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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    Agroecosystem patterns and land management co-develop through environment, management, and land-use interactions
    Caulfield, Mark E. ; Fonte, Steven J. ; Groot, Jeroen C.J. ; Vanek, Steven J. ; Sherwood, Stephen ; Oyarzun, Pedro ; Borja, Ross Mary ; Dumble, Sam ; Tittonell, Pablo - \ 2020
    Ecosphere 11 (2020)4. - ISSN 2150-8925
    co-development - Ecuador - elevation - environmental gradients - farm management - socio-ecological systems - soil organic carbon

    A poor understanding of the interactions between biophysical and social elements within rural mountainous landscapes can lead to suboptimal management and recommendations. The objective of this study was to contribute to more contextualized natural resource management in a rural landscape in the Ecuadorian Andes by (1) identifying biophysical patterns in soil properties, biodiversity, and C stocks that emerge from natural landscape pedogenic processes, resulting from elevation-induced climate gradients, erosion and soil textural patterns, and (2) assessing farm management and land-use effects on and their interactions with these biophysical patterns. Our findings revealed that the climate and soil texture gradients within the landscape led to an exponential increase in SOC with elevation moderated by slope gradient, indicating significant erosion processes. Farmers adapted their farm management according to the observed environmental patterns creating three distinct management zones. Differentiated agricultural management in these zones and asymmetrical distribution of land-uses in turn were observed to significantly influence soil and agroecosystem properties. For example, available P was found to be significantly higher in the upper and middle agricultural management zones (24.0 and 28.7 mg/kg, respectively), where agricultural inputs were higher compared to the lower agricultural management zone (8.9 mg/kg, P < 0.001). Mixed hedgerows, on the other hand, displayed significantly higher Shannon index scores for ground vegetation (1.8) and soil macrofauna (2.0) compared to agricultural land-uses (1.0 and 1.7). Our results provide important insights into how agroecosystem patterns and land management co-developed through complex environment, management, and land-use interactions.

    Simple parametric tests for trait–environment association
    Braak, Cajo J.F. ter; Peres-Neto, Pedro R. ; Dray, Stéphane - \ 2018
    Journal of Vegetation Science 29 (2018)5. - ISSN 1100-9233 - p. 801 - 811.
    community ecology - community-level test - CWM of traits - environmental gradients - fourth-corner - functional traits - modified test - species niche centroid - species-level test - statistical ecology - trait–environment relationship

    Question: The CWM approach is an easy way of analysing trait–environment association by regressing (or correlating) the mean trait per plot against an environmental variable and assessing the statistical significance of the slope or the associated correlation coefficient. However, the CWM approach does not yield valid tests, as random traits (or random indicator values) are far too often judged significantly related to the environmental variable, even when the trait and environmental variable are extrinsic to (not derived from) the community data. Existing solutions are the ZS-modified test (Zelený & Schaffers,) and the max (or sequential) test based on the fourth-corner correlation. Both tests are based on permutations which become cumbersome when many tests need to be carried out and many permutations are required, as in methods that correct for multiple testing. The main goal of this study was to compare these existing permutation-based solutions and to develop a quick and easy parametric test that can replace them. Methods: This study decomposes the fourth-corner correlation in two ways, which suggests a simple parametric approach consisting of assessing the significances of two linear regressions, one plot-level test as in the CWM approach and one species-level test, the reverse of the CWM approach, that regresses the environmental mean per species (i.e. the species niche centroid) on to the trait. The tests are combined by taking the maximum p-value. The type I error rates and power of this parametric max test are examined by simulation of one- and two-dimensional Gaussian models and log-linear models. Results: The ZS-modified test and the fourth-corner max test are conservative in different scenarios, the ZS-modified test being even more conservative than the fourth-corner. The new parametric max test is shown to control the type I error and has equal or even higher power than permutation tests based on the fourth-corner, the ZS-modified test and variants thereof. A weighted version of the new test showed inflated type I error. Conclusion: The combination of two simple regressions is a good alternative to the fourth-corner and the ZS-modified test. This combination is also applicable when multiple trait measurements are made per plot.

    Data from: Taxonomic and functional turnover are decoupled in European peat bogs
    Robroek, Bjorn J.M. ; Jassey, Vincent E.J. ; Payne, Richard J. ; Martí, Magalí ; Bragazza, Luca ; Bleeker, Albert ; Buttler, Alexandre ; Caporn, Simon J.M. ; Dise, Nancy B. ; Kattge, Jens ; Zajac, Katarzyna ; Svensson, Bo H. ; Ruijven, J. van; Verhoeven, Jos T.A. - \ 2017
    Utrecht University
    community ecology - species diversity - functional diversity - plant functional traits - peatland ecology - environmental gradients - climate change - Andromeda polifolia - Betula nana - Carex pauciflora - Drosera anglica - Drosera rotundifolia - Empetrum nigrum - Rubus chamaemorus - Scheuchzeria palustris - Vaccinium oxycoccus - Vaccinium uliginosum - Vaccinium microcarpon - Calluna vulgaris - Eriophorum angustifolium - Erica tetralix - Molinia caerulea - Narthecium ossifragum - Trichophorum cespitosum - Eriophorum vaginatum - Rhynchospora alba - Sphagnum angustifolium - Sphagnum balticum - Sphagnum fallax - Sphagnum fuscum - Sphagnum majus - Sphagnum rubellum - Sphagnum capillifolium - Sphagnum austinii - Sphagnum cuspidatum - Sphagnum flexuosum - Sphagnum papillosum - Sphagnum magellanicum - Sphagnum pulchrum - Sphagnum tenellum - Dicranales - Hypnales - Bryales - Cladonia spp. - Polytrichales
    In peatland ecosystems, plant communities mediate a globally significant carbon store. The effects of global environmental change on plant assemblages are expected to be a factor in determining how ecosystem functions such as carbon uptake will respond. Using vegetation data from 56 Sphagnum-dominated peat bogs across Europe, we show that in these ecosystems plant species aggregate into two major clusters that are each defined by shared response to environmental conditions. Across environmental gradients, we find significant taxonomic turnover in both clusters. However, functional identity and functional redundancy of the community as a whole remain unchanged. This strongly suggests that in peat bogs, species turnover across environmental gradients is restricted to functionally similar species. Our results demonstrate that plant taxonomic and functional turnover are decoupled, which may allow these peat bogs to maintain ecosystem functioning when subject to future environmental change.
    Old-growth Neotropical forests are shifting in species and trait composition
    Sande, M.T. van der; Arets, E.J.M.M. ; Pena Claros, M. ; Avila, L.A. ; Roopsind, A. ; Mazzei, L. ; Ascarrunz, N. ; Finegan, B. ; Alarcón, A. ; Caceres-Siani, Yasmani ; Licona, J.C. ; Ruschel, A.R. ; Toledo, M. ; Poorter, L. - \ 2016
    Wageningen UR
    disturbance - drought - environmental gradients - forest dynamicsfunctional traits - global change - rainfall - resource availability - soil fertility
    This dataset contains the underlaying data for the study: Tropical forests have long been thought to be in stable state, but recent insights indicate that global change is leading to shifts in forest dynamics and species composition. These shifts may be driven by environmental changes such as increased resource availability, increased drought stress, and/or recovery from past disturbances. The relative importance of these drivers can be inferred from analysing changes in trait values of tree communities. Here, we evaluate a decade of change in species and trait composition across five old-growth Neotropical forests in Bolivia, Brazil, Guyana and Costa Rica that cover large gradients in rainfall and soil fertility. To identify the drivers of compositional change, we used data from 29 permanent sample plots and measurements of 15 leaf, stem and whole-plant traits that are important for plant performance and should respond to global change drivers. We found that forests differ strongly in their community-mean trait values, resulting from differences in soil fertility and annual rainfall seasonality. The abundance of deciduous species with high specific leaf area increases from wet to dry forests. The community-mean wood density is high in the driest forests to protect xylem vessels against drought-cavitation, and is high in nutrient poor forests to increase wood longevity and enhance nutrient residence time in the plant. The species composition changed over time in three of the forests, and the community-mean wood density increased and the specific leaf area decreased in all forests, indicating that these forests are changing towards later successional stages dominated by slow-growing, shade-tolerant species. We did not see changes in other traits that could reflect responses to increased drought stress, such as increased drought-deciduousness or decreased maximum adult size, or that could reflect increased resource availability (CO2, rainfall or nitrogen). Changes in species and trait composition in these forests are, therefore, most likely caused by recovery from past disturbances. These compositional changes may also lead to shifts in ecosystem processes, such as a lower carbon sequestration and “slower” forest dynamics. For 29 permanent sample plots in two census years across five old-growth Neotropical forests in Bolivia, Brazil, Guyana and Costa Rica, the following data are available: values of 15 leaf, stem and whole-plant traits at the community-level, and the plot scores along two principal component axes that represent species composition.
    Seperating the role of biotic interactions and climate in determining adaptive response of plants to climate change
    Tomiolo, S. ; Putten, W.H. van der; Tielbörger, K. - \ 2015
    Ecology 96 (2015)5. - ISSN 0012-9658 - p. 1298 - 1308.
    local adaptation - environmental gradients - positive interactions - species interactions - soil feedback - ecological responses - aridity gradient - global change - evolutionary - communities
    Altered rainfall regimes will greatly affect the response of plant species to climate change. However, little is known about how direct effects of changing precipitation on plant performance may depend on other abiotic factors and biotic interactions. We used reciprocal transplants between climatically very different sites with simultaneous manipulation of soil, plant population origin, and neighbor conditions to evaluate local adaptation and possible adaptive response of four Eastern Mediterranean annual plant species to climate change. The effect of site on plant performance was negligible, but soil origin had a strong effect on fecundity, most likely due to differential water retaining ability. Competition by neighbors strongly reduced fitness. We separated the effects of the abiotic and biotic soil properties on plant performance by repeating the field experiment in a greenhouse under homogenous environmental conditions and including a soil biota manipulation treatment. As in the field, plant performance differed among soil origins and neighbor treatments. Moreover, we found plant species-specific responses to soil biota that may be best explained by the differential sensitivity to negative and positive soil biota effects. Overall, under the conditions of our experiment with two contrasting sites, biotic interactions had a strong effect on plant fitness that interacted with and eventually overrode climate. Because climate and biotic interactions covary, reciprocal transplants and climate gradient studies should consider soil biotic interactions and abiotic conditions when evaluating climate change effects on plant performance.
    Amazonian Dark Earth shapes the understory plant community in a Bolivian Amazonian Forest
    Quintero-Vallejo, E. ; Klomberg, Y. ; Bongers, F. ; Poorter, L. ; Toledo, M. ; Pena Claros, M. - \ 2015
    Biotropica 47 (2015)2. - ISSN 0006-3606 - p. 152 - 161.
    mesoscale distribution patterns - anthropogenic soils - environmental gradients - species composition - brazilian amazonia - tropical forest - diversity - ferns - specialization - landscape
    Amazonian Dark Earths (ADE) are the result of human modification of the Amazonian landscape since pre-Columbian times. ADE are characterized by increased soil fertility compared to natural soils. In the Amazonian forest, soil fertility influences understory herb and fern species composition. However, little research has been done to evaluate the effect of ADE on the composition of the understory community. We evaluated the effects of ADE and soil in 36 plots (150 m × 4 m) established in a Bolivian moist forest (La Chonta). For each plot, we determined soil nutrients, and the composition, richness, and abundance of terrestrial fern, angiosperm herb, and understory palm species. We found that the presence of ADE created a gradient in soil nutrients and pH that affected the understory species composition especially of ferns and palms. Additionally, the higher nutrient concentration and more neutral soil pH on ADE soils caused a decrease of ferns species richness. We therefore conclude that the current composition of the understory community in this particular Bolivian forest is a reflection of past human modifications of the soil.
    Rainfall and temperature affect tree species distributions in Ghana
    Amissah, L. ; Mohren, G.M.J. ; Bongers, F. ; Hawthorne, W.D. ; Poorter, L. - \ 2014
    Journal of Tropical Ecology 30 (2014)5. - ISSN 0266-4674 - p. 435 - 446.
    tropical forest trees - response curves - environmental gradients - distribution patterns - logistic-regression - continuum theory - soil nutrients - amazon forest - drought - growth
    We evaluated the relative importance of annual rainfall, temperature and their seasonality to tree species distribution in Ghana. We used species presence/absence data from 2505 1-ha plots systematically distributed over Ghana's forests. Logistic regression was used to determine species responses to four climatic variables generated from the Worldclim database. The distribution of 95% of 20 species was significantly associated with annual rainfall, 60% with rainfall seasonality, 45% with isothermality and 40% with temperature seasonality. Annual rainfall explained on average most of the variation (17%, range = 0.5–52%) in species distribution, followed by rainfall seasonality 5% (range = 0.5–27%), isothermality 4% (range = 0.8–24%) and temperature seasonality 1% (range = 0.4–4.5%). Our results suggest that, out of the climatic variables investigated, rainfall is the main factor determining tree species distribution in Ghana; temperature also influences the distribution of a number of species, although it explains much less of the variation. The reduction in annual rainfall that prevailing climate-change scenarios predict for the region will result in a shift in the distribution of most species, whereas the predicted increase in temperature variation is likely to have little effect.
    Biogeographic patterns of base-rich fen vegetation across Europe
    Jiménez-Alfaro, B. ; Hájek, M. ; Ejrnaes, R. ; Rodwell, J. ; Pawlikowski, P. ; Weeda, E.J. - \ 2014
    Applied Vegetation Science 17 (2014)2. - ISSN 1402-2001 - p. 367 - 380.
    environmental gradients - ecological gradients - plant associations - vascular plants - temperate zone - plot size - north - classification - mires - water
    Questions What is the distribution of base-rich fen vegetation and the specialist species along European biogeographic regions? How do the gradients in species composition correlate to geography and climate at continental scale? What are the implications of such patterns for the classification of these habitats? Location Fifteen countries of Central, Western and Northern Europe. Methods We compiled a vegetation plot database of base-rich fens and related communities including vascular plants and bryophytes. The initial data set with 6943 plots was filtered according to the presence of specialists using discriminant analysis. We used DCA to analyse the correlation of species composition with geography and climate, and kriging interpolation for mapping gradients in the study area. Modified TWINSPAN was used to detect major vegetation groups. The results of the whole data set (plot size 1–100 m2) were compared with those obtained from two subsets with plots of 1–5 m2 and 6–30 m2. Results Most of the specialists were distributed among all the biogeographic regions, but many were more represented in the Alpine than in the Atlantic, Boreal and Continental regions. Variation in species composition was mainly correlated to temperature, precipitation and latitude in the three data sets, showing a major gradient from (1) alpine belt fens characterized by spring species to (2) small sedge fens mainly distributed in mountain regions and (3) boreo-temperate fens reflecting waterlogged conditions. Conclusions Base-rich fen communities are widely distributed across European biogeographic regions, but the Alpine region can be considered as the compositional centre of this vegetation type. Large-scale gradients of species composition are mainly explained by climate, while the influence of latitude is probably correlated to increasing water table in the boreo-temperate regions. These gradients can be better understood by differentiating three major vegetation types, which should be considered when establishing classification systems of base-rich fens in Europe.
    Geomorphology and flooding shape fish distribution in a large-scale temperate floodplain
    Gorski, K. ; Buijse, A.D. ; Winter, H.V. ; Leeuw, J.J. de; Compton, T.J. ; Zolotarev, D.V. ; Verreth, J.A.J. ; Nagelkerke, L.A.J. - \ 2013
    River Research and Applications 29 (2013)10. - ISSN 1535-1459 - p. 1226 - 1236.
    boosted regression trees - amazon river-floodplain - mississippi river - water-quality - environmental gradients - assemblage structure - species richness - aquatic habitats - orinoco river - oxbow lakes
    Natural river-floodplain systems are characterized by their dynamic hydrology and diverse geomorphology resulting in a wide range of habitats that support high fish diversity and production. Various factors (e.g. hydrological dynamics, water quality, and biotic processes) have been proposed to explain fish distribution in large river floodplains, but it is still widely acknowledged that the mechanisms involved may vary in diverse floodplain systems and that they are not fully understood. To determine how flooding dynamics and floodplain geomorphology influence fish species distributions across the Volga-Akhtuba floodplain, Russian Federation, we examined the distributions of eight species with respect to variables reflecting floodplain hydrology and geomorphology. On the basis of fish catches in 40 floodplain water bodies at the end of summer in 2006–2008, we found that frequency of occurrence of most fish species remained stable along the time. The distribution of fish species was strongly influenced by the size and shape of water bodies as well as flood extent. Therefore, the long-term flood variability that drives the geomorphic heterogeneity of the floodplain creates suitable habitats across ranges of fish flow guilds (rheophilic, eurytopic, and limnophilic), resulting in high diversity of the floodplain ichthyofauna. We conclude that this diverse habitat availability is a highly significant factor influencing fish distribution in the Volga-Akhtuba floodplain.
    Distributional congruence of mammalian herbivores in the Trans-Himalayan Mountains
    Namgail, T. ; Wieren, S.E. van; Prins, H.H.T. - \ 2013
    Current Zoology 59 (2013)1. - ISSN 1674-5507 - p. 116 - 124.
    cross-taxon congruence - species richness - environmental gradients - distribution patterns - iberian peninsula - blue sheep - conservation - ladakh - similarity - biogeography
    Large-scale distribution and diversity patterns of mammalian herbivores, especially less charismatic species in alpine environments remain little understood. We studied distributional congruence of mammalian herbivores in the Trans-Himalayan region of Ladakh to see if the distributions of less prominent and smaller herbivores can be determined from those of larger and more prominent herbivores like ungulates. Using a similarity index, we assessed shared distributions of species in 20x20 km2 grid-cells in an area of about 80,000 km2. We used the Unweighted Pair-Group Method with Arithmetic Average (UPGMA) to classify mammalian herbivores into groups with similar distributions. We then used the G-test of independence to look for statistical significance of the groups obtained. We identified six groups of mammalian herbivores with distributions more similar than expected at random. The largest group was composed of nine species whereas the other large group comprised six species. Canonical Correspondence Analysis (CCA), used to relate the groups with environmental features, showed that the largest group occurred in higher and flatter areas, while the other large group occurred in lower and steeper areas. Large herbivores like ungulates can be used as surrogate for less prominent small herbivores while identifying areas for latter’s protection in the inaccessible mountainous regions of the Trans-Himalaya
    Distribution patterns of tropical woody species in response to climatic and edaphic gradients
    Toledo, M. ; Peña-Claros, M. ; Bongers, F. ; Alarcón, A. ; Balcázar, J. ; Chubiña, J. ; Leaño, C. ; Licona, J.C. ; Poorter, L. - \ 2012
    Journal of Ecology 100 (2012)1. - ISSN 0022-0477 - p. 253 - 263.
    rain-forest - environmental gradients - logistic-regression - continuum theory - moist forest - soil factors - tree - drought - abundance - curves
    1. The analysis of species distribution patterns along environmental gradients is important for understanding the diversity and ecology of plants and species responses to climate change, but detailed data are surprisingly scarce for the tropics. 2. Here, we analyse the distribution of 100 woody species over 220 1-ha forest plots distributed over an area of c. 160 000 km2, across large environmental gradients in lowland Bolivia and evaluate the relative importance of climate and soils in shaping species distribution addressing four multivariate environmental axes (rainfall amount and distribution, temperature, soil fertility and soil texture). 3. Although species abundance was positively related to species frequency (the number of plots in which the species is found), this relationship was rather weak, which challenges the view that most tropical forests are dominated at large scales by a few common species. 4. Species responded clearly to environmental gradients, and for most of the species (65%), climatic and soil conditions could explain most of the variation in occurrence (R2 > 0.50), which challenges the idea that most tropical tree species are habitat generalists. 5. Climate was a stronger driver of species distribution than soils; 91% of the species were affected by rainfall (distribution), 72% by temperature, 47% by soil fertility and 44% by soil texture. In contrast to our expectation, few species showed a typical unimodal response to the environmental gradients.6. Synthesis. Tropical tree species specialize for different parts of the environmental gradients, and climate is a stronger driver of species distribution than soils. Because climate change scenarios predict increases in annual temperature and a stronger dry season for tropical forests, we may expect potentially large shifts in the distribution of tropical trees
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