric water line in some wells are indicating that recharge occurs at the granite/basalt interface through lateral flow paths in and below the clay. A soil moisture routing (SMR) model showed that most recharge occurs on the granitic mountains. The basaltic aquifer receives recharge from these sedimentary zones around the granite/basalt interface. The identification of these types of areas is of major importance for future managed-aquifer recharge solutions to solve problems of groundwater depletion.
    Identifying groundwater recharge pathways in the Moscow sub-basin
    Candel, J.H.J. ; Brooks, E.S. ; Verhoeff, Eric ; Dobre, Mariana ; Sanchez-Murillo, Ricardo ; Grader, Jr., George W. ; Dijksma, R. - \ 2016
    Continual groundwater decline over the last 80 years in the Moscow-Pullman basin is motivating communities to explore a wide range of strategies ranging from reservoir development to direct injection to aquifers to ensure a sustainable regional water supply. Historic pumping records indicate the shallow Wanapum aquifer in the Moscow region does receive recharge however it is less certain that the deeper Grand Ronde aquifer is receiving any significant recharge. Moreover there is not a clear consensus in the region of the location of the major aquifer recharge flow paths. In this study we used both distributed hydrologic modeling based on detailed soil mapping and stable isotope tracers to explore and evaluate potential groundwater recharge pathways in the Moscow sub-basin. Modelling results indicate that subsurface water flow off the forested granitics in eastern margin of the sub-basin is likely a significant source of recharge. Biweekly water samples taken from 22 wells and 2 springs and high frequency streamflow and precipitation samples collected over a two year period throughout the Moscow sub-basin were analyzed for stable isotopes of hydrogen and oxygen. Frequency analysis of these stable isotope data suggest the some wells are receiving recharge. Furthermore many of these wells exist on the eastern margin of the sub-basin lending further support to the hypothesis that this region should be considered to be a critical ground recharge zone.
    Quo Vadimus : Integrating fishers' knowledge research in science and management
    Stephenson, Robert L. ; Paul, Stacy ; Pastoors, M.A. ; Kraan, M.L. ; Holm, Petter ; Wiber, M. ; Mackinson, S. ; Dankel, D.J. ; Brooks, K. ; Benson, Ashleen - \ 2016
    ICES Journal of Marine Science 73 (2016)6. - ISSN 1054-3139 - p. 1459 - 1465.
    collaborative research - cooperative research - fishers' knowledge research - integrating fishers' knowledge - local knowledge - participatory research - stakeholder involvement
    Fishers' knowledge research (FKR) aims to enhance the use of experiential knowledge of fish harvesters in fisheries research, assessment, and management. Fishery participants are able to provide unique knowledge, and that knowledge forms an important part of “best available information” for fisheries science and management. Fishers' knowledge includes, but is much greater than, basic biological fishery information. It includes ecological, economic, social, and institutional knowledge, as well as experience and critical analysis of experiential knowledge. We suggest that FKR, which may in the past have been defined quite narrowly, be defined more broadly to include both fishery observations and fishers “experiential knowledge” provided across a spectrum of arrangements of fisher participation. FKR is part of the new and different information required in evolving “ecosystem-based” and “integrated” management approaches. FKR is a necessary element in the integration of ecological, economic, social, and institutional considerations of future management. Fishers' knowledge may be added to traditional assessment with appropriate analysis and explicit recognition of the intended use of the information, but fishers' knowledge is best implemented in a participatory process designed to receive and use it. Co-generation of knowledge in appropriately designed processes facilitates development and use of fishers' knowledge and facilitates the participation of fishers in assessment and management, and is suggested as best practice in improved fisheries governance.
    Projecting Global Biodiversity Indicators under Future Development Scenarios
    Visconti, Piero ; Bakkenes, Michel ; Baisero, Daniele ; Brooks, Thomas ; Butchart, Stuart H.M. ; Joppa, Lucas ; Alkemade, Rob ; Marco, Moreno Di; Santini, Luca ; Hoffmann, Michael ; Maiorano, Luigi ; Pressey, Robert L. ; Arponen, Anni ; Boitani, Luigi ; Reside, April E. ; Vuuren, Detlef P. van; Rondinini, Carlo - \ 2016
    Conservation Letters 9 (2016)1. - ISSN 1755-263X - p. 5 - 13.
    Biodiversity indicators - Biodiversity scenarios - Carnivores - Climate change - Extinction risk - Geometric Mean Abundance - Land-use change - Red List Index - Ungulates

    To address the ongoing global biodiversity crisis, governments have set strategic objectives and have adopted indicators to monitor progress toward their achievement. Projecting the likely impacts on biodiversity of different policy decisions allows decision makers to understand if and how these targets can be met. We projected trends in two widely used indicators of population abundance Geometric Mean Abundance, equivalent to the Living Planet Index and extinction risk (the Red List Index) under different climate and land-use change scenarios. Testing these on terrestrial carnivore and ungulate species, we found that both indicators decline steadily, and by 2050, under a Business-as-usual (BAU) scenario, geometric mean population abundance declines by 18-35% while extinction risk increases for 8-23% of the species, depending on assumptions about species responses to climate change. BAU will therefore fail Convention on Biological Diversity target 12 of improving the conservation status of known threatened species. An alternative sustainable development scenario reduces both extinction risk and population losses compared with BAU and could lead to population increases. Our approach to model species responses to global changes brings the focus of scenarios directly to the species level, thus taking into account an additional dimension of biodiversity and paving the way for including stronger ecological foundations into future biodiversity scenario assessments.

    Preventieve maatregelen tegen huisvliegen in vleeskuikenstallen
    Mul, M.F. ; Smallegange, R.C. ; Brooks, Mike - \ 2015
    Wageningen : Wageningen UR Livestock Research (Livestock Research rapport 836) - 28
    De huisvlieg (Musca domestica) speelt een belangrijke rol in de overdracht van Campylobacter spp. naar vleeskuikens en andere landbouwhuisdieren. Door het weren van vliegen uit een vleeskuikenstal met behulp van vliegennetten werd in Denemarken het percentage Campylobacter-positieve koppels van 43,3% (drie jaren zonder vliegennetten) gereduceerd naar 9,9% (vier jaren met vliegennetten). Dit rapport beschrijft een aantal maatregelen en mogelijkheden voor het weren van vliegen uit vleeskuikenstallen.
    Epidemic predictions in an imperfect world : Modelling disease spread with partial data
    Dawson, P.M. ; Werkman, Marleen ; Brooks-Pollock, Ellen ; Tildesley, M.J. - \ 2015
    Proceedings of the Royal Society. B: Biological Sciences 282 (2015)1808. - ISSN 0962-8452 - 9 p.
    Epidemics - Livestock networks - Partial datav

    ‘Big-data’ epidemic models are being increasingly used to influence government policy to help with control and eradication of infectious diseases. In the case of livestock, detailed movement records have been used to parametrize realistic transmission models. While livestock movement data are readily available in the UK and other countries in the EU, in many countries around theworld, such detailed data are not available. By using a comprehensive database of the UK cattle trade network, we implement various sampling strategies to determine the quantity of network data required to give accurate epidemiological predictions. It is found that by targeting nodes with the highest number of movements, accurate predictions on the size and spatial spread of epidemics can be made. This work has implications for countries such as the USA, where access to data is limited, and developing countries that may lack the resources to collect a full dataset on livestock movements.

    Altered food-cue processing in chronically ill and recovered women with anorexia nervosa
    Sanders, N. ; Smeets, P.A.M. ; Elburg, A.A. van; Danner, U.N. ; Meer, F. van; Hoek, H.W. ; Adan, R.A.H. - \ 2015
    Frontiers in Behavioral Neuroscience 9 (2015). - ISSN 1662-5153 - 12 p.
    default mode network - high-calorie foods - eating-disorders - functional-anatomy - reward - fmri - stimuli - leptin - energy - cortex
    Anorexia nervosa (AN) is a severe mental disorder characterized by food restriction and weight loss. This study aimed to test the model posed by Brooks et al. (2012a,b) that women suffering from chronic AN show decreased food-cue processing activity in brain regions associated with energy balance and food reward (bottom-up; BU) and increased activity in brain regions associated with cognitive control (top-down; TD) when compared with long-term recovered AN (REC) and healthy controls (HC). Three groups of women, 15 AN (mean illness duration 7.8 ± 4.1 years), 14 REC (mean duration of recovery 4.7 ± 2.7 years) and 15 HC viewed alternating blocks of food and non-food images preceded by a short instruction during functional magnetic resonance imaging (fMRI), after fasting overnight. Functional region of interests (fROIs) were defined in BU (e.g., striatum, hippocampus, amygdala, hypothalamus, and cerebellum), TD (e.g., medial and lateral prefrontal cortex, and anterior cingulate), the insula, and visual processing areas (VPA). Food-cue processing activation was extracted from all fROIs and compared between the groups. In addition, functional connectivity between the fROIs was examined by modular partitioning of the correlation matrix of all fROIs. We could not confirm the hypothesis that BU areas are activated to a lesser extent in AN upon visual processing of food images. Among the BU areas the caudate showed higher activation in both patient groups compared to HC. In accordance with Brooks et al.’s model, we did find evidence for increased TD control in AN and REC. The functional connectivity analysis yielded two clusters in HC and REC, but three clusters in AN. In HC, fROIs across BU, TD, and VPA areas clustered; in AN, one cluster span across BU, TD, and insula; one across BU, TD, and VPA areas; and one was confined to the VPA network. In REC, BU, TD, and VPA or VPA and insula clustered. In conclusion, despite weight recovery, neural processing of food cues is also altered in recovered AN patients.
    Eight challenges in modelling infectious livestock diseases
    Brooks-Pollock, E. ; Jong, M. de; Keeling, M.J. ; Klinkenberg, D. ; Wood, J.L.N. - \ 2015
    Epidemics 10 (2015). - ISSN 1755-4365 - p. 1 - 5.
    mouth-disease - great-britain - bovine tuberculosis - virus transmission - avian influenza - dynamic-model - uk foot - cattle - epidemic - impact
    The transmission of infectious diseases of livestock does not differ in principle from disease transmission in any other animals, apart from that the aim of control is ultimately economic, with the influence of social, political and welfare constraints often poorly defined. Modelling of livestock diseases suffers simultaneously from a wealth and a lack of data. On the one hand, the ability to conduct transmission experiments, detailed within-host studies and track individual animals between geocoded locations make livestock diseases a particularly rich potential source of realistic data for illuminating biological mechanisms of transmission and conducting explicit analyses of contact networks. On the other hand, scarcity of funding, as compared to human diseases, often results in incomplete and partial data for many livestock diseases and regions of the world. In this overview of challenges in livestock disease modelling, we highlight eight areas unique to livestock that, if addressed, would mark major progress in the area.
    Spiritual values
    Wild, R. ; Verschuuren, B. ; Dudley, N. - \ 2014
    In: Applications of Key Biodiversity Areas: End-user consultations / Dudley, N., Boucher, J.L., Cuttelod, A., Brooks, T.M., Langhammer, P.F., Gland : IUCN - ISBN 9782831716886 - p. 99 - 101.
    Publishing for the Protected Area Community: A vision for PARKS from its editorial board
    Amend, T. ; Brooks, T. ; Choudhury, B.C. ; Verschuuren, B. - \ 2014
    PARKS: the International of Protected Areas and Conservation 20 (2014)2. - ISSN 0960-233X - p. 7 - 12.
    In this editorial essay, members of the Editorial Board of PARKS review the status of conservation literature. Three problems are identified: 1) the growing gap between the formal conservation literature and the so-called ‘grey literature’ of project reports, studies and working papers; 2) the effectiveness of the majority of conservation literature in promoting good conservation; and 3) the lack of open access to much of the conservation literature currently available. The article sets out the vision of this journal: PARKS, the International Journal of Protected Areas and Conservation, published by the International Union for Conservation of Nature (IUCN) expert World Commission on Protected Areas (WCPA). PARKS aims to encourage new writers, including younger researchers, conservation professionals who do not generally write for peer-reviewed publications and people from developing countries, including indigenous and local people, to share their best practices in protected area management. PARKS is published twice a year as an online, open-access and peer reviewed journal and welcomes submissions of papers from all protected area professionals worldwide.
    Modeling water potentials and flows in the soil-plant system comparing hydraulic resistances and transpiration reduction fuctions
    Jong, Q. de; Dam, J.C. van; Durigon, A. ; Santos, M.A. dos; Metselaar, K. - \ 2013
    Vadose Zone Journal 12 (2013)3. - ISSN 1539-1663 - 20 p.
    root-water - polymer tensiometers - simulation-model - stress - conductivity - extraction - maize - architecture - transport - movement
    Crop transpiration depends on resistances in the soil–plant–atmosphere system. We present a new deterministic root water uptake model to estimate transpiration and compare it with two other models. We show the sensitivity of actual transpiration to parameters like soil and plant hydraulic properties and root length density distribution with depth. Transpiration reduction functions are often used in hydrological modeling to estimate actual transpiration as a function of soil water status. Empirical reduction functions are most frequently used due to the higher data needs and computational requirements of mechanistic models. Empirical models, however, lack a description of physical mechanisms and their parameters require extensive calibration. We derive a process-based reduction function predicting system potentials, resistances, and water flows. An analytical solution for a special case of Brooks and Corey soils is presented. A numerical version of the reduction function for van Genuchten soils was implemented in the Soil–Water–Atmosphere–Plant (SWAP) hydrological model, allowing predictions for layered soil profiles and root length density variations over depth. The analytical and numerical versions of the model allow an increasingly quantitative insight into the mechanism of root water uptake, such as the existence of a maximum root water uptake rate as a function of soil water status, soil hydraulic properties, root length density, and root radius, in addition to the fact that sensitivity of simulated root water uptake to the radial root conductivity and axial conductance decrease when root length density increases. The approach can be used for the estimation of threshold values for empirical reduction functions.
    International biodiversity offsets
    Peterson, Annah L. ; Hill, Chloe ; Gallagher, Louise A. - \ 2011
    In: Ecosystem Services and Global Trade of Natural Resources / Koellner, Thomas, Taylor and Francis - ISBN 9780415485838 - p. 225 - 241.
    Introduction Intensifying patterns of international trade resulting from globalization create significant challenges for conservation efforts (see Chapter 2 for a more nuanced discussion of the relationship between globalization and conservation). By increasing primary commodity imports (meat, wood, coffee, sugar, etc.), developed nations are indirectly exporting environmental pressures to resource-rich developing countries in the form of heightened land-use change largely manifesting as deforestation and, consequently, increased biodiversity loss (see Chapter 6). Compounding these international drivers of extinction are more local pressures stemming from overpopulation, poverty and a general lack of local incentives for conservation. Together, global and local development pressures have contributed to the growth of the current species extinction rate to between 100 and 1,000 times faster than the historic average (Pimm and Brooks 2000).
    (Flash) Floods on 27 Augustus 2010 in lowland catchments in The Netherlands and Germany
    Brauer, C.C. ; Teuling, A.J. ; Overeem, A. ; Velde, Y. van der; Hazenberg, P. ; Warmerdam, P.M.M. ; Uijlenhoet, R. ; Hobbelt, L.G. - \ 2011
    On 26 August 2010 the eastern part of The Netherlands and the bordering part of Germany were struck by a series of rainfall events. Over an area of 740 km2 more than 120 mm of rainfall were observed in 24 h. This extreme event resulted in local flooding of city centres, highways and agricultural fields, and considerable financial loss. We investigated the unprecedented flash flood triggered by this exceptionally heavy rainfall event in the 6.5 km2 Hupsel Brook catchment, which has been the experimental watershed employed by Wageningen University since the 1960s. This study aims to improve our understanding of the dynamics of such lowland flash floods. We present a detailed hydrometeorological analysis of this extreme event, focusing on its synoptic meteorological characteristics, its space-time rainfall dynamics as observed with rain gauges, weather radar and a microwave link, as well as the measured soil moisture, groundwater and discharge response of the catchment. We found that the response of the Hupsel Brook catchment can be divided into four phases: (1) soil moisture reservoir filling, (2) groundwater response, (3) surface depression filling and surface runoff and (4) backwater feedback. During this extreme event some thresholds became apparent that do not play a role during average conditions and are not incorporated in rainfall-runoff models. Because of the large spatial extent of the rainfall event, many brooks and rivers in the Netherlands and Germany flooded. With data from several catchments we investigated the influence of rainfall and catchment characteristics (such as slope, size and land use) on the reaction of discharge to rainfall.
    Baseline leptin and leptin reduction predict improvements in metabolic variables and long-term fat loss in obese children and adolescents: a prospective study of an inpatient weight-loss program
    Murer, S.B. ; Knopfli, B.H. ; Aeberli, I. ; Jung, A. ; Wildhaber, J. ; Wildhaber-Brooks, J. ; Zimmermann, M.B. - \ 2011
    American Journal of Clinical Nutrition 93 (2011)4. - ISSN 0002-9165 - p. 695 - 702.
    blood-brain-barrier - serum leptin - body-weight - insulin-resistance - loss maintenance - plasma leptin - overweight - adiposity - life - intervention
    Background: It is unclear whether high plasma leptin in obese individuals represents leptin resistance or whether individuals with marked reductions in leptin concentrations in response to weight loss may be at greater risk of regaining weight. Moreover, whether changes in leptin predict metabolic improvements during weight loss is uncertain. Objective: The objective was to prospectively examine associations between plasma leptin, body fat, and weight and metabolic risk factors in obese children during weight loss. Design: In obese children and adolescents [n = 203; mean age: 14.1 y, >98th body mass index (BMI) percentile for age and sex] participating in a 2-mo inpatient weight-loss program, we measured changes in body composition (by dual-energy X-ray absorptiometry), plasma leptin, insulin, and lipids. After discharge, anthropometric measures and plasma leptin were remeasured at 6 (n = 139) and 12 (n = 100) mo. Results: During the 2-mo program, mean (±SD) weight and fat loss were 13.9 ± 4.0 kg and 9.2 ± 2.5 kg, respectively; and mean plasma leptin decreased by 76%. Weight and fat loss were sustained, and no significant differences in BMI-SD score (SDS) or body composition were found between 12 and 2 mo. Baseline leptin was a negative predictor for percentage fat loss at 2, 6, and 12 mo (P <0.05). The percentage change in leptin during the 2-mo intervention positively correlated with the relative change in fasting insulin, the relative change in LDL cholesterol at 2 mo, percentage fat loss, and change in BMI-SDS at 2 and 6 mo (P <0.02). Conclusions: Even in obese children with strongly elevated baseline leptin, large leptin reductions that predict short- and long-term loss of body fat and improvements in lipids and insulin sensitivity can be achieved. Thus, increased plasma leptin in obese children may not necessarily reflect leptin resistance; many children appear to remain leptin sensitive at this age.
    Groundwater recharge in Pleistocene sediments overlying basalt aquifers in the Palouse Basin, USA: modeling of distributed recharge potential and identification of water pathways
    Dijksma, R. ; Brooks, E.S. ; Boll, J. - \ 2011
    Hydrogeology Journal 19 (2011)2. - ISSN 1431-2174 - p. 489 - 500.
    system - tables - smr
    Groundwater levels in basalt aquifers around the world have been declining for many years. Understanding water pathways is needed for solutions like artificial drainage. Water supply in the Palouse Basin, Washington and Idaho, USA, primarily relies on basalt aquifers. This study presents a combination of modeling and field observations to understand the spatial distribution of recharge pathways in the overlying Pleistocene sediments. A spatially distributed model was used to quantify potential recharge rates. The model shows clearly that recharge predominantly occurs through non-argilic soils and soils that are not underlain by fine-grained sediments, i.e. the upper area of the watershed. A field survey was conducted to determine recharge pathways from this area. It revealed 83 perennial springs. Drillings near springs showed connection of coarse-grained layers within the fine-grained Sediments of Bovill to these springs. Such layers, with streambed-like features, act as paleo-channels. Water from one of these coarse-grained layers had a similar electrical conductivity (200 µS cm–1) to water from a downstream perennial spring, also suggesting the existence of a lateral conduit for deep percolation water.
    During Rapid Weight Loss in Obese Children, Reductions in TSH Predict Improvements in Insulin Sensitivity Independent of Changes in Body Weight or Fat
    Aeberli, I. ; Jung, A. ; Murer, S.B. ; Wildhaber, J. ; Wildhaber-Brooks, J. ; Knopfli, B.H. ; Zimmermann, M.B. - \ 2010
    Journal of Clinical Endocrinology and Metabolism 95 (2010)12. - ISSN 0021-972X - p. 5412 - 5418.
    coronary-heart-disease - subclinical hypothyroidism - thyroid-function - reference range - morbid-obesity - in-vivo - leptin - risk - adolescents - population
    Background: Although serum TSH is often elevated in obesity and may be linked to disorders of lipid and glucose metabolism, the clinical relevance of these relationships remains unclear. Subjects: Subjects were obese children and adolescents (n = 206; mean age 14 yr) undergoing rapid weight and fat loss in a standardized, multidisciplinary, 2-month, in-patient weight loss program. Design: This was a prospective study that determined thyroid function, glucose and lipid parameters, leptin, anthropometric measures, and body composition measured by dual-energy x-ray absorption at baseline and at the end of the intervention. Results: At baseline, 52% of children had TSH concentrations in the high normal range (> 2.5 mU/liter), but TSH was not correlated with body weight, body mass index SD scores, lean body mass, or body fat percentage. At baseline, independent of adiposity, TSH significantly correlated with total cholesterol (P = 0.008), low-density lipoprotein cholesterol (P = 0.013), fasting insulin (P = 0.010), homeostatic model assessment (HOMA) (P = 0.004), and leptin (P = 0.006). During the intervention, mean body fat, TSH, HOMA, and fasting insulin decreased by 21, 11, 53, and 54%, respectively. Change (Delta) in TSH did not correlate with Delta body weight or Delta body composition, but Delta TSH significantly correlated with, Delta fasting insulin and Delta HOMA, independent of Delta body weight or Delta body composition (P <0.05). Conclusion: TSH concentrations are elevated in obese children but are not correlated with the amount of excess body weight or fat. During weight loss, independent of changes in body weight or composition, decreases in elevated serum TSH predict decreases in fasting insulin and HOMA. These findings suggest interventions that target high TSH concentrations during weight loss in obese subjects may improve insulin sensitivity. (J Clin Endocrinol Metab 95: 5412-5418, 2010)
    The Bayesian vantage for dealing with uncertainty
    Evans, D. ; Newman, D.J. ; Lavine, M.C. ; Jaworski, J.C. ; Toll, J. ; Brooks, B.W. ; Brock, T.C.M. - \ 2010
    In: Application of uncertainty analysis to ecological risks of pesticides / Warren-Hicks, W.J., Hart, A, Boca Raton, London, New York : SETAC Press & CRC Press, Taylor & Francis Group - ISBN 9781439807347 - p. 71 - 87.
    Historical water management in the river basin of the Baaksche Beek and the adaptations to the water system as a result of change in land use
    Massop, H.T.L. ; Gaast, J.W.J. van der - \ 2009
    Physics and Chemistry of the Earth 34 (2009)3. - ISSN 1474-7065 - p. 192 - 199.
    In the 19th and the first part of the 20th century large parts of the sandy area of The Netherlands were transformed from heath and woodland into agricultural areas. These areas were made suitable for agricultural use by significantly adapting the existing water systems (improving existing brooks, digging new watercourses, etc.). Adaptations will once again be needed, as climate change will increase both precipitation and the peak flow flood waves in the Dutch large rivers. New, pre-emptive adaptations of the current waters system are needed to maintain good agricultural and living conditions, and to prevent catastrophes. Study of the reaction of the water system as a result of previous adaptations is directly relevant to current planning, since such study should reveal the likely long-term outcomes of future adaptations necessitated by climate change
    Voorkom vliegen, voordat je ze ziet vliegen!
    Mul, M.F. ; Brooks, M.D. ; Berg, A.W.H. - \ 2009
    BioKennis bericht Varkensvlees 9 (2009). - 4
    biologische landbouw - varkenshouderij - varkensstallen - diergezondheid - dierenwelzijn - plagenbestrijding - diptera - ziekteoverdracht - bedrijfshygiëne - organic farming - pig farming - pig housing - animal health - animal welfare - pest control - diptera - disease transmission - industrial hygiene
    Vliegen in de stal zijn hinderlijk en kunnen gezondheidsproblemen bij varkens veroorzaken. Wageningen UR Livestock Research heeft het afgelopen jaar de vliegenoverlast en bestrijdingsmethoden geïnventariseerd op biologische varkensbedrijven. Nu is het onderzoek gericht op het voorkomen en weren van vliegen. Dit bioKennisbericht geeft een overzicht van ontwikkelingsplaatsen van vliegen in de stal en tips om vliegenoverlast te voorkomen
    A simple approach to identify critical source areas for phosphorus leaching in the Netherlands
    Salm, C. van der; Schoumans, O.F. ; Walvoort, D.J.J. ; Groenendijk, P. ; Pleijter, M. - \ 2009
    Geophysical Research Abstracts 2009 (2009)11. - ISSN 1029-7006 - p. EGU2009 - 3623.
    High soil phopshorus contents in agricultural soils in the Netherlands cause excessive losses of P to surfacewaters. The reductions in P application rates in the present manure policy are not sufficient to reach surfacewater quality standards resulting from the European Water Framework Directive in all catchments by 2015.Accordingly, additional measures have to be considered to further reduce P loading to surface water. For a costeffective implementation of these measures an instrument to identify critical source areas for phosphorus leachingis indispensable. In the Netherlands phosphorus leaching at a national scale is simulated with a comprehensivemechanistic simulation model (STONE, Wolf et al., 2005) focusing on changes in P leaching with time. Theidentification of critical source areas requires simulations at a high spatial resolution. STONE is less suitable forthis purpose, because of the large number of input parameters required by this complex model. For this reason, asimple model (PLEASE: Phosphorus LEAching from Soils to the Environment; Schoumans et al., in prep.) hasbeen developed based on the same mechanistic process description for inorganic P as the complex model STONEand a simplified description of the lateral flow of water from soil to surface waters. With this model P leachingto surface waters can be calculated using readily available information of field characteristics like depth of thegroundwater table, precipitation surplus and P status and phosphorus adsorption capacity of the soil.To evaluate the performance of the model, it was applied to the Netherlands using the same input as thenational model. Parameterised in this way, PLEASE is a metamodel of STONE. The model was also testedon two small catchments: a catchment with sandy soils and high P accumulation and a clay catchment with amoderate P accumulation. The application at the national scale showed that the overall order of magnitude ofthe calculated leaching fluxes was quite comparable with results of the complex model. However, for individualfields, differences between the two models are sometimes considerable due to differences in the distribution ofthe lateral water fluxes with depth. The application at the catchment scale showed a good agreement betweenmeasured and simulated year average discharge of water and phosphorus. The simulated maps of P leaching forthe two catchments appeared to be plausible with highest P leaching fluxes in intensively used agricultural fieldsin wet areas close to brooks and rivers.Wolf, J. et al. (2005), The integrated modeling system STONE for calculating nutrient emissions fromagriculture in the Netherlands. Environmental Modeling and Software 18, 597-617.Schoumans, O.F., P. Groenendijk and C. van der Salm (in prep.). PLEASE: A simple procedure to determineP losses by leaching
    Assumption 0 analysis: comparative phylogenetic studies in the age of complexity
    Brooks, D.R. ; Veller, M.G.P. van - \ 2008
    Annals of the Missouri Botanical Garden 95 (2008)2. - ISSN 0026-6493 - p. 201 - 223.
    emerging infectious-diseases - a-posteriori methods - vicariance biogeography - historical biogeography - island biogeography - parsimony analysis - cladistic-analysis - contemporary time - area cladograms - species concept
    Darwin's panoramic view of biology encompassed two metaphors: the phylogenetic tree, pointing to relatively linear (and divergent) complexity, and the tangled bank, pointing to reticulated (and convergent) complexity. The emergence of phylogenetic systematics half a century ago made it possible to investigate linear complexity in biology. Assumption 0, first proposed in 1986, is not needed for cases of simple evolutionary patterns, but must be invoked when there are complex evolutionary patterns whose hallmark is reticulated relationships. A corollary of Assumption 0, the duplication convention, was proposed in 1990, permitting standard phylogenetic systematic ontology to be used in discovering reticulated evolutionary histories. In 2004, a new algorithm, phylogenetic analysis for comparing trees (PACT), was developed specifically for use in analyses invoking Assumption 0. PACT can help discern complex evolutionary explanations for historical biogeographical, coevolutionary, phylogenetic, and tokogenetic processes
    The shape of the transpiration reduction function under plant water stress
    Metselaar, K. ; Jong van Lier, Q. de - \ 2007
    Vadose Zone Journal 6 (2007)1. - ISSN 1539-1663 - p. 124 - 139.
    bodemwater - bodem-plant relaties - transpiratie - modellen - soil water - soil plant relationships - transpiration - models - available soil-water - leaf-area - balance model - root-system - crop growth - transport - wheat - evaporation - irrigation - responses
    Assuming transpiration to be reduced after a critical pressure head (usually chosen as −1.5 MPa or −150 m) at the root surface has been reached, transpiration rates in this so-called falling-rate phase were analyzed numerically for soils described by the van Genuchten–Mualem equations (numerical soils). The analysis was based on the differential equation describing radial flow to a single root.
    Assuming transpiration to be reduced after a critical pressure head ( usually chosen as -1.5 MPa or -150 m) at the root surface has been reached, transpiration rates in this so-called falling-rate phase were analyzed numerically for soils described by the van Genuchten-Mualem equations ( numerical soils). The analysis was based on the differential equation describing radial flow to a single root. Numerically, the system was simulated by an implicit scheme. It is shown that, at limiting hydraulic conditions, relative transpiration ( ratio between actual and potential transpiration) is equal to relative matric flux potential ( ratio between actual matric flux potential and matric flux potential at the onset of limiting hydraulic conditions). Given this equality, transpiration reduction functions as a function of soil water content and as a function of time are presented for five types of analytical soils: a constant diffusivity, Green and Ampt, Brooks and Corey, versatile nonlinear, and exponential soil. While in the case of constant diffusivity, relative transpiration decreases as a linear function of water content, for the remaining four cases the decrease is a concave function of soil water content. Numerical simulations also result in a concave shape, unless the difference between water content at the onset of limiting hydraulic conditions and at permanent wilting is very small, for example, at high root densities. These discrepancies may be explained by the relative importance of a transition period between the constant- and falling-rate phases.
    Plant species and functional group effects on abiotic and microbial soil properties and plant-soil feedback responses in two grasslands
    Bezemer, T.M. ; Lawson, C.S. ; Hedlund, K. ; Edwards, A.R. ; Brooks, A.J. ; Igual, J.M. ; Mortimer, S.R. ; Putten, W.H. van der - \ 2006
    Journal of Ecology 94 (2006)5. - ISSN 0022-0477 - p. 893 - 904.
    fatty-acid analysis - community structure - diversity - rhizosphere - vegetation - biota - dynamics - biomass - succession - management
    1 Plant species differ in their capacity to influence soil organic matter, soil nutrient availability and the composition of soil microbial communities. Their influences on soil properties result in net positive or negative feedback effects, which influence plant performance and plant community composition. 2 For two grassland systems, one on a sandy soil in the Netherlands and one on a chalk soil in the United Kingdom, we investigated how individual plant species grown in monocultures changed abiotic and biotic soil conditions. Then, we determined feedback effects of these soils to plants of the same or different species. Feedback effects were analysed at the level of plant species and plant taxonomic groups (grasses vs. forbs). 3 In the sandy soils, plant species differed in their effects on soil chemical properties, in particular potassium levels, but PLFA (phospholipid fatty acid) signatures of the soil microbial community did not differ between plant species. The effects of soil chemical properties were even greater when grasses and forbs were compared, especially because potassium levels were lower in grass monocultures. 4 In the chalk soil, there were no effects of plant species on soil chemical properties, but PLFA profiles differed significantly between soils from different monocultures. PLFA profiles differed between species, rather than between grasses and forbs. 5 In the feedback experiment, all plant species in sandy soils grew less vigorously in soils conditioned by grasses than in soils conditioned by forbs. These effects correlated significantly with soil chemical properties. None of the seven plant species showed significant differences between performance in soil conditioned by the same vs. other plant species. 6 In the chalk soil, Sanguisorba minor and in particular Briza media performed best in soil collected from conspecifics, while Bromus erectus performed best in soil from heterospecifics. There was no distinctive pattern between soils collected from forb and grass monocultures, and plant performance could not be related to soil chemical properties or PLFA signatures. 7 Our study shows that mechanisms of plant-soil feedback can depend on plant species, plant taxonomic (or functional) groups and site-specific differences in abiotic and biotic soil properties. Understanding how plant species can influence their rhizosphere, and how other plant species respond to these changes, will greatly enhance our understanding of the functioning and stability of ecosystems.
    Fermentation of wheat: effects of backslopping different proportions of pre-fermented wheat on the microbial and chemical composition
    Moran, C.A. ; Scholten, R.H.J. ; Tricarico, J.M. ; Brooks, P.H. ; Verstegen, M.W.A. - \ 2006
    Archives of Animal Nutrition 60 (2006)2. - ISSN 1745-039X - p. 158 - 169.
    liquid compound diets - 6-day storage period - fed ad-libitum - organic-acids - coproducts - feed - pigs - performance - food
    The objective of the study was to examine effect of backslop on the chemical and microbiological characteristics of fermented wheat (FW). Coarsely ground wheat was mixed with water (1:3 wt/wt) and inoculated with 6 log cfu ml(-1) each of an overnight culture of Lactobacillus plantarum and Pediococcus pentosaceus. Four fermentation treatments were conducted in 45 1, closed, PVC containers over 48 hours. Three treatments investigated the benefits of the addition of previously fermented wheat (backslopping, BSL) at different proportions (0.20, 0.33 or 0.42 kg) to freshly prepared wheat. The control treatment contained no addition of BSL. Elimination of coliforms from the FW within 48 h was only achieved through backslopping; where coliform bacteria counts decreased from approximately 6.5 log10 cfu ml(-1) to less than 3 log10 cfu ml(-1). There was no apparent advantage in increasing the backslop proportion above 0.20. However, the exclusion of coliform bacteria required the pH to remain below 4.0 for at a minimum of 24 h. The results of these studies indicate that fermentation of wheat has the potential to reduce the risk of feed-borne colibacillosis and provides a practical alternative to producers that cannot ferment multiple diets or have limited fermentation capacity.
    Inter-laboratory variation in in vitro gas production profiles of some selected feeds, using both manual and automated methods
    Rymer, C. ; Williams, B.A. ; Brooks, A.E. ; Davies, D.R. ; Givens, D.I. - \ 2005
    Animal Feed Science and Technology 123-124 (2005)1. - ISSN 0377-8401 - p. 225 - 241.
    temperature dried grass - neutral detergent fiber - fatty-acid production - fermentation kinetics - ruminant feeds - rumen fluid - pressure transducer - forages - degradability - degradation
    A study was conducted to estimate variation among laboratories and between manual and automated techniques of measuring pressure on the resulting gas production profiles (GPP). Eight feeds (molassed sugarbeet feed, grass silage, maize silage, soyabean hulls, maize gluten feed, whole crop wheat silage, wheat, glucose) were milled to pass a 1 mm screen and sent to three laboratories (ADAS Nutritional Sciences Research Unit, UK; Institute of Grassland and Environmental Research (IGER), UK; Wageningen University, The Netherlands). Each laboratory measured GPP over 144 h using standardised procedures with manual pressure transducers (MPT) and automated pressure systems (APS). The APS at ADAS used a pressure transducer and bottles in a shaking water bath, while the APS at Wageningen and IGER used a pressure sensor and bottles held in a stationary rack. Apparent dry matter degradability (ADDM) was estimated at the end of the incubation. GPP were fitted to a modified Michaelis¿Menten model assuming a single phase of gas production, and GPP were described in terms of the asymptotic volume of gas produced (A), the time to half A (B), the time of maximum gas production rate (tRM gas) and maximum gas production rate (RM gas). There were effects (P
    An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm
    Armstrong, R. ; Whisson, S.C. ; Pritchard, L. ; Bos, J.I.B. ; Venter, E. ; Avrova, A.O. ; Rehmany, A.P. ; Bohme, U. ; Brooks, K. ; Cherevach, I. ; Hamlin, N. ; White, B. ; Fraser, A. ; Lord, A. ; Quail, M.A. ; Churcher, C. ; Hall, N. ; Berriman, M. ; Huang, S. ; Kamoun, S. ; Beynon, J.L. ; Birch, P.R.J. - \ 2005
    Proceedings of the National Academy of Sciences of the United States of America 102 (2005)21. - ISSN 0027-8424 - p. 7766 - 7771.
    phytophthora-infestans - comparative genomics - disease resistance - potato famine - plant-cells - arabidopsis - evolution - products - elicitor - fungus
    Plants sense phosphate (Pi) deficiency and initiate signaling that controls adaptive responses necessary for Pi acquisition. Herein, evidence establishes that AtSIZ1 is a plant small ubiquitin-like modifier (SUMO) E3 ligase and is a focal controller of Pi starvation-dependent responses. T-DNA insertional mutated alleles of AtSIZ1 (At5g60410) cause Arabidopsis to exhibit exaggerated prototypical Pi starvation responses, including cessation of primary root growth, extensive lateral root and root hair development, increase in root/shoot mass ratio, and greater anthocyanin accumulation, even though intracellular Pi levels in siz1 plants were similar to wild type. AtSIZ1 has SUMO E3 ligase activity in vitro, and immunoblot analysis revealed that the protein sumoylation profile is impaired in siz1 plants. AtSIZ1-GFP was localized to nuclear foci. Steadystate transcript abundances of Pi starvation-responsive genes AtPT2, AtPS2, and AtPS3 were moderate but clearly greater in siz1 seedlings than in wild type, where Pi is sufficient. Pi starvation induced the expression of these genes to the same extent in siz1 and wild-type seedlings. However, two other Pi starvation-responsive genes, AtIPS1 and AtRNS1, are induced more slowly in siz1 seedlings by Pi limitation. PHR1, a MYB transcriptional activator of AtIPS1 and AtRNS1, is an AtSIZ1 sumoylation target. These results indicate that AtSIZ1 is a SUMO E3 ligase and that sumoylation is a control mechanism that acts both negatively and positively on different Pi deficiency responses
    Tight coupling between leaf area index and foliage N content in arctic plant communities
    Wijk, M.T. van; Williams, M. ; Shaver, G.R. - \ 2005
    Oecologia 142 (2005)3. - ISSN 0029-8549 - p. 421 - 427.
    brooks-range-foothills - tundra ecosystems - northern alaska - tussock tundra - responses - biomass - productivity - toposequence - vegetation - landscape
    The large spatial heterogeneity of arctic landscapes complicates efforts to quantify key processes of these ecosystems, for example productivity, at the landscape level. Robust relationships that help to simplify and explain observed patterns, are thus powerful tools for understanding and predicting vegetation distribution and dynamics. Here we present the same linear relationship between Leaf area index (LAI) and Total foliar nitrogen (TFN), the two factors determining the photosynthetic capacity of vegetation, across a wide range of tundra vegetation types in both northern Sweden and Alaska between leaf area indices of 0 and 1 m(2) m(-2), which is essentially the entire range of leaf area index values for the Arctic as a whole. Surprisingly, this simple relationship arises as an emergent property at the plant community level, whereas at the species level a large variability in leaf traits exists. As the relationship between LAI and TFN exists among such varied ecosystems, the arctic environment must impose tight constraints on vegetation canopy development. This relationship simplifies the quantification of vegetation productivity of arctic vegetation types as the two most important drivers of productivity can be estimated reliably from remotely sensed NDVI images.
    Report on the infauna sampling by TDI Brooks. Visit to Nigeria June 27th until June 30th 2004
    Boois, I.J. de - \ 2004
    IJmuiden : RIVO (Report C060/04) - 12 p.
    Ending a decade of deception: a valiant failure, a not-so-valiant failure, and a success story
    Brooks, D.R. ; Dowling, A.P.G. ; Veller, M.G.P. van; Hoberg, E.P. - \ 2004
    Cladistics-The International Journal of the Willi Hennig Society 20 (2004)1. - ISSN 0748-3007 - p. 32 - 46.
    brooks parsimony analysis - host-parasite coevolution - a-posteriori methods - historical biogeography - vicariance biogeography - cladistic biogeography - phylogenetic biogeography - associations - assumptions - speciation
    Prior studies involving two methods, Brooks Parsimony Analysis (BPA) and TreeMap, have found BPA to be the more reliable method. Recent criticisms leveled at these studies argue that the tests were unfairly created and biased in favor of BPA. The authors of a recent critique offered new exemplars to demonstrate flaws in BPA, plus a simple fix to correct the flaws found in TreeMap. A re-evaluation of their exemplars clearly shows that the authors' calculations are incorrect, their understanding of the methods is lacking, and that their simple fix does not work. Additional analyses using TreeMap 2.02 are run to show that TreeMap 2.02, like TreeMap 1.0, cannot adequately deal with widespread parasites, contrary to the claims of its supporters. Furthermore, the exemplars corroborate previous findings that BPA, when calculated correctly, is more reliable than TreeMap1.0 and TreeMap 2.02 and therefore the method of choice in coevolutionary and biogeographic studies
    Critique of parsimony analysis of endemicity as a method of historical biogeography
    Brooks, D.R. ; Veller, M.G.P. van - \ 2003
    Journal of Biogeography 30 (2003). - ISSN 0305-0270 - p. 819 - 825.
    vicariance biogeography - area relationships - a-posteriori - speciation - evolution - dispersal - associations - assumption-2 - coevolution - parasites
    Aim Assess the value of parsimony analysis of endemism as either an a priori (cladistic) and an a posteriori (phylogenetic) method of historical biogeography. Location World-wide. Methods Parsimony analysis of endemicity (PAE) and Brooks parsimony analysis (BPA). Results Parsimony analysis of endemicity is capable of finding correct and unambiguous area relationships only under scenarios of vicariance in combination with non-response to vicariance or extinction. An empirical comparison between PAE and BPA, using the poeciliid fish genera Heterandria and Xiphophorus , demonstrates that PAE fails to document much of the historical complexity in this relatively simple system. Main Conclusions The a priori assumptions of PAE are far more restrictive than those made by other a priori methods, limiting its utility as a method of cladistic biogeography. The inability of PAE to detect perfect vicariance or biogeographical histories involving dispersal, renders it unsuitable as a method of phylogenetic biogeography.
    A priori and a posteriori methods in comparative evolutionary studies of host-parasite associations
    Dowling, A.P.G. ; Veller, M.G.P. van; Hoberg, E.P. ; Brooks, D.R. - \ 2003
    Cladistics-The International Journal of the Willi Hennig Society 19 (2003). - ISSN 0748-3007 - p. 240 - 253.
    historical biogeography - vicariance biogeography - cladistic biogeography - parsimony analysis - area cladograms - phylogenetic systematics - component analysis - coevolution - speciation - statements
    Brooks parsimony analysis (BPA) and reconciliation methods in studies of host-parasite associations differ fundamentally, despite using the same null hypothesis. Reconciliation methods may eliminate or modify input data to maximize fit of single parasite clades to a null hypothesis of cospeciation, by invoking different a priori assumptions, including a known host phylogeny. By examining the degree of phylogenetic congruence among multiple parasite clades, using hosts as analogs of taxa but not presuming a host phylogeny or any degree of cospeciation a priori, BPA modifies the null hypothesis of cospeciation if necessary to maintain the integrity of the input data. Two exemplars illustrate critical empirical differences between reconciliation methods and BPA: (1) reconciliation methods rather than BPA may select the incorrect general host cladogram for a set of data from different clades of parasites, (2) BPA rather than reconciliation methods provides the most parsimonious interpretation of all available data, and (3) secondary BPA, proposed in 1990, when applied to data sets in which host-switching produces hosts with reticulate histories, provides the most parsimonious and biologically realistic interpretations of general host cladograms. The extent to which these general host cladograms, based on cospeciation among different parasite clades inhabiting the same hosts, correspond to host phylogeny can be tested, a posteriori, by comparison with a host phylogeny generated from nonparasite data. These observations lead to the conclusion that BPA and reconciliation methods are designed to implement different research programs based on different epistemologies. BPA is an a posteriori method that is designed to assess the host context of parasite speciation events, whereas reconciliation methods are a priori methods that are designed to fit parasite phylogenies to a host phylogeny. Host-switching events are essential for explaining complex histories of host-parasite associations. BPA assumes coevolutionary complexity (historical contingency), relying on parsimony as an a posteriori explanatory tool to summarize complex results, whereas reconciliation methods, which embody formalized assumptions of maximum cospeciation, are based on a priori conceptual parsimony. Modifications of basic reconciliation methods, embodied in TreeMap 1.0 and TreeMap 2.02, represent the addition of weighting schemes in which the researcher specifies allowed departures from cospeciation a priori, with the result that TreeMap results more closely agree with BPA results than do reconciled tree analysis results. (C) 2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.
    Cladistic and phylogenetic biogeography: the art and the science of discovery
    Veller, M.G.P. van; Brooks, D.R. ; Zandee, R. - \ 2003
    Journal of Biogeography 30 (2003). - ISSN 0305-0270 - p. 319 - 329.
    historical biogeography - vicariance biogeography - parsimony analysis - area cladograms - component analysis - a-posteriori - speciation - statements - dispersal - assumption-1
    All methods used in historical biogeographical analysis aim to obtain resolved area cladograms that represent historical relationships among areas in which monophyletic groups of taxa are distributed. When neither widespread nor sympatric taxa are present in the distribution of a monophyletic group, all methods obtain the same resolved area cladogram that conforms to a simple vicariance scenario. In most cases, however, the distribution of monophyletic groups of taxa is not that simple. A priori and a posteriori methods of historical biogeography differ in the way in which they deal with widespread and sympatric taxa. A posteriori methods are empirically superior to a priori methods, as they provide a more parsimonious accounting of the input data, do not eliminate or modify input data, and do not suffer from internal inconsistencies in implementation. When factual errors are corrected, the exemplar presented by M.C. Ebach & C.J. Humphries (Journal of Biogeography, 2002, 29, 427) purporting to show inconsistencies in implementation by a posteriori methods actually corroborates the opposite. The rationale for preferring a priori methods thus corresponds to ontological rather than to epistemological considerations. We herein identify two different research programmes, cladistic biogeography (associated with a priori methods) and phylogenetic biogeography (associated with a posteriori methods). The aim of cladistic biogeography is to fit all elements of all taxon–area cladograms to a single set of area relationships, maintaining historical singularity of areas. The aim of phylogenetic biogeography is to document, most parsimoniously, the geographical context of speciation events. The recent contribution by M.C. Ebach & C.J. Humphries (Journal of Biogeography, 2002, 29, 427) makes it clear that cladistic biogeography using a priori methods is an inductivist/verificationist research programme, whereas phylogenetic biogeography is hypothetico-deductivist/falsificationist. Cladistic biogeography can become hypothetic-deductive by using a posteriori methods of analysis
    Assessing modes of speciation : range asymmetry and biogeographical congruence
    Green, M.D. ; Veller, M.G.P. van; Brooks, D.R. - \ 2002
    Cladistics-The International Journal of the Willi Hennig Society 18 (2002). - ISSN 0748-3007 - p. 112 - 124.
    Lynch [1989, in "Speciation and Its Consequences" (D. Otte and J. A. Endler, Eds.), pp. 527–553, Sinauer, Sunderland, MA, proposed a methodology for assessing the frequency of occurrence of various modes of initiating species formation, using a combination of phylogenetic relationships and relative size of geographic ranges for sister species and sister groups. Historical biogeography provides an alternative criterion for assessing modes of species formation. Species whose distributions conform to a general (replicated in multiple clades) pattern of area relationships are deemed to be the result of vicariance (including microvicariance) regardless of the details of current geographic range. Species exhibiting unique biogeographic distributions are the result of peripheral isolates speciation and postspeciation dispersal. Lineage duplications indicate sympatric speciation. An empirical assessment of this alternative approach was performed using the most recent phylogenetic trees and geographical distribution data on the Mesoamerican poeciliid fish comprising the genera Xiphophorus and Heterandria. The single area cladogram produced by secondary Brooks Parsimony Analysis indicates 3 vicariant events (accounting for seven extant species and the common ancestor of the northern swordtails, which are not further analyzed) and at least 13 episodes of peripheral isolates speciation. Two of the 10 areas considered in previous analyses are vicariant areas of endemism, 1 is historically unique due to a single episode of peripheral isolates speciation, and the remaining 7 have reticulated histories of speciation. The results corroborate inferences of speciation modes made by Lynch for the same data.
    A posteriori and a priori methodologies for testing hypotheses of causal processes in vicariance biogeography
    Veller, M.G.P. van; Kornet, D.J. ; Zandee, M. - \ 2002
    Cladistics-The International Journal of the Willi Hennig Society 18 (2002). - ISSN 0748-3007 - p. 207 - 217.
    Methods used in vicariance biogeography fall into the categories of a posteriori methods (e.g., Component Compatibility Analysis and Brooks Parsimony Analysis) and a priori methods (e.g., Component Analysis, Reconciled Tree Analysis, and Three Area Statement Analysis). Each category corresponds to a particular methodology that arrives at general area cladograms by testing null hypotheses in a particular way. A posteriori methods assume the process of vicariance only (A0) as a common cause of the distribution of different monophyletic groups of taxa under the null hypothesis. Whenever a parsimony analysis of combined data from these monophyletic groups results in a general area cladogram with homoplasy, the null hypothesis is rejected and extinction and dispersal are invoked a posteriori as ad hoc process explanations. A priori methods assume not only vicariance (A0) but also combinations of vicariance with the processes of extinction (A1) and dispersal (A2) as possible causes of the distribution of the taxa of different monophyletic groups. Each assumed set of processes corresponds to a different null hypothesis. Under the assumption of independence and thus additivity of the processes involved, the sets of area cladograms obtained under A0, A1, and A2 from data of each monophyletic group must be inclusive (requirement I). Whenever no congruent area cladograms are found in the intersection of sets of area cladograms derived under the same assumption for different monophyletic groups (II), the corresponding null hypothesis is rejected.
    The effect of laboratory on the rate and extent of gas production in vitro
    Rymer, C. ; Williams, B.A. ; Brooks, A.E. ; Givens, D.I. - \ 2000
    In: Proceedings of the BSAS Winter Meeting in Scarborough, Scarborough 20-22 March 2000. - Scarborough : BSAS, 2000 - p. 45 - 45.
    Quantification of uncertainty in climate change impact assessment
    Downing, T.E. ; Barrow, E.M. ; Brooks, R.J. ; Butterfield, R.E. ; Carter, T.R. ; Harisson, P.A. ; Hulme, M. ; Oleson, J.E. ; Porter, J.R. ; Schellberg, J. ; Semenov, M.A. ; Vinther, F.P. ; Wheeler, T.R. ; Wolf, J. - \ 2000
    In: Climate Change, Climatic Variability and Agriculture in Europe / Downing, T.E., Harrison, P.A., Butterfield, R.E., Lonsdale, K.G., Oxford, UK : Environmental Change Institute - ISBN 9781874370222 - p. 435 - 441.
    Review and comparison of scaling-up methods
    Butterfield, R.E. ; Bindi, M. ; Brooks, R.J. ; Carter, T.R. ; Delecolle, R. ; Downing, T.E. ; Harnos, Z. ; Harrison, P.A. ; Iglesias, A. ; Olesen, J.E. ; Orr, J.L. ; Semenov, M.A. ; Wolf, J. - \ 2000
    In: Climatic Change, Climatic Variability and Agriculture in Europe / Downing, T.E., Harrison, P.A., Butterfield, R.E., Lonsdale, K.G., Oxford, UK : Environmental Change Institute - ISBN 9781874370222 - p. 393 - 414.
    ABC transporters and their impact on pathogenesis and drug sensitivity
    Andrade, A.C. ; Zwiers, L.H. ; Waard, M.A. de - \ 1999
    In: Pesticide Chemistry and BioScience / Brooks, G.T., Roberts, T.R., - p. 221 - 235.
    A protocol to evaluate the effectiveness of odor control additives.
    Miner, R. ; Godwin, D. ; Brooks, P. ; Rulkens, W. ; Kielich, C. - \ 1995
    In: Proc. 7th Int. Symp. on Agricultural and food processing wastes, C.C. Ross (ed.). Chicago - p. 13 - 25.
    Computer supported reconnaissance planning : implementing a planning methodology with geographical information system in Noord-Brabant, the Netherlands
    Eweg, R. - \ 1994
    Agricultural University. Promotor(en): F. Kleefmann; H.F.L. Ottens. - Wageningen : WAU - ISBN 9789054852582 - 227
    ruimtelijke ordening - planning - beleid - ontwikkeling - geografische informatiesystemen - nederland - noord-brabant - physical planning - planning - policy - development - geographical information systems - netherlands - noord-brabant

    Goal
    One of the themes of the research at the Department of Physical Planning and Rural Development in Wageningen Agricultural University is the planning within the field of tension between sustainability and flexibility. This research has resulted in a method called the 'reconnaissance planning approach', first described by Kleefmann, in which possible directions of development are formulated for an area. The aim of this approach is not only to find the best possible spatial organization for an area, but also to encourage the discussion about the normative choices that underlie a planning process. Information systems are regarded as valuable means to operationalize this methodology.

    Another Wageningen researcher, van Lammeren, developed a prototype of a planning support system named RISOR. The structure of the RISOR system was based on an analysis of the planning methodology as described by Kleefmann. The research described in this thesis is a further elaboration of the work done by van Lammeren and Kleefmann.
    Its main goal was:

    'To operationalize the methodology of 'searching for possible directions of development' (i.e. the reconnaissance planning approach), at a regional level, using Geographical Information Systems. From the results of a case study, it should be possible to evaluate the concept of the planning support system RISOR and to assess that system's structure in terms of its capacity to store the knowledge used and generated during the case study in an accessible way'.
    This goal was expressed in three questions:
    - how can the reconnaissance planning approach be operationalized at a regional level?
    - how can Geographical Information Systems support such an operationalization?
    - is the structure of the prototype of RISOR sufficient to store the knowledge acquired during the planning process?

    At the beginning of the research, a study area had to be chosen. The choice was determined by methodological considerations, availability of data and opportunities for cooperation with colleagues during the research. These considerations resulted in the catchment areas of the lowland brooks Beerze, Reuse] and Voorste Stroom in the province of Noord Brabant being selected as the study area. For practical reasons, the research was limited to agriculture and nature, particularly their physical aspects. Additionally, some economic information was derived from economic statistics.

    Methodology
    In the case study, a reconnaissance planning process was carried out, within the constraints described above and the practical and methodological constraints connected with the laboratory situation in which the process was carried out. Because of the conceptual nature of the planning theory and RISOR, plus the limited experience regarding GIS applications in planning and the constraints of the available facilities, this research was exploratory in nature.

    The aim of the research was to carry out a reconnaissance planning process with the help of GIS and to describe systematically the main knowledge types discemed by the RISOR information system: object, normative and process knowledge. The methods used during the planning process constitute the 'method knowledge'. Subsequently, these knowledge types had to be stored in the databases of RISOR.

    The object knowledge was generated by collecting and digitizing. The planning process began with the formulation of normative notions for the plan construction and the drawing up of the accompanying plans. Final stages of the process were the visualization and the evaluation of the resulting plans. The planning process was done using GIS. Finally, the knowledge used in and resulting from the case study was stored in the RISOR system. To make this possible, the planning process carried out had to be described in terms of the RISOR concept.

    Results
    The spatial organization in the study area, i.e. the object of planning, was described according to the systematics of a theoretical model of the socio-physical organization. So that they could be inserted in the GIS, these theoretical models were formalized. Both types of models constitute the basic object knowledge used in the case study.

    In this case study, three types of normative knowledge were discerned, based on their abstractness and on statements regarding the planning process. The most abstract normative knowledge was called 'intention'. Two intentions were formulated:
    1 . an anthropocentric intention, with privately owned means of production and a governing body that 'follows' the market, from a technocratic position,
    2. an ecocentric intention, with privately owned means of production and a governing body that 'guides' the market in a sociocratic way.

    In the process knowledge, the normative, object and method knowledge are integrated. A systematic description of the planning process constitutes the process knowledge. A description of the various (GIS) methods and techniques which had been employed formed part of the process knowledge. The planning process in the case study was unfolded into four phases: description, interpretation, concrete intentions and plan generation. It was preceded by the formulation of intentions and followed by the decision-making phase. These six phases were taken as a guideline for the systematic description of the planning process. The resulting maps of the plans show the possible spatial organizations for the two normative intentions. The final part of the case study involved storing the knowledge categories in the RISOR system.

    Conclusions
    In answer to the question of how GIS could support an operationalization of the reconnaissance planning approach, it is concluded from the experiences obtained during the case study that the raster software used in that study was an adequate too] to model the object and the segments of the planning process itself. Its speed, ability to handle large quantities of complex data and to evaluate the results of each step, and the facilities for registering the process with the help of command files proved essential. Furthermore, it is concluded that at the start of a GISsupported planning process, a suitable methodology and analysis model have to be chosen to serve as a basis for that process; it should be carefully considered if and where the use of GIS will support the process.

    Another conclusion is that GIS can only be used for activities that can be described in formal models, and therefore it is not to be expected that an entire planning process can be automated. The development of knowledge systems will probably not only lead to more attention being paid to the knowledge used in the planning process, but will also allow the experience and expertise of specialists and other planners that was developed in earlier projects to be exploited. The advantage of the reconnaissance planning approach is that by using it the planning process will lose its 'black box' character, and that GIS will enable the discussion of the spatial models resulting from a planning exercise to be brought forward and will enlarge the scope for discussing the process itself.

    Although the overall conclusion is that the structure of the RISOR system satisfied the requirements for storing the types of knowledge acquired during the case study, the system could still be improved further by making its classification of the knowledge and access to the database more flexible, adding modules for storing information about the method knowledge, and increasing its user-friendliness.

    Regarding the planning methodology, it is concluded that the case study was not a true replication of a reconnaissance planning approach, as it was not the result of interdisciplinary teamwork, the intentions were not the result of a political discussion and there was no final discussion and decision about the resulting spatial models. Nevertheless, the case study illustrated the first section of a reconnaissance planning process, restricted by constraints on time and available labour. It certainly demonstrated that reconnaissance planning could be operationalized at a regional level using GIS, within the constraints of the laboratory setting of the study.

    As the changing position of government in society seems to advocate exploratory planning exercises, the applicability of the reconnaissance planning approach in practice was discussed. It is concluded that the application of reconnaissance planning exercises would strengthen the process of searching for the most appropriate and desired future spatial development.

    Refuge Begonias : taxonomy, phylogeny and historical biogeography of Begonia sect. Loasibegonia and sect. Scutobegonia in relation to glacial rain forest refuges in Africa
    Sosef, M.S.M. - \ 1994
    Agricultural University. Promotor(en): L.J.G. van der Maesen, co-promotor(en): J.J.F.E. de Wilde. - S.l. : s.n. - ISBN 9789054852438 - 306
    begoniaceae - taxonomie - plantengeografie - begoniaceae - taxonomy - phytogeography - cum laude

    Begonia is a genus of + 1000 species and is represented in all tropical areas. In Wageningen, under the guidance of dr J.J.F.E. de Wilde, the continental African begonias are being studied. Continental Africa has some 120 species, divided over 10 sections, and compared with the amount of species on other continents it is poor. A study on two of those sections with a total of 40 species is recorded in this work. The status of these species was in urgent need of revision, and it was questionable whether the two sections could be upheld.
    Some other important research questions are related to the theory on glacial rain forest refuges.

    The taxonomic level achieving the rank of section or genus is rather arbitrarily defined and it is being applied differently throughout the plant kingdom.
    In this study, species are approached according to the biological species concept. Subspecies are regarded as evolutionary entities separated in space, while varieties occur sympatrically.

    An extensive morphological study is the basis for distinguishing the separate species. The two sections are characterized a.o. by a creeping rhizome, a monochasial inflorescence with strongly reduced axes, indehiscent fruits, and male and female flowers with 2 perianth segments that are often bright yellow. Important diagnostic features for the separate species are found in the shape of the ovary and in the shape and the indumentum of the leaves. No clear delimitation between the two sections could be made on the basis of exclusively macromorphological characters (but see below).

    Former studies revealed a wide variety of leaf anatomical characters within Begonia. A leaf anatomical investigation of the species treated here was performed. Its primary objective was to acquire supplementary characters for the phylogenetic analysis, in order to obtain a more concrete and broader basis. The second objective was to investigate whether anatomical differences between the two sections could be identified.

    Leaf anatomy was studied by means of electron microscope research and the analysis of transverse sections. The results are considered to be satisfactory, as both goals mentioned above were reached. It was demonstrated that even within this group of closely related species a wide variety of anatomical characteristics exists, which in many cases support phylogenetic relationships already advanced upon the results of the macromorphological study.

    Important leaf anatomical characters are:
    - the presence or absence of a cuticula structure on the hairs,
    - the presence of short, sausage-shaped, often clustered glandular hairs or of longer, solitary, r-shaped ones,
    - the presence of sclerenchyma around the vasculary bundles,
    - the size of the epidermal cells in relation to that of the cells of the palisade parenchyma below them.
    Some leaf anatomical characters may be regarded as adaptations to the often deeply shaded habitat conditions in which the plants grow naturally.

    Anatomical characteristics of the ovary were investigated and also used for the phylogenetic analysis. Some important ones are the shape of the placentae, the shape of the septa and the arrangement of the ovules.
    The vascularisation within the ovary was analysed through series of cross sections. Former research suggested the activity of 2 separate meristems in shaping the ovary. This view was supported by research performed at Wageningen on the vascularisation within species of the section Tetraphila. The vascularisation of the species studied here does, however, not support this hypothesis and suggests a 'normal' development from carpels.
    The anatomical structure of papillae on the style also shows variation which is indicative for common descent.

    Micromorphological characters of the seeds were investigated earlier by colleagues in Amsterdam and they proved to be useful in delimiting sections within the genus Begonia. Some relevant characters were selected and added to the datamatrix used in the phylogenetic analysis.

    Species of the sections studied here have been artificially hybridized in the past, both mutually and with species from quite different sections. Some putative natural hybrids have also been observed. In only one case this possibly concerned hybridization with a species from a different section, viz. the closely related Filicibegonia.
    Most species of the sections Loasibegonia and Scutobegonia grow on medium to heavily shaded sites in humid tropical rain forest. They are terrestrial and occur on comparatively acid, often clayey soils with a low Mg-content.
    Many of the species are difficult to cultivate and demand a high relative humidity, a light, comparatively acid substrate and protection against direct sunlight.
    Generally, the species flower during distinct periods, usually twice a year. The flowers of several species show sleeping movements and are closed during parts of the day and night. It is still quite uncertain how pollination takes place, although insect pollination is the most likely possibility. Maturation of the fruit often takes several months. The seeds are released close to the mother plant from slowly disintegrating fruits and seed dispersal therefore does not seem to be very effective.

    Taxonomy strives after a stable and natural system of classification. A strict reflection of genealogical relationships in nomenclature is not compatible with its stability. The acceptance of a certain kind of paraphyletic clades as genera offers a solution.
    Most likely the two sections studied here form together a monophyletic group. The section Filicibegonia represents the most plausible outgroup.
    On account of a theoretical presupposition, a particular treatment of polytypic characters in a phylogenetic analysis is being proposed.
    A datamatrix for the 40 species and 132 characters was drawn up and analysed by means of cladistic methods. A first analysis yielded a very instable result with a comparatively large amount of 'weak' characters. That is why a weighting method was developed and applied. It diminishes the influence of 'weak' characters on the final cladogram structure. After application of this method 7 monophyletic subgroups could be identified. In addition, two of those were analysed separately in order to reveal their ingroup structure. The definite position of 5 species remained uncertain. The ultimately accepted phylogenetic tree is less parsimonous than the initial one.
    The most important conclusion that may be drawn from the genealogical relations is, that the sections Loasibegonia and Scutobegonia represent 2 monophyletic groups and therefore they should be upheld. Synapomorphic characters for the section Loasibegonia are the juicy petioles and the short, sausage- shaped glandular hairs. The presence of a thin epidermis, sclerenchyma around the tertiary nerves, a cuticula structure on the hairs, long r-shaped glandular hairs and an obtuse operculum of the seed is characteristic for species belonging to the section Scutobegonia.

    During the last glacial (± 70,000 - 12,000 year B.P.) in tropical Africa it was considerably cooler, + 4°C, and there was much less precipitation than at present. As a result the area of lowland rain forest presumably shrank considerably and ultimately disintegrated into a number of small refuges, situated as islands within an area occupied by more drought-resistant vegetation. Under these circumstances the area of montane rain forest probably expanded locally. Consequently, when speaking of rain forest refuges, one must make a clear distinction between lowland and montane rain forest.
    The Begonia species studied here are practically all confined to shaded, humid places in tropical lowland rain forest. During the last glacial, they will have survived almost exclusively in the refuges. Since, moreover, their seed dispersal seems not to be very effective, the location of the former refuges may be deduced from their present-day distribution.
    Begonia taxa happen to occur concentrated indeed within the main refuge localities postulated by other researchers, viz. in Liberia/Ivory Coast, in Cameroon/Gabon and in eastern Zaire. Within the Cameroon/Gabon area some 5 or 6 smaller areas with a high number of endemics can be denoted. These coincide remarkably well with the areas earlier indicated as possible refuges on the basis of other data. This strong conformity supports the view that these begonias may be regarded as dependable indicators of former refuges. As such they point to the possibility that also the Mayombe area and possibly the Doudou Mountains represent former lowland rain forest refuges.
    The existance of geographically isolated refuges formed a stimulant for speciation processes. Because of their short life cycle and the plasticity of their characters, the present species should be capable to evolve rapidly. Whether this has indeed happened under the influence of the development of refuges is an important question, that is studied next by means of a historical biogeographic analysis.
    Because it is plausible that the localities of former refuges will have retained a high degree of biodiversity into our days, knowledge about their location is of prime importance for nature conservation activities.

    By means of historical biogeographical research it is attempted to reconstruct the geological and climatological developments, using the phylogeny in combination with the distribution patterns of taxa. Nowadays, cladistic methods are often used, and among these Brooks Parsimony Analysis is considered theoretically the most suitable.
    In all, 25 areas of endemism have been demarcated. A first analysis lead to a poor result due to the comparatively large quantity of areas lacking their own endemic Begonia taxa. Eliminating these areas from the analysis yielded a better result, which was, however, still not optimal owing to the uncertain position within the areagram of the Doudou Mountains. Disregarding the latter area yielded an acceptable result. Eliminating areas seems to lead to good results in the present case, but the precise theoretical consequences of such actions need to be further investigated.
    A core area, composed of some 5 areas in Cameroon and Gabon, can be identified in all analyses that were performed. It coincides comfortably with the 'Lower Guinea' region often cited in floristical studies.
    Because the analyses show that sister species rarely occupy adjacent areas, remarkably few vicariance events seem to have occurred. If vicariance did occur during the last and previous glacials, this is perhaps concealed at present because of renewed dispersal after each occasion. The relationships between the areas seem to be more of a reflection of floristic similarity, rather than of a common history.
    There are indications for the presence of a demarcation line along the Sanaga River and another one across Equatorial Guinea.

    A revision of the sections Loasibegonia and Scutobegonia, including a key to the taxa, is presented. The taxa are accompanied by extensive descriptions, drawings, distribution maps, ecological notes and other relevant data. Recently, 14 new species have been published. In the present work the following additional new taxa are described and new combinations proposed:
    Begonia letouzeyi Sosef
    Begonia prismatocarpa W.J. Hooker subsp. delobata Sosef
    Begonia prismatocarpa W.J. Hooker subsp. petraea (A. Chev.) Sosef
    Begonia quadrialata Warb. subsp. quadrialata var. pilosa Sosef
    Begonia quadrialata Warb. subsp. nimbaensis Sosef
    Begonia quadrialata Warb. subsp. dusenii (Warb.)
    Sosef Begonia scapigera Hook.f. subsp. australis Sosef
    The section Loasibegonia now comprises 19 species, 10 subspecies and 2 varieties. The section Scutobegonia has 21 species and 2 varieties.

    Landschapsecologie en ruimtelijke organisatie in riviersystemen : een onderzoek naar de landschapsecologie van riviersystemen en de overheidszorg daarvoor in planning en beleid
    Jongman, R.H.G. - \ 1993
    Agricultural University. Promotor(en): F. Kleefmann; C.W. Stortenbeker. - S.l. : Jongman - ISBN 9789054851523 - 142
    landschap - landschapsecologie - ruimtelijke ordening - planning - beleid - ontwikkeling - landschapsbouw - stroomgebieden - nederland - landscape - landscape ecology - physical planning - planning - policy - development - landscaping - watersheds - netherlands

    Landscape ecological research in the Netherlands has been fruitful because of the mutual exchange of ideas and results of fundamental and applied research. This research project has been focused on methodologies for application of fundamental landscape ecological research in planning for land use and water use with emphasis on nature conservation aspects. The object of research has been the river system, because the river system is both a fundamental landscape ecological unit and an administration unit.

    The theoretical concept of planning is based on the model of spatial organisation; this model has been worked out by differentiating the rather simple physical aspects into a 'spatial ecological structure'.This model is based on the idea that all species have an ecological web and that these webs together make the - natural - landscape. The main patterns and processes in the spatial ecological structure of river systems are climate and water discharge. Within this context organisms create their ecological webs and these webs together constitute the spatial ecological structure. This spatial ecological structure can be modified by man. Man-through his social organization has an important impact by ecological changes that modify the spatial ecological structure into a manmade physical organisation. It is a model of the interference between sustainability and dynamics. The spatial ecological structure has been used as the guiding principle for the landscape ecological analysis and the interference of landscape ecological processes with changes in society. Within this context the research questions have been formulated as:
    * the definition of the main processes in river systems that determine ecological development in time and space and its translation into guiding principles and constraints for nature conservation;
    * evaluation of planning and management of rivers and its related nature in the context of its objectives.
    To answer these questions several research projects have been carried out, that have all been published in the period 1990-1992. They concerned both questions and emphasised different aspects of the spatial ecological structure. The research projects are:

    Ecological classification of the climate of the Rhine catchment ( Int. J Biometeorology 1990, 34:194-203 ).
    In this research an ordination and classification has been carried out on the climate of the Rhine catchment based on data from meteorological stations. The objective of the classification is to provide an ecological interpretation of climate data. The climate of northern France, Belgium, Luxembourg, The Netherlands, The Federal Republic of Germany and northern Switzerland is divided into 5 classes, of which two, the atlantic and the subcontinental are subdivided further into subclasses.

    The climate classes can be interpreted ecologically and are correlated with floristic and vegetation data. The Rhine valley has a distinctive and characteristic climate. Interpolation of the classification has not been carried out, because of the uneven geographical spread of the sites in the dataset.

    The position of the Rhine valley as a separate subclass is striking. For the use of climatic data for modelling changes in climate in relation to hydrological effects, this will have minor implications, because the valley is just a section of the total drainage basin. For ecological interpretation of the Rhine catchment however, it will be of major importance, because also climatically the Rhine valley seems to function as a major ecological stream corridor in western Europe. Land use changes or climatic changes in this corridor might improve or hamper its functioning as such. Other rivers do not seem to be characterised by climatic differences in the same way and may not function as climate related stream corridors. They possibly do not have such pronounced effect on the surrounding landscape or insufficient climatic data are lacking to conclude on this.

    Vegetation, river management and land use in the Dutch Rhine floodplains (Regulated Rivers 1992 7(3):279-289.
    In this project the relation between vegetation and historical changes in ecological processes has been investigated. The floodplains of the Lower Rhine are situated in a densely populated area of The Netherlands. Although they are intensively used, the floodplains still fulfil important ecological functions. The lower Rhine is the downstream sedimentation zone of the River Rhine and its floodplains are characterised by river transported vascular flora originating from southern and eastern Europe.

    Using multivariate methods data from literature and field data on grasslands and former river beds have been analyzed to find trends in ecological changes. The consequence of continued sedimentation and diminished erosion is an increased drying out of the floodplains. Excavation and recultivation of former excavated land does not reverse the losses in flora and vegetation. Statistically there is a negative relationship between the characteristic dry fluvial flora and recultivated land.

    Also the natural transversal river gradient disappears together with its characteristic ecological diversity. Aquatic environments in the floodplains have been changed completely since the regulation works started in the 19th century. Most former river beds have disappeared by silting up. Data on short term vegetation succession confirm the long term analysis of map data.

    Dutch floodplain policy, regulation of landscape ecological processes ( Landschap 1992 9(l):17-29 ).
    In this project the relation between floodplain vegetation and the management of ecological processes has been investigated. Rivers are landscape ecological systems, characterised by dynamic processes. Floodplains are very important in the ecological functioning of the river system. The Rhine is a regulated river situated in a densely populated area. The Dutch Lower Rhine is the downstream sedimentation area of the river. Here the floodplains are strongly influenced by man during the last decades. In general there is a process of drying out going on in both the Upper Rhine and the Lower Rhine. River dynamics in the floodplains can be analyzed on basic processes as period and time of discharge, stream velocity, relative altitude and morphology.

    The importance of the floodplains has been recognised by all administrative levels and nature conservation and nature development has become a policy objective. To develop and execute a river floodplain policy translation of river dynamics into practical planning and management is needed. Little experience is available on the effectiveness of the means for policy execution. The available knowledge shows, that at this moment neither physical planning nor water management but only protection by Nature Conservation Law can be used to handle extreme cases.

    Conservation of brooks in small watersheds: a case for planning (Landscape and Urban Planning 1990 19:55-68).
    In this research project a simple regional water balance model has been made of the two regions in the Veluwe in order to qualify the consequences of adjacent land use and urban activities for the objectives of the National Park. Nature conservation is under stress in The Netherlands because of intensive land use and related water use. One of the main problems for the brook systems is planning of water use in order to maintain a locally high water-table.

    From a study of the water balance it is shown, that extraction in some parts of the research area causes water shortage for brook discharge. Water extraction is inevitable because of the dense population in the fringes of the national park. This leads to the conclusion that integration of research and co-ordination of physical planning and water use planning is needed to realise a sound nature conservation policy for this area.

    Landscape ecological and spatial impacts of climate change in two areas in the Netherlands (Earth surface processes and Landforms 1991 16:639-652).
    Possible impact of climatic change on the water balance has been analyzed for the river Dommel and the Veluwe, an area drained by many very small brooks. The water balance has been calculated for the winter and the summer period. With help of four scenarios, based on GCM's, climate data from the dry year 1976 and land use scenarios the impact of climatic change and a possible superposed effect of acid precipitation is analyzed. The results show that although the yearly changes in the water balance are small in some cases, in all cases the fluctuations in the water balance between winter and summer period increase. Changes in precipitation and evapotranspiration are multiplied in water storage and runoff. This will have an important impact on water use planning and management.

    River systems: a leading part in a changing climate (Milieu 1992 7(3):68-75)
    A review has been made of research carried out on the impact of climate change in rivers. Climate change will influence the environment in Europe not only by changes in CO 2 -content and temperature, but also by changes in hydrology. Rivers might appear to be very sensitive to climatic variability and climate change. Most important impact is expected to be a change in mean discharge, extreme events and seasonality of runoff, which can cause important changes in erosion and sedimentation in various parts of Europe, quality of both ground water and surface water, functioning of the aquatic and semiterrestrial ecosystems and the availability of water resources.
    Consequences of climate change combined with potential synergistic effects of acidification will be dealt with sooner or later through the water system in many parts of Europe. Wise use of water, based on thorough analysis of the hydrological system and international co-operation at the level of river catchments are of utmost importance for anticipation on possible changes.

    From this research it can be concluded, that the natural basis for planning can be considered as a spatial ecological structure made by natural ecological processes and related patterns. Such a framework can be used as a guiding principle for landscape ecological modelling and the analysis of the impact of land use changes.
    The concept of Ecological Main Structure as developed in The Netherlands is a policy concept. Its scientific basis can be found in the spatial ecological structure of catchments. However, for the pleistocene pail of the Netherlands it can be concluded from the analysis that the objectives of the Dutch Ecological Main Structure can only partly be reached. Natural development can best be achieved for whole catchments because of the strong interaction between all land use. A complicating factor is that all large Dutch rivers and many lowland streams originate from headwaters in other countries. This makes international co-ordination necessary.

    Dry grasslands in the floodplains of the major dutch rivers are significantly related with sites flooded less than two days a year and significantly not related with excavated and recultivated soils. They are severely under threat of extinction. Former river beds tend to silt up and especially the open oxbows and the tidal oxbows have disappeared. Both tendencies have important consequences for nature conservation strategy in the river area and especially for nature redevelopment projects.
    The use of physical planning regulations to maintain aquatic nature and wetlands has not yet been very successful, nor in planning nor in implementation and management. Intensive co-operation between the water boards and the municipalities is needed both in planning and in management of waters.
    The climate of the Rhine catchment can be differentiated into several types among which that of the Rhine valley. This can be of importance for research on the impact of climate change. However, it is not yet clear if other rivers have a comparable corridor.
    Consequences of climate change combined with potential synergistic effects of acidification will be dealt with sooner or later through the water system in many parts of Europe. Wise use of water, based on thorough analysis of the hydrological system and international co-operation at the level of river catchments are of utmost importance for anticipation on possible changes.

    Conservation of brooks in small watersheds: a case for planning.
    Jongman, R.H.G. - \ 1990
    Landscape and Urban Planning 19 (1990). - ISSN 0169-2046 - p. 55 - 68.
    Een model voor de simulatie van het fysische rijpingsproces van gronden in de IJsselmeerpolders
    Rijniersce, K. - \ 1983
    Landbouwhogeschool Wageningen. Promotor(en): R.H.A. van Duin, co-promotor(en): W.H. van der Molen. - Wageningen : Rijniersce - ISBN 9789012042994 - 156
    computersimulatie - mechanische eigenschappen - fysische eigenschappen - simulatie - simulatiemodellen - bodemvorming - bodemwatergehalte - nederland - flevoland - computer simulation - mechanical properties - physical properties - simulation - simulation models - soil formation - soil water content - netherlands - flevoland
    SUMMARY

    Introduction

    Subaqueous sediments, rich in clay and organic matter have a high watercontent and are unaerated and almost impermeable just after emergence. Such a sediment is inaccessible due to the low bearing capacity. Plant growth is restricted to a pioneer vegetation of plants, which are able to provide the oxygen demand of their own roots. Due to evapotranspiration in periods with a rainfall deficit the water content of the sediment decreases irreversibly. By capillary forces the soil particles are drawn to each other, so the bulk density increases. As a result, the surface will subside and crack formation starts. Water transport to open-field drains and tile-drains is then possible via the cracks. This dewatering-process is known as 'ripening'. Ripening can be subdivided into a physical, a chemical and a microbiological part. The physical part of the process, which can be considered as the motor of the entire process, is the topic of this study.

    Knowledge about this process is necessary to be able to predict the qualities of not yet reclaimed sediments and their rate of subsidence. Since the start of the IJsselmeerpolder project, research has been carried out to increase this knowledge. In the first period emphasis was given to research concerning dewatering-measures that had to be taken to obtain a ripened soil as fast as possible. Also much research was focused on the subsidence-rates. A first attempt for a quantitative integrated approach of the physical ripening process was given by SEGEREN (1966).

    To improve this quantitative insight, including the process effecting factors a numerical simulation model has been developed, based on a conceptual approach.

    Description of the process of physical soil ripening

    The soil profile in the IJsselmeerpolders can be roughly characterised as a layer of Holocene, mostly rich in clay and organic matter, with a thickness from nearly nil to over 7 m, underlain by Pleistocene, mostly sandy deposits (figure 3 and 4). The clay fraction is composed of app. 60% illite, 20% smectite and 20% kaolinite. The sediments are rich in calciumcarbonate, so they remain basic after reclamation.

    Just after emergence the water contents of the sediments are very high. At that moment app. 2.2 grams of water are bound by 1 gram of clay. In a completely ripened topsoil just 0.3-0.4 grammes of water are found per gram clay. The water content has been found to be linearly related to the clay and organic matter content during all the ripening stages (Eq. 2.1. ZUUR; 1958).

    The process of physical soil ripening can be approached by using waterbalances. The progress in ripening is positively influenced by periods with a high rainfall deficit and by discharge of water in periods with a rainfall surplus. During the ripening process the pF-curve, the permeability and the thickness of a layer change considerably. The formation of a waterbalance for a ripening soil is complicated by these changes.

    Under the climatic conditions in the Netherlands in an average year an evaporation surplus is found in summer and a rainfall excess in winter (figure 10). For the evaporation surplus in summer, which determines the progress in ripening, an average value of 163 mm is found, if the difference between the evaporation of a free water surface and the rainfall is taken into account. In very dry summers a value of 500 mm can be reached.

    In dry periods water is drawn from the soil by evapotranspiration. The soil layers close to the surface lose their water the most and the first, even if the soil is kept bare.

    Due to the difference in elevation between the water levels in the polders and in the surrounding lakes, seepage is found locally. Seepage has a negative effect on ripening. The amount of seepage is difficult to determine. Especially the non-discharged part of the seepage, which is responsible for a retardation of the ripening process, is difficult to measure.

    The permeability of an unripened soil is found to be app. 1.7.10 -4m.d -1. This value is found for different types of determination. No relation could be found between the permeability and the pore space or the clay and organic matter content. The permeability of a ripening soil increases by crack-formation up to values above 100 m.d -1. This 'crack-permeability' is completely determined by the existence of the cracks. The permeability of the compact soil between the cracks remains at the mentioned low value.

    The depth of the cracks increase during the process of ripening. For that reason the groundwater levels found for a certain amount of discharge will be lowered during ripening. So the progress in ripening can be illustrated by using so called Q-y figures of successive years. In these figures the relation between the discharge Q and the groundwater level y is given (figure 15 and 16).

    In the IJsselmeerpolders ripening is stimulated by the installation of dewatering-methods, such as ditches, open-field drains and subsurface tile drains and by the exploitation of the soils with arable crops. The usual scheme of crop rotation in the IJsselmeerpoiders is: oil seed rape, winter wheat and spring barley in the first three years, followed by oil seed rape or oats in the fourth year. By using crops, which can be harvested in summer, damage to the soil structure is prevented.

    Problems in the determination of relevant parameters

    Research on the process of physical soil ripening is hampered by several causes. Even on the often rather uniform soil layers in the IJsselmeerpolders an important variation in the results of laboratory measurements is found due to the non-uniformity of the samples. Due to unwanted but inevitable ripening during experiments, some parameters in an unripened soil can not be measured in the right way. The very low permeability of the soil makes it almost impossible to obtain correct values for groundwater levels. An area with unripened soils is difficult to enter, due to the low bearing capacity and to the lack of fixed points, like roads, church towers etc. For the above mentioned reasons it is very difficult to obtain sufficient data over a long period.

    Numerical simulation of physical soil ripening

    The development of the simulation model has proceeded by the formulation of a number of points of departure. The most important ones are:
    - insight in this process can only be achieved by a conceptual model
    - the soil moisture suction ψmust be used as the 'master variable', not only defining the storage and the permeabilities but also the rate of compaction
    - physical soil ripening can be simulated with a one-dimensional model
    - a cracked soil must be divided into cracks and compact soil; the parameters of the soil must be related to the compact soil.

    In the model, the soil profile is divided into layers, thin (0.5-2.0 cm) layers in the topsoil and thicker (up to 5 cm) layers in the subsoil. Every layer is defined by its clay and organic matter content and its bulk density. The content of solid parts in each layer remains the same during the simulation, so the thickness is variable.

    To allow a simulation of app. 10 years with acceptable costs, a new calculation method has been developed to find the ψ-profile on every time step. The calculation of this ψ- profile and all the ψ-dependant parameters is performed in the following way.

    A first estimate is chosen for ψin the uppermost layer. Based on this estimated value it is calculated which amount is delivered in this first layer. The delivered amount depends on the suction difference and the possible compaction. The difference between the needed and the delivered amount is transported from or to the second layer. This flux defines the value of ψin this layer, using Darcy's law. This procedure is repeated for all layers. At the last layer the integrated amounts of needed and delivered water must be equal, except for a small inaccuracy, which can be chosen. If the amounts are not equal, the total calculation is repeated, using a new estimate for ψin the first layer. The process of iteration is repeated until the given accuracy is reached. It is proved that the calculated solution for the ψ-profile is the only possible solution.

    The potential evaporation is calculated by multiplying the open water evaporation by a reduction factor, depending on the soil cover (Eq 4.19). When the soil suction in the topsoil reaches high values, the actual evaporation can have a smaller value than the potential one, due to a decreasing permeability.

    The potential transpiration is calculated by multiplying the difference between the open water evaporation and the actual evaporation by a reduction factor. Values for this reduction factor, related to the stage of development and the kind of crop for the months of the year, are given (table g). The withdrawal by the plant roots (the sink- term) is calculated, using a method given by HOOGLAND et al. (1981). This method is based on a preference for extraction in the upper layers and on the assumption that a certain maximum amount can be withdrawn from a volume unit of soil in a unit of time. The withdrawal is reduced if the soil suction exceeds values of 500 cm. A method has been developed to calculate pF-curves, using a data-base of pF-curves, determined in the laboratory. The pF-curves of clay soils (>8% clay) are defined by the bulk density and the clay and organic matter content. The pF-curves of sandy soils are only defined by the coarseness of the sand. The advantage of these calculation methods is that no pF-curves have to be delivered as input, an important advantage for ripening soils with changing pF-curves It is proved that a good agreement exists between the calculated and determinated pF-curves (tables 10 and 11).

    Approximation methods have also been developed for the relation between the soil suction ψand the permeability k. For the sandy soils the relations are obtained using the BROOKS and COREY-method. The saturated permeability is calculated for these soils with the formula given by KOZENY (Eq. 4.39). For the clay soils it is assumed that the saturated permeability remains on a value of 1.7 . 10 -4m.d -1, and the k-ψrelationship can be given as k = aψ -n. A linear relation was found between log a and the exponent n (Eq. 4.41). The value for the exponent n appeared to be related to the clay-content (Eq. 4.42). The approximation methods for both the pF-curves and the permeability are only valid for the compact soil.

    A new formula has been developed to calculate the rate of compaction (Eq. 4.52). This formula is based on the assumption of an existing relation between the logarithm of the grain stress in the soil and the pore space. Due to the compaction the bulk density will increase. As a result the surface will subside and cracks will be formed. A relation is given to calculate the distribution of the compaction over subsidence and crack-formation (Eq. 4.63). It is indicated that only subsidence can appear as a result of compaction if a soft layer is loaded by the upper layers. In this case developing cracks will be closed, due to this load and the weakness of the soil. A relation between the waterfactor n of the first non-cracked layer and the overburden pressure is given (figure 39).

    To save costs a simplified method has been developed to calculate the rewetting of the profile. An exact calculation of ψ-profiles during this rewetting-process is not essential for a ripening model.

    Validation and use of the model

    The developed simulation model is calibrated and tested, using measured data from research areas for subsidence in Zuidelijk Flevoland. Calibration was necessary while the values of two parameters in formula 4.55 could not be found in another way. Although more parameters had to be estimated, the calibration is restricted to these two parameters.

    Just a few research areas in Flevoland were suitable for testing. Even for these areas, on which many parameters had been measured, several input parameters had to be estimated. The amounts of rainfall and evaporation had not been recorded on the spot and had to be calculated using data of surrounding meteorological stations (Eq. 5.1).

    The results of the simulations are compared with the data, measured in the field. Most attention is given to a comparison between measured and calculated values for the depth of the cracks and the subsidence. The agreement between the measured and the calculated values is rather good (a.o. figure 52 and 53). A sensitivity analysis has been carried out to investigate the influence on the results of:
    - the length of the time step
    - the saturated and unsaturated permeabilities
    - the maximum rate of water withdrawal by plant roots
    - the constant K 2 in the compaction formula 4.55

    In particular a change in permeability proved to have an impressive influence on the results.

    Seven variants have been simulated to illustrate the application-possibilities of the developed model. A good ripened soil can be obtained if the soil is kept bare and the extraction of water occurs only by evaporation of the bare soil. A permanent grass vegetation instead of the normal crop rotation shows a slower progress in ripening of the soil. If, next to it, the dewatering depth is also restricted to 0.3 m, the progress in ripening is even slower.

    Nevertheless the groundwater depths in this variant are found in summer on a low level (figure 57). A very good ripened soil can be obtained if the soil is covered by a forest. Rather high groundwater levels are found in summer if any seepage is present (table 25). Seepage proved to have a negative influence on the progress of ripening. Progress is also diminished if a 4 cm thick sand layer, unpenetratable for plant roots, is assumed on a depth of 40 to 44 cm. The layers below this sand layer remain wet due to a decreased capillary rise, so they subside less (figure 59). A very fast ripening progress is found under dry climatic conditions. A variant has been simulated, using climatic data as found in the Rumanian Danube-delta.

    Limitations of the model

    A simulation model is defined as a simplified representation of a process in reality. A number of factors, influencing the process in reality, which are not taken into account in the model, are elucidated. The effects of frost, tillage activities and clay transport are not included in the model. It is assumed that a good simulation of the process of physical soil ripening is possible with a model in which these factors are not considered.

    All relations between parameters are based on research results as found in the IJsselmeerpolders As a result the application of the model in its present form is restricted to that area. Especially the mineralogical composition of the clay fraction will effect the process. Nevertheless the approach of the problem can be used as an example when developing a simulation model for physical soil ripening in other parts of the world.

    Artificial brooks on the Veluwe. An analysis of their use, significances and functioning to come to a policy of long-term protection
    Jongman, R.H.G. - \ 1982
    In: Proc. 6th.international symposium on problems of Landscape Ecological research, October 1982, Piestany Czechoslovakia
    The JH titre in the Colorado beetle in relation to reproduction e and diapause
    Kort, C.A.D. de; Khan, M.A. ; Bergot, B.J. ; Schooley, D.A. - \ 1981
    In: 'Juvenile Hormone Biochemistry' / Pratt, G.E., Brooks, G.T.,
    Dual response of corpora allata from Locusta migratoria after in vivo and in vitro exposure to precocene II
    Schooneveld, H. ; Orshan, L. - \ 1981
    In: 'Juvenile Hormone Bicchemistry' / Pratt, G.E., Brooks, G.T.,
    Comparison with the brooks and corey method
    Bloemen, G.W. - \ 1978
    Wageningen : I.C.W. (Nota / Instituut voor Cultuurtechniek en Waterhuishouding 1064) - 18
    horizontale stroming - capillaire opstijging - permeabiliteit - hysterese - bodemstructuur - bodemtextuur - pf-curve - horizontal flow - capillary rise - permeability - hysteresis - soil structure - soil texture - pf-curve
    Assessment of the n-values in a formula of brooks and corey for the calculation of hydraulic conductivity from grain size distribution - Pt. 2
    Bloemen, G.W. - \ 1977
    Wageningen : I.C.W. (Nota / Instituut voor Cultuurtechniek en Waterhuishouding 962) - 16
    horizontale stroming - capillaire opstijging - permeabiliteit - hysterese - bodemstructuur - bodemtextuur - pf-curve - horizontal flow - capillary rise - permeability - hysteresis - soil structure - soil texture - pf-curve
    Real and theoretical values of the exponent in a formula of brooks and corey for the calculation of hydraulic conductivities - Pt. 1
    Bloemen, G.W. - \ 1977
    Wageningen : I.C.W. (Nota / Instituut voor Cultuurtechniek en Waterhuishouding 952) - 14
    horizontale stroming - capillaire opstijging - permeabiliteit - hysterese - bodemstructuur - bodemtextuur - pf-curve - horizontal flow - capillary rise - permeability - hysteresis - soil structure - soil texture - pf-curve
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