Interpretation and predictions of the emergent neutrality model: A reply to Barabás et al
Vergnon, R.O.H. ; Nes, E.H. van; Scheffer, M. - \ 2013
Oikos 122 (2013)11. - ISSN 0030-1299 - p. 1573 - 1575.
species-diversity - biodiversity - maintenance - similarity - transients - evolution - niches
Formulated in 2006, Scheffer and van Nes' Emergent neutrality model predicts that competing species might self-organize into groups of species similar in their traits. Recently, Vergnon et al. showed that the model consistently generates multimodal species abundance distributions, in accordance with empirical data. Barabás et al. argue that Emergent neutrality model relies on unmodeled, 'hidden' species differences. They also suggest that an Emergent neutrality model explicitly integrating such differences may fail to generate multimodal species abundance distributions, while other models can robustly produce those patterns. Here we demonstrate that density dependence - the process deemed problematic by Barabás et al. - may permanently maintain groups of similar species without need for additional species differences. More broadly, we make it clear that density dependence is not the only likely mechanism that could allow the permanent coexistence of similar species in the Emergent neutrality framework. We welcome the finding that models other than Emergent neutrality can generate multimodal abundance distributions and we briefly discuss their novelty and relevance.
Species richness declines and biotic homogenisation have slowed down for NW-European pollinators and plants.
Carvalheiro, L.G. ; Kunin, W.E. ; Keil, P. ; Aguirre-Gutiérrez, J. ; Ellis, W.N. ; Fox, R. ; Groom, Q. ; Hennekens, S. ; Landuyt, W. Van; Maes, D. ; Meutter, F. Van de; Michez, D. ; Rasmont, P. ; Ode, B. ; Potts, S.G. ; Reemer, M. ; Roberts, S.P.M. ; Schaminée, J. ; Wallis de Vries, M.F. ; Biesmeijer, J.C. - \ 2013
Ecology Letters 16 (2013)7. - ISSN 1461-023X - p. 870 - 878.
agri-environment schemes - global biodiversity - british butterflies - diversity - abundance - britain - scale - netherlands - indicators - similarity
Concern about biodiversity loss has led to increased public investment in conservation. Whereas there is a widespread perception that such initiatives have been unsuccessful, there are few quantitative tests of this perception. Here, we evaluate whether rates of biodiversity change have altered in recent decades in three European countries (Great Britain, Netherlands and Belgium) for plants and flower visiting insects. We compared four 20-year periods, comparing periods of rapid land-use intensification and natural habitat loss (1930–1990) with a period of increased conservation investment (post-1990). We found that extensive species richness loss and biotic homogenisation occurred before 1990, whereas these negative trends became substantially less accentuated during recent decades, being partially reversed for certain taxa (e.g. bees in Great Britain and Netherlands). These results highlight the potential to maintain or even restore current species assemblages (which despite past extinctions are still of great conservation value), at least in regions where large-scale land-use intensification and natural habitat loss has ceased.
Surface Temperature and Surface-Layer Turbulence in a Convective Boundary Layer
Garai, A. ; Pardyjak, E. ; Steeneveld, G.J. ; Kleissl, J. - \ 2013
Boundary-Layer Meteorology 148 (2013)1. - ISSN 0006-8314 - p. 51 - 72.
sensible heat-flux - energy balance algorithm - renewal analysis - model - grass - flow - environment - similarity - canopies - density
Previous laboratory and atmospheric experiments have shown that turbulence influences the surface temperature in a convective boundary layer. The main objective of this study is to examine land-atmosphere coupled heat transport mechanism for different stability conditions. High frequency infrared imagery and sonic anemometer measurements were obtained during the boundary layer late afternoon and sunset turbulence (BLLAST) experimental campaign. Temporal turbulence data in the surface-layer are then analyzed jointly with spatial surface-temperature imagery. The surface-temperature structures (identified using surface-temperature fluctuations) are strongly linked to atmospheric turbulence as manifested in several findings. The surface-temperature coherent structures move at an advection speed similar to the upper surface-layer or mixed-layer wind speed, with a decreasing trend with increase in stability. Also, with increasing instability the streamwise surface-temperature structure size decreases and the structures become more circular. The sequencing of surface- and air-temperature patterns is further examined through conditional averaging. Surface heating causes the initiation of warm ejection events followed by cold sweep events that result in surface cooling. The ejection events occur about 25 % of the time, but account for 60–70 % of the total sensible heat flux and cause fluctuations of up to 30 % in the ground heat flux. Cross-correlation analysis between air and surface temperature confirms the validity of a scalar footprint model.
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
The impact of regulatory heterogeneity on agri-food trade
Winchester, N. ; Rau, M.L. ; Goetz, C. ; Larue, B. ; Otsuki, T. ; Shutes, K. ; Wieck, C. ; Burnquist, H.L. ; Pinto de Souza, M.J. ; Nunes de Faria, R. - \ 2012
The World Economy 35 (2012)8. - ISSN 0378-5920 - p. 973 - 993.
general coefficient - agricultural trade - similarity - agreements - patterns - gravity - model - sps
We estimate the impact of regulatory heterogeneity on agri-food trade using a gravity analysis that relies on detailed data on non-tariff measures (NTMs) collected by the NTM-Impact project. The data cover a broad range of import requirements for agricultural and food products for the EU and nine of its major trade partners. We find that trade is significantly reduced when importing countries have stricter maximum residue limits (MRLs) for plant products than exporting countries. For most other measures, due to their qualitative nature, we were unable to infer whether the importer has stricter standards relative to the exporter, and we do not find a robust relationship between these measures and trade. Our findings suggest that, at least for some import standards, harmonising regulations will increase trade. We also conclude that tariff reductions remain an effective means to increase trade even when NTMs abound.
Emergent neutrality leads to multimodal species abundance distributions
Vergnon, R. ; Nes, E.H. van; Scheffer, M. - \ 2012
Nature Communications 3 (2012). - ISSN 2041-1723 - 6 p.
body-size - community - biodiversity - coexistence - diversity - ecology - model - similarity - paradox - niche
Recent analyses of data sampled in communities ranging from corals and fossil brachiopods to birds and phytoplankton suggest that their species abundance distributions have multiple modes, a pattern predicted by none of the existing theories. Here we show that the multimodal pattern is consistent with predictions from the theory of emergent neutrality. This adds to the observations, suggesting that natural communities may be shaped by the evolutionary emergence of groups of similar species that coexist in niches. Such self-organized similarity unifies niche and neutral theories of biodiversity.
Spatial variation in ditch bank plant species composition at the regional level: the role of environment and dispersal
Leng, X. ; Musters, C.J.M. ; Snoo, G.R. de - \ 2010
Journal of Vegetation Science 21 (2010)5. - ISSN 1100-9233 - p. 868 - 875.
seed dispersal - beta-diversity - similarity - distance - conservation - patterns - ecology - communities - biodiversity - forests
Questions: Can patterns of species similarity on ditch banks be explained by environmental and dispersal factors and, if so, to what extent? Does the pattern of distance decay differ among different species groups (all species versus target species of conservation interest; species of different dispersal type)? Location: Krimpenerwaard, the Netherlands. Methods: In 2006-2007, ditch bank vegetation data on 130 terrestrial herbaceous species were collected on 72 plots. Species similarity was measured and related to environmental distance (soil type and nutrient level) and dispersal distance (geographic distance and limitation of dispersal by water, wind and agricultural activities) as explanatory factors using multiple regression on distance matrices (MRM). Differences in rates of distance decay in species similarity among different subsets of data (species groups) were investigated using randomization tests. Results: In all species, patterns of similarity of composition are influenced mainly by variations in dispersal, while for target species these are due to combined effects of environmental and dispersal variation. Compared with species using other dispersal mechanisms, water-dispersed species had half the rate of distance decay. Conclusions: For all species considered here, dispersal limitation seems more responsible for the spatial variation in species composition than environmental determinism. Conservation management focused on plant species diversity would be more successful in areas adjacent to those where a similar management regime is already in force. For target species of conservation interest, besides dispersal limitation, environmental determinants like nutrient level are also important. As a means of conserving such target species, therefore, focusing on reducing nutrient levels and facilitating species dispersal will be more effective than current management practices, which mainly focus on reducing fertilizer inputs.
The paradox of the clumps mathematically explained
Fort, H. ; Scheffer, M. ; Nes, E.H. van - \ 2009
Theoretical Ecology 2 (2009)3. - ISSN 1874-1738 - p. 171 - 176.
similarity - neutrality
The lumpy distribution of species along a continuous one-dimensional niche axis recently found by Scheffer and van Nes (Scheffer and van Ness 2006) is explained mathematically. We show that it emerges simply from the eigenvalue and eigenvectors of the community matrix. Both the transient patterns—lumps and gaps between them—as well as the asymptotic equilibrium are explained. If the species are evenly distributed along the niche axis, the emergence of these patterns can be demonstrated analytically. The more general case, of randomly distributed species, shows only slight deviations and is illustrated by numerical simulation. This is a robust result whenever the finiteness of the niche is taken into account: it can be extended to different analytic dependence of the interaction coefficients with the distance on the niche axis (i.e., different kernel interactions), different boundary conditions, etc. We also found that there is a critical value both for the width of the species distribution s and the number of species n below which the clusterization disappears
Assignment of releves to pre-defined classes by supervised clustering of plant communities using a new composite index
Tongeren, O. ; Gremmen, N. ; Hennekens, S.M. - \ 2008
Journal of Vegetation Science 19 (2008)4. - ISSN 1100-9233 - p. 525 - 536.
phytosociological classification - neural-networks - vegetation - program - similarity - prediction - tables - units
Question: How does a newly designed method of supervised clustering perform in the assignment of releve ( species composition) data to a previously established classification. How do the results compare to the assignment by experts and to the assignment using a completely different numerical method? Material: Releves analysed represent 4186 Czech grassland plots and 4990 plots from a wide variety of vegetation types ( 359 different associations or basal communities) in The Netherlands. For both data sets we had at our disposal an expert classification, and for the Czech data we also had available a numerical classification as well as a classification based on a neural network method ( multi- layer perceptron). Methods: Two distance indices, one qualitative and one quantitative, are combined into a single index by weighted multiplication. The composite index is a distance index for the dissimilarity between releves and vegetation types. For both data sets the classifications by the new method were compared with the existing classifications. Results: For the Czech grasslands we correctly classified 81% of the plots to the classes of an expert classification at the alliance level and 71% to the classes of the numerical classification. Correct classification rates for the Dutch releves were 64, 78 and 83 % for the lowest ( subassociation or association), association, and alliance level, respectively. Conclusion: Our method performs well in assigning community composition records to previously established classes. Its performance is comparable to the performance of other methods of supervised clustering. Compared with a multi- layer perceptron ( a type of artificial neural network), fewer parameters have to be estimated. Our method does not need the original releve data for the types, but uses synoptic tables. Another practical advantage is the provision of directly interpretable information on the contributions of separate species to the result.
Solubilization, Activation, and Insecticidal Activity of Bacillus thuringiensis Serovar thompsoni HD542 Crystal Proteins
Naimov, S. ; Boncheva, R. ; Karlova, R.B. ; Dukiandjiev, S. ; Minkov, I. ; Maagd, R.A. de - \ 2008
Applied and Environmental Microbiology 74 (2008)23. - ISSN 0099-2240 - p. 7145 - 7151.
forming toxin aerolysin - septicum alpha-toxin - subsp thompsoni - delta-endotoxin - cydia-pomonella - codling moth - similarity - resistance - potato - domain
Cry15Aa protein, produced by Bacillus thuringiensis serovar thompsoni HD542 in a crystal together with a 40 kDa accompanying protein is one of a small group of non-typical, less well-studied members of the Cry family of insecticidal proteins, and may provide an alternative for the more commonly used Cry proteins in insect pest management. In this paper we describe the characterization of the Cry15Aa and 40 kDa protein's biochemical and insecticidal properties and the mode of action. Both proteins were solubilized above pH10 in vitro. Incubation of solubilized crystal proteins with trypsin or insect midgut extracts rapidly processed the 40 kDa protein to fragments too small to be detected by SDS-PAGE, whereas the Cry15 protein yielded a stable product of approximately 30 kDa. Protein N-terminal sequencing showed that Cry15 processing occurs exclusively at the C-terminal end. Cry15 protein showed in vitro hemolytic activity, which was greatly enhanced by preincubation with trypsin or insect gut extract. Larvae of the lepidopteran insects Manduca sexta, Cydia pomonella, and Pieris brassicae were susceptible to crystals and pre-solubilization of the crystals enhanced activity to P. brassicae. Activity for all three species was enhanced by pre-incubation with trypsin. Larvae of Helicoverpa armigera and Spodoptera exigua were relatively insensitive to crystals and activity against these insects was not enhanced by prior solubilization or trypsin treatment. The 40 kDa crystal protein showed no activity in the insects tested, nor did its addition or co-expression in E. coli increase the activity of Cry15 in insecticidal and hemolytic assays.
Less lineages - more trait variation: phylogenetically clustered plant communities are functionally more diverse
Prinzing, A. ; Reiffers, R.C. ; Braakhekke, W.G. ; Hennekens, S.M. ; Tackenberg, O. ; Ozinga, W.A. ; Schaminée, J.H.J. ; Groenendael, J.M. van - \ 2008
Ecology Letters 11 (2008)8. - ISSN 1461-023X - p. 809 - 819.
environmental-conditions - niche - evolution - similarity - phylogeny - grassland - depends - signal - scale
Functional diversity within communities may influence ecosystem functioning, but which factors drive functional diversity? We hypothesize that communities assembled from many phylogenetic lineages show large functional diversity if assembly is random, but low functional diversity if assembly is controlled by interactions between species within lineages. We combined > 9000 descriptions of Dutch plant communities, a species-level phylogeny, and information on 16 functional traits (including eight dispersal traits). We found that all traits were conserved within lineages, but nevertheless communities assembled from many lineages showed a smaller variation in trait-states of most traits (including dispersal traits) than communities assembled from few lineages. Hence, within lineages, species are not randomly assembled into communities, contradicting Neutral Theory. In fact, we find evidence for evolutionary divergence in trait-states as well as present-day mutual exclusion among related, similar species, suggesting that functional diversity of communities increased due to past and present interactions between species within lineages.
Genetic diversity of maize (Zea mays L. ssp. mays) in communities of the western highlands of Guatemala: geographical patterns and processes.
Etten, J. van; Fuentes, M.R. ; Molina, L.G. ; Ponciano, K.M. - \ 2008
Genetic Resources and Crop Evolution 55 (2008)2. - ISSN 0925-9864 - p. 303 - 317.
natural-populations - similarity - markers - mexico - flow
This study concerns spatial genetic patterning, seed flow and the impact of modern varieties in maize populations in Chimaltenango, Guatemala. It uses a collection of 79 maize seed samples from farmers in the area and five samples derived from modern varieties. Bulked SSR markers employed with bulked samples (ten plants) were used. Genetic distances between populations based on these SSR data were used as a measure of co-ancestry. The study describes the genetic variation in space, assesses the association of maize diversity with spatial and environmental descriptors and quantitative traits, and provides a test of the impact of improved varieties. Maize diversity showed significant isolation-by-distance locally, but not regionally. This was interpreted as evidence for a difference between local and regional mechanisms of seed exchange; regional exchange is more related to innovation. There was also a significant association with altitude and ear/grain characteristics (related to racial classifications). Also, consistent evidence for the influence of modern varieties of maize was found, although its impact was limited spatially. It is argued that the spatial distributions of maize diversity are important to consider for germplasm collection, but should be seen as a recent outcome of dynamic processes.
Wind profiles, momentum fluxes and roughness lengths at Cabauw revisited
Verkaik, J.W. ; Holtslag, A.A.M. - \ 2007
Boundary-Layer Meteorology 122 (2007)3. - ISSN 0006-8314 - p. 701 - 719.
grenslaagmeteorologie - windsnelheid - fluctuaties - experimenten - boundary-layer meteorology - wind speed - fluctuations - experiments - atmospheric boundary-layer - surface-layer - complex terrain - land-surface - parameterization - similarity - turbulence - footprint - location - exchange
We describe the results of an experiment focusing on wind speed and momentum fluxes in the atmospheric boundary layer up to 200 m. The measurements were conducted in 1996 at the Cabauw site in the Netherlands. Momentum fluxes are measured using the K-Gill Propeller Vane. Estimates of the roughness length are derived using various techniques from the wind speed and flux measurements, and the observed differences are explained by considering the source area of the meteorological parameters. A clear rough-to-smooth transition is found in the wind speed profiles at Cabauw. The internal boundary layer reaches the lowest k-vane (20 m) only in the south-west direction where the obstacle-free fetch is about 2 km. The internal boundary layer is also reflected in the roughness lengths derived from the wind speed profiles. The lower part of the profile (<40 m) is not in equilibrium and no reliable roughness analysis can be given. The upper part of the profile can be linked to a large-scale roughness length. Roughness lengths derived from the horizontal wind speed variance and gustiness have large footprints and therefore represent a large-scale average roughness. The drag coefficient is more locally determined but still represents a large-scale roughness length when it is measured above the local internal boundary layer. The roughness length at inhomogeneous sites can therefore be determined best from drag coefficient measurements just above the local internal boundary layers directly, or indirectly from horizontal wind speed variance or gustiness. In addition, the momentum and heat fluxes along the tower are analysed and these show significant variation with height related to stability and possibly surface heterogeneity. It appears that the dimensionless wind speed gradients scale well with local fluxes for the variety of conditions considered, including the unstable cases.
Internal versus external preference analysis : an exploratory study on end-user evaluation
Kleef, E. van; Trijp, H.C.M. van; Luning, P.A. - \ 2006
Food Quality and Preference 17 (2006)5. - ISSN 0950-3293 - p. 387 - 399.
d-marketing interface - product development - consumer perceptions - information - similarity - model - thinking - quality - credibility - antecedents
Internal and external preference analysis emphasise fundamentally different perspectives on the same data. We extend the literature on comparisons between internal and external preference analysis by incorporating the perspective of the end user of the preference analysis results. From a conceptual analysis of the methodological similarities and differences between these two techniques, we develop and implement a framework for end-user evaluation of preference analysis output in terms of perceived actionability for food technology, marketing and creative purposes as well as comprehensibility and perceived appropriateness at the marketing¿R&D interface. Overall, this exploratory study suggests that end-users find information from external analysis more actionable for food technological tasks. Internal preference analysis holds a clear advantage on marketing actionability and new product creativity. No preference technique holds a clear advantage on marketing¿R&D interface appropriateness and comprehensibility. Rather than recommending applying both techniques, we suggest several ways forward in better exploiting the synergy between these two approaches.
Variance Method to Determine Turbulent Fluxes of Momentum And Sensible Heat in The Stable Atmospheric Surface Layer
Debruin, H.A.R. ; Hartogensis, O.K. - \ 2005
Boundary-Layer Meteorology 116 (2005)2. - ISSN 0006-8314 - p. 385 - 392.
nocturnal boundary-layer - sonic anemometer - eddy-correlation - temperature - similarity - cases-99
Evidence is presented that in the stable atmospheric surface layer turbulent fluxes of heat and momentum can be determined from the standard deviations of longitudinal wind velocity and temperature, ¿u and ¿T respectively, measured at a single level. An attractive aspect of this method is that it yields fluxes from measurements that can be obtained with two-dimensional sonic anemometers. These instruments are increasingly being used at official weather stations, where they replace the standard cup anemometer-wind vane system. With methods such as the one described in this note, a widespread, good quality, flux network can be established, which would greatly benefit the modelling community. It is shown that a 'variance' dimensionless height (¿¿) defined from ¿uand ¿Tis highly related to the 'conventional' dimensionless stability parameter ¿ = z/L, where is height and L is the Obukhov length. Empirical functions for ¿¿ are proposed that allow direct calculation of heat and momentum fluxes from ¿u and ¿F. The method performs fairly well also during a night of intermittent turbulence.
Effects of water vapour on the structure parameter of the refractive index for near-infrared radiation
Moene, A.F. - \ 2003
Boundary-Layer Meteorology 107 (2003). - ISSN 0006-8314 - p. 635 - 653.
surface-layer turbulence - humidity fluctuations - boundary-layer - temperature - scintillation - fluxes - similarity - quantities - spectrum - moisture
The refractive index of air (n) mainly depends on temperature and water vapour content. For near-infrared radiation, temperature is the main determining factor. To determine the structure parameter of temperature (C-T(2)) from the structure parameter of the refractive index (C-n(2)), the influence of water vapour content on n needs to be taken into account as a correction. Three levels of approximation are presented. The first involves the standard deviations of T and q (sigma(T) and sigma(q)) as well as the correlation coefficient between T and q (R-Tq). The second approximation involves R-Tq and the Bowen ratio (beta), and the last uses only the Bowen ratio. The latter is the classical Bowen ratio correction. Evaluation of the validity of the assumptions used in the derivation reveals that a large error may be introduced (for situations with R-Tq1, the correction is small, and all three approximations give errors of less than 1% in C-T(2). When C-T(2) is used to compute the sensible heat flux, the influence of the quality of the correction for water vapour fluctuations on the measured energy balance is small: for small \beta\, the correction is large, but the absolute value of the heat flux is small, whereas for large \beta\, the correction is insignificant.
Scale variability of atmospheric surface layer fluxes of energy and carbon over a tropical rain forest in southwest Amazonia; 1 diurnal conditions
Randow, C. von; Sá, L.D.A. ; Gannabathula, P.S.S.D. ; Manzi, A.O. ; Arlino, P.R.A. ; Kruijt, B. - \ 2002
Journal of Geophysical Research: Atmospheres 107 (2002)020. - ISSN 2169-897X - p. 8062 - 8062.
boundary-layer - wavelet analysis - turbulence - temperature - decomposition - similarity - modulation - canopies - aircraft - spectra
The aim of this study is to investigate the low-frequency characteristics of diurnal turbulent scalar spectra and cospectra near the Amazonian rain forest during the wet and dry seasons. This is because the available turbulent data are often nonstationary and there is no clear spectral gap to separate data into "mean" and "turbulent" parts. Daubechies-8 orthogonal wavelet is used to scale project turbulent signals in order to provide scale variance and covariance estimations. Based on the characteristics of the scale dependence of the scalar fluxes, some classification criteria of this scale dependence are investigated. The total scalar covariance of each 4-hour data run is partitioned in categories of scale covariance contributions. This permits the study of some statistical characteristics of the scalar turbulent fields in each one of these classes and, thus, to give an insight and a possible explanation of the origin of the variability of the scalar fields close to the Amazonian forest. The results have shown that a two-category classification is the most appropriate to describe the kind of observed fluctuations: "turbulent" and "mesoscale" contributions. The largest contribution of the sensible heat, latent heat, and CO2 covariance contributions occurs in the "turbulent" length scales. Mesoscale eddy motions, however, can contribute up to 30% of the total covariances under weak wind conditions. Analysis of scale correlation coefficient [r(Tvq)] between virtual temperature (Tv) and humidity (q) signals shows that the scale patterns of Tv and q variability are not similar and r(Tvq) <1 for all analyzed scales. Scale humidity skewness calculations are negative during the dry season and positive during the wet season. This suggests that different boundary layer moisture regimes occur during the dry and wet seasons.