239 Works

Source code for R tutorials and dataset for empirical case study on Malurus elegans (red-winged fairy wren)

Martijn Van De Pol & Lyanne Brouwer
Biological processes exhibit complex temporal dependencies due to the sequential nature of allocation decisions in organisms’ life-cycles, feedback loops, and two-way causality. Consequently, longitudinal data often contain cross-lags: the predictor variable depends on the response variable of the previous time-step. Although statisticians have warned that regression models that ignore such covariate endogeneity in time series are likely to be inappropriate, this has received relatively little attention in biology. Furthermore, the resulting degree of estimation bias...

Measuring the contribution of evolution to community trait structure in freshwater zooplankton

Lynn Govaert, Luc De Meester, Steven Declerck, Sarah Rousseaux & Jelena H. Pantel
There are currently few predictions about when evolutionary processes are likely to play an important role in structuring community features.Determining predictors that indicate when evolution is expected to impact ecological processes in natural landscapes can help researchers identify eco-evolutionary 'hotspots', where eco-evolutionary interactions are more likely to occur. Using data collected from a survey in freshwater cladoceran communities, landscape population genetic data, and phenotypic trait data measured in a common garden, we applied a Bayesian...

Data from: Cyanophage propagation in the freshwater cyanobacterium Phormidium is constrained by phosphorus limitation and enhanced by elevated pCO2

Dedmer Van De Waal, Kai Cheng, Thijs Frenken & Corina P. D. Brussaard
Intensification of human activities has led to changes in the availabilities of CO2 and nutrients in freshwater ecosystems, which may greatly alter the physiological status of phytoplankton. Viruses require hosts for their reproduction and shifts in phytoplankton host physiology through global environmental change may thus affect viral infections as well. Various studies have investigated the impacts of single environmental factors on phytoplankton virus propagation, yet little is known about the impacts of multiple factors, particularly...

Invasive earthworms reduce chemical defense and increase herbivory and pathogen infection in native trees

Madhav Thakur, Tom Kuenne, Sybille Unsicker, Arjen Biere, Olga Ferlian, Ulrich Pruschitzki, Lise Thouvenot, Manfred Turke & Nico Eisenhauer
Recent research shows that earthworms can alter defense traits of plants against herbivores and pathogens by affecting soil biochemistry. Yet, the effects of invasive earthworms on defense traits of native plants from previously earthworm-free ecosystems as well as the consequences for multitrophic interactions are virtually unknown. Here we use a combination of an observational study and a complementary experimental study to investigate the effects of invasive earthworms on leaf defense traits, herbivore damage, and pathogen...

Resilience of rhizosphere microbial predators and their prey communities after an extreme heat event

Madhav Thakur, Wim Van Der Putten, Fariha Apon, Ezio Angelini, Branko Vres & Stefan Geisen
Climate change is known to disrupt aboveground food chains when the various trophic layers respond differently to warming. However, little is known about belowground food chains involving microbial preys and their predators. Here, we study how climate warming- induced heat shocks influence resistance (change immediately after a disturbance) and resilience (ability to recover back to pre-disturbance levels) in rhizosphere microbial communities. We used three species of rhizosphere protists as microbial predators and six different rhizosphere...

Inconsistent effects of agricultural practices on soil fungal communities across twelve European long‐term experiments

S. Emilia Hannula, D. P. Di Lonardo, B. T. Christensen, F.V. Crotty, A. Elsen, P.J. Erp, E.M. Hansen, G. H. Rubæk, M. Tits, Z. Toth & A. J. Termorshuizen
Cropping practices have a great potential to improve soil quality through changes in soil biota. Yet the effects of these soil improving cropping systems on soil fungal communities are not well known. Here, we analysed soil fungal communities using standardized measurements in 12 long‐term experiments and 20 agricultural treatments across Europe. We were interested in whether the same practices (i.e. tillage, fertilization, organic amendments and cover crops) applied across different sites have predictable and repeatable...

Timing of increased temperature sensitivity coincides with nervous system development in winter moth embryos

Natalie Van Dis, Maurijn Van Der Zee, Roelof Hut, Bregje Wertheim & Marcel Visser
Climate change is rapidly altering the environment and many species will need to genetically adapt their seasonal timing to keep up with these changes. Insect development rate is largely influenced by temperature, but we know little about the mechanisms underlying temperature sensitivity of development. Here we investigate seasonal timing of egg hatching in the winter moth, one of the few species which has been found to genetically adapt to climate change, likely through selection on...

Data from: Stay or fly away? Impact of human disturbance on shorebird individuals and populations

Henk-Jan Van Der Kolk
These data comprise the data of four chapters from the PhD thesis from van der Kolk (2021) entitled ‘Stay or fly away? Impact of human disturbance on shorebird individuals and populations.’ The thesis focusses on quantifying the impacts of human disturbance on oystercatchers. This dataset contains data from chapters 4, 5, 7 and 10. For Chapter 4 field observations were done to observe how shorebirds responded to aircraft overflights at different sites. The data provides...

Effects of soil phosphorus, light, AMF and jasmonic acid on growth and defense of Plantago lanceolata

Arjen Biere, Minggang Wang & Laiye Qu
This dataset contains data from a two-part greenhouse experiments described in the paper: “Qu, L., Wang, M., and Biere, A. (2021) Interactive effects of Mycorrhizae, Soil Phosphorus and Light on Growth and Induction and Priming of Defense in Plantago lanceolata. Frontiers in Plant Science 12: 647372”. The experiment investigates the effects of a factorial combination of three factors: inoculation with AMF (the arbuscular mycorrhizal fungus Funneliformis mosseae; yes/no), soil phosphorus level (Soil P, 10.5 vs....

List of known SNP positions (based on SNP chip data) for base quality score recalibration of alignments for whole-genome resequencing and whole-genome bisulfite sequencing data from great tits (Parus major)

Melanie Lindner, Veronika N Laine & Marcel E Visser
The profiling of epigenetic marks like DNA methylation has become a central aspect of studies in evolution and ecology. Bisulfite sequencing is commonly used for assessing genome-wide DNA methylation at single nucleotide resolution but these data can also provide information on genetic variants like single nucleotide polymorphisms (SNPs). However, bisulfite conversion causes unmethylated cytosines to appear as thymines, complicating the alignment and subsequent SNP calling. Several tools have been developed to overcome this challenge, but...

Large wild herbivores slow down the rapid decline of plant diversity in a tropical forest biodiversity hotspot

Nacho Villar & Emilia Patricia Medici
1. The UN declaration of the Decade of Ecosystem Restoration 2021-2030 emphasizes the need for effective measures to restore ecosystems and safeguard biodiversity. Large herbivores regulate many ecosystem processes and functions, yet their potential as a nature-based solution to buffer against long-term temporal declines in biodiversity associated to global change and restore diversity in secondary forests remains unknown. 2. By means of an exclusion experiment, we tested experimentally the buffering effects of large wild herbivores...

Plant community legacy effects on nutrient cycling, fungal decomposer communities and decomposition in a temperate grassland

Renske Jongen, S. Emilia Hannula, Jonathan R. De Long, Robin Heinen, Martine Huberty, Katja Steinauer & T. Martijn Bezemer
Soil legacies mediated by plant species-specific microbial communities are major drivers of plant community dynamics. Most soil legacy studies focus on the role of pathogens and mutualists in driving these processes, while much less is known about plant litter-mediated changes to the soil microbial community. Here, we used an existing plant-soil feedback field experiment in which plant communities with different growth strategies (i.e., fast versus slow) and different proportions of functional groups (grasses versus forbs)...

Data for: Telomere dynamics in relation to experimentally increased locomotion costs and fitness in great tits

Simon Verhulst, Els Atema & Arie J. Van Noordwijk
Evidence that telomere length (TL) and dynamics can be interpreted as proxy for ‘life stress’ experienced by individuals stems largely from correlational studies. We tested for effects of an experimental increase of workload on telomere dynamics by equipping male great tits (Parus major) with a 0.9 gram backpack for a full year. In addition, we analysed associations between natural life-history variation, TL and TL dynamics. Carrying 5% extra weight for a year did not significantly...

Postnatal growth rate varies with latitude in range-expanding geese – the role of plasticity and day length

Michiel P. Boom, Henk P. Van Der Jeugd, Boas Steffani, Bart A. Nolet, Kjell Larsson & Götz Eichhorn
This dataset contains data from an analysis of differences in growth rate among three different barnacle populations breeding at different latitudes, described in the paper: Boom, Michiel P., van der Jeugd, H.P., Steffani, B., Nolet, B.A., Larsson, K., & Eichhorn, G. (2021), Postnatal growth rate varies with latitude in range-expanding geese – the role of plasticity and day length. Journal of Animal Ecology. The postnatal growth period is a crucial life stage, with potential lifelong...

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Resource Types

  • Dataset


  • Nederlands Instituut voor Ecologie
  • Wageningen University & Research
  • Netherlands Institute of Ecology
  • University of Groningen
  • Utrecht University
  • University of Amsterdam
  • Radboud University Nijmegen
  • Leiden University
  • VU University Amsterdam
  • University of Turku