240 Works

Data from: Response of bats to light with different spectra: light-shy and agile bat presence is affected by white and green, but not red light

Kamiel Spoelstra, Roy H. A. Van Grunsven, Jip J. C. Ramakers, Kim B. Ferguson, Thomas Raap, Maurice Donners, Elmar M. Veenendaal & Marcel E. Visser
Artificial light at night has shown a remarkable increase over the past decades. Effects are reported for many species groups, and include changes in presence, behaviour, physiology and life-history traits. Among these, bats are strongly affected, and how bat species react to light is likely to vary with light colour. Different spectra may therefore be applied to reduce negative impacts. We used a unique set-up of eight field sites to study the response of bats...

Data from: Disentangling plastic and genetic changes in body mass of Siberian jays

Phillip Gienapp & Juha Merilä
Spatial and temporal phenotypic differentiation in mean body size is of commonplace occurrence, but the underlying causes remain often unclear: both genetic differentiation in response to selection (or drift) and environmentally induced plasticity can create similar phenotypic patterns. Studying changes in body mass in Siberian jays (Perisoreus infaustus) over three decades, we discovered that mean body mass declined drastically (ca. 10%) over the first two decades, but increased markedly thereafter back to almost the initial...

Data from: Recent natural selection causes adaptive evolution of an avian polygenic trait

Mirte Bosse, Lewis G. Spurgin, Veronika N. Laine, Ella F. Cole, Josh A. Firth, Phillip Gienapp, Andrew G. Gosler, Keith McMahon, Jocelyn Poissant, Irene Verhagen, Martien A. M. Groenen, Kees Van Oers, Ben C. Sheldon, Marcel E. Visser & Jon Slate
We used extensive data from a long-term study of great tits (Parus major) in the United Kingdom and Netherlands to better understand how genetic signatures of selection translate into variation in fitness and phenotypes. We found that genomic regions under differential selection contained candidate genes for bill morphology and used genetic architecture analyses to confirm that these genes, especially the collagen gene COL4A5, explained variation in bill length. COL4A5 variation was associated with reproductive success,...

Data from: Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates

Kees Van Oers, Anna W. Santure, Isabelle De Cauwer, Nikkie E. M. Van Bers, Richard P. M. A. Crooijmans, Ben C. Sheldon, Marcel E. Visser, Jon Slate & Martien A. M. Groenen
Linking variation in quantitative traits to variation in the genome is an important, but challenging task in the study of life-history evolution. Linkage maps provide a valuable tool for the unravelling of such trait-gene associations. Moreover, they give insight into recombination landscapes and between- species karyotype evolution. Here we used genotype data, generated from a 10k SNP-chip, of over 2000 individuals to produce high-density linkage maps of the great tit (Parus major), a passerine bird,...

Data from: Resistance and recovery of methane-oxidizing communities depends on stress regime and history; a microcosm study

Henri Van Kruistum, Paul L. E. Bodelier, Adrian Ho, Marion Meima-Franke & Annelies J. Veraart
Although soil microbes are responsible for important ecosystem functions, and soils are under increasing environmental pressure, little is known about their resistance and resilience to multiple stressors. Here, we test resistance and recovery of soil methane-oxidizing communities to two different, repeated, perturbations: soil drying, ammonium addition and their combination. In replicated soil microcosms we measured methane oxidation before and after perturbations, while monitoring microbial abundance and community composition using quantitative PCR assays for the bacterial...

Data from: Evidence from pyrosequencing indicates that natural variation in animal personality is associated with DRD4 DNA methylation

Eveline C. Verhulst, A. Christa Mateman, Mathijs V. Zwier, Samuel P. Caro, Koen J. F. Verhoeven, Kees Van Oers & Koen J.F. Verhoeven
Personality traits are heritable and respond to natural selection, but are at the same time influenced by the ontogenetic environment. Epigenetic effects, such as DNA methylation, have been proposed as a key mechanism to control personality variation. However, to date little is known about the contribution of epigenetic effects to natural variation in behaviour. Here, we show that great tit (Parus major) lines artificially selected for divergent exploratory behaviour for four generations differ in their...

Data from: Hydrology, shore morphology and species traits affect seed dispersal, germination and community assembly in shoreline plant communities

Casper H. A. Van Leeuwen, Judith M. Sarneel, José Van Paassen, Winnie J. Rip & Elisabeth S. Bakker
1.Seed dispersal and germination are two primary processes influencing plant community assembly. On freshwater shores, water levels regulate both processes. However, it is still unclear how water levels, shore morphology and species traits interactively affect seed dispersal and germination, and how these interactions determine plant community assembly. We hypothesize that a drawdown water regime enhances seed establishment compared to a year-round stable water level, that this increases species richness and diversity, and that this is...

Data from: A mechanistic assessment of the relationship between gut morphology and endozoochorous seed dispersal by waterfowl

Erik Kleyheeg, Bart A. Nolet, Sandra Otero-Ojea & Merel B. Soons
Many plants and invertebrates rely on internal transport by animals for long-distance dispersal. Their dispersal capacity is greatly influenced by interactions with the animal’s digestive tract. Omnivorous birds adjust their digestive tract morphology to seasonally variable diets. We performed feeding trials in waterfowl to unravel how changing organ size, in combination with seed size, affects dispersal potential. We subjected captive mallards to mimics of summer (animal-based), winter (plant-based) and intermediate diets, and analysed gut passage...

Data from: Symbiotic polydnavirus and venom reveal parasitoid to its hyperparasitoids

Feng Zhu, Antonino Cusumano, Janneke Bloem, Berhane T. Weldegergis, Alexandre Villela, Nina E. Fatouros, Joop J.A. Van Loon, Marcel Dicke, Jeffrey A. Harvey, Heiko Vogel & Erik H. Poelman
Symbiotic relationships may provide organisms with key innovations that aid in the establishment of new niches. For example, during oviposition, some species of parasitoid wasps, whose larvae develop inside the bodies of other insects, inject polydnaviruses into their hosts. These symbiotic viruses disrupt host immune responses, allowing the parasitoid’s progeny to survive. Here, we show that symbiotic polydnaviruses also have a downside to the parasitoid’s progeny by initiating a multi-trophic chain of interactions that reveals...

Data from: Body stores persist as fitness correlate in a long-distance migrant released from food constraints

Adriaan M. Dokter, Wimke Fokkema, Steven K. Bekker, Willem Bouten, Barwoldt S. Ebbinge, Gerard Müskens, Han Olff, Henk P. Van Der Jeugd, Bart A. Nolet & Barwolt S Ebbinge
Long-distance migratory birds rely on acquisition of body reserves to fuel their migration and reproduction. Breeding success depends on the amount of body reserve acquired prior to migration, which is thought to increase with access to food at the fuelling site. Here we studied how food abundance during fuelling affected time budgets and reproductive success. In a regime of plenty, we expected that (1) limitations on food harvesting would become lifted, allowing birds to frequently...

Data from: Plant functional diversity and nutrient availability can improve restoration of floating fens via facilitation, complementarity and selection effects

Jeroen P. Van Zuidam, Casper H.A. Van Leeuwen, Elisabeth S. Bakker, Jos T.A. Verhoeven, Stephanie IJff, Edwin T.H.M. Peeters, Bastiaan G. Van Zuidam, Merel B. Soons, Edwin T. H. M. Peeters, Casper H. A. Van Leeuwen & Jos T. A. Verhoeven
1. Peat-forming wetlands, and particularly floating fens forming the initial stages of these ecosystems, are globally declining due to excavation, dehydration and eutrophication. Restoration of these valuable ecosystems typically involves re-establishment of early-successional open-water stages with oligotrophic conditions that are characteristic for these systems. However, restoration success is notoriously limited and a potential solution may be to initiate succession by re-introduction of target plant species. Knowledge is needed on (a) which plant functional groups should...

Data from: More salt, please: global patterns, responses, and impacts of foliar sodium in grasslands

Elizabeth T. Borer, Eric M. Lind, Jennifer Firn, Eric W. Seabloom, T. Michael Anderson, Elizabeth S. Bakker, Lori Biederman, Kimberly J. La Pierre, Andrew S. MacDougall, Joslin L. Moore, Anita C. Risch, Martin Schutz & Carly J. Stevens
Sodium is unique among abundant elemental nutrients, because most plant species do not require it for growth or development, whereas animals physiologically require sodium. Foliar sodium influences consumption rates by animals and can structure herbivores across landscapes. We quantified foliar sodium in 201 locally abundant, herbaceous species representing 32 families and, at 26 sites on four continents, experimentally manipulated vertebrate herbivores and elemental nutrients to determine their effect on foliar sodium. Foliar sodium varied taxonomically...

Data from: Interactions between functionally diverse fungal mutualists inconsistently affect plant performance and competition

Madhav P. Thakur, Vera Quast, Nichole M. Van Dam, Nico Eisenhauer, Christiane Roscher, Arjen Biere & Ainhoa Martinez-Medina
Plants form mutualistic relationship with a variety of belowground fungal species. Such a mutualistic relationship can enhance plant growth and resistance to pathogens. Yet, we know little about how interactions between functionally diverse groups of fungal mutualists affect plant performance and competition. We experimentally determined the effects of interaction between two functional groups of belowground fungi that form mutualistic relationship with plants, arbuscular mycorrhizal (AM) fungi and Trichoderma, on interspecific competition between pairs of closely...

Data from: Negative effects of litter richness on root decomposition in the presence of detritivores

Yinong Li, Xi Chen, Ciska GF Veen, Nico Eisenhauer, Yu Liang, Xiaomei Zhou, Naili Zhang, Keping Ma & G. F. Ciska Veen
1. Decomposition is a vital process underlying many ecosystem functions. Although a growing number of studies have tested how litter richness affects the decomposition of aboveground plant organs, knowledge remains limited about the decomposition of root mixtures. Here, we used a field experiment in a subtropical forest to investigate how species richness in root litter mixtures (air-dried fresh fine roots) affects the decomposition of root litter material. 2. Based on the concept of resource complementarity,...

Data from: Sensitivity of global soil carbon stocks to combined nutrient enrichment

Thomas W. Crowther, Charlotte Riggs, Eric M. Lind, Elizabeth T. Borer, Eric W. Seabloom, Sarah E. Hobbie, E. R. Jasper Wubs, Peter B. Adler, Jennifer Firn, Laureano Gherardi, Nicole Hagenah, Kirsten S. Hofmockel, Johannes M. H. Knops, Rebecca L. McCulley, Andrew MacDougall, Pablo L. Peri, Suzanne M. Prober, Carly J. Stevens & Devin Routh
Soil stores approximately twice as much carbon as the atmosphere and fluctuations in the size of the soil carbon pool directly influence climate conditions. We used the Nutrient Network global change experiment to examine how anthropogenic nutrient enrichment might influence grassland soil carbon storage at a global scale. In isolation, enrichment of nitrogen and phosphorous had minimal impacts on soil carbon storage. However, when these nutrients were added in combination with potassium and micronutrients, soil...

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....

Anthropogenic noise impairs foraging for cryptic prey via cross-sensory interference

Wouter Halfwerk & Kees Van Oers
Anthropogenic noise levels are globally rising with profound impacts on ecosystems and the species that live in them. Masking or distraction by noise can interfere with relevant sounds and thereby impact ecological interactions between individuals of the same or different species. Predator-prey dynamics are particularly likely to be influenced by rising noise levels, with important population- and community-level consequences, as species may differentially adapt to noise disturbance. Acoustic noise can, however, also impair the use...

Data from: Cumulative energetic costs of military aircraft, recreational and natural disturbance in roosting shorebirds

Henk-Jan Van Der Kolk, K. L. Krijgsveld, H. Linssen, R. Diertens, D. Dolman, M. Jans, M. Frauendorf, B. J. Ens & M. Van De Pol
Knowing the consequences of disturbance for multiple species and all disturbance sources is crucial to mitigate disturbance impacts in densely populated areas. However, studies that observe the complete disturbance landscape to estimate cumulative costs of disturbance are scarce. Therefore, we quantified responses, frequencies and energetic costs of disturbance of four shorebird species on five high tide roosts in the Wadden Sea. Roosts were located either in a military air force training area or were predominantly...

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...

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...

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...

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...

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...

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)...

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...

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