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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    Dynamics of adaptation in experimental yeast populations exposed to gradual and abrupt change in heavy metal concentration
    Gorter, Florien ; Aarts, Mark ; Zwaan, B.J. ; Visser, J.A.G.M. de - \ 2015
    Wageningen UR
    adaptation - ecology - evolutionary - microbial - Environmental variability - evolution - fitness - genetics - population - dynamics - fungi - heavy metals - pleiotropy
    Directional environmental change is a ubiquitous phenomenon that may have profound effects on all living organisms. However, it is unclear how different rates of such change affect the dynamics and outcome of evolution. We studied this question using experimental evolution of heavy metal tolerance in the baker´s yeast Saccharomyces cerevisiae. To this end, we grew replicate lines of yeast for 500 generations in the presence of (i) a constant high concentration of cadmium, nickel or zinc, or (ii) a gradually increasing concentration of these metals. We found that gradual environmental change leads to a delay in fitness increase compared to abrupt change, but not necessarily to a different fitness of evolutionary endpoints. For the non-essential metal cadmium this delay is due to reduced fitness differences between genotypes at low metal concentrations, consistent with directional selection to minimize intracellular concentrations of this metal. In contrast, for the essential metals nickel and zinc different genotypes are selected at different concentrations, consistent with stabilizing selection to maintain constant intracellular concentrations of these metals. These findings indicate diverse fitness consequences of evolved tolerance mechanisms for essential and non-essential metals, and imply that the rate of environmental change and the nature of the stressor are crucial determinants of evolutionary dynamics.
    DNA methylation and sex allocation in the parasitoid wasp Nasonia vitripennis
    Cook, N. ; Pannebakker, B.A. ; Tauber, E. ; Shuker, D.M. - \ 2015
    Wageningen UR
    behavior - evolution - reproductive - genetics - evolutionary - sex - allocation - ratio
    The role of epigenetics in the control and evolution of behavior is being increasingly recognized. Here we test whether DNA methylation influences patterns of adaptive sex allocation in the parasitoid wasp Nasonia vitripennis. Female N. vitripennis allocate offspring sex broadly in line with local mate competition (LMC) theory. However, recent theory has highlighted how genomic conflict may influence sex allocation under LMC, conflict that requires parent-of-origin information to be retained by alleles through some form of epigenetic signal. We manipulated whole-genome DNA methylation in N. vitripennis females using the hypomethylating agent 5-aza-2′-deoxycytidine. Across two replicated experiments, we show that disruption of DNA methylation does not ablate the facultative sex allocation response of females, as sex ratios still vary with cofoundress number as in the classical theory. However, sex ratios are generally shifted upward when DNA methylation is disrupted. Our data are consistent with predictions from genomic conflict over sex allocation theory and suggest that sex ratios may be closer to the optimum for maternally inherited alleles.
    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.
    Remarkably divergent regions punctuate the genome assembly of the Caenorhabditis elegans Hawaiian strain CB4856
    Thompson, O.A. ; Snoek, L.B. ; Nijveen, H. ; Sterken, M.G. ; Volkers, R.J.M. ; Brenchley, R. ; Hof, A. van 't; Bevers, R.P.J. ; Cossins, A.R. ; Yanai, I. ; Hajnal, A. ; Schmid, T. ; Perkins, J.D. ; Spencer, D. ; Kruglyak, L. ; Andersen, E.C. ; Moerman, D.G. ; Hillier, L.W. ; Kammenga, J.E. ; Waterston, R.H. - \ 2015
    Genetics 200 (2015)3. - ISSN 0016-6731 - p. 975 - 989.
    natural variation data - c. elegans - arabidopsis-thaliana - gene - polymorphism - populations - diversity - nematodes - dna - evolutionary
    The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population and evolutionary studies. To enhance the utility of the strain, we have generated a draft sequence of the CB4856 genome, exploiting a variety of resources and strategies. The CB4856 genome when compared against the N2 reference has 327,050 single nucleotide variants (SNVs) and 79,529 insertion-deletion events (indels) that result in a total of 3.3 megabasepairs (Mb) of N2 sequence missing from CB4856 and 1.4 Mb of sequence present in CB4856 not present in N2. As previously reported, the density of SNVs varies along the chromosomes, with the arms of chromosomes showing greater average variation than the centers. In addition, we find 61 regions totaling 2.8 Mb, distributed across all six chromosomes, that have a greatly elevated SNV density, ranging from 2% to 16% SNVs. A survey of other wild isolates show that the two alternative haplotypes for each region are widely distributed, suggesting they have been maintained by balancing selection over long evolutionary times. These divergent regions contain an abundance of genes from large rapidly evolving families encoding F-box, MATH, BATH, seven-transmembrane G-coupled receptors, and nuclear hormone receptors suggesting that they provide selective advantages in natural environments. The draft sequence makes available a comprehensive catalog of sequence differences between the CB4856 and N2 strains that will facilitate the molecular dissection of their phenotypic differences. Our work also emphasizes the importance of going beyond simple alignment of reads to a reference genome when assessing differences between genomes.
    Repeated parallel evolution reveals limiting similarity in subterranean diving beetles
    Vergnon, R. ; Leijs, R. ; Nes, Egbert van; Scheffer, M. - \ 2013
    Wageningen UR
    community - structure - competition - ecology - evolutionary
    The theory of limiting similarity predicts that co-occurring species must be sufficiently different to coexist. Although this idea is a staple of community ecology, convincing empirical evidence has been scarce. Here we examine 34 subterranean beetle communities in arid inland Australia that share the same habitat type but have evolved in complete isolation over the past 5 million years. Although these communities come from a range of phylogenetic origins, we find that they have almost invariably evolved to share a similar size structure. The relative positions of coexisting species on the body size axis were significantly more regular across communities than would be expected by chance, with a size ratio, on average, of 1.6 between coexisting species. By contrast, species’ absolute body sizes varied substantially from one community to the next. This suggests that self-organized spacing according to limiting-similarity theory, as opposed to evolution toward preexisting fixed niches, shaped the communities. Using a model starting from random sets of founder species, we demonstrate that the patterns are indeed consistent with evolutionary self-organization. For less isolated habitats, the same model predicts the coexistence of multiple species in each regularly spaced functional group. Limiting similarity, therefore, may also be compatible with the coexistence of many redundant species.
    Phylogenetics of Stelis and closely related genera (Orchidaceae: Pleurothallidinae)
    Karremans, A.P. ; Bakker, F.T. ; Pupulin, F. ; Solano-Gomez, R. ; Smulders, M.J.M. - \ 2013
    Plant Systematics and Evolution 299 (2013)1. - ISSN 0378-2697 - p. 151 - 176.
    consensus networks - trees - dna - evolutionary - collections - inference - mrbayes - nuclear
    Stelis, one of the largest genera within Pleurothallidinae, was recently recircumscribed to include a few hundred more species, most of which had previously been assigned to Pleurothallis. Here, a new phylogenetic analysis of Stelis and closely related genera based on DNA sequences from nuclear ITS and chloroplast matK, based on a much larger sample, is presented; it includes more than 100 species assigned to Stelis and covers all proposed groupings within the genus, many of which have not previously been represented. Clades are proposed to enable easier discussion of groups of closely related species; each clade is characterized morphologically, ecologically, and geographically to explain the evidence found in the molecular analysis. Discussion of the evolutionary trends of character states found in the genus in its broad sense is given. The current taxonomy of the group is given and the possible taxonomical implications of the findings presented here are discussed.
    The predictive adaptive response: modeling the life history evolution of the butterfly, Bicyclus anynana, in seasonal environments
    Heuvel, J. van den; Saastamoinen, M. ; Brakefield, P.M. ; Kirkwood, T.B.L. ; Zwaan, B.J. - \ 2012
    Wageningen UR
    ecology - evolutionary - evolution - physiological - life history - modeling - individual based - stochastic spatial - phenotypic plasticy - polymorphism - resource allocation - theory - trade offs
    A predictive adaptive response (PAR) is a type of developmental plasticity where the response to an environmental cue is not immediately advantageous but instead is later in life. The PAR is a way for organisms to maximize fitness in varying environments. Insects living in seasonal environments are valuable model systems for testing the existence and form of PAR. Previous manipulations of the larval and the adult environments of the butterfly Bicyclus anynana have shown that individuals that were food restricted during the larval stage coped better with forced flight during the adult stage compared to those with optimal conditions in the larval stage. Here, we describe a state-dependent energy allocation model, which we use to test whether such a response to food restriction could be adaptive in nature where this butterfly exhibits seasonal cycles. The results from the model confirm the responses obtained in our previous experimental work and show how such an outcome was facilitated by resource allocation patterns to the thorax during the pupal stage. We conclude that for B. anynana, early-stage cues can direct development toward a better adapted phenotype later in life and, therefore, that a PAR has evolved in this species.
    De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology
    Nijkamp, J.F. ; Broek, M. van den; Datema, E. ; Kok, S. de; Bosman, L. ; Luttik, M.A. ; Daran-Lapujade, P. ; Vongsangnak, W. ; Nielsen, J. ; Heijne, W.H.M. ; Klaassen, P. ; Paddon, C.J. ; Platt, D. ; Kotter, P. ; Ham, R.C.H.J. van; Reinders, M.J.T. ; Pronk, J.T. ; Ridder, D. de; Daran, J.M. - \ 2012
    Microbial Cell Factories 11 (2012). - ISSN 1475-2859
    l-arabinose - alcoholic fermentation - biotin-prototrophy - chemostat cultures - gene prediction - yeast genome - glucose - evolutionary - protein - xylose
    Saccharomyces cerevisiae CEN.PK 113-7D is widely used for metabolic engineering and systems biology research in industry and academia. We sequenced, assembled, annotated and analyzed its genome. Single-nucleotide variations (SNV), insertions/deletions (indels) and differences in genome organization compared to the reference strain S. cerevisiae S288C were analyzed. In addition to a few large deletions and duplications, nearly 3000 indels were identified in the CEN.PK113-7D genome relative to S288C. These differences were overrepresented in genes whose functions are related to transcriptional regulation and chromatin remodelling. Some of these variations were caused by unstable tandem repeats, suggesting an innate evolvability of the corresponding genes. Besides a previously characterized mutation in adenylate cyclase, the CEN. PK113-7D genome sequence revealed a significant enrichment of non-synonymous mutations in genes encoding for components of the cAMP signalling pathway. Some phenotypic characteristics of the CEN. PK113-7D strains were explained by the presence of additional specific metabolic genes relative to S288C. In particular, the presence of the BIO1 and BIO6 genes correlated with a biotin prototrophy of CEN. PK113-7D. Furthermore, the copy number, chromosomal location and sequences of the MAL loci were resolved. The assembled sequence reveals that CEN. PK113-7D has a mosaic genome that combines characteristics of laboratory strains and wild-industrial strains.
    Fungal Planet description sheets: 107-127
    Crous, P.W. ; Summerell, B.A. ; Shivas, R.G. ; Burgess, T.I. ; Decock, C.A. ; Dreyer, L.L. ; Granke, L.L. ; Guest, D.I. ; Hardy, G.E.St.J. ; Hausbeck, M.K. ; Hüberli, D. ; Jung, T. ; Koukol, O. ; Lennox, C.L. ; Liew, E.C.Y. ; Lombard, L. ; McTaggart, A.R. ; Pryke, J.S. ; Roets, F. ; Saude, C. ; Shuttleworth, L.A. ; Stukely, M.J.C. ; Vánky, K. ; Webster, B.J. ; Windstam, S.T. ; Groenewald, J.Z. - \ 2012
    Persoonia 28 (2012). - ISSN 0031-5850 - p. 138 - 182.
    sp-nov - allied genera - south-africa - diaporthales - eucalyptus - genus - cryphonectriaceae - gnomoniaceae - reevaluation - evolutionary
    Novel species of microfungi described in the present study include the following from Australia: Phytophthora amnicola from still water, Gnomoniopsis smithogilvyi from Castanea sp., Pseudoplagiostoma corymbiae from Corymbia sp., Diaporthe eucalyptorum from Eucalyptus sp., Sporisorium andrewmitchellii from Enneapogon aff. lindleyanus, Myrmecridium banksiae from Banksia, and Pilidiella wangiensis from Eucalyptus sp. Several species are also described from South Africa, namely: Gondwanamyces wingfieldii from Protea caffra, Montagnula aloes from Aloe sp., Diaporthe canthii from Canthium inerne, Phyllosticta ericarum from Erica gracilis, Coleophoma proteae from Protea caffra, Toxicocladosporium strelitziae from Strelitzia reginae, and Devriesia agapanthi from Agapanthus africanus. Other species include Phytophthora asparagi from Asparagus officinalis (USA), and Diaporthe passiflorae from Passiflora edulis (South America). Furthermore, novel genera of coelomycetes include Chrysocrypta corymbiae from Corymbia sp. (Australia), Trinosporium guianense, isolated as a contaminant (French Guiana), and Xenosonderhenia syzygii, from Syzygium cordatum (South Africa). Pseudopenidiella piceae from Picea abies (Czech Republic), and Phaeocercospora colophospermi from Colophospermum mopane (South Africa) represent novel genera of hyphomycetes. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.
    Normative contestation in transitions ‘in the making’: Animal welfare concerns and system innovation in pig husbandry
    Elzen, B. ; Geels, F. ; Leeuwis, C. ; Mierlo, B. van - \ 2011
    Research Policy 40 (2011)2. - ISSN 0048-7333 - p. 263 - 275.
    sociotechnical transition - social-movements - dynamics - transformation - evolutionary - performance
    Previous studies of system innovations mainly focused on historical cases that were driven by commercial motivations of pioneers and entrepreneurs. This article investigates a system innovation in the making that is driven by normative concerns, such as sustainability or animal welfare, initially formulated by outsiders like special-interest groups. Our central research question is: How, when and why is normative contestation of existing regimes effective in influencing the orientation of transitions in the making? The conceptual framework enriches innovation studies and the multi-level perspective with insights from social movement theory (SMT) and political science. SMT is used to analyze the build up of normative pressure (through framing, resource mobilization, and political opportunity structures). From political science we use the notion of multiple streams, in our analysis a problem, regulatory, market and technology stream.The research design consists of a comparative case study of pig husbandry systems. One case analyses the sub-sector of pregnant sows where normative pressures, after several decades, led to the changes advocated by the contestants. The second case concerns the sub-sector of pig fattening where normative pressure was less successful. The difference is partly explained by the normative pressure for pregnant sows being larger than for fattening pigs. The other part of the explanation is that in the first case normative pressure aligned better with the three other streams (regulatory, market and technology) to lead to the changes desired by the contestants.
    The quest for orthologs: finding the corresponding gene across genomes
    Kuzniar, A. ; Ham, R.C.H.J. van; Pongor, S. ; Leunissen, J.A.M. - \ 2008
    Trends in Genetics 24 (2008)11. - ISSN 0168-9525 - p. 539 - 551.
    phylogenetic trees - network propagation - eukaryotic genomes - protein families - database - evolutionary - classification - life - phylogenomics - inference
    Orthology is a key evolutionary concept in many areas of genomic research. It provides a framework for subjects as diverse as the evolution of genomes, gene functions, cellular networks and functional genome annotation. Although orthologous proteins usually perform equivalent functions in different species, establishing true orthologous relationships requires a phylogenetic approach, which combines both trees and graphs (networks) using reliable species phylogeny and available genomic data from more than two species, and an insight into the processes of molecular evolution. Here, we evaluate the available bioinformatics tools and provide a set of guidelines to aid researchers in choosing the most appropriate tool for any situation.
    Small CRISPR RNAs guide antiviral defense in prokaryotes
    Brouns, S.J.J. ; Jore, M.M. ; Lundgren, M. ; Westra, E.R. ; Slijkhuis, R.J. ; Snijders, A.P. ; Dickman, M.J. ; Makarova, K.S. ; Koonin, E.V. ; Oost, J. van der - \ 2008
    Science 321 (2008)5891. - ISSN 0036-8075 - p. 960 - 964.
    provides acquired-resistance - streptococcus-thermophilus - repeats - identification - elements - dna - evolutionary - sequence - viruses - system
    Prokaryotes acquire virus resistance by integrating short fragments of viral nucleic acid into clusters of regularly interspaced short palindromic repeats (CRISPRs). Here we show how virus-derived sequences contained in CRISPRs are used by CRISPR-associated (Cas) proteins from the host to mediate an antiviral response that counteracts infection. After transcription of the CRISPR, a complex of Cas proteins termed Cascade cleaves a CRISPR RNA precursor in each repeat and retains the cleavage products containing the virus-derived sequence. Assisted by the helicase Cas3, these mature CRISPR RNAs then serve as small guide RNAs that enable Cascade to interfere with virus proliferation. Our results demonstrate that the formation of mature guide RNAs by the CRISPR RNA endonuclease subunit of Cascade is a mechanistic requirement for antiviral defense
    Onion thrips, Thrips tabaci, have gut bacteria that are closely related to the symbionts of the western flower thrips, Frankliniella occidentalis
    Vries, E.J. de; Wurff, A.W.G. van der; Jacobs, G. ; Breeuwer, J.A.J. - \ 2008
    Journal of Insect Science 8 (2008). - ISSN 1536-2442 - p. 1 - 11.
    microbial ecology - thysanoptera - transmission - insects - growth - evolutionary - association - resistance - wolbachia - termites
    It has been shown that many insects have Enterobacteriaceae bacteria in their gut system. The western flower thrips, Frankliniella occidentalis Pergande [Thysanoptera: Thripidae], has a symbiotic relation with Erwinia species gut bacteria. To determine if other Thripidae species have similar bacterial symbionts, the onion thrips, Thrips tabaci, was studied because, like F. occidentalis, it is phytophagous. Contrary to F. occidentalis, T. tabaci is endemic in Europe and biotypes have been described. Bacteria were isolated from the majority of populations and biotypes of T. tabaci examined. Bacteria were present in high numbers in most individuals of the populations studied. Like F. occidentalis, T. tabaci contained one type of bacterium that clearly outnumbered all other types present in the gut. This bacterium was identified as an Erwinia species, as was also the case for F. occidentalis. However, its biochemical characteristics and 16S rDNA sequence differed from the bacteria present in F. occidentalis.
    Host feeding in insect parasitoids: why destructively feed upon a host that excretes an alternative?
    Burger, W. ; Reijnen, T.M. ; Lenteren, J.C. van; Vet, L.E.M. - \ 2004
    Entomologia Experimentalis et Applicata 112 (2004)3. - ISSN 0013-8703 - p. 207 - 215.
    trialeurodes-vaporariorum homoptera - encarsia-formosa hymenoptera - alfalfa weevil coleoptera - aphytis-melinus - honeydew sugars - aphelinidae - aleyrodidae - food - strategies - evolutionary
    Host feeding is the consumption of host tissue by the adult female parasitoid. We studied the function of destructive host feeding and its advantage over non-destructive feeding on host-derived honeydew in the whitefly parasitoid Encarsia formosa Gahan (Hymenoptera: Aphelinidae). We allowed parasitoids to oviposit until they attempted to host feed. We either prevented or allowed host feeding. Parasitoids had access to sucrose solution, with or without additional access to honeydew. Parasitoids that were allowed to host feed did not have a higher egg load 20 or 48 h after host feeding than parasitoids prevented from host feeding. Host feeding did not increase the number of eggs matured within these periods, nor did the time spent host feeding positively affect any of these response variables. On the other hand, the presence of honeydew did have a positive effect on egg load 20 and 48 h after host feeding compared with parasitoids deprived of honeydew. Parasitoids with access to honeydew matured more eggs within these periods than honeydew-deprived parasitoids. Host feeding increased life expectancy, but this effect was nullified when honeydew was supplied after the host-feeding attempt. In conclusion, feeding on honeydew could be an advantageous alternative to host feeding in terms of egg quantity and longevity. This applies especially to parasitoids exploiting Homoptera, because these parasitoids can obtain honeydew from the host itself. It is possible that destructive host feeding has evolved to enable females to sustain the production of high-quality anhydropic eggs, which may be important in the parasitoid's natural environment. We argue that future studies should take natural alternative food sources into more consideration.
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