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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A decade of uncertainty: Resolving the phyologenetic position of Diclinanona (Annonaceae), inlcuding taxonomic notes and a key to the species
Erkens, R.H.J. ; Chatrou, L.W. ; Chaowasku, T. ; Westra, L.I.T. ; Maas, J.W. ; Maas, P.J.M. - \ 2014
Taxon 63 (2014)6. - ISSN 0040-0262 - p. 1244 - 1252.
palms sheds light - historical biogeography - global biogeography - evolution - diversification - speciation - genus - taxa - biodiversity - convergence
The molecular phylogenetic placement of Diclinanona (Annonaceae) has been debated in the literature for a decade. On the basis of morphological studies the genus was thought to be related to genera now all placed in subfam. Annonoideae. This early hypothesis was supported by the first phylogenetic analyses of Annonaceae. However, more recently a placement in subfam. Malmeoideae was hypothesised based on an analysis of more plastid data, thus contradicting older but also new morphological findings and previous phylogenetic work. The current study uses newly sequenced plastid data for two species of Diclinanona to show that the earlier hypothesised placement was correct and discusses the (little) anatomical and morphological data on Diclinanona that is available in a phylogenetic framework. Furthermore, an online revision of the three species of Diclinanona is presented in order to update the taxonomic knowledge of this genus.
Repeated parallel evolution reveals limiting similarity in subterranean diving beetles
Vergnon, R.O.H. ; Leijs, P. ; Nes, E.H. van; Scheffer, M. - \ 2013
American Naturalist 182 (2013)1. - ISSN 0003-0147 - p. 67 - 75.
species-diversity - competition - dytiscidae - patterns - convergence - coexistence - coleoptera - divergence - morphology - community
The theory of limiting similarity predicts that co-occurring species must be sufficiently different to coexist. Although this idea is a staple of community ecology, convincing empirical evidence has been scarce. Here we examine 34 subterranean beetle communities in arid inland Australia that share the same habitat type but have evolved in complete isolation over the past 5 million years. Although these communities come from a range of phylogenetic origins, we find that they have almost invariably evolved to share a similar size structure. The relative positions of coexisting species on the body size axis were significantly more regular across communities than would be expected by chance, with a size ratio, on average, of 1.6 between coexisting species. By contrast, species' absolute body sizes varied substantially from one community to the next. This suggests that self-organized spacing according to limiting-similarity theory, as opposed to evolution toward preexisting fixed niches, shaped the communities. Using a model starting from random sets of founder species, we demonstrate that the patterns are indeed consistent with evolutionary self-organization. For less isolated habitats, the same model predicts the coexistence of multiple species in each regularly spaced functional group. Limiting similarity, therefore, may also be compatible with the coexistence of many redundant species. © 2013 by The University of Chicago.
Facilitating Learning in Multidisciplinary Groups with Transactive CSCL Scripts
Noroozi, O. ; Teasley, S.D. ; Biemans, H.J.A. ; Weinberger, A. ; Mulder, M. - \ 2013
International Journal of Computer-Supported Collaborative Learning 8 (2013)2. - ISSN 1556-1607 - p. 189 - 223.
argumentative knowledge construction - decision-making - memory-systems - macro-scripts - information - performance - organizations - environments - convergence - classroom
Knowledge sharing and transfer are essential for learning in groups, especially when group members have different disciplinary expertise and collaborate online. Computer-Supported Collaborative Learning (CSCL) environments have been designed to facilitate transactive knowledge sharing and transfer in collaborative problem-solving settings. This study investigates how knowledge sharing and transfer can be facilitated using CSCL scripts supporting transactive memory and discussion in a multidisciplinary problem-solving setting. We also examine the effects of these CSCL scripts on the quality of both joint and individual problem-solution plans. In a laboratory experiment, 120 university students were randomly divided into pairs based only on their disciplinary backgrounds (each pair had one partner with a background in water management and one partner with a background in international development studies). These dyads were then randomly assigned to one of four conditions: transactive memory script, transactive discussion script, both scripts, or no scripts (control). Learning partners were asked to analyze, discuss, and solve an authentic problem that required knowledge of both their domains, i.e., applying the concept of community-based social marketing in fostering sustainable agricultural water management. The results showed interaction effects for the transactive memory and discussion scripts on transactive knowledge sharing and transfer. Furthermore, transactive memory and discussion scripts individually, but not in combination, led to better quality demonstrated in both joint and individual problem solutions. We discuss how these results advance the research investigating the value of using scripts delivered in CSCL systems for supporting knowledge sharing and transfer.
Scripting for construction of a transactive memory system in multidisciplinary CSCL environments
Noroozi, O. ; Biemans, H.J.A. ; Weinberger, A. ; Mulder, M. ; Chizari, M. - \ 2013
Learning and Instruction 25 (2013)1. - ISSN 0959-4752 - p. 1 - 12.
argumentative knowledge construction - functional roles - group efficiency - convergence - performance - tools
Establishing a Transactive Memory System (TMS) is essential for groups of learners, when they are multidisciplinary and collaborate online. Environments for Computer-Supported Collaborative Learning (CSCL) could be designed to facilitate the TMS. This study investigates how various aspects of a TMS (i.e., specialization, coordination, and trust) can be facilitated using a transactive memory script that spans three interdependent processes (i.e., encoding, storage, and retrieval) in multidisciplinary CSCL. Sixty university students were assigned to multidisciplinary pairs based on their disciplines (water management or international development). These pairs were randomly assigned to a scripted or non-scripted condition and asked to discuss and solve a problem case. The script facilitated construction of a TMS, fostered learners' knowledge transfer and convergence, and improved the quality of problem solution plans. Specialization and coordination aspects of the TMS were mediators for the impacts of the script on joint but not individual problem solution plans.
A combination of functionally different plant traits provides a means to quantitatively predict a broad range of species assemblages in NW Europe
Douma, J.C. ; Aerts, R. ; Witte, J.P.M. ; Bekker, R.M. ; Kunzmann, D. ; Metselaar, K. ; Bodegom, P.M. van - \ 2012
Ecography 35 (2012)4. - ISSN 0906-7590 - p. 364 - 373.
vegetatietypen - plantenecologie - vegetation types - plant ecology - relative growth-rate - community ecology - strategies - diversity - convergence - divergence - patterns - model - components - nitrogen
Assembly theory predicts that filtering processes will select species by their attributes to build a community. Some filters increase functional similarity among species, while others lead to dissimilarity. Assuming converging processes to be dominant within habitats, we tested in this study whether species assemblages across a wide range of habitats can be distinguished quantitatively by their mean trait compositions. In addition, we investigated how many and which traits are needed to describe the differences between species assemblages best. The approach has been applied on a dataset that included 12 plant traits and 7644 vegetation releves covering a wide range of habitats in the Netherlands. We demonstrate that due to the dominant role of converging processes 1) the functional composition can explain up to 80% of the floristic differences between species assemblages using seven plant traits, showing that plant trait combinations provide a powerful tool for predicting the occurrence of species assemblages across different habitats; 2) to achieve a high performance, traits should be taken from different strategy components, i.e. traits that are functionally orthogonal, which does not necessarily coincide with low trait-trait correlations; 3) the different strategy components identified in this study correspond to the strategy components of some conventional plant ecological strategy schemes (PESS) schemes to describe the variation between individual species. However, some PESS merge traits into one strategy component that are shown to be functionally different when predicting species assemblages. If such PESS is used to predict assemblages, this leads to a loss in predictive capacity. Potentially, our new approach is globally applicable to quantify community assembly patterns. However this needs to be tested.
A plastid DNA phylogeny of Dasymaschalon (Annonaceae) and allied genera: Evidence for generic non-monophyly and the parallel evolutionary loss of inner petals
Wang, M. ; Thomas, D.C. ; Su, Y. ; Meinke, S. ; Chatrou, L.W. ; Saunders, R.M.K. - \ 2012
Taxon 61 (2012)3. - ISSN 0040-0262 - p. 545 - 558.
molecular phylogenetics - genetic interactions - bayesian-inference - uvaria annonaceae - mixed models - trees - convergence - mrbayes
Dasymaschalon and the closely related genera Desmos, Friesodielsia and Monanthotaxis together comprise ca. 170 species of trees, shrubs and woody climbers distributed in tropical Africa and tropical Asia. These genera form the desmoid clade, which, because of the presence of diverse flower and fruit syndromes including different types of pollination chambers and moniliform monocarps, offers an opportunity to investigate potentially ecologically significant shifts in flower and fruit characters. Despite its morphological diversity, however, generic delimitation within the desmoid clade is problematic and the intergeneric relationships of the constituent genera are only poorly understood. Bayesian, maximum likelihood and maximum parsimony analyses of plastid DNA sequence data ( matK, psbA-trnH, ndhF, rbcL, trnL-F; ca. 5.4 kb; 52 taxa) were used to clarify phylogenetic relationships within the desmoid clade. The evolution and taxonomic utility of selected fruit and flower characters was investigated with likelihood and parsimony ancestral character reconstructions. The results indicate problems in the current delimitations of Dasymaschalon and Friesodielsia. Friesodielsia as currently circumscribed is polyphyletic, with African Friesodielsia species allied to the African genus Monanthotaxis, and only distantly related to Asian representatives. The majority of Dasymaschalon species form a strongly supported clade, but three species are more closely related to Asian species of Friesodielsia. Ancestral character reconstructions indicate that seed number and monocarp shape are of limited value in generic circumscriptions, and that the three-petalled corolla characteristic of Dasymaschalon evolved independently twice within the desmoid clade. Disruptions to homeotic gene expression or strong selective pressure for a partial enclosure of the mature stamens and carpels by the corolla are hypothesised to underlie the parallel evolution of pollination chambers formed by outer petal homologues subsequent to inner petal loss
Trait assembly of woody plants in communities across sub-alpine gradients: Identifying the role of limiting similarity
Yan, B. ; Zhang, J. ; Liu, Y. ; Li, Z. ; Huang, X. ; Yang, W. ; Prinzing, A. - \ 2012
Journal of Vegetation Science 23 (2012)4. - ISSN 1100-9233 - p. 698 - 708.
functional traits - amazonian forest - neutral theory - niche - coexistence - height - growth - consequences - convergence - equivalence
Questions - Plant species can be assembled into communities through habitat filtering or species competition, but their relative roles are still debated. We do not know whether there is limited similarity between co-existing species when accounting for the parallel effect of abiotic habitat filtering and biotic competition. By accounting for such effects, we test the predictions of three theories (classic niche theory, the Hubbell neutrality theory and the Scheffer and van Nes theory) of community assembly. Location - Two vegetation transitions (a grazing gradient and a timber line ecotone) in a sub-alpine area of western Sichuan Province, China (31° 51'N, 102° 41'E). Methods - We used a null model to investigate the above plant community assembly theories on two sub-alpine gradients of woody vegetation. In the null model, species traits were constrained between the maximum and minimum trait values of observed communities to test the principle of limiting similarity between co-existing species by testing for even spacing of traits. We analysed traits characterizing growth strategies of stems, leaves and twigs, measured at the level of individuals in situ. Results - After accounting for variations in trait range, it became evident that six out of eight traits showed significantly uneven spacing within some plots, notably towards the forest end of the gradient, i.e. under increased competition pressure among woody plants. The Wilcoxon rank test showed that seven out of eight traits were significantly unevenly spaced within plots. The two transitions studied showed surprisingly similar patterns, despite their dissimilar precise drivers.
Industrial concentration and price-cost margin of the Indonesian food and beverages sector
Setiawan, M. ; Emvalomatis, G. ; Oude Lansink, A.G.J.M. - \ 2012
Applied Economics 44 (2012)29. - ISSN 0003-6846 - p. 3805 - 3814.
market-structure - cyclical fluctuations - manufacturing-industries - competition policy - performance - conduct - convergence - tests - panel
This article investigates trends in industrial concentration and its relationship with the price-cost margin in 54 subsectors of the Indonesian food and beverages sector in the period 1995 to 2006. This study uses firm-level survey data provided by the Indonesian Bureau of Central Statistics (BPS), classified at the five-digit International Standard Industrial Classification (ISIC) Level. The results show a significant increase in industrial concentration in 1995 to 1999, which coincided with the period of the economic crisis in Indonesia. After 1999, the industrial concentration exhibits a slightly decreasing long-term trend. Furthermore, the industrial concentration for all subsectors tends to converge to the same value in the long run. Additionally, results show that higher industrial concentration yields a higher price-cost margin. Finally, the introduction of the competition law in 1999 has slightly lowered industrial concentration and the price-cost margin
The increasing multifunctionality of Agricultural Raw Materials: Three dilemmas for Innovation and Adoption
Boehlje, M. ; Bröring, S. - \ 2011
International Food and Agribusiness Management Review 14 (2011)2. - ISSN 1096-7508 - p. 1 - 16.
sustainability - convergence - diffusion - industry - systems - foods
Agricultural raw materials are increasingly being used for multiple industries or sectors beyond the traditional fiber and nutrition industries: energy in the form of ethanol and biodiesel, industrial products such as polymers and bio-based synthetic chemicals and fibers, and pharmaceutical/health products such as functional foods, growth hormones and organ transplants. A combination of the new science of biotechnology, the new potential end uses of the products of that science and the broadened social/public goals that these products can respond to surfaces at least three fundamental challenges or dilemmas: (1) the competing goals dilemma, (2) the incumbent vs. new entrant competition dilemma, and (3) the industry boundaries dilemma. This paper reviews the innovation and adoption research related to renewables and the bio-economy, and then frames the three dilemmas with the objective of identifying important research issues and the conceptual frameworks that might be useful to analyze these issues.
Inter-regional output distribution: a comparison of Russian and Chinese experience
Herzfeld, T. - \ 2008
Post-Communist Economies 20 (2008)4. - ISSN 1463-1377 - p. 431 - 447.
regional economic-performance - growth - convergence - inequality - reforms - multimodality - federalism - evolution - tests
Several studies report increasing inter-regional inequality in transition countries over the course of economic reforms, but most of them fail to look at the underlying dynamics. Using the cases of Russia and China, this article analyses the evolution of inter-regional output distribution during economic transition. One non-parametric method, kernel density estimation, and one parametric method, a Markov chain transition matrix, are used to evaluate the shape of the inter-regional output distribution and to evaluate regions' mobility within this distribution. Estimated distributions for both countries are skewed with long right tails. Whereas the distribution for Russian regions shows multiple modes, the hypothesis of unimodality could not be rejected for Chinese regions over the last two decades. Stationary distributions of the Markov chain transition matrices support this finding. It turns out that increasing inequality and multimodality in both countries are driven by a few outliers with very distinct characteristics
Differential Evolution Markov Chain with snooker updater and fewer chains
Braak, C.J.F. ter; Vrugt, J.A. - \ 2008
Statistics and Computing 18 (2008)4. - ISSN 0960-3174 - p. 435 - 446.
monte-carlo - algorithms - optimization - convergence - spaces - mcmc
Differential Evolution Markov Chain (DE-MC) is an adaptive MCMC algorithm, in which multiple chains are run in parallel. Standard DE-MC requires at least N=2d chains to be run in parallel, where d is the dimensionality of the posterior. This paper extends DE-MC with a snooker updater and shows by simulation and real examples that DE-MC can work for d up to 50–100 with fewer parallel chains (e.g. N=3) by exploiting information from their past by generating jumps from differences of pairs of past states. This approach extends the practical applicability of DE-MC and is shown to be about 5–26 times more efficient than the optimal Normal random walk Metropolis sampler for the 97.5% point of a variable from a 25–50 dimensional Student t 3 distribution. In a nonlinear mixed effects model example the approach outperformed a block-updater geared to the specific features of the model
Regulatory Federalism and the Distribution of Air Pollutant Emissions
Bulte, E.H. ; List, J. ; Strazicich, M. - \ 2007
Journal of Regional Science 47 (2007)1. - ISSN 0022-4146 - p. 155 - 178.
environmental kuznets curve - unit-root hypothesis - time-series analysis - oil-price shock - economic-growth - great crash - us states - community characteristics - convergence - tests
Recent empirical work suggests that (i) incomes are converging through time, and (ii) income and pollution levels are linked. This paper weds these two literatures by examining the spatial and temporal distribution of pollution. After establishing that theoretical predictions about whether pollution will converge are critically linked to certain structural parameters, we explore pollution convergence using state-level data on two important pollutants¿nitrogen oxides and sulfur oxides¿from 1929 to 1999. We find stronger evidence of converging emission rates during the federal pollution control years (1970¿1999) than during the local control years (1929¿1969). These results suggest that income convergence alone may not be sufficient to induce convergence of pollutant emissions.
Investigations on multimodal sensory integration: Texture, taste, and ortho- and retronasal olfactory stimuli in concert
Bult, J.H.F. ; Wijk, R.A. de; Hummel, T. - \ 2007
Neuroscience Letters 411 (2007)1. - ISSN 0304-3940 - p. 6 - 10.
flavor release - human brain - perception - viscosity - sweetness - smell - convergence - sucrose
Perceptual interactions between odour and oral texture were explored in a study in which a cream odour was presented ortho- or retronasally at well-defined moments whilst milk-like foods with different viscosities, produced by adding a thickener, were present in the mouth. Gaseous (odour) and liquid (texture) pulses were presented using a specially-developed computer-controlled system of air-dilution olfactometry and pumps. Odour pulses, lasting 2 s, were presented either during a 3-s period in which a liquid filled the oral cavity, during a 3-s period in which the liquid was manipulated orally or during the swallowing of the liquid. Subjects rated the intensity of overall flavour, thickness and creaminess. Perceived flavour intensity was reduced with increasing viscosity of the liquid, irrespective of whether or not the odour was presented ortho- or retronasally. The odour stimulus increased the intensities of thickness and creaminess, but only when the odour was presented retronasally that is as if the odour would have originated from the liquid. Furthermore, this enhancement was most pronounced when odours coincided with swallowing, less pronounced when odours coincided with oral manipulation and absent when presented during mouth filling. The results suggest that cross-modal interactions are the rule rather than the exception, provided that multi-modal sensory integration has occurred.
A Markov Chain Monte Carlo version of the genetic algorithm Differential Evolution: easy Bayesian computing for real parameter spaces
Braak, C.J.F. ter - \ 2006
Statistics and Computing 16 (2006)3. - ISSN 0960-3174 - p. 239 - 249.
convergence - hastings - models
Differential Evolution (DE) is a simple genetic algorithm for numerical optimization in real parameter spaces. In a statistical context one would not just want the optimum but also its uncertainty. The uncertainty distribution can be obtained by a Bayesian analysis (after specifying prior and likelihood) using Markov Chain Monte Carlo (MCMC) simulation. This paper integrates the essential ideas of DE and MCMC, resulting in Differential Evolution Markov Chain (DE-MC). DE-MC is a population MCMC algorithm, in which multiple chains are run in parallel. DE-MC solves an important problem in MCMC, namely that of choosing an appropriate scale and orientation for the jumping distribution. In DE-MC the jumps are simply a fixed multiple of the differences of two random parameter vectors that are currently in the population. The selection process of DE-MC works via the usual Metropolis ratio which defines the probability with which a proposal is accepted. In tests with known uncertainty distributions, the efficiency of DE-MC with respect to random walk Metropolis with optimal multivariate Normal jumps ranged from 68% for small population sizes to 100% for large population sizes and even to 500% for the 97.5% point of a variable from a 50-dimensional Student distribution. Two Bayesian examples illustrate the potential of DE-MC in practice. DE-MC is shown to facilitate multidimensional updates in a multi-chain “Metropolis-within-Gibbs” sampling approach. The advantage of DE-MC over conventional MCMC are simplicity, speed of calculation and convergence, even for nearly collinear parameters and multimodal densities.
Trade policies and development of less-favoured areas: evidence from the literature
Oskam, A.J. ; Komen, M.H.C. ; Wobst, P. ; Yalew, A. - \ 2004
Food Policy 29 (2004)4. - ISSN 0306-9192 - p. 445 - 466.
developing-countries - economic-performance - wto negotiations - growth - africa - liberalization - exports - impact - convergence - investment
The links between international markets and production and consumption decisions in less-favoured areas (LFAs) often appear rather loose. Hence, it may be questioned whether international trade and economic growth effects trickle down to LFAs. This paper explores the evidence in the literature in which direction and to what extent trade policy may effect the development of LFAs. The literature on modern trade and growth theory spell out conditions of sustained economic growth that are, nearly by definition, opposite to the conditions that hold for LFAs. Although the institutional economics literature is very much focused at the country level, it is clear that for LFAs with inadequate institutions and infrastructure, the effects of trade-led growth is often irrelevant. Further trade liberalisation will entail small or even detrimental effects for LFAs, with an exception for products suffering from tariff escalation and/or peak tariffs. The prevailing problem seems to be the lacking supply response to (international) price changes. The literature contains evidence that long-term growth strategies for less-favoured areas require the development of institutions and infrastructure
Spatial Econometric data analysis: moving beyond traditional models
Florax, R.J.G.M. ; Vlist, A.J. van der - \ 2003
International Regional Science Review 26 (2003)3. - ISSN 0160-0176 - p. 223 - 243.
linear-regression models - autoregressive models - bayesian-estimation - moments estimation - expansion method - economic-growth - house prices - autocorrelation - dependence - convergence
This article appraises recent advances in the spatial econometric literature. It serves as the introduction too collection of new papers on spatial econometric data analysis brought together in this special issue, dealing specifically with new extensions to the spatial econometric modeling perspective. Although the initial development of the field of spatial econometrics has been rather slow, the Dixit-Stiglitz revolution and the emergence of the New Economy Geography have been instrumental in uplifting the significance and the use of spatial data analysis techniques. Concurrent developments in other social sciences parallel this situation in economics. The upsurge in spatial econometrics is, among other things, driven by the recognition that traditional spatial econometric models are insufficient to capture modern theoretical developments. Therefore, this issue brings together a collection of articles on space-time and discrete choice modeling, spatial nonstationarity, and the methodology and empirics of regional economic growth models.
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