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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    Microbial invasions in terrestrial ecosystems
    Thakur, Madhav P. ; Putten, Wim H. van der; Cobben, Marleen M.P. ; Kleunen, Mark van; Geisen, Stefan - \ 2019
    Nature Reviews Microbiology (2019). - ISSN 1740-1526 - p. 1 - 11.

    Human travel and global trade have tremendously increased the spread of invasive microorganisms in new regions. Experimental and observational studies in terrestrial ecosystems are beginning to shed light on processes of microbial invasions, their ecological impacts and implications for ecosystem functioning. We provide examples of terrestrial invasive microorganisms, including bacteria, fungi, oomycetes and other protists, and viruses, and discuss the impacts of pathogenic and non-pathogenic invasive microorganisms at levels ranging from host species to ecosystems. This Review highlights that despite the recent progress in microbial invasion research, we are only beginning to understand how alien microorganisms interact with native microorganisms, and the implications of those interactions. Finally, we propose three research themes — microbial interactions, impacts and climate change — to make microbial invasion research a truly integrative discipline.

    Modeling water quality in the Anthropocene: directions for the next-generation aquatic ecosystem models
    Mooij, W.M. ; Wijk, Dianneke van; Beusen, A.H.W. ; Brederveld, R.J. ; Chang, M. ; Cobben, Marleen M.P. ; DeAngelis, D.L. ; Downing, A.S. ; Janssen, A.B.G. ; Hengeveld, G.M. - \ 2019
    Current Opinion in Environmental Sustainability 36 (2019). - ISSN 1877-3435 - p. 85 - 95.
    Everything changes and nothing stands still” (Heraclitus). Here we review three major improvements to freshwater aquatic ecosystem models — and ecological models in general — as water quality scenario analysis tools towards a sustainable future. To tackle the rapid and deeply connected dynamics characteristic of the Anthropocene, we argue for the inclusion of eco-evolutionary, novel ecosystem and social-ecological dynamics. These dynamics arise from adaptive responses in organisms and ecosystems to global environmental change and act at different integration levels and different time scales. We provide reasons and means to incorporate each improvement into aquatic ecosystem models. Throughout this study we refer to Lake Victoria as a microcosm of the evolving novel social-ecological systems of the Anthropocene. The Lake Victoria case clearly shows how interlinked eco-evolutionary, novel ecosystem and social-ecological dynamics are, and demonstrates the need for transdisciplinary research approaches towards global sustainability.
    Maternal Effects in a Wild Songbird Are Environmentally Plastic but Only Marginally Alter the Rate of Adaptation
    Ramakers, Jip J.C. ; Cobben, Marleen M.P. ; Bijma, Piter ; Reed, Thomas E. ; Visser, Marcel E. ; Gienapp, Phillip - \ 2018
    American Naturalist 191 (2018)5. - ISSN 0003-0147 - p. E000 - E000.
    adaptation - environmental shift - evolutionary dynamics - maternal inheritance - plastic maternal effect - quantitative genetics
    Despite ample evidence for the presence of maternal effects (MEs) in a variety of traits and strong theoretical indications for their evolutionary consequences, empirical evidence to what extent MEs can influence evolutionary responses to selection remains ambiguous. We tested the degree to which MEs can alter the rate of adaptation of a key life-history trait, clutch size, using an individual-based model approach parameterized with experimental data from a long-term study of great tits (Parus major). We modeled two types of MEs: (i) an environmentally plastic ME, in which the relationship between maternal and offspring clutch size depended on the maternal environment via offspring condition, and (ii) a fixed ME, in which this relationship was constant. Although both types of ME affected the rate of adaptation following an abrupt environmental shift, the overall effects were small. We conclude that evolutionary consequences of MEs are modest at best in our study system, at least for the trait and the particular type of ME we considered here. A closer link between theoretical and empirical work on MEs would hence be useful to obtain accurate predictions about the evolutionary consequences of MEs more generally.
    Data from: Maternal effects in a wild songbird are environmentally plastic but only marginally alter the rate of adaptation
    Ramakers, J.J.C. ; Cobben, M.M.P. ; Bijma, P. ; Reed, T.E. ; Visser, M.E. ; Gienapp, P. - \ 2017
    Wageningen University & Research
    adaptation - bird - evolution - experimental - fitness - genetics - quantative - maternal effects
    Despite ample evidence for the presence of maternal effects (MEs) in a variety of traits and strong theoretical indications for their evolutionary consequences, empirical evidence to what extent MEs can influence evolutionary responses to selection remains ambiguous. We tested the degree to which MEs can alter the rate of adaptation of a key life-history trait, clutch size, using an individual-based model approach parameterized with experimental data from a long-term study of great tits (Parus major). We modeled two types of MEs: (i) an environmentally plastic ME, in which the relationship between maternal and offspring clutch size depended on the maternal environment via offspring condition, and (ii) a fixed ME, in which this relationship was constant. Although both types of ME affected the rate of adaptation following an abrupt environmental shift, the overall effects were small. We conclude that evolutionary consequences of MEs are modest at best in our study system, at least for the trait and the particular type of ME we considered here. A closer link between theoretical and empirical work on MEs would hence be useful to obtain accurate predictions about the evolutionary consequences of MEs more generally.
    Spatial sorting and range shifts: consequences for evolutionary potential and genetic signature of a dispersal trait
    Cobben, M.M.P. ; Verboom, J. ; Opdam, P.F.M. ; Hoekstra, R.F. ; Jochem, R. ; Smulders, M.J.M. - \ 2015
    Journal of Theoretical Biology 373 (2015). - ISSN 0022-5193 - p. 92 - 99.
    woodpecker dendrocopos-medius - climate-change - wave-front - expanding population - local adaptation - metapopulation - diversity - expansion - edge - extinction
    Species are shifting their ranges under climate change, with genetic and evolutionary consequences. As a result, the spatial distribution of genetic diversity in a species’ range can show a signature of range expansion. This genetic signature takes time to decay after the range stops expanding and it is important to take that lag time into account when interpreting contemporary spatial patterns of genetic diversity. In addition, the return to spatial equilibrium on an ecologically relevant timescale will depend on migration of genetic diversity across the species’ range. However, during a range shift alleles may go extinct at the retracting range margin due to spatial sorting. Here we studied the spatial pattern of genotypes that differ in dispersal rate across the species range before, during and after a range shift, assessed the effect of range retraction on this pattern, and quantified the duration of the ephemeral genetic signature of range expansion for this trait. We performed simulation experiments with an individual-based metapopulation model under several contemporary climate change scenarios. The results show an increase of the number of individuals with high dispersal rate. If the temperature increased long enough the allele coding for low dispersal rate would go extinct. The duration of the genetic signature of range expansion after stabilisation of the species’ distribution lasted up to 1200 generations after a temperature increase for 60 years at the contemporary rate. This depended on the total displacement of the climate optimum, as the product of the rate of temperature increase and its duration. So genetic data collected in the field do not necessarily reflect current selection pressures but can be affected by historic changes in species distribution, long after the establishment of the current species’ range. Return to equilibrium patterns may be hampered by loss of evolutionary potential during range shift.
    Landscape diversity enhances the resilience of populations, ecosystems and local economy in rural areas
    Schippers, P. ; Heide, C.M. van der; Koelewijn, H.P. ; Schouten, M.A.H. ; Smulders, M.J.M. ; Cobben, M.M.P. ; Sterk, M. ; Vos, C.C. ; Verboom, J. - \ 2015
    Landscape Ecology 30 (2015)2. - ISSN 0921-2973 - p. 193 - 202.
    climate-change - genetic diversity - patch size - habitat fragmentation - ecological resilience - response diversity - biodiversity - conservation - reserves - services
    Context In today’s world, rapid environmental and economic developments and changes pose major threats to ecosystems and economic systems. Objective In this context we explore if resilience can be increased by the spatial configuration of the rural landscape in an integrated ecological-genetic-economic way. Methods We study the concept of landscape diversity from genetic, ecological and economic perspectives. Results We show that small-scale landscapes are potentially more resilient than large-scale landscapes, provided that ecosystem patch sizes are sufficiently large to support genetic diversity and ecosystem and economic functions. The basic premise underlying this finding is that more variation in a landscape generally leads to greater genetic and species diversity. This, in turn, stabilizes populations and strengthens the different ecosystem elements in the landscape. Greater variation in ecosystem elements provides for more varied ecosystem services, which may enhance the resilience of the local economy. Conclusion We conclude that a resilient landscape is shaped within the context of economic and ecological possibilities and constraints, and is determined by landscape diversity and spatial organisation.
    Robustness and accuracy of Maxent niche modelling for Lactuca species distributions in light of collecting expeditions
    Cobben, M.M.P. ; Treuren, R. van; Castaneda-Alvarez, N.P. ; Khoury, C.K. ; Kik, C. ; Hintum, T.J.L. van - \ 2015
    Plant genetic resources: characterization and utilization 13 (2015)2. - ISSN 1479-2621 - p. 153 - 161.
    genetic-resources - absence data - prediction - asteraceae - lettuce
    Niche modelling software can be used to assess the probability of detecting a population of a plant species at a certain location. In this study, we used the distribution of the wild relatives of lettuce (Lactuca spp.) to investigate the applicability of Maxent species distribution models for collecting missions. Geographic origin data of genebank and herbarium specimens and climatic data of the origin locations were used as input. For Lactuca saligna, we varied the input data by omitting the specimens from different parts of the known distribution area to assess the robustness of the predicted distributions. Furthermore, we examined the accuracy of the modelling by comparing the predicted probabilities of population presence against recent expedition data for the endemic Lactuca georgica and the cosmopolitan Lactuca serriola. We found Maxent to be quite robust in its predictions, although its usefulness was higher for endemic taxa than for more widespread species. The exclusion of occurrence data from the perceived range margins of the species can result in important information about local adaptation to distinct climatic conditions. We discuss the potential for enhanced use of Maxent in germplasm collecting planning.
    Climate change and crop wild relatives: can species track their suitable environment and what do they lose in the process
    Cobben, M.M.P. ; Treuren, R. van; Hintum, T.J.L. van - \ 2013
    Plant genetic resources: characterization and utilization 11 (2013)3. - ISSN 1479-2621 - p. 234 - 237.
    range expansion - metapopulation - landscapes - diversity - shift
    Crop wild relatives are an increasingly important source of plant genetic resources for plant breeders. Several studies have estimated the effects of climate change on the distribution of crop wild relatives, using species distribution models. In this approach, two important aspects, i.e. species' dispersal capacity and founder effects, are currently not taken into account. Neglecting these aspects can lead to an underestimation of the climate change-induced threat to the size of the species range and the conservation of range-wide levels of genetic diversity. This paper presents two recommendations for the interpretation of the results obtained with these models. The integration of process-based simulation models and statistical species distribution models will facilitate the inclusion of dispersal processes and founder effects in future assessments of the resilience of plant genetic resources under climate change.
    Warmer klimaat oorzaak genetische erosie
    Cobben, Marleen - \ 2012
    colonization - fauna - habitats - climatic change
    Wrong place, wrong time: climate change-induced range shift across fragmented habitat causes maladaptation and declined population size in a modelled bird species
    Cobben, M.M.P. ; Verboom, J. ; Opdam, P.F.M. ; Hoekstra, R.F. ; Jochem, R. ; Smulders, M.J.M. - \ 2012
    Global Change Biology 18 (2012)8. - ISSN 1354-1013 - p. 2419 - 2428.
    vogels - habitatfragmentatie - klimaatverandering - modellen - birds - habitat fragmentation - climatic change - models - expanding population - genetic diversity - wave-front - metapopulation - mutations - dispersal - evolution - expansion - adaptation - survival
    Many species are locally adapted to decreased habitat quality at their range margins, and therefore show genetic differences throughout their ranges. Under contemporary climate change, range shifts may affect evolutionary processes at the expanding range margin due to founder events. Additionally, populations that are affected by such founder events will, in the course of time, become located in the range centre. Recent studies investigated evolutionary changes at the expanding range margin, but have not assessed eventual effects across the species’ range. We explored the possible influence of range shift on the level of adaptation throughout the species’ total range. For this we used a spatially explicit, individual-based simulation model of a woodland bird, parameterised after the middle spotted woodpecker (Dendrocopus medius) in fragmented habitat. We simulated its range under climate change, and incorporated genetic differences at a single locus that determined the individual's degree of adaptation to optimal temperature conditions. Generalist individuals had a large thermal tolerance but relatively low overall fitness, while climate specialists had high fitness combined with a small thermal tolerance. In equilibrium, the populations in the range centre were comprised of the specialists, while the generalists dominated the margins. In contrast, under temperature increase, the generalist numbers increased at the expanding margin and eventually also occupied the centre of the shifting range, while the specialists were located in the retracting margins. This was caused by founder events and led to overall maladaptation of the species, which resulted in a reduced metapopulation size and thus impeded the species’ persistence. We therefore found no evidence for a complementary effect of local adaptation and range shifts on species’ survival. Instead we showed that founder events can cause local maladaptation which can amplify throughout the species’ range, and, as such, hamper the species’ persistence under climate change
    Adapt, move or perish : the interaction of genetics and demography in fragmented populations under climate change
    Cobben, M.M.P. - \ 2012
    Wageningen University. Promotor(en): Rolf Hoekstra; Paul Opdam, co-promotor(en): Rene Smulders; Jana Verboom-Vasiljev. - S.l. : s.n. - ISBN 9789461731999 - 132
    dendrocopos - habitats - habitatfragmentatie - biodiversiteit - populaties - klimaatverandering - adaptatie - genetica - demografie - modellen - verspreiding - dendrocopos - habitats - habitat fragmentation - biodiversity - populations - climatic change - adaptation - genetics - demography - models - dispersal
    In reactie op klimaatverandering verschuift van veel soorten het areaal, maar het is duidelijk dat dit voor lang niet alle soorten snel genoeg gaat. Habitatfragmentatie zal in het algemeen de noodzakelijke areaalverschuivingen vertragen. Er is geopperd dat de combinatie van areaalverschuivingen en de lokale aanpassing van soorten aan de veranderende omstandigheden hun overleving positief zal beïnvloeden
    Landscape prerequisites for the survival of a modelled metapopulation and its neutral genetic diversity are affected by climate change
    Cobben, M.M.P. ; Verboom, J. ; Opdam, P.F.M. ; Hoekstra, R.F. ; Jochem, R. ; Smulders, M.J.M. - \ 2012
    Landscape Ecology 27 (2012). - ISSN 0921-2973 - p. 227 - 237.
    klimaatverandering - metapopulaties - kolonisatie - modellen - climatic change - metapopulations - colonization - models - frog rana-arvalis - population - biodiversity - differentiation - implementation - connectivity - adaptation - divergence - migration - responses
    In response to climate change a species may move, adapt, or go extinct. For the adaptability of a population its genetic diversity is essential, but climate change-induced range shifts can cause a loss of genetic diversity. We investigated how landscape structure affects the level and distribution of genetic diversity in metapopulations subject to climate change-induced range shifts. For this we used the spatially explicit, individual-based model METAPHOR which simulates metapopulation demography and genetics under different temperature increase scenarios. The results indicated that increasing total habitat area may enhance the maintenance of the genetic diversity in metapopulations while they are shifting their range under climate change. However, the results also showed that a high level of total habitat area did not prevent the populations in the newly colonised habitat area of being depleted of much of the original genetic diversity. We therefore conclude that enhancing landscape connectivity may lead to a delayed loss of genetic diversity in metapopulations under climate change, but that additional measures would be necessary to ensure its long-term conservation. Importantly, our simulations also show that a landscape which could be regarded as well-structured under stable climatic conditions, may be inferior for the conservation of genetic diversity during a range shift. This is important information for landscape management when developing strategies for the in situ conservation of genetic variation in natural populations under climate change.
    Projected climate change causes loss and redistribution of neutral genetic diversity in a model metapopulation of a medium-good disperser
    Cobben, M.M.P. ; Verboom, J. ; Opdam, P.F.M. ; Hoekstra, R.F. ; Jochem, R. ; Arens, P. ; Smulders, M.J.M. - \ 2011
    Ecography 34 (2011)6. - ISSN 0906-7590 - p. 920 - 932.
    klimaatverandering - vegetatie - biodiversiteit - climatic change - vegetation - biodiversity - woodpecker dendrocopos-medius - environmental stochasticity - habitat fragmentation - expanding population - landscape genetics - wave-front - colonization - adaptation - extinction - mutations
    Climate change causes species ranges to shift geographically as individuals colonise new suitable temperature zones or fail to reproduce where climate conditions fall below tolerance levels. Little is known about the potential loss of genetic diversity in such dynamic ranges. We investigated the level and distribution of neutral genetic diversity in shifting metapopulations during three scenarios of temperature increase projected for this century and at various degrees of weather variability. We used an individual-based and spatially explicit metapopulation model in which temperature zones were simulated to move across a fragmented landscape following different climate change scenarios. Although the connectivity between habitat patches allowed the species, modelled after the middle spotted woodpecker Dendrocopos medius, to move along with the shifting temperature range, existing neutral genetic diversity was lost under all three temperature increase scenarios. This was independent of the loss of individuals. The explanation for this effect is that only a part of the original genetic variation moved into the newly colonised habitat. Under increased weather variability the number of individuals and the number of alleles per locus were persistently lower. However, the pattern of changes in allele distributions under temperature zone shifts was the same under all weather variability levels. Genetic differentiation between populations had a tendency to increase at metapopulation range margins, but decreased again when population sizes increased in time. Increased weather variability led to increased variation around the mean genetic differentiation across the metapopulation. Our results illustrate the usefulness of more realistic models for studying the effects of climate change on metapopulations. They indicate that biodiversity monitoring indices based on species occurrence and abundance are not a good proxy for the trend in the level of genetic diversity. Further, the results underline the importance of conserving areas where species have existed for a long time as modern refugia for genetic diversity.
    Landscape genetics of fragmented forests: anticipating climate change by facilitating migration
    Smulders, M.J.M. ; Cobben, M.M.P. ; Arens, P.F.P. ; Verboom, J. - \ 2009
    iForest : Biogeosciences and Forestry 2 (2009). - ISSN 1971-7458 - p. 128 - 132.
    habitatfragmentatie - soortendiversiteit - klimaatverandering - habitat fragmentation - species diversity - climatic change
    Habitat fragmentation is a threat to the survival of species and causes population decline, as isolated populations are more susceptible to demographic and genetic stochasticity. This can be compensated for by sufficient spatial connectivity between habitat patches to allow dispersal of individuals among populations. In that case such a network of populations may effectively form a metapopulation. In this paper we discuss some aspects of metapopulation theory, notably with respect to maintaining genetic diversity in fragmented forest patches. In addition we will discuss recent studies that explore ways for forest management to anticipate and mitigate the expected climate change, in relation to range shifts and colonisation opportunities
    Genetic factors in metapopulation survival : introduction to a PhD-project
    Cobben, M.M.P. ; Arens, P.F.P. ; Verboom, J. ; Smulders, M.J.M. - \ 2008
    habitats - populatiegenetica - demografie - distributie - conservering - genetische diversiteit - klimaatverandering - simulatiemodellen - metapopulaties - ecologische hoofdstructuur - habitats - population genetics - demography - distribution - conservation - genetic diversity - climatic change - simulation models - metapopulations - ecological network
    Short introduction to a PhD project. Which factors determine the level and distribution of genetic diversity in fragmented populations, and how are these affected by increased temperature and weather variability? METAPHOR, a stochastic, spatially explicit, individual-based simulation model for demography of fragmented populations, will be extended with a genetic module to explore these research questions
    Adapt, move or perish : genetic processes in fragmented populations under climate change
    Cobben, M.M.P. ; Arens, P.F.P. ; Smulders, M.J.M. ; Verboom, J. ; Opdam, P.F.M. ; Hoekstra, R.F. - \ 2007
    habitats - demografie - distributie - populatiegenetica - genetische diversiteit - klimaatverandering - simulatiemodellen - metapopulaties - ecologische hoofdstructuur - habitats - demography - distribution - population genetics - genetic diversity - climatic change - simulation models - metapopulations - ecological network
    Poster presentation of a PhD project. Which factors determine the level and distribution of genetic diversity in fragmented populations, and how are these affected by increased temperature and weather variability? METAPHOR, a stochastic, spatially explicit, individual-based simulation model for demography of fragmented populations, will be extended with a genetic module to explore these research questions
    Influence of a dipping preservative treatment on the performance of wood finished with waterborne coatings.
    Meijer, M. de; Creemers, J. ; Cobben, W. ; Ahola, P. - \ 1998
    In: 29th Annual meeting of the Int. Research Group on Wood Preservation, Maastricht, The Netherlands (1998)
    Sequential sampling to measure the infiltration rate within relatively homogeneous soil units.
    Stein, A. ; Bouma, J. ; Kroonenberg, S.B. ; Cobben, S. - \ 1989
    Catena 16 (1989). - ISSN 0341-8162 - p. 91 - 100.
    hydraulisch geleidingsvermogen - infiltratie - meting - permeabiliteit - bemonsteren - kwel - bodem - grondanalyse - hydraulic conductivity - infiltration - measurement - permeability - sampling - seepage - soil - soil analysis
    In memoriam R.H. Cobben (1925-1987), een biografie en een bibliografie.
    Vrijer, P.W.F. de - \ 1988
    Entomologische Berichten 48 (1988). - ISSN 0013-8827 - p. 165 - 169.
    Taxonomic analysis of ecological and behavioural species differentiation in Hemiptera.
    Cobben, R.H. ; Vrijer, P.W.F. de; Bieman, C.F.M. den - \ 1987
    In: Systematics and evolution: a matter of diversity / Hovenkamp, P., - p. 81 - 95.
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