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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    Epigenetic differences linked to phenotypic variation in field and common garden grown Scabiosa columbaria plants
    Groot, Maartje P. ; Wagemaker, Niels ; Ouborg, Joop ; Verhoeven, Koen J.F. ; Vergeer, P. - \ 2018
    Ecology and Evolution 8 (2018)6. - ISSN 2045-7758 - p. 3505 - 3517.
    Populations often differ in phenotype and these differences can be caused by adaptation by natural selection, random neutral processes, and environmental responses. The most straightforward way to divide mechanisms that influence phenotypic variation is heritable variation and environmental‐induced variation (e.g., plasticity). While genetic variation is responsible for most heritable phenotypic variation, part of this is also caused by nongenetic inheritance. Epigenetic processes may be one of the underlying mechanisms of plasticity and nongenetic inheritance and can therefore possibly contribute to heritable differences through drift and selection. Epigenetic variation may be influenced directly by the environment, and part of this variation can be transmitted to next generations. Field screenings combined with common garden experiments will add valuable insights into epigenetic differentiation, epigenetic memory and can help to reveal part of the relative importance of epigenetics in explaining trait variation. We explored both genetic and epigenetic diversity, structure and differentiation in the field and a common garden for five British and five French Scabiosa columbaria populations. Genetic and epigenetic variation was subsequently correlated with trait variation. Populations showed significant epigenetic differentiation between populations and countries in the field, but also when grown in a common garden. By comparing the epigenetic variation between field and common garden‐grown plants, we showed that a considerable part of the epigenetic memory differed from the field‐grown plants and was presumably environmentally induced. The memory component can consist of heritable variation in methylation that is not sensitive to environments and possibly genetically based, or environmentally induced variation that is heritable, or a combination of both. Additionally, random epimutations might be responsible for some differences as well. By comparing epigenetic variation in both the field and common environment, our study provides useful insight into the environmental and genetic components of epigenetic variation.
    Transgenerational effects of mild heat in Arabidopsis thaliana show strong genotype specificity that is explained by climate at origin
    Groot, Maartje P. ; Kubisch, Alexander ; Ouborg, Joop ; Pagel, Jorn ; Schmid, Karl J. ; Vergeer, P. ; Lampei, Christian - \ 2017
    New Phytologist 215 (2017)3. - ISSN 0028-646X - p. 1221 - 1234.
    Transgenerational environmental effects can trigger strong phenotypic variation. However, it is unclear how cues from different preceding generations interact. Also, little is known about the genetic variation for these life history traits.
    Here, we present the effects of grandparental and parental mild heat, and their combination, on four traits of the third‐generation phenotype of 14 Arabidopsis thaliana genotypes. We tested for correlations of these effects with climate and constructed a conceptual model to identify the environmental conditions that favour the parental effect on flowering time.
    We observed strong evidence for genotype‐specific transgenerational effects. On average, A. thaliana accustomed to mild heat produced more seeds after two generations. Parental effects overruled grandparental effects in all traits except reproductive biomass. Flowering was generally accelerated by all transgenerational effects. Notably, the parental effect triggered earliest flowering in genotypes adapted to dry summers. Accordingly, this parental effect was favoured in the model when early summer heat terminated the growing season and environments were correlated across generations.
    Our results suggest that A. thaliana can partly accustom to mild heat over two generations and genotype‐specific parental effects show non‐random evolutionary divergence across populations that may support climate change adaptation in the Mediterranean.
    Data from: Effects of multi-generational stress exposure and offspring environment on the expression and persistence of transgenerational effects in Arabidopsis thaliana
    Groot, M. ; Kooke, R. ; Knoben, Nieke ; Vergeer, P. ; Keurentjes, J.J.B. ; Ouborg, N.J. ; Verhoeven, Koen J.F. - \ 2016
    Wageningen University & Research
    grandparental effects - great-parental effects - parental effects - salt stress - transgenerational plasticity
    Phenotype data of A. thaliana plants grown in either a field environment or in a climate chamber environment. In the climate chamber environment plants were grown under control conditions or salt stress.
    How Can Genomic Tools Contribute to the Conservation of Endangered Organisms
    Pertoldi, Cino ; Randi, Ettore ; Ruiz-González, Aritz ; Vergeer, Philippine ; Ouborg, Joop - \ 2016
    International journal of genomcs 2016 (2016). - ISSN 2314-436X - 2 p.
    Effects of Multi-Generational Stress Exposure and Offspring Environment on the Expression and Persistence of Transgenerational Effects in Arabidopsis thaliana
    Groot, Maartje P. ; Kooke, R. ; Knoben, Nieke ; Vergeer, P. ; Keurentjes, J.J.B. ; Ouborg, N.J. ; Verhoeven, Koen J.F. - \ 2016
    PLoS ONE 11 (2016)3. - ISSN 1932-6203 - 16 p.
    Plant phenotypes can be affected by environments experienced by their parents. Parental environmental effects are reported for the first offspring generation and some studies showed persisting environmental effects in second and further offspring generations. However, the expression of these transgenerational effects proved context-dependent and their reproducibility can be low. Here we study the context-dependency of transgenerational effects by evaluating parental and transgenerational effects under a range of parental induction and offspring evaluation conditions. We systematically evaluated two factors that can influence the expression of transgenerational effects: single- versus multiple-generation exposure and offspring environment. For this purpose, we exposed a single homozygous Arabidopsis thaliana Col-0 line to salt stress for up to three generations and evaluated offspring performance under control and salt conditions in a climate chamber and in a natural environment. Parental as well as transgenerational effects were observed in almost all traits and all environments and traced back as far as great-grandparental environments. The length of exposure exerted strong effects; multiple-generation exposure often reduced the expression of the parental effect compared to single-generation exposure. Furthermore, the expression of transgenerational effects strongly depended on offspring environment for rosette diameter and flowering time, with opposite effects observed in field and greenhouse evaluation environments. Our results provide important new insights into the occurrence of transgenerational effects and contribute to a better understanding of the context-dependency of these effects.
    epiGBSBS: reference-free reduced representation bisulfite sequencing
    Gurp, T. van; Wagemaker, C.A.M. ; Wouters, B. ; Vergeer, P. ; Ouborg, N.J. ; Verhoeven, Koen J.F. - \ 2016
    Nature Methods : techniques for life scientists and chemists 13 (2016). - ISSN 1548-7091 - p. 322 - 324.
    We describe epiGBSBS, a reduced representation bisulfite sequencing method for cost-effective exploration and comparative analysis of DNADNADNA methylation and genetic variation in hundreds of samples de novo. This method uses genotyping by sequencing of bisulfite-converted DNADNADNA followed by reliable de novo reference construction, mapping, variant calling, and distinction of single-nucleotide polymorphisms (SNSNPs) versus methylation variation (software is available at https://github.com/thomasvangurp/epiGBS). The output can be loaded directly into a genome browser for visualization and into RnBeads for analysis of differential methylation.
    Within and between population variation in inbreeding depression in the locally threatened perennial Scabiosa columbaria
    Angeloni, F. ; Vergeer, P. ; Wagemaker, C.A.M. ; Ouborg, N.J. - \ 2014
    Conservation Genetics 15 (2014)2. - ISSN 1566-0621 - p. 331 - 342.
    among-family variation - false discovery rate - self-fertilization - life-history - genetic differentiation - grassland plant - mating systems - size - extinction - conservation
    Inbreeding depression plays a central role within the conservation genetics paradigm. Until now inbreeding depression is incorporated into models of population viability as a mean value (e.g. number of lethal equivalents) for all traits in a population. In this study of the locally threatened perennial plant species Scabiosa columbaria we investigated both the mean and the variance among families of inbreeding depression in eight life history traits for five natural populations varying in size from 300 to more than 120,000 individuals. Significant inbreeding depression was found in all populations and all traits. The mean inbreeding depression value per trait was never correlated to population size. Within each population, highly significant variation in inbreeding depression between families (VIFLID) was found. Per trait, families with inbreeding depression next to families with outbreeding depression were often found within the same population. Inbreeding depression at the family level was in many cases not correlated among traits and independent of correlations between traits themselves. VIFLID was negatively correlated with population size: in two traits these correlations were significant. The results underline that inbreeding depression is a complex, highly dynamic phenomenon. Models of viability should incorporate inbreeding depression distributions, with a trait specific mean and variance. Moreover, models of metapopulation dynamics should incorporate genotype quality as factor in colonization success.
    Early root overproduction not triggered by nutrients decisive for competitive success belowground
    Padilla, F.M. ; Mommer, L. ; Caluwe, H. de; Smit-Tiekstra, A.E. ; Wagemaker, C.A.M. ; Ouborg, N.J. ; Kroon, H. de - \ 2013
    PLoS ONE 8 (2013)1. - ISSN 1932-6203 - 9 p.
    interspecific competition - plant diversity - niche differentiation - negative feedback - species-diversity - seed yield - productivity - communities - maintenance - mechanisms
    Background - Theory predicts that plant species win competition for a shared resource by more quickly preempting the resource in hotspots and by depleting resource levels to lower concentrations than its competitors. Competition in natural grasslands largely occurs belowground, but information regarding root interactions is limited, as molecular methods quantifying species abundance belowground have only recently become available. Principal Findings - In monoculture, the grass Festuca rubra had higher root densities and a faster rate of soil nitrate depletion than Plantago lanceolata, projecting the first as a better competitor for nutrients. However, Festuca lost in competition with Plantago. Plantago not only replaced the lower root mass of its competitor, but strongly overproduced roots: with only half of the plants in mixture than in monoculture, Plantago root densities in mixture were similar or higher than those in its monocultures. These responses occurred equally in a nutrient-rich and nutrient-poor soil layer, and commenced immediately at the start of the experiment when root densities were still low and soil nutrient concentrations high. Conclusions/Significance - Our results suggest that species may achieve competitive superiority for nutrients by root growth stimulation prior to nutrient depletion, induced by the presence of a competitor species, rather than by a better ability to compete for nutrients per se. The root overproduction by which interspecific neighbors are suppressed independent of nutrient acquisition is consistent with predictions from game theory. Our results emphasize that root competition may be driven by other mechanisms than is currently assumed. The long-term consequences of these mechanisms for community dynamics are discussed.
    Belowground DNA-based techniques: untangling the network of plant root interactions
    Mommer, L. ; Dumbrell, A.J. ; Wagemaker, C.A.M. ; Ouborg, N.J. - \ 2011
    Plant and Soil 348 (2011)1-2. - ISSN 0032-079X - p. 115 - 121.
    molecular-identification - niche differentiation - species composition - soil - biodiversity - diversity - markers - distributions - competition - depth
    The east-west-north colonization history of the Mediterranean and Europe by the coastal plant Carex extensa (Cyperaceae)
    Escudero, M. ; Vargas, P. ; Arens, P. ; Ouborg, N.J. ; Luceno, M. - \ 2010
    Molecular Ecology 19 (2010)2. - ISSN 0962-1083 - p. 352 - 370.
    population genetic-structure - length polymorphism markers - messinian salinity crisis - sedges carex - phylogeographical structure - molecular evolution - microsatellite data - computer-program - chloroplast dna - cakile-maritima
    Coastal plants are ideal models for studying the colonization routes of species because of the simple linear distributions of these species. Carex extensa occurs mainly in salt marshes along the Mediterranean and European coasts. Variation in cpDNA sequences, amplified fragment length polymorphisms (AFLPs) and simple sequence repeats (SSRs) of 24 populations were analysed to reconstruct its colonization history. Phylogenetic relationships indicate that C. extensa together with the South American Carex vixdentata and the southern African Carex ecklonii form a monophyletic group of halophilic species. Analyses of divergence times suggest that early lineage diversification may have occurred between the late Miocene and the late Pliocene (Messinian crisis). Phylogenetic and network analyses of cpDNA variation revealed the monophyly of the species and an ancestral haplotype contained in populations of the eastern Mediterranean. The AFLP and SSR analyses support a pattern of variation compatible with these two lineages. These analyses also show higher levels of genetic diversity and differentiation in the eastern population group, which underwent an east-to-west Mediterranean colonization. Quaternary climatic oscillations appear to have been responsible for the split between these two lineages. Secondary contacts may have taken place in areas near the Ligurian Sea in agreement with the gene flow detected in Corsican populations. The AFLP and SSR data accord with the 'tabula rasa' hypothesis in which a recent and rapid colonization of northern Europe took place from the western Mediterranean after the Last Glacial Maximum. The unbalanced west-east vs. west-north colonization may be as a result of 'high density blocking' effect
    Unveiling below-ground species abundance in a biodiversity experiment: a test of vertical niche differentiation among grassland species
    Mommer, L. ; Ruijven, J. van; Berendse, F. ; Ouborg, N.J. - \ 2010
    Journal of Ecology 98 (2010)5. - ISSN 0022-0477 - p. 1117 - 1127.
    plant diversity - interspecific competition - root competition - microbial communities - soil feedbacks - productivity - biomass - rhizosphere - complementarity - pathogens
    1. Plant diversity has profound effects on primary production. Plant diversity has been shown to correlate with increased primary production in nutrient-limited grassland ecosystems. This overyielding has been attributed to vertical niche differentiation among species below-ground, allowing for complementarity in resource capture. However, a rigorous test of this longstanding hypothesis is lacking because roots of different species could not be distinguished in diverse communities. 2. Here, we present the first application of a DNA-based technique that quantifies species abundances in multispecies root samples. We were thus able to compare root distributions in monocultures of two grasses and two forbs with root distributions in four-species mixtures. In order to investigate if vertical niche differentiation is driven by soil nutrient depletion, the topsoil layer of the communities were either nutrient-rich or -poor. 3. Immediately in the first year, 40% more root biomass was produced in mixtures than expected from the monocultures, together with significant below-ground complementarity effects, probably preceding above-ground overyielding. This below-ground overyielding appeared not to be the result of vertical niche differentiation, as rooting depth of the community tended to decrease, rather than increase in mixtures compared to monocultures. Roots thus tended to clump in the very dense topsoil layer rather than segregate over the whole profile in mixtures. The below-ground overyielding was mainly driven by enhanced root investments of one species, Anthoxanthum odoratum, in the densely rooted topsoil layer without retarding the growth of the other species. 4. Synthesis. Conventional ecological mechanisms, such as competition for nutrients, do not seem to be able to explain the increased root investments of A. odoratum in mixtures compared to monocultures, with apparently little effect on the root growth of the other species. Instead, the observed root responses are consistent with species-specific root recognition responses. From a community perspective, the observed early below-ground overyielding may initiate the recently reported increased soil organic matter, mineralization and N availability and thus may ultimately be responsible for the higher productivity at high plant species diversity.
    Gene flow and genetic structure of the aquatic macrophyte Sparganium emersum in a linear unidirectional river
    Pollux, B.J.A. ; Luteijn, A. ; Groenendael, J.M. Van; Ouborg, N.J. - \ 2009
    Freshwater Biology 54 (2009)1. - ISSN 0046-5070 - p. 64 - 76.
    Assignment tests - Asymmetric bidirectional dispersal - Hydrochory - One-dimensional ecosystems - Zoochory

    1. River systems offer special environments for the dispersal of aquatic plants because of the unidirectional (downstream) flow and linear arrangement of suitable habitats. 2. To examine the effect of this flow on microevolutionary processes in the unbranched bur-reed (Sparganium emersum) we studied the genetic variation within and among nine (sub)populations along a 103 km stretch of the Niers River (Germany-The Netherlands), using amplified fragment length polymorphisms. 3. Genetic diversity in S. emersum populations increased significantly downstream, suggesting an effect of flow on the pattern of intrapopulation genetic diversity. 4. Gene flow in the Niers River is asymmetrically bidirectional, with gene flow being approximately 3.5 times higher in a downstream direction. The observed asymmetry is probably caused by frequent hydrochoric dispersal towards downstream locations on the one hand, and sporadic zoochoric dispersal in an upstream direction on the other. The spread of vegetative propagules (leaf and stem fragments) is probably not an important mode of dispersal for S. emersum, suggesting that gene flow is mainly via seed dispersal. Realized dispersal distances exceeded 60 km, revealing a potential for long-distance dispersal in S. emersum. 5. There was no correlation between geographical and genetic distances among the nine S. emersum populations (i.e. no isolation by distance), which may be due to the occurrence of long-distance dispersal and/or colonization and extinction dynamics in the Niers River. 6. Overall, the genetic population structure and regional dispersal patterns of S. emersum in the Niers River are best explained by a linear metapopulation model. Our study shows that flow can exert a strong influence on population genetic processes of plants inhabiting stream systems.

    Intraspecific variation of seed floating ability in Sparganium emersum suggests a bimodal dispersal strategy
    Pollux, B.J.A. ; Verbruggen, E. ; Groenendael, J.M. Van; Ouborg, N.J. - \ 2009
    Aquatic Botany 90 (2009)2. - ISSN 0304-3770 - p. 199 - 203.
    Buoyancy - Cryptic seed heteromorphism - Germination - Hydrochory - Long-distance dispersal - Seed mass

    Water-mediated spread of seeds (hydrochory) plays an important role in the dispersal of aquatic plants. In this study we investigate intraspecific variation in floating ability and germination capacity of Sparganium emersum seeds in relation to seed mass, within three natural populations along the Rur River (the Netherlands-Germany). Our results suggest that S. emersum produces two types of seeds: (i) short-floating seeds (SFS) that sink within 4 weeks (approximately 71% of all seeds), and (ii) long-floating seeds (LFS) that float at least for 6 months (approximately 28% of all seeds). Our study further shows that short-floating seeds display a significantly higher germination (%) (SFS = 89.9% vs LFS = 32.6%), a faster germination rate (SFS = 8.71 ± 3.3 vs LFS = 9.32 ± 3.1 days to germination) and a higher mean seed mass (SFS = 15.17 ± 4.5 vs LFS = 11.25 ± 3.8 mg), compared to long-floating seeds. It is argued that the production of these two types of seeds by S. emersum plants, each type with a different potential for water-mediated dispersal, represents a bimodal hydrochoric dispersal strategy.

    Phylogenetic analyses of the leaf beetle genus Galerucella: evidence for host switching at speciation?
    Borghuis, A. ; Madsen, O. ; Ouborg, N.J. ; Groenendael, J. van - \ 2009
    Molecular Phylogenetics and Evolution 53 (2009)2. - ISSN 1055-7903 - p. 361 - 367.
    sympatric speciation - reproductive isolation - race formation - genetic differentiation - quantitative traits - nymphaeae - evolution - chrysomelidae - coleoptera - insects
    It is still the subject of lively debate whether sympatric speciation is a general mode of speciation as opposed to allopatric speciation. In herbivorous insects, host switching, i.e. colonization of, and adaptation to, a new host by a herbivore, has been proposed as one of the driving mechanisms of sympatric speciation. Evidence for host switching as a speciation driving mechanism can be inferred from phylogenies of herbivores and host plants: if the host plant phylogeny is randomly distributed over the herbivore phylogeny, this indicates host switching. The Chrysomelid beetle genus Galerucella is a good taxon to study for evidence of host switching, because several closely related Galerucella species form sympatric species complexes associated with various unrelated plant species. Here we present the phylogenetic relationships of 10 species in the genus Galerucella, based on the mitochondrial gene fragments of the NADH-2 (410 bp) and CO-I (659 bp) genes, and analyzed with Bayesian, Maximum Likelihood and Maximum Parsimony methods. The resulting molecular phylogenetic tree proved to be largely congruent with morphologically based taxonomy. The host-associated taxa of the Galerucella nymphaeae species complex are not defined as distinct gene pools under the phylogenetic species concept (PSC), however, the species complex as a whole is. Two results indicate the contribution of host switching to the speciation of Galerucella: (1) the host-associated taxa of the G. nymphaeae species complex have diverged very recently and (2) constrained ML analyses showed that host use constraints led to a significantly different Galerucella tree compared to unconstrained analyses. This evidence for host switching, together with the observation that several sister taxa using unrelated host plants live in sympatry, suggests that sympatric speciation by host race formation can be an important mode of speciation in this genus
    Consequences of intraspecific seed-size variation in Sparganium emersum for dispersal by fish
    Pollux, B.J.A. ; Ouborg, N.J. ; Groenendael, J.M. Van; Klaassen, M. - \ 2007
    Functional Ecology 21 (2007)6. - ISSN 0269-8463 - p. 1084 - 1091.
    Endozoochory - Ichthyochory - Seed mass - Seed size selection - Seed traits

    1. The potential for seed dispersal by fish (ichthyochory) is likely to vary within aquatic plant species, depending on intraspecific variation in phenotypic seed traits. 2. We studied the effect of seed size variation within the unbranched burreed (Sparganium emersum) on the potential for internal dispersal by the common carp (Cyprinus carpio), by feeding them light (< 10 mg), medium (10-20 mg) and heavy (> 20 mg) seeds, seed mass being positively related to seed size. 3. We hypothesized: (i) that ingestion, retention time, survival during gut passage and viability after gut passage of S. emersum seeds would be affected by seed size; and (ii) that this would translate into intraspecific variation in dispersal probability and dispersal distance among seed size categories. 4. Ingestion was negatively related to seed size, while survival during gut passage was positively related to seed size. Seed viability after gut passage was not affected by seed size. Since the negative effect of ingestion was counterbalanced by an equally strong but positive effect on seed survival, the probability of dispersal did not differ between the tested seed-size categories. 5. The time that seeds remained in the digestive tract of carp did not differ between seed sizes, suggesting equal potential dispersal distances for all seeds. Based on optimum swimming speeds of carp, ranging from 0.9 to 1.8 km h-1, maximum dispersal distances will most likely range from 13.5 to 27 km. 6. This study highlights the importance of studying all stages of the endozoochorous dispersal process in order to estimate the effect of a phenotypic seed trait on plant dispersal.

    Reproductive strategy, clonal structure and genetic diversity in populations of the aquatic macrophyte Sparganium emersum in river systems
    Pollux, B.J.A. ; Jong, M.D.E. ; Steegh, A. ; Verbruggen, E. ; Groenendael, J.M. Van; Ouborg, N.J. - \ 2007
    Molecular Ecology 16 (2007)2. - ISSN 0962-1083 - p. 313 - 325.
    Dispersal - Hydrochory - Sexual reproduction - Vegetative reproduction - Waterfowl - Zoochory

    Many aquatic and riparian plant species are characterized by the ability to reproduce both sexually and asexually. Yet, little is known about how spatial variation in sexual and asexual reproduction affects the genotypic diversity within populations of aquatic and riparian plants. We used six polymorphic microsatellites to examine the genetic diversity within and differentiation among 17 populations (606 individuals) of Sparganium emersum, in two Dutch-German rivers. Our study revealed a striking difference between rivers in the mode of reproduction (sexual vs. asexual) within S. emersum populations. The mode of reproduction was strongly related to locally reigning hydrodynamic conditions. Sexually reproducing populations exhibited a greater number of multilocus genotypes compared to asexual populations. The regional population structure suggested higher levels of gene flow among sexually reproducing populations compared to clonal populations. Gene flow was mainly mediated via hydrochoric dispersal of generative propagules (seeds), impeding genetic differentiation among populations even over river distances up to 50 km. Although evidence for hydrochoric dispersal of vegetative propagules (clonal plant fragments) was found, this mechanism appeared to be relatively less important. Bayesian-based assignment procedures revealed a number of immigrants, originating from outside our study area, suggesting intercatchment plant dispersal, possibly the result of waterfowl-mediated seed dispersal. This study demonstrates how variation in local environmental conditions in river systems, resulting in shifting balances of sexual vs. asexual reproduction within populations, will affect the genotypic diversity within populations. This study furthermore cautions against generalizations about dispersal of riparian plant species in river systems.

    Microarray challenges in ecology
    Kammenga, J.E. ; Herman, M.A. ; Ouborg, N.J. ; Johnson, L. ; Breitling, R. - \ 2007
    Trends in Ecology and Evolution 22 (2007)5. - ISSN 0169-5347 - p. 273 - 279.
    gene-expression profiles - drosophila-melanogaster - ectomycorrhizal fungus - nicotiana-attenuata - natural-populations - cdna microarrays - evolution - arabidopsis - genomics - patterns
    Microarrays are used to measure simultaneously the amount of mRNAs transcribed from many genes. They were originally designed for gene expression profiling in relatively simple biological systems, such as cell lines and model systems under constant laboratory conditions. This poses a challenge to ecologists who increasingly want to use microarrays to unravel the genetic mechanisms underlying complex interactions among organisms and between organisms and their environment. Here, we discuss typical experimental and statistical problems that arise when analyzing genome-wide expression profiles in an ecological context. We show that experimental design and environmental confounders greatly influence the identification of candidate genes in ecological microarray studies, and that following several simple recommendations could facilitate the analysis of microarray data in ecological settings.
    The effect of seed morphology on the potential dispersal of aquatic macrophytes by the common carp (Cyprinus carpio)
    Pollux, B.J.A. ; Jong, M. De; Steegh, A. ; Ouborg, N.J. ; Groenendael, J.M. Van; Klaassen, M. - \ 2006
    Freshwater Biology 51 (2006)11. - ISSN 0046-5070 - p. 2063 - 2071.
    Endozoochory - Gut passage - Ichthyochory - Postdispersal establishment - Retention time

    1. The potential for seed dispersal by fish (ichthyochory) will vary among aquatic plants because of differences in seed size and morphology. 2. To examine how seed morphology influences the probability of dispersal by the common carp (Cyprinus carpio), we studied seed ingestion, retention time and subsequent egestion and germination of seeds of Sparganium emersum and Sagittaria sagittifolia, two aquatic plant species with similar sized but morphologically different seeds. 3. We compared dispersal probabilities between the two plant species, in which the probability of dispersal is assumed to be a function of the probabilities of seed ingestion, egestion and germination, and the dispersal distance is assumed to be a function of seed egestion rate over time. 4. We found that, although the soft seeds of S. sagittifolia had an approximately 1.5 times higher probability of being ingested by the carp than the hard seeds of S. emersum (83.15% ± 1.8% versus 56.16% ± 2.7%, respectively), the latter had an almost twofold higher probability of surviving the passage through the digestive tract (38.58% ± 2.7% versus 20.97% ± 1.5%, respectively). Patterns of seed egestion over time did not differ between the two plant species, despite the difference in seed morphology. Gut passage had a different effect on seed germination between plant species. Compared with non-ingested controls, seeds of S. emersum showed a 12.6% increase in germination and a 2.1 day acceleration in germination rate, whereas seeds of S. sagittifolia displayed a 47.3% decrease and 5.1 day delay, respectively. 5. Our results suggest that seed morphology affects the dispersal probability and postdispersal establishment, but not the dispersal distance, of aquatic plants that are dispersed by fish.

    Isolation and characterization of microsatellites in Sparganium emersum and cross-species amplification in the related species S. erectum
    Pollux, B.J.A. ; Ouborg, N.J. - \ 2006
    Molecular Ecology Notes 6 (2006)2. - ISSN 1471-8278 - p. 530 - 532.
    Dispersal - Gene flow - Microsatellites - Null alleles - Population genetics

    We developed seven novel polymorphic microsatellite loci for the aquatic macrophyte Sparganium emersum (Sparganiaceae). These were characterized on 62 individuals collected from nine different populations. In this set of individuals, seven to 20 alleles per locus were detected and observed heterozygosity ranged between 0.16 and 0.95. Cross-species amplification was tested in the related species Sparganium erectum, and was successful for five of the seven microsatellite loci.

    The effect of turf cutting on plant and arbuscular mycorrhizal spore recolonisation: Implications for heathland restoration
    Vergeer, P. ; Berg, L.J.L. van den; Baar, J. ; Ouborg, N.J. ; Roelofs, J.G.M. - \ 2006
    Biological Conservation 129 (2006)2. - ISSN 0006-3207 - p. 226 - 235.
    community structure - calluna heathland - arnica-montana - species-diversity - nutrient-uptake - fungi - soil - succession - infection - biodiversity
    In two natural heathland vegetations, we analysed the effect of turf cutting on spore numbers of arbuscular mycorrhizal fungi (AMF). Next to this, we performed a controlled factorial experiment to examine the role of AMF for germination and establishment of Arnica montana in both turf cut and non-turf cut situations. AMF spore numbers decreased with soil depth, and, along with the topsoil, almost all AMF spores were removed with the removal of the acidified and/or eutrophied organic layer. Recolonisation of AMF spore numbers after turf cutting was slow: spore numbers of approximately 60-95 spores g(-1) dry soil were found two and a half years after turf cutting, corresponding with 55-70% of AMF spore numbers found in natural field populations of A. montana. Since AMF colonisation increased establishment and biomass, and decreased mortality of A. montana, it was suggested that lack of AMF after turf removal might complicate the establishment of this herbaceous species. Removal of organic material as a management measure should therefore carefully be applied, taking in consideration the low recolonisation rates of AMF as this can markedly effect the success of restoration.
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