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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Data from: Low abundant soil bacteria can be metabolically versatile and fast growing
Kurm, V. ; Putten, W.H. van der; Boer, W. de; Naus-Wiezer, Suzanne ; Hol, W.H.G. - \ 2016
bacterial abundance - life-history traits - phylogeny
The abundance of species is assumed to depend on their life history traits, such as growth rate and resource specialization. However, this assumption has not been tested for bacteria. Here we investigate how abundance of soil bacteria relates to slow growth and substrate specialization (oligotrophy) versus fast growth and substrate generalization (copiotrophy). We collected 47 saprotrophic soil bacterial isolates of differing abundances and measured their growth rate and the ability to use a variety of single carbon sources. Opposite to our expectation, there was no relationship between abundance in soil and the measured growth rate or substrate utilization profile (SUP). However, isolates with lower growth rates used fewer substrates than faster growing ones supporting the assumption that growth rate may relate to substrate specialization. Interestingly, growth rate and SUP were correlated with phylogeny, rather than with abundance in soil. Most markedly, Gammaproteobacteria on average grew significantly faster and were able to use more substrates than other bacterial classes, whereas Alphaproteobacteria were growing relatively slowly and used fewer substrates. This finding suggests that growth and substrate utilization are phylogenetically deeply conserved. We conclude that growth rate and substrate utilization of soil bacteria are not general determinants of their abundance. Future studies on explaining bacterial abundance need to determine how other factors, such as competition, predation and abiotic factors may contribute to rarity or abundance in soil bacteria.
The laboratory domestication of Caenorhabditis elegans
Sterken, M.G. ; Snoek, L.B. ; Kammenga, J.E. ; Andersen, E.C. - \ 2015
Trends in Genetics 31 (2015)6. - ISSN 0168-9525 - p. 224 - 231.
life-history traits - c. elegans - natural variation - social-behavior - npr-1 - genetics - yeast - environment - populations - diversity
Model organisms are of great importance to our understanding of basic biology and to making advances in biomedical research. However, the influence of laboratory cultivation on these organisms is underappreciated, and especially how that environment can affect research outcomes. Recent experiments led to insights into how the widely used laboratory reference strain of the nematode Caenorhabditis elegans compares with natural strains. Here we describe potential selective pressures that led to the fixation of laboratory-derived alleles for the genes npr1, glb-5, and nath-10. These alleles influence a large number of traits, resulting in behaviors that affect experimental interpretations. Furthermore, strong phenotypic effects caused by these laboratory-derived alleles hinder the discovery of natural alleles. We highlight strategies to reduce the influence of laboratory-derived alleles and to harness the full power of C. elegans.
Effects of seed traits for the potential of seed dispersal by fish with contrasting modes of feeding
Boedeltje, G. ; Spannings, T. ; Flik, G. ; Pollux, B.J.A. ; Sibbing, F.A. ; Verberk, W.C.E.P. - \ 2015
Freshwater Biology 60 (2015)5. - ISSN 0046-5070 - p. 944 - 959.
carp cyprinus-carpio - life-history traits - common carp - digestive-tract - ruppia-maritima - wetland plants - size - fruit - germination - floodplain
For aquatic and riparian plants, the important role of fish in seed dispersal is increasingly recognised. While the propensity of seeds to disperse is known to be a function of morphological, physical and chemical traits of the seed, in the case of fish-mediated seed dispersal (ichthyochory), it is largely unknown how seed traits modulate the potential for seed ingestion and their subsequent survival through the gut. Furthermore, which seed traits are important may vary among fish species. To evaluate the role of both seed and fish traits in ichthyochory, we fed seeds of 19 aquatic and riparian plant species to fish with differing feeding mechanisms. Cyprinus carpio (common carp) has a pharyngeal ‘mill’, which it uses physically to crush hard food, while Oreochromis mossambicus (Mozambique tilapia) has only tiny oral and pharyngeal teeth and instead relies more on chemical digestion. A number of seed traits, including hardness, size and shape, were important determinants of the potential of seeds for ichthyochory. Certain traits (e.g. seed dimensions) were more important during ingestion, whereas other traits were more important for seed survival and subsequent germination (e.g. seed hardness, mucilaginous coat). Compared to controls, germination of retrieved seeds in carp was lower in 10 and higher in two plant species, whereas for tilapia, it was lower in seven and higher in three species. Overlap between these plant species was low, indicating clear difference between the fish studied in their potential for seed dispersal. Carp increased in size during the experiment and concomitant decreases in seed survival and retrieval were found, suggesting that body size and the correlated bite force is an important fish trait in ichthyochory. Overall, seed hardness, size and shape appear crucial for the survival of seeds passing through the guts of carp and tilapia. Beyond this general pattern, a greater complexity of trait-performance relationships appeared: different seed traits are involved during each of the stages of ichthyochory. Moreover, the importance of seed traits differed between carp and tilapia, with some traits having interactive and contrasting effects in both fish species. Aquatic plants with floating seeds adapted to hydrochorous dispersal were less likely to be dispersed by tilapia than plants with non-floating seeds, suggesting a dispersal trade-off between ichthyochory and hydrochory. Thus, depending on their seed characteristics, fish may offer an additional dispersal route to aquatic and riparian plants.
Widespread Genomic Incompatibilities in Caenorhabditis elegans
Snoek, L.B. ; Orbidans, H.E. ; Stastna, J. ; Aartse, A. ; Rodriguez Sanchez, M. ; Riksen, J.A.G. ; Kammenga, J.E. ; Harvey, S.C. - \ 2014
G3 : Genes Genomes Genetics 4 (2014)10. - ISSN 2160-1836 - p. 1813 - 1823.
cryptic genetic-variation - natural variation data - life-history traits - c. elegans - outbreeding depression - hybrid sterility - reproductive isolation - tribolium-castaneum - population-genetics - synthetic lethals
In the Bateson-Dobzhansky-Muller (BDM) model of speciation, incompatibilities emerge from the deleterious interactions between alleles that are neutral or advantageous in the original genetic backgrounds, i.e. negative epistatic effects. Within species such interactions are responsible for outbreeding depression and F2 (hybrid) breakdown. We sought to identify BDM incompatibilities in the nematode Caenorhabditis elegans by looking for genomic regions that disrupt egg laying; a complex, highly regulated and coordinated phenotype. Investigation of introgression lines and recombinant inbred lines derived from the isolates CB4856 and N2 uncovered multiple incompatibility quantitative trait loci (QTL). These QTL produce a synthetic egg-laying defective phenotype not seen in CB4856 and N2 nor in other wild isolates. For two of the QTL regions, results are inconsistent with a model of pairwise interaction between two loci, suggesting that the incompatibilities are a consequence of complex interactions between multiple loci. Analysis of additional life history traits indicates that the QTL regions identified in these screens are associated with effects on other traits such as lifespan and reproduction, suggesting that the incompatibilities are likely to be deleterious. Taken together, these results indicate that numerous BDM incompatibilities that could contribute to reproductive isolation can be detected and mapped within C. elegans.
WormQTL HD—a web database for linking human disease to natural variation data in C. elegans
Velde, K.J. van der; Haan, M. de; Zych, K. ; Arends, D. ; Snoek, L.B. ; Kammenga, J.E. ; Jansen, R.C. ; Swertz, M.A. ; Li, Y. - \ 2014
Nucleic acids research 42 (2014)D1. - ISSN 0305-1048 - p. D794 - D801.
life-history traits - caenorhabditis-elegans - systems biology - stress-response - genotype - genome - qtl - environment - identification - polymorphism
Interactions between proteins are highly conserved across species. As a result, the molecular basis of multiple diseases affecting humans can be studied in model organisms that offer many alternative experimental opportunities. One such organism— Caenorhabditis elegans—has been used to produce much molecular quantitative genetics and systems biology data over the past decade. We present WormQTLHD (Human Disease), a database that quantitatively and systematically links expression Quantitative Trait Loci (eQTL) findings in C. elegans to gene–disease associations in man. WormQTLHD, available online at http://www.wormqtl-hd.org, is a user-friendly set of tools to reveal functionally coherent, evolutionary conserved gene networks. These can be used to predict novel gene-to-gene associations and the functions of genes underlying the disease of interest. We created a new database that links C. elegans eQTL data sets to human diseases (34 337 gene–disease associations from OMIM, DGA, GWAS Central and NHGRI GWAS Catalogue) based on overlapping sets of orthologous genes associated to phenotypes in these two species. We utilized QTL results, high-throughput molecular phenotypes, classical phenotypes and genotype data covering different developmental stages and environments from WormQTL database. All software is available as open source, built on MOLGENIS and xQTL workbench.
Do plant traits retrieved from a database accurately predict on-site measurements?
Cordlandwehr, V. ; Meredith, R.L. ; Ozinga, W.A. ; Bekker, R.M. ; Groenendael, J.M. van; Bakker, J.P. - \ 2013
Journal of Ecology 101 (2013)3. - ISSN 0022-0477 - p. 662 - 670.
northwest european flora - life-history traits - land-use change - intraspecific variability - functional diversity - aboveground biomass - relative importance - leaf traits - communities - ecology
1. Trait-based approaches are increasingly used to obtain an insight into the functional aspects of plant communities. Since measuring traits can be time-consuming, large international databases of plant traits are being compiled to share the effort. From these databases, average trait values are often extracted per species by averaging trait values of individuals over multiple populations and habitats. However, the accuracy of such aggregated information from regional databases as a surrogate for on-site measurements has seldom been tested. 2. For the local species pool (aggregated at the habitat-level) and the plant communities on the plots (aggregated at the community-level), we quantified how accurately trait values for each species measured at the plot (plot scale) and those averaged per species and site (site scale) can be estimated from those retrieved from a North-west-European trait database. We analysed three widely used plant traits, canopy height (CH), leaf dry matter content (LDMC) and specific leaf area (SLA), of species occurring in a wet meadow and a salt marsh. 3. Database values more accurately predicted traits aggregated at the habitat-level than those aggregated at the community-level. In addition, traits with lower plasticity, such as LDMC, were more accurately predicted by database values. The performance of database values also depended upon the habitat studied, for example, habitat-level SLA values were accurately predicted by database values in the wet meadow but inaccurately predicted in the salt marsh. 4. Synthesis. This study reveals that the accuracy of traits retrieved from a database depends on the level of aggregation (lower at community-level), the trait (lower in plastic traits) and the habitat type (lower in extreme habitats). For studies focussing on processes mainly acting at the site scale (e.g. trait–environment relationships), traits retrieved from a regional database and filtered according to habitat will probably lead to good results. Whereas studying processes acting at the plot scale (e.g. niche partitioning), requires the additional effort of measuring traits on-site.
Gene-environment and protein degradation signatures characterize genomic and phenotypic diversity in wild Caenorhabditis elegans populations
Volkers, J.M. ; Snoek, L.B. ; Hellenberg Hubar, C.J. van; Coopman, R. ; Chen, W. ; Yang, Wentao ; Sterken, M.G. ; Schulenburg, H. ; Braeckman, B. ; Kammenga, J.E. - \ 2013
BMC Biology 11 (2013). - ISSN 1741-7007 - 13 p.
life-history traits - c. elegans - natural variation - nucleotide polymorphism - microarray data - reveals - toxicity - genotype - specificity - infection
Background: Analyzing and understanding the relationship between genotypes and phenotypes is at the heart of genetics. Research on the nematode Caenorhabditis elegans has been instrumental for unraveling genotype-phenotype relations, and has important implications for understanding the biology of mammals, but almost all studies, including forward and reverse genetic screens, are limited by investigations in only one canonical genotype. This hampers the detection and functional analysis of allelic variants, which play a key role in controlling many complex traits. It is therefore essential to explore the full potential of the natural genetic variation and evolutionary context of the genotype-phenotype map in wild C. elegans populations. Results: We used multiple wild C. elegans populations freshly isolated from local sites to investigate gene sequence polymorphisms and a multitude of phenotypes including the transcriptome, fitness, and behavioral traits. The genotype, transcriptome, and a number of fitness traits showed a direct link with the original site of the strains. The separation between the isolation sites was prevalent on all chromosomes, but chromosome V was the largest contributor to this variation. These results were supported by a differential food preference of the wild isolates for naturally co-existing bacterial species. Comparing polymorphic genes between the populations with a set of genes extracted from 19 different studies on gene expression in C. elegans exposed to biotic and abiotic factors, such as bacteria, osmotic pressure, and temperature, revealed a significant enrichment for genes involved in gene-environment interactions and protein degradation. Conclusions: We found that wild C. elegans populations are characterized by gene-environment signatures, and we have unlocked a wealth of genotype-phenotype relations for the first time. Studying natural isolates provides a treasure trove of evidence compared with that unearthed by the current research in C. elegans, which covers only a diminutive part of the myriad of genotype-phenotype relations that are present in the wild.
Effects of resources and mortality on the growth and reproduction of Nile perch in Lake Victoria
Downing, A.S. ; Nes, E.H. van; Wolfshaar, K.E. van de; Scheffer, M. ; Mooij, W.M. - \ 2013
Freshwater Biology 58 (2013)4. - ISSN 0046-5070 - p. 828 - 840.
lates-niloticus l - size-structured populations - life-history traits - haplochromine cichlids - east-africa - mwanza gulf - nyanza-gulf - competition - predation - dynamics
1. A collapse of Nile perch stocks of Lake Victoria could affect up to 30 million people. Furthermore, changes in Nile perch population size-structure and stocks make the threat of collapse imminent. However, whether eutrophication or fishing will be the bane of Nile perch is still debated. 2. Here, we attempt to unravel how changes in food resources, a side effect of eutrophication, and fishing mortality determine fish population growth and size structures. We parameterised a physiologically structured model to Nile perch, analysed the influence of ontogenetic diet shifts and relative resource abundances on existence boundaries of Nile perch and described the populations on either side of these boundaries. 3. Our results showed that ignoring ontogenetic diet shifts can lead to over-estimating the maximum sustainable mortality of a fish population. Size distributions can be indicators of processes driving population dynamics. However, the vulnerability of stocks to fishing mortality is dependent on its environment and is not always reflected in size distributions. 4. We suggest that the ecosystem, instead of populations, should be used to monitor long-term effects of human impact.
WormQTL—public archive and analysis web portal for natural variation data in Caenorhabditis spp
Snoek, L.B. ; Velde, K.J. van der; Arends, D. ; Li, Y. ; Beyer, A. ; Elvin, M. ; Fisher, J. ; Hajnal, A. ; Hengartner, M. ; Poulin, G. ; Rodriguez Sanchez, M. ; Schmid, T. ; Schrimpf, S. ; Xue, F. ; Jansen, R.C. ; Kammenga, J.E. ; Swertz, M.A. - \ 2013
Nucleic acids research 41 (2013)D1. - ISSN 0305-1048 - p. D738 - D743.
life-history traits - c. elegans - systems biology - qtl - polymorphism - genotype - environment - plasticity - platform - genome
Here, we present WormQTL (http://www.wormqtl.org), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a valuable amount of phenotypic, high-throughput molecular and genotypic data across different developmental worm stages and environments in hundreds of C. elegans strains. WormQTL provides a workbench of analysis tools for genotype–phenotype linkage and association mapping based on but not limited to R/qtl (http://www.rqtl.org). All data can be uploaded and downloaded using simple delimited text or Excel formats and are accessible via a public web user interface for biologists and R statistic and web service interfaces for bioinformaticians, based on open source MOLGENIS and xQTL workbench software. WormQTL welcomes data submissions from other worm researchers.
Long-term effects of scrub clearance and litter removal on the re-establishment of dry alvar grassland species
Bakker, J.P. ; Rosén, E. ; Ozinga, W.A. ; Bretfeld, M. ; Feldt, T. ; Stahl, J. - \ 2012
Annales Botanici Fennici 49 (2012)1-2. - ISSN 0003-3847 - p. 21 - 30.
northwest european flora - life-history traits - chalk grassland - seedling recruitment - limestone grassland - plant-communities - bryophyte layer - establishment - dispersal - emergence
Many characteristic dry alvar grassland species disappear after cessation of livestock grazing as a result of encroachment by Juniperus communis. We studied the re-establishment of these species after scrub clearance with and without the removal of the layer of litter and mosses in long-term (14 years) permanent plots. Most of the species belonging to the community species pool of dry alvar grassland species before clearance were found in permanent plots between 2 and 14 years after the clearance. A large part originated from vegetative spread of already occurring species in the established vegetation in the surroundings. Only a small part of the long-term persistent soil seed bank resulted in the re-establishment of alvar species. There was no significant difference in the traits soil seed bank, seed weight and long-distance dispersal by wind, dung or fur of animals of established and non-established species. Removal of litter and mosses positively affected the re-establishment of alvar species
Aging Uncouples Heritability and Expression-QTL in Caenorhabditis elegans
Viñuela Rodriguez, A. ; Snoek, L.B. ; Riksen, J.A.G. ; Kammenga, J.E. - \ 2012
G3 : Genes Genomes Genetics 2 (2012)5. - ISSN 2160-1836 - p. 597 - 605.
quantitative trait loci - cdna microarray data - life-history traits - gene-expression - c-elegans - age - arabidopsis - genomics - normalization - plasticity
The number and distribution of gene expression QTL (eQTL) represent the genetic architecture of many complex traits, including common human diseases. We previously reported that the heritable eQTL patterns are highly dynamic with age in an N2 × CB4856 recombinant inbred population of the nematode Caenorhabditis elegans. In particular, we showed that the number of eQTL decreased with age. Here, we investigated the reason for this decrease by combining gene expression profiles at three ages in the wild types N2 and CB4856 with the reported expression profiles of the RIL population. We determined heritability and transgression (when gene expression levels in the RILs are more extreme than the parents) and investigated their relation with eQTL changes with age. Transgressive segregation was widespread but depended on physiological age. The percentage of genes with an eQTL increased with a higher heritability in young worms. However, for old worms this percentage hardly increased. Using a single marker approach, we found that almost 20% of genes with heritability >0.9 had an eQTL in developing worms. Surprisingly, only 10% was found in old worms. Using a multimarker approach, this percentage increased to almost 30% for both age groups. Comparison of the single marker to a multiple marker eQTL mapping indicated that heritable regulation of gene expression becomes more polygenic in aging worms due to multiple loci and possible epistatic interactions. We conclude that linkage studies should account for the relation between increased polygenic regulation and diminished effects at older ages.
Developing European conservation and mitigation tools for pollination services: approaches of the STEP (Status and Trends of European Pollinators) project
Potts, S.G. ; Biesmeijer, J.C. ; Bommarco, R. ; Felicioli, A. ; Fischer, M. ; Jokinen, P. ; Kleijn, D. ; Klein, A.M. ; Kunin, W.E. ; Neumann, P. ; Penev, L.D. ; Petanidou, T. ; Rasmont, P. ; Roberts, S.P.M. ; Smith, H.G. ; Sorensen, P.B. ; Steffan-Dewenter, I. ; Vaissiere, B.E. ; Vila, M. ; Vujic, A. ; Woyciechowski, M. ; Zobel, M. ; Settele, J. ; Schweiger, O. - \ 2011
Journal of Apicultural Research 50 (2011)2. - ISSN 0021-8839 - p. 152 - 164.
life-history traits - agri-environment schemes - different spatial scales - bee population-dynamics - agricultural landscapes - pollen limitation - land-use - fragmented habitats - plant reproduction - species responses
Pollinating insects form a key component of European biodiversity, and provide a vital ecosystem service to crops and wild plants. There is growing evidence of declines in both wild and domesticated pollinators, and parallel declines in plants relying upon them. The STEP project (Status and Trends of European Pollinators, 2010-2015, www.stepproject.net) is documenting critical elements in the nature and extent of these declines, examining key functional traits associated with pollination deficits, and developing a Red List for some European pollinator groups. Together these activities are laying the groundwork for future pollinator monitoring programmes. STEP is also assessing the relative importance of potential drivers of pollinator declines, including climate change, habitat loss and fragmentation, agrochemicals, pathogens, alien species, light pollution, and their interactions. We are measuring the ecological and economic impacts of declining pollinator services and floral resources, including effects on wild plant populations, crop production and human nutrition. STEP is reviewing existing and potential mitigation options, and providing novel tests of their effectiveness across Europe. Our work is building upon existing and newly developed datasets and models, complemented by spatially-replicated campaigns of field research to fill gaps in current knowledge. Findings are being integrated into a policy-relevant framework to create evidence-based decision support tools. STEP is establishing communication links to a wide range of stakeholders across Europe and beyond, including policy makers, beekeepers, farmers, academics and the general public. Taken together, the STEP research programme aims to improve our understanding of the nature, causes, consequences and potential mitigation of declines in pollination services at local, national, continental and global scales.
A fitness assay for comparing RNAi effects across multiple C. elegans genotypes
Elvin, M. ; Snoek, L.B. ; Frejno, M. ; Klemstein, U. ; Kammenga, J.E. ; Poulin, G. - \ 2011
BMC Genomics 12 (2011). - ISSN 1471-2164 - 14 p.
life-history traits - caenorhabditis-elegans - gene - interference - rde-1
Background - RNAi technology by feeding of E. coli containing dsRNA in C. elegans has significantly contributed to further our understanding of many different fields, including genetics, molecular biology, developmental biology and functional genomics. Most of this research has been carried out in a single genotype or genetic background. However, RNAi effects in one genotype do not reveal the allelic effects that segregate in natural populations and contribute to phenotypic variation. Results - Here we present a method that allows for rapidly comparing RNAi effects among diverse genotypes at an improved high throughput rate. It is based on assessing the fitness of a population of worms by measuring the rate at which E. coli is consumed. Critically, we demonstrate the analytical power of this method by QTL mapping the loss of RNAi sensitivity (in the germline) in a recombinant inbred population derived from a cross between Bristol and a natural isolate from Hawaii. Hawaii has lost RNAi sensitivity in the germline. We found that polymorphisms in ppw-1 contribute to this loss of RNAi sensitivity, but that other loci are also likely to be important. Conclusions - In summary, we have established a fast method that improves the throughput of RNAi in liquid, that generates quantitative data, that is easy to implement in most laboratories, and importantly that enables QTL mapping using RNAi.
Evolution of sexual dimorphism in the Lepidoptera
Allen, C.E. ; Zwaan, B.J. ; Brakefield, P.M. - \ 2011
Annual Review of Entomology 56 (2011). - ISSN 0066-4170 - p. 445 - 464.
butterfly bicyclus-anynana - western white butterflies - wing pattern evolution - life-history traits - female mate choice - size dimorphism - papilio-polyxenes - neotropical butterflies - heliconius butterflies - phenotypic plasticity
Among the animals, the Lepidoptera (moths and butterflies) are second only to beetles in number of described species and are known for their striking intra- and interspecific diversity. Within species, sexual dimorphism is a source of variation in life history (e.g., sexual size dimorphism and protandry), morphology (e.g., wing shape and color pattern), and behavior (e.g., chemical and visual signaling). Sexual selection and mating systems have been considered the primary forces driving the evolution of sexual dimorphism in the Lepidoptera, and alternative hypotheses have been neglected. Here, we examine opportunities for sexual selection, natural selection, and the interplay between the two forces in the evolution of sexual differences in the moths and butterflies. Our primary goal is to identify mechanisms that either facilitate or constrain the evolution of sexual dimorphism, rather than to resolve any perceived controversy between hypotheses that may not be mutually exclusive
A strategy in searching for stress tolerance-correlated characteristics in nematodes while accounting for phylogenetic interdependence
Holterman, M.H.M. ; Korthals, G.W. ; Doroszuk, A. ; Megen, H.H.B. van; Bakker, J. ; Bongers, A.M.T. ; Helder, J. ; Wurff, A.W.G. van der - \ 2011
Nematology 13 (2011)3. - ISSN 1388-5545 - p. 261 - 275.
life-history traits - maturity index - central brazil - evolution - community - size - disturbance - allocation - stability - patterns
Biological indicators are highly relevant for assessing the condition of a soil as they are integrative; they reflect the overall impact of physical, chemical and biological changes. Indigenous soil organisms are preferable to other test organisms because the diversity and condition of indigenous soil organisms reflect both acute and chronic effects of soil disturbances. Nematodes are ubiquitous, speciose, easily extractable and present in extremely high numbers. Given the ever increasing amount of sequence data, DNA barcode-based community analysis will soon be possible and a next step would be to define objective criteria for the ecological grouping of soil nematodes. Here, we present a framework to ascertain which traits are correlated with a tolerance to stress. For this, a field study on the effects of pH and copper on nematode communities was re-analysed. Changes in abundances of individual genera were correlated with a number of potentially stress tolerance-related characteristics. The generalised least squares (GLS) method was used to account for the phylogenetic dependence of the data. Only the relationship between the ability to enter a survival stage and tolerance to copper at pH 6.1 was found to be significant, but the quantity of missing data probably had a negative impact on the analyses. This study did, however, clearly demonstrate the importance of accounting for the effects of phylogenetic dependence in the data. When the phylogeny was taken into account, we observed an average change in P value of 0.196 (and in some cases as much as 0.6) for the correlations of possible stress-related characteristics and Cu or pH tolerance. This research constitutes a proof-of-principle for a transparent method to relate stress tolerance to (ecological) characteristics. The usefulness of this powerful method should become even clearer when substantially higher numbers of individuals are analysed (as facilitated by using DNA barcodes) and when missing data are filled in
Genetic architecture of rainbow trout survival from egg to adult
Vehvilainen, H. ; Kause, A. ; Quiton, C. ; Kuukka-Anttila, H. ; Koskinen, H. ; Paananen, T. - \ 2010
Genetics Research 92 (2010)01. - ISSN 0016-6723 - p. 1 - 11.
life-history traits - sire composite population - infectious salmon anemia - scottish blackface sheep - atlantic salmon - crassostrea-gigas - pacific oyster - environment interactions - quantitative genetics - increase resistance
Survival from birth to a reproductive adult is a challenge that only robust individuals resistant to a variety of mortality factors will overcome. To assess whether survival traits share genetic architecture throughout the life cycle, we estimated genetic correlations for survival within fingerling stage, and across egg, fingerling and grow-out stages in farmed rainbow trout. Genetic parameters of survival at three life cycle stages were estimated for 249 166 individuals originating from ten year classes of a pedigreed population. Despite being an important fitness component, survival traits harboured significant but modest amount of genetic variation (h2=0·07–0·27). Weak associations between survival during egg-fry and fingerling periods, between early and late fingerling periods (rG=0·30) and generally low genetic correlations between fingerling and grow-out survival (mean rG=0·06) suggested that life-stage specific survival traits are best regarded as separate traits. However, in the sub-set of data with detailed time of death records, positive genetic correlations between early and late fingerling survival (rG=0·89) showed that during certain years the best genotypes in the early period were also among the best in the late period. That survival across fingerling period can be genetically the same, trait was indicated also by only slightly higher heritability (h2=0·15) estimated with the survival analysis of time to death during fingerling period compared to the analysis treating fingerling survival as a binary character (h2=0·11). The results imply that (1) inherited resistance against unknown mortality factors exists, but (2) ranking of genotypes changes across life stages.
How species traits and affinity to urban land use control large-scale species frequency
Knapp, S. ; Kuhn, I. ; Bakker, J.P. ; Kleyer, M. ; Klotz, S. ; Ozinga, W.A. ; Poschlod, P. ; Thompson, K. ; Thuiller, W. ; Romermann, C. - \ 2009
Diversity and Distributions 15 (2009)3. - ISSN 1366-9516 - p. 533 - 546.
life-history traits - indicator values - spatial autocorrelation - plant ecology - models - patterns - europe - areas - flora - biodiversity
Although urban areas only occupy c. 2.8% of the earth's land surface, urbanization threatens biodiversity as areas of high human population density often coincide with high biodiversity. Therefore, nature conservation should concentrate on both remote areas and densely populated regions. Protecting rare plant species in rural and urban areas can contribute to the protection of biodiversity. We therefore need to understand why species are rare. Studies on causes of rarity often concentrate on either plant traits or extrinsic threats (such as habitat fragmentation or nitrogen enrichment). However, there are only a few studies that combine traits and extrinsic threats, although such analyses might clarify causes of rarity. We assessed how the affinity of vascular plant species to urban land use ('urbanity') interacts with plant traits in determining species frequency. Germany, resolution c. 12 km x 11 km. Species with a low frequency may be rare because they occur in rare habitats or because of other reasons, although their habitat is frequent. Therefore, we calculated the frequency of species corrected for habitat frequency, i.e. relative species frequency. We explained relative species frequency by the interactions of species traits and species affinity to urban land use using generalized linear models. Simultaneous autoregressive error models controlled for phylogenetic relationships of species. Relative species frequency depends on species affinity to urban land use, independent of the different interactions between traits and urbanity used as predictors. The higher the urbanity the higher is species frequency. Urbanity interacts with species preferences towards temperature and soil acidity. Moreover, dispersal, nitrogen preferences and origin explain relative species frequency, amongst others. Many rare species, especially those preferring cool or acidic habitats might already have disappeared from urban areas. Analyses that combine species traits and environmental effects can explain the causes of rarity and help to derive better conservation strategies.
A genome-wide library of CB4856/N2 introgression lines of Caenorhabditis elegans
Doroszuk, A. ; Snoek, L.B. ; Fradin, E. ; Riksen, J.A.G. ; Kammenga, J.E. - \ 2009
Nucleic acids research 37 (2009)16. - ISSN 0305-1048 - p. e110 - e110.
quantitative trait locus - life-history traits - genotype-environment interactions - natural variation - c-elegans - consomic strains - complex traits - qtl - architecture - polymorphism
Recombinant inbred lines (RILs) derived from Caenorhabditis elegans wild-type N2 and CB4856 are increasingly being used for mapping genes underlying complex traits. To speed up mapping and gene discovery, introgression lines (ILs) offer a powerful tool for more efficient QTL identification. We constructed a library of 90 ILs, each carrying a single homozygous CB4856 genomic segment introgressed into the genetic background of N2. The ILs were genotyped by 123 single-nucleotide polymorphism (SNP) markers. The proportion of the CB4856 segments in most lines does not exceed 3%, and together the introgressions cover 96% of the CB4856 genome. The value of the IL library was demonstrated by identifying novel loci underlying natural variation in two ageing-related traits, i.e. lifespan and pharyngeal pumping rate. Bin mapping of lifespan resulted in six QTLs, which all have a lifespan-shortening effect on the CB4856 allele. We found five QTLs for the decrease in pumping rate, of which four colocated with QTLs found for average lifespan. This suggests pleiotropic or closely linked QTL associated with lifespan and pumping rate. Overall, the presented IL library provides a versatile resource toward easier and efficient fine mapping and functional analyses of loci and genes underlying complex traits in C. elegans
Chemical complexity of volatiles from plants induced by multiple attack
Dicke, M. ; Loon, J.J.A. van; Soler, R. - \ 2009
Nature Chemical Biology 5 (2009)5. - ISSN 1552-4450 - p. 317 - 324.
arbuscular mycorrhizal fungi - tritrophic interaction webs - life-history traits - lima-bean leaves - jasmonic acid - nicotiana-attenuata - arabidopsis-thaliana - indirect defense - natural enemies - foraging efficiency
The attack of a plant by herbivorous arthropods can result in considerable changes in the plant's chemical phenotype. The emission of so-called herbivore-induced plant volatiles (HIPV) results in the attraction of carnivorous enemies of the herbivores that induced these changes. HIPV induction has predominantly been investigated for interactions between one plant and one attacker. However, in nature plants are exposed to a variety of attackers, either simultaneously or sequentially, in shoots and roots, causing much more complex interactions than have usually been investigated in the context of HIPV. To develop an integrated view of how plants respond to their environment, we need to know more about the ways in which multiple attackers can enhance, attenuate, or otherwise alter HIPV responses. A multidisciplinary approach will allow us to investigate the underlying mechanisms of HIPV emission in terms of phytohormones, transcriptional responses and biosynthesis of metabolites in an effort to understand these complex plant-arthropod interactions.
Dispersal failure contributes to plant losses in NW Europe
Ozinga, W.A. ; Römermann, C. ; Bekker, R.M. ; Prinzing, A. ; Tamis, W.L.M. ; Schaminée, J.H.J. ; Hennekens, S.M. ; Thompson, K. ; Poschlod, P. ; Kleyer, M. ; Bakker, J.P. ; Groenendael, J.M. van - \ 2009
Ecology Letters 12 (2009)1. - ISSN 1461-023X - p. 66 - 74.
vegetatietypen - dispersie - plantengemeenschappen - noordwest-europa - vegetation types - dispersion - plant communities - northwestern europe - life-history traits - species richness - environmental-conditions - conservation - diversity - communities - extinction - landscape - ecology - fragmentation
The ongoing decline of many plant species in Northwest Europe indicates that traditional conservation measures to improve the habitat quality, although useful, are not enough to halt diversity losses. Using recent databases, we show for the first time that differences between species in adaptations to various dispersal vectors, in combination with changes in the availability of these vectors, contribute significantly to explaining losses in plant diversity in Northwest Europe in the 20th century. Species with water- or fur-assisted dispersal are over-represented among declining species, while others (wind- or bird-assisted dispersal) are under-represented. Our analysis indicates that the 'colonization deficit' due to a degraded dispersal infrastructure is no less important in explaining plant diversity losses than the more commonly accepted effect of eutrophication and associated niche-based processes. Our findings call for measures that aim to restore the dispersal infrastructure across entire regions and that go beyond current conservation practices
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