Richner N.,Agroscope Institute for Sustainability science ISS |
Holderegger R.,Swiss Federal Institute of forest |
Holderegger R.,Universitatsstrasse 16 |
Linder H.P.,University of Zürich |
Walter T.,Agroscope Institute for Sustainability science ISS
Weed Research | Year: 2015
Changing agricultural practices have dramatically altered the arable flora of Europe since the Second World War. We conducted a meta-analysis of the available literature to assess the dynamics of species richness and species traits in the arable flora across Europe during this time period. We found a total of 32 publications, yielding 53 data sets with an average number of 252 studied plots per data set. Average species number per plot of arable plants across all data sets declined by about 20%. However, twelve data sets showed an increase in average species number per plot, including all studies starting after 1980. Plant species preferring nutrient-rich sites, neophytes and monocotyledons generally increased since 1980, while characteristic or threatened species of arable weed communities further declined. This temporal development of the European arable flora suggests that the changes happening in agricultural management since the 1980s, such as organic farming and reduced pesticide input, may have helped slow the decline of the arable flora in terms of species number, but not in terms of characteristic or threatened arable weeds. Hence, more specific measures are necessary to stop decline of the latter, making sure that these measures are advantageous for rare and characteristic arable species, but not for harmful weeds. Weed Research © 2015 European Weed Research Society.
Herrmann M.,Swiss Federal Institute of forest |
Holderegger R.,Swiss Federal Institute of forest |
Holderegger R.,Universitatsstrasse 16 |
Van Strien M.J.,Swiss Federal Institute of forest |
Van Strien M.J.,Universitatsstrasse 16
Molecular Ecology Resources | Year: 2013
The use of procedures for the automated scoring of amplified fragment length polymorphisms (AFLP) fragments has recently increased. Corresponding software does not only automatically score the presence or absence of AFLP fragments, but also allows an evaluation of how different settings of scoring parameters influence subsequent population genetic analyses. In this study, we used the automated scoring package rawgeno to evaluate how five scoring parameters influence the number of polymorphic bins and estimates of pairwise genetic differentiation between populations (Fst). Steps were implemented in r to automatically run the scoring process in rawgeno for a set of different parameter combinations. While we found the scoring parameters minimum bin width and minimum number of samples per bin to have only weak influence on pairwise Fst values, maximum bin width and bin reproducibility had much stronger effects. The minimum average bin fluorescence scoring parameter affected Fst values in an only moderate way. At a range of scoring parameters around the default settings of rawgeno, the number of polymorphic bins as well as pairwise Fst values stayed rather constant. This study thus shows the particularities of AFLP scoring, be it either manual or automatical, can have profound effects on subsequent population genetic analysis. © 2012 Blackwell Publishing Ltd.
Na H.,University of Aarhus |
Lever M.A.,University of Aarhus |
Lever M.A.,Universitatsstrasse 16 |
Kjeldsen K.U.,University of Aarhus |
And 2 more authors.
Environmental Microbiology Reports | Year: 2015
Stable isotope probing (SIP) of deoxyribonucleic acid (DNA) was used to identify microbes incorporating 13C-labeled acetate in sulfate-reducing sediment from Aarhus Bay, Denmark. Sediment was incubated in medium containing 10mM sulfate and different 13C-acetate (10, 1, 0.1mM) concentrations. The resultant changes in microbial community composition were monitored in total and SIP-fractionated DNA during long-term incubations. Chemical analyses demonstrated metabolic activity in all sediment slurries, with sulfate-reducing activity largely determined by initial acetate concentrations. Sequencing of 16S rRNA gene PCR amplicons showed that the incubations shifted the bacterial but not the archaeal community composition. After 3 months of incubation, only sediment slurries incubated with 10mM 13C-acetate showed detectable 13C-DNA labeling. Based on 16S rRNA and dsrB gene PCR amplicon sequencing, the 13C-labeled DNA pool was dominated by a single type of sulfate reducer representing a novel genus in the family Desulfobacteraceae. In addition, members of the uncultivated Crenarchaeotal group C3 were enriched in the 13C-labeled DNA. Our results were reproducible across biological replicate experiments and provide new information about the identities of uncultured acetate-consuming bacteria and archaea in marine sediments. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.
Winqvist C.,Swedish University of Agricultural Sciences |
Bengtsson J.,Swedish University of Agricultural Sciences |
Aavik T.,University of Tartu |
Aavik T.,Universitatsstrasse 16 |
And 12 more authors.
Journal of Applied Ecology | Year: 2011
1. Organic farming in Europe has been shown to enhance biodiversity locally, but potential interactions with the surrounding landscape and the potential effects on ecosystem services are less well known. 2. In cereal fields on 153 farms in five European regions, we examined how the species richness and abundance of wild plants, ground beetles and breeding birds, and the biological control potential of the area, were affected by organic and conventional farming, and how these effects were modified by landscape complexity (percentage of arable crops within 1000m of the study plots). Information on biodiversity was gathered from vegetation plots, pitfall traps and by bird territory mapping. The biological control potential was measured as the percentage of glued, live aphids removed from plastic labels exposed in cereal fields for 24h. 3. Predation on aphids was highest in organic fields in complex landscapes, and declined with increasing landscape homogeneity. The biological control potential in conventional fields was not affected by landscape complexity, and in homogenous landscapes it was higher in conventional fields than in organic fields, as indicated by an interaction between farming practice and landscape complexity. 4. A simplification of the landscape, from 20% to 100% arable land, reduced plant species richness by about 16% and cover by 14% in organic fields, and 33% and 5·5% in conventional fields. For birds, landscape simplification reduced species richness and abundance by 34% and 32% in organic fields and by 45·5% and 39% in conventional fields. Ground beetles were more abundant in simple landscapes, but were unaffected by farming practice. 5. Synthesis and applications. This Europe-wide study shows that organic farming enhanced the biodiversity of plants and birds in all landscapes, but only improved the potential for biological control in heterogeneous landscapes. These mixed results stress the importance of taking both local management and regional landscape complexity into consideration when developing future agri-environment schemes, and suggest that local-regional interactions may affect other ecosystem services and functions. This study also shows that it is not enough to design and monitor agri-environment schemes on the basis of biodiversity, but that ecosystem services should be considered too. © 2011 The Authors. Journal of Applied Ecology © 2011 British Ecological Society.
Hartmann K.,University of Tasmania |
Wong D.,Dalhousie University |
Stadler T.,Universitatsstrasse 16
Systematic Biology | Year: 2010
A wide range of evolutionary models for species-level (and higher) diversification have been developed. These models can be used to test evolutionary hypotheses and provide comparisons with phylogenetic trees constructed from real data. To carry out these tests and comparisons, it is often necessary to sample, or simulate, trees from the evolutionary models. Sampling trees from these models is more complicated than it may appear at first glance, necessitating careful consideration and mathematical rigor. Seemingly straightforward sampling methods may produce trees that have systematically biased shapes or branch lengths. This is particularly problematic as there is no simple method for determining whether the sampled trees are appropriate. In this paper, we show why a commonly used simple sampling approach (SSA)-simulating trees forward in time until n species are first reached-should only be applied to the simplest pure birth model, the Yule model. We provide an alternative general sampling approach (GSA) that can be applied to most other models. Furthermore, we introduce the constant-rate birth-death model sampling approach, which samples trees very efficiently from a widely used class of models. We explore the bias produced by SSA and identify situations in which this bias is particularly pronounced. We show that using SSA can lead to erroneous conclusions: When using the inappropriate SSA, the variance of a gradually evolving trait does not correlate with the age of the tree; when the correct GSA is used, the trait variance correlates with tree age. The algorithms presented here are available in the Perl Bio:Phylo package, as a stand-alone program TreeSample, and in the R TreeSim package. © The Author(s) 2010.
Stadler T.,Universitatsstrasse 16 |
Degnan J.H.,University of Canterbury |
Degnan J.H.,National Institute of Mathematical and Biological Synthesis
Algorithms for Molecular Biology | Year: 2012
Background: The ancestries of genes form gene trees which do not necessarily have the same topology as the species tree due to incomplete lineage sorting. Available algorithms determining the probability of a gene tree given a species tree require exponential computational runtime.Results: In this paper, we provide a polynomial time algorithm to calculate the probability of a ranked gene tree topology for a given species tree, where a ranked tree topology is a tree topology with the internal vertices being ordered. The probability of a gene tree topology can thus be calculated in polynomial time if the number of orderings of the internal vertices is a polynomial number. However, the complexity of calculating the probability of a gene tree topology with an exponential number of rankings for a given species tree remains unknown.Conclusions: Polynomial algorithms for calculating ranked gene tree probabilities may become useful in developing methodology to infer species trees based on a collection of gene trees, leading to a more accurate reconstruction of ancestral species relationships. © 2012 Stadler and Degnan; licensee BioMed Central Ltd.
Sbilordo S.H.,University of Zürich |
Sbilordo S.H.,Universitatsstrasse 16 |
Martin O.Y.,Universitatsstrasse 16 |
Ward P.I.,University of Zürich
Journal of Insect Science | Year: 2010
Knowledge of karyotypical characteristics of a species is essential for understanding how sexually selected and sexually antagonistic traits evolve. The yellow dung fly Scathophaga stercoraria L. (Diptera: Scathophagidae) is an established model system for studies of sexual selection and sexual conflict, but karyotypical data are lacking to date. Here, the karyotype of S. stercoraria was characterized using conventional Giemsa-staining and C-banding techniques. The diploid chromosome set consists of 6 pairs of bi-armed meta- or submetacentric chromosomes. The sex chromosomes are the largest chromosomes and constitute 30% of the total length of the diploid set in females and about 25% in males. Males are the heterogametic sex, and the length of the Y chromosome is about three-quarters of that of the X chromosome. C-banding revealed that both sex chromosomes are largely heterochromatic. In contrast, in the five autosome pairs, heterochromatin is limited to narrow bands in the centromeric regions. This karyotypic information will help provide a more profound understanding of the inheritance of phenotypic variation in reproductive traits and the chromosomal locations of underlying genes.
Kaeser A.,Universitatsstrasse 16 |
Bernasconi J.,Universitatsstrasse 16 |
Zimmermann W.,Universitatsstrasse 16
Forest Policy and Economics | Year: 2013
New forms of governance are detected in the Swiss forest reserve policy, a policy in the field of forest biodiversity, and they have helped its implementation. A survey on the implementation status of the Swiss forest reserve concept in the cantons shows that (1) governance elements are clearly favored over traditional command-and-control regulations, (2) 6.6% of the Swiss forest area is delimited forest reserves, (3) large forest reserves are still missing in most of the cantons. Impeding factors can be a lack of conviction of the forest owners, a complicated ownership structure or the weak financial condition of a canton. Improvements may be achieved by increasing consultation and financial incentives or through a purchase of ecologically valuable areas by the Confederation and the cantons. Until now, the Swiss forest reserve policy lacks integration with interacting policies such as climate policy. Climate change could promote forest reserves as sinks for carbon dioxide. Yet this could be counteracted by the support of timber as renewable energy. Integration between forest reserve policy and interacting policies needs to be strengthened, especially with respect to the biodiversity policy (national biodiversity strategy; Convention on Biological Diversity). © 2012 Elsevier B.V.
PubMed | Universitatsstrasse 16
Type: Journal Article | Journal: Algorithms for molecular biology : AMB | Year: 2013
The ancestries of genes form gene trees which do not necessarily have the same topology as the species tree due to incomplete lineage sorting. Available algorithms determining the probability of a gene tree given a species tree require exponential computational runtime.In this paper, we provide a polynomial time algorithm to calculate the probability of a ranked gene tree topology for a given species tree, where a ranked tree topology is a tree topology with the internal vertices being ordered. The probability of a gene tree topology can thus be calculated in polynomial time if the number of orderings of the internal vertices is a polynomial number. However, the complexity of calculating the probability of a gene tree topology with an exponential number of rankings for a given species tree remains unknown.Polynomial algorithms for calculating ranked gene tree probabilities may become useful in developing methodology to infer species trees based on a collection of gene trees, leading to a more accurate reconstruction of ancestral species relationships.