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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    Human-induced changes in Indonesian peatlands increase drought severity
    Taufik, M. ; Minasny, B. ; Mcbratney, A.B. ; Dam, J.C. Van; Jones, P.D. ; Lanen, H.A.J. Van - \ 2020
    Environmental Research Letters 15 (2020)8. - ISSN 1748-9318
    canalization - drought amplification - hydrological drought - land-use change - peat degradation

    Indonesian peatlands are critical to the global carbon cycle, but they also support a large number of local economies. Intense forest clearing and draining in these peatlands is causing severe ecological and environmental impacts. Most studies highlighted increased carbon emission in the region through drought and large-scale fires, further accelerating peatland degradation. Yet, little is known about the long-term impacts of human-induced disturbance on peatland hydrology in the tropics. Here we show that converting natural peat forests to plantations can significantly alter the hydrological system far worse than previously recognized, leading to amplified moisture stress and drought severity. This study quantified how human-induced changes to Indonesian peatlands have affected drought severity. Through field observations and modelling, we demonstrate that canalization doubled drought severity; logging and starting plantations even quadrupled drought severity. Recognizing the importance of peatlands to Indonesia, proper management, and rehabilitating peatlands remain the only viable option for continued plantation use.

    Data from: Modelling the co-evolution of indirect genetic effects and inherited variability
    Marjanovic, J. ; Mulder, H.A. ; Rönnegård, L. ; Bijma, P. - \ 2018
    Wageningen University & Research
    inherited variability - canalization - indirect genetic effects - social interactions - competition
    When individuals interact, their phenotypes may be affected by genes in their social partners, a phenomenon known as Indirect Genetic Effects (IGEs). In aquaculture species and some plants, competition not only affects trait levels of individuals, but also inflates variation of trait values among individuals. Variability of trait values has been studied as a quantitative trait in itself, and is often referred to as inherited variability. Although the observed phenotypic relationship between competition and variability suggests an underlying genetic relationship, models of IGE and inherited variability do not allow for such relationship. Models of trait levels show IGEs may considerably change heritable variation in trait values. Currently, we lack the tools to investigate whether this result extends to inherited variability. Here we present a model that integrates IGEs and inherited variability. In this model, the target phenotype, say growth rate, is a function of genetic and environmental effects of the focal individual and of the difference in trait values between the social partner and the focal individual, multiplied by a regression coefficient. The regression coefficient is a genetic trait which is measure of cooperation; a negative value indicates competition, a positive value cooperation, and an increasing value due to selection indicates the evolution of cooperation. Our simulations show that the model results in increased variability of body weight with increase of competition. When competition decreases, variability becomes significantly smaller. Our findings suggest we may have been overlooking an entire level of genetic variation in variability, the one due to IGEs
    Polar auxin transport: models and mechanisms
    Berkel, K. van; Boer, R.J. de; Scheres, B. ; Tusscher, K. ten - \ 2013
    Development 140 (2013)11. - ISSN 0950-1991 - p. 2253 - 2268.
    pattern-formation - plant development - pin proteins - arabidopsis - efflux - phyllotaxis - root - canalization - endocytosis - growth
    Spatial patterns of the hormone auxin are important drivers of plant development. The observed feedback between the active, directed transport that generates auxin patterns and the auxin distribution that influences transport orientation has rendered this a popular subject for modelling studies. Here we propose a new mathematical framework for the analysis of polar auxin transport and present a detailed mathematical analysis of published models. We show that most models allow for self-organised patterning for similar biological assumptions, and find that the pattern generated is typically unidirectional, unless additional assumptions or mechanisms are incorporated. Our analysis thus suggests that current models cannot explain the bidirectional fountain-type patterns found in plant meristems in a fully self-organised manner, and we discuss future research directions to address the gaps in our understanding of auxin transport mechanisms.
    Quantitative genetic analysis of responses to larval food limitation in a polyphenic butterfly indicates environment- and trait-specific effects
    Saastamoinen, M. ; Brommer, J.E. ; Brakefield, P.M. ; Zwaan, B.J. - \ 2013
    Ecology and Evolution 3 (2013)10. - ISSN 2045-7758 - p. 3576 - 3589.
    bicyclus-anynana - phenotypic plasticity - life-history - adaptive responses - reaction norms - evolution - growth - genotype - evolvability - canalization
    Different components of heritability, including genetic variance (VG), are influenced by environmental conditions. Here, we assessed phenotypic responses of life-history traits to two different developmental conditions, temperature and food limitation. The former represents an environment that defines seasonal polyphenism in our study organism, the tropical butterfly Bicyclus anynana, whereas the latter represents a more unpredictable environment. We quantified heritabilities using restricted maximum likelihood (REML) procedures within an “Information Theoretical” framework in a full-sib design. Whereas development time, pupal mass, and resting metabolic rate showed no genotype-by-environment interaction for genetic variation, for thorax ratio and fat percentage the heritability increased under the cool temperature, dry season environment. Additionally, for fat percentage heritability estimates increased under food limitation. Hence, the traits most intimately related to polyphenism in B. anynana show the most environmental-specific heritabilities as well as some indication of cross-environmental genetic correlations. This may reflect a footprint of natural selection and our future research is aimed to uncover the genes and processes involved in this through studying season and condition-dependent gene expression
    Simulation of Organ Patterning on the Floral Meristem Using a Polar Auxin Transport Model
    Mourik, S. van; Kaufmann, K. ; Dijk, A.D.J. van; Angenent, G.C. ; Merks, R.M.H. ; Molenaar, J. - \ 2012
    PLoS ONE 7 (2012)1. - ISSN 1932-6203 - 9 p.
    flower development - arabidopsis-thaliana - phyllotaxis - efflux - flux - canalization - initiation - leaf
    An intriguing phenomenon in plant development is the timing and positioning of lateral organ initiation, which is a fundamental aspect of plant architecture. Although important progress has been made in elucidating the role of auxin transport in the vegetative shoot to explain the phyllotaxis of leaf formation in a spiral fashion, a model study of the role of auxin transport in whorled organ patterning in the expanding floral meristem is not available yet. We present an initial simulation approach to study the mechanisms that are expected to play an important role. Starting point is a confocal imaging study of Arabidopsis floral meristems at consecutive time points during flower development. These images reveal auxin accumulation patterns at the positions of the organs, which strongly suggests that the role of auxin in the floral meristem is similar to the role it plays in the shoot apical meristem. This is the basis for a simulation study of auxin transport through a growing floral meristem, which may answer the question whether auxin transport can in itself be responsible for the typical whorled floral pattern. We combined a cellular growth model for the meristem with a polar auxin transport model. The model predicts that sepals are initiated by auxin maxima arising early during meristem outgrowth. These form a pre-pattern relative to which a series of smaller auxin maxima are positioned, which partially overlap with the anlagen of petals, stamens, and carpels. We adjusted the model parameters corresponding to properties of floral mutants and found that the model predictions agree with the observed mutant patterns. The predicted timing of the primordia outgrowth and the timing and positioning of the sepal primordia show remarkable similarities with a developing flower in nature
    Translating environmental gradients into discontinuous reaction norms via hormone signalling in a polyphenic butterfly
    Oostra, V. ; Jong, M.A. de; Invergo, B.M. ; Kesbeke, F. ; Wende, F. ; Brakefield, P.M. ; Zwaan, B.J. - \ 2011
    Proceedings of the Royal Society. B: Biological Sciences 278 (2011)1706. - ISSN 0962-8452 - p. 789 - 797.
    bicyclus-anynana - phenotypic plasticity - developmental plasticity - drosophila-melanogaster - starvation resistance - artificial selection - eyespot size - evolution - responses - canalization
    Polyphenisms—the expression of discrete phenotypic morphs in response to environmental variation—are examples of phenotypic plasticity that may potentially be adaptive in the face of predictable environmental heterogeneity. In the butterfly Bicyclus anynana, we examine the hormonal regulation of phenotypic plasticity that involves divergent developmental trajectories into distinct adult morphs for a suite of traits as an adaptation to contrasting seasonal environments. This polyphenism is induced by temperature during development and mediated by ecdysteroid hormones. We reared larvae at separate temperatures spanning the natural range of seasonal environments and measured reaction norms for ecdysteroids, juvenile hormones (JHs) and adult fitness traits. Timing of peak ecdysteroid, but not JH titres, showed a binary response to the linear temperature gradient. Several adult traits (e.g. relative abdomen mass) responded in a similar, dimorphic manner, while others (e.g. wing pattern) showed a linear response. This study demonstrates that hormone dynamics can translate a linear environmental gradient into a discrete signal and, thus, that polyphenic differences between adult morphs can already be programmed at the stage of hormone signalling during development. The range of phenotypic responses observed within the suite of traits indicates both shared regulation and independent, trait-specific sensitivity to the hormone signal.
    Estimation of genetic variation in residual variance in female and male broiler chickens
    Mulder, H.A. ; Hill, W.G. ; Vereijken, A. ; Veerkamp, R.F. - \ 2009
    Animal 3 (2009)12. - ISSN 1751-7311 - p. 1673 - 1680.
    environmental variability - tribolium-castaneum - weight traits - birth-weight - pupa weight - litter size - selection - heterogeneity - canalization - mice
    In breeding programs, robustness of animals and uniformity of end product can be improved by exploiting genetic variation in residual variance. Residual variance can be defined as environmental variance after accounting for all identifiable effects. The aims of this study were to estimate genetic variance in residual variance of body weight, and to estimate genetic correlations between body weight itself and its residual variance and between female and male residual variance for broilers. The data sets comprised 26 972 female and 24 407 male body weight records. Variance components were estimated with ASREML. Estimates of the heritability of residual variance were in the range 0.029 (s.e.50.003) to 0.047 (s.e.50.004). The genetic coefficients of variation were high, between 0.35 and 0.57. Heritabilities were higher in females than in males. Accounting for heterogeneous residual variance increased the heritabilities for body weight as well. Genetic correlations between body weight and its residual variance were 20.41 (s.e.50.032) and 20.45 (s.e.50.040), respectively, in females and males. The genetic correlation between female and male residual variance was 0.11 (s.e.50.089), indicating that female and male residual variance are different traits. Results indicate good opportunities to simultaneously increase the mean and improve uniformity of body weight of broilers by selection.
    Prediction of breeding values and selection responses with genetic heterogeneity of environmental variance
    Mulder, H.A. ; Bijma, P. ; Hill, W.G. - \ 2007
    Genetics 175 (2007). - ISSN 0016-6731 - p. 1895 - 1910.
    stabilizing selection - disruptive selection - tribolium-castaneum - quantitative traits - residual variance - pupa weight - canalization - variability - plasticity - drosophila
    There is empirical evidence that genotypes differ not only in mean, but also in environmental variance of the traits they affect. Genetic heterogeneity of environmental variance may indicate genetic differences in environmental sensitivity. The aim of this study was to develop a general framework for prediction of breeding values and selection responses in mean and environmental variance with genetic heterogeneity of environmental variance. Both means and environmental variances were treated as heritable traits. Breeding values and selection responses were predicted with little bias using linear, quadratic and cubic regression on individual phenotype, or using linear regression on the mean and within-family variance of a group of relatives. A measure of heritability was proposed for environmental variance to standardize results in the literature and to facilitate comparisons to "conventional" traits. Genetic heterogeneity of environmental variance can be considered as a trait with a low heritability. Although a large amount of information is necessary to accurately estimate breeding values for environmental variance, response in environmental variance can be substantial, even with mass selection. The methods developed allow use of the well-known selection index framework to evaluate breeding strategies and effects of natural selection that simultaneously change the mean and the variance
    Phenotypic plasticity of elytron length in wingless two-spot ladybird beetles Adalia bipunctata (Coleoptera: Coccinellidae)
    Lommen, S.T.E. ; Jong, P.W. de; Brakefield, P.M. - \ 2005
    European Journal of Entomology 102 (2005)3. - ISSN 1210-5759 - p. 553 - 556.
    nigropilosus uzel thysanoptera - drosophila-melanogaster - canalization - temperature - cricket - form - polymorphism - populations - heteroptera - characters
    Winglessness in the two-spot ladybird beetle Adalia bipunctata (L.) is determined by a single locus with the wingless allele recessive to the winged wildtype allele. The expression of the wingless trait is highly variable, with individuals missing a variable part of elytra and flight wings; the elytra and wings appear to be truncated rather than miniature in form. The degree of winglessness is partly determined genetically. Here we report on the phenotypic plasticity of the degree of winglessness. The environmental effect on elytron length relative to maximal elytron length in wingless phenotypes was studied by rearing offspring of single pair crosses of this form at a low (19°C) or high (29°C) temperature. Offspring reared at 19°C showed relatively longer elytra than those reared at 29°C
    Perspective: Evolution and detection of genetic robustness
    Visser, J.A.G.M. de; Hermisson, J. ; Wagner, G.P. ; Ancel Meyers, L. ; Bagheri-Chaichian, H. ; Blanchard, J.L. ; Chao, L. ; Cheverud, J.M. ; Elena, S.F. ; Fontana, W. ; Gibson, G. ; Hansen, T.F. ; Krakauer, D. ; Lewontin, R.C. ; Ofria, C. ; Rice, S.H. ; Dassow, G. von; Wagner, A. ; Whitlock, M.C. - \ 2003
    Evolution 57 (2003)9. - ISSN 0014-3820 - p. 1959 - 1972.
    drosophila-melanogaster - developmental stability - deleterious mutations - fitness components - heat-shock - canalization - dominance - epistasis - selection - plasticity
    Robustness is the invariance of phenotypes in the face of perturbation. The robustness of phenotypes appears at various levels of biological organization, including gene expression, protein folding, metabolic flux, physiological homeostasis, development, and even organismal fitness. The mechanisms underlying robustness are diverse, ranging from thermodynamic stability at the RNA and protein level to behavior at the organismal level. Phenotypes can be robust either against heritable perturbations (e.g., mutations) or nonheritable perturbations (e.g., the weather). Here we primarily focus on the first kind of robustness-genetic robustness-and survey three growing avenues of research: (1) measuring genetic robustness in nature and in the laboratory; (2) understanding the evolution of genetic robustness; and (3) exploring the implications of genetic robustness for future evolution.
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