59 Works

Data from: Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus Batrachochytrium dendrobatidis

Allison Q. Byrne, Andrew P. Rothstein, Thomas J. Poorten, Jesse Erens, Matthew L. Settles & Erica Bree Rosenblum
One of the most devastating emerging pathogens of wildlife is the chytrid fungus, Batrachochytrium dendrobatidis (Bd), which affects hundreds of amphibian species around the world. Genomic data from pure Bd cultures has advanced our understanding of Bd phylogenetics, genomic architecture, and mechanisms of virulence. However pure cultures are laborious to obtain and whole genome sequencing is comparatively expensive, so relatively few isolates have been genetically characterized. Thus we still know little about the genetic diversity...

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: EuMIXFOR empirical forest mensuration and ring width data from pure and mixed stands of Scots pine (Pinus sylvestris L.) and European beech (Fagus sylvatica L.) through Europe

Michael Heym, Ricardo Ruíz-Peinado, Miren Del Río, Kamil Bielak, David I. Forrester, Gerald Dirnberger, Ignacio Barbeito, Gediminas Brazaitis, Indrė Ruškytė, Lluís Coll, Marek Fabrika, Lars Drössler, Magnus Löf, Hubert Sterba, Václav Hurt, Viktor Kurylak, Fabio Lombardi, Dejan Stojanović, Jan Den Ouden, Renzo Motta, Maciej Pach, Jerzy Skrzyszewski, Quentin Ponette, Géraud De Streel, Vit Sramek … & Hans Pretzsch
This data set provides unique empirical data from triplets of Scots pine (Pinus sylvestris L.) and European beech (Fagus sylvatica L.) across Europe. Dendrometric variables are provided for 32 triplets, 96 plots, 7555 trees and 4695 core samples. These data contribute to our understanding of mixed stand dynamics.

Data from: Remote sensing of plant trait responses to field-based plant–soil feedback using UAV-based optical sensors

Bob Van Der Meij, Lammert Kooistra, Juha Suomalainen, Janna M. Barel & Gerlinde B. De Deyn
Plant responses to biotic and abiotic legacies left in soil by preceding plants is known as plant–soil feedback (PSF). PSF is an important mechanism to explain plant community dynamics and plant performance in natural and agricultural systems. However, most PSF studies are short-term and small-scale due to practical constraints for field-scale quantification of PSF effects, yet field experiments are warranted to assess actual PSF effects under less controlled conditions. Here we used unmanned aerial vehicle...

Data from: Fire coral clones demonstrate phenotypic plasticity among reef habitats

Caroline Eve Dubé, Emilie Boissin, Jeffrey A. Maynard & Serge Planes
Clonal populations are often characterized by reduced levels of genotypic diversity, which can translate into lower numbers of functional phenotypes, both of which impede adaptation. Study of partially clonal animals enables examination of the environmental settings under which clonal reproduction is favoured. Here, we gathered genotypic and phenotypic information from 3,651 georeferenced colonies of the fire coral Millepora platyphylla in five habitats with different hydrodynamic regimes in Moorea, French Polynesia. In the upper slope where...

Data from: Temporal carry-over effects in sequential plant–soil feedbacks

Jasper R. Wubs, T. Martijn Bezemer & E. R. Jasper Wubs
Plant-soil feedbacks (PSF) strongly influence plant performance. However, to what extent these PSF effects are persistent in the soil and how they are altered by species that subsequently condition the soil is unclear. Here we test how conspecific and heterospecific soil-conditioning effects interact across different soil-conditioning phases. We conducted a fully factorial glasshouse experiment where six plant species conditioned soils in two consecutive phases and measured the performance of Jacobaea vulgaris. The species that conditioned...

Data from: Warming advances top-down control and reduces producer biomass in a freshwater plankton community

Mandy Velthuis, Lisette N. De Senerpont Domis, Thijs Frenken, Susanne Stephan, Garabet Kazanjian, Ralf Aben, Sabine Hilt, Sarian Kosten, Ellen Van Donk & Dedmer B. Van De Waal
Global warming has been shown to affect ecosystems worldwide. Warming may, for instance, disrupt plant herbivore synchrony and bird phenology in terrestrial systems, reduce primary production in oceans, and promote toxic cyanobacterial blooms in freshwater lakes. Responses of communities will not only depend on direct species-specific temperature effects, but also on indirect effects related to bottom-up and top-down processes. Here, we investigated the impact of warming on freshwater phytoplankton community dynamics, and assessed the relative...

Data from: Vegetation recovery in tidal marshes reveals critical slowing down under increased inundation

Jim Van Belzen, Johan Van De Koppel, Matthew L. Kirwan, Daphne Van Der Wal, Peter M. J. Herman, Vasilis Dakos, Sonia Kéfi, Marten Scheffer, Glenn R. Guntenspergen & Tjeerd J. Bouma
A declining rate of recovery following disturbance has been proposed as an important early warning for impending tipping points in complex systems. Despite extensive theoretical and laboratory studies, this ‘critical slowing down’ remains largely untested in the complex settings of real-world ecosystems. Here, we provide both observational and experimental support of critical slowing down along natural stress gradients in tidal marsh ecosystems. Time series of aerial images of European marsh development reveal a consistent lengthening...

Data from: Admixture between released and wild game birds: a changing genetic landscape in European mallards (Anas platyrhynchos)

Pär Söderquist, Johan Elmberg, Gunnar Gunnarsson, Carl-Gustaf Thulin, Jocelyn Champagnon, Matthieu Guillemain, Jakub Kreisinger, Herbert H. T. Prins, Richard P. M. A. Crooijmans & Robert H. S. Kraus
Disruption of naturally evolved spatial patterns of genetic variation and local adaptations is a growing concern in wildlife management and conservation. During the last decade, releases of native taxa with potentially non-native genotypes have received increased attention. This has mostly concerned conservation programs, but releases are also widely carried out to boost harvest opportunities. The mallard, Anas platyrhynchos, is one of few terrestrial migratory vertebrates subjected to large-scale releases for hunting purposes. It is the...

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: Trait-dependent distributional shifts in fruiting of common British fungi

Alan C. Gange, Einar Heegaard, Lynne Boddy, Carrie Andrew, Paul Kirk, Rune Halvorsen, Thomas W. Kuyper, Claus Bässler, Jeffrey Diez, Jacob Heilman-Clausen, Klaus Høiland, Ulf Büntgen & Håvard Kauserud
Despite the dramatic phenological responses of fungal fruiting to recent climate warming, it is unknown whether spatial distributions of fungi have changed and to what extent such changes are influenced by fungal traits, such as ectomycorrhizal (ECM) or saprotrophic lifestyles, spore characteristics, or fruit body size. Our overall aim was to understand how climate and fungal traits determine whether and how species-specific fungal fruit body abundances have shifted across latitudes over time, using the UK...

Data from: Frequency tuning and directional sensitivity of tympanal vibrations in the field cricket Gryllus bimaculatus

Martin J. Lankheet, Uroš Cerkvenik, Ole N. Larsen & Johan L. Van Leeuwen
Female field crickets use phonotaxis to locate males by their calling song. Male song production and female behavioural sensitivity form a pair of matched frequency filters, which in Gryllus bimaculatus are tuned to a frequency of about 4.7 kHz. Directional sensitivity is supported by an elaborate system of acoustic tracheae, which make the ears function as pressure difference receivers. As a result, phase differences between left and right sound inputs are transformed into vibration amplitude...

Data from: Feeding preference as a main determinant of microscale patchiness among terrestrial nematodes

Casper W. Quist, Gerrit Gort, Christian Mulder, Ruud H. P. Wilbers, Aad J. Termorshuizen, Jaap Bakker & Johannes Helder
Soil biota are responsible for essential ecosystem services such as carbon storage, nutrient cycling and water retention. However, assessment of the condition of soil biota is hampered by an overwhelming level of diversity. With representatives in all trophic levels of the food web, nematode communities can be used as bio-indicators. Accurate assessment of nematode assemblages requires insight in the distribution of specimens with distinct food preferences. With the availability of taxon-specific quantitative-PCR assays, distribution patterns...

Data from: The differential impact of a native and a non-native ragwort species (Senecioneae) on the first and second trophic level of the rhizosphere food web

Paula Harkes, Ava Verhoeven, Mark G. Sterken, L. Basten Snoek, Sven J. J. Van Den Elsen, Paul J. W. Mooijman, Casper W. Quist, Mariëtte T. W. Vervoort & Johannes Helder
Whereas the impact of exotic plant species on above-ground biota is relatively well-documented, far less is known about the effects of non-indigenous plants on the first and second trophic level of the rhizosphere food web. Here, rhizosphere communities of the invasive narrow-leaved ragwort Senecio inaequidens and the native tansy ragwort Jacobaea vulgaris, co-occurring in three semi-natural habitats are compared. For both species, two life stages were taken into consideration. Quantitative PCR assays for the analyses...

Data from: Woodland ectomycorrhizal fungi benefit from large-scale reduction of nitrogen deposition in the Netherlands

Arco J. Van Strien, Menno Boomsluiter, Machiel E. Noordeloos, Richard J. T. Verweij & Thomas W. Kuyper
1.Woodland ectomycorrhizal (ECM) fungal species declined considerably in the Netherlands in the late 20th century, mainly due to raised levels of atmospheric nitrogen deposition. Environmental measures have been taken to reduce this deposition, but it remains unclear whether and to what extent ECM species have benefitted from this. 2.We hypothesised that ECM species, especially those species that are known to be nitrophobic, i.e. sensitive to nitrogen loading, have recovered to some extent from the reduction...

Data from: Detecting environment-dependent diversification from phylogenies: a simulation study and some empirical illustrations

Eric Lewitus & Hélène Morlon
Understanding the relative influence of various abiotic and biotic variables on diversification dynamics is a major goal of macroevolutionary studies. Recently, phylogenetic approaches have been developed that make it possible to estimate the role of various environmental variables on diversification using time-calibrated species trees, paleoenvironmental data, and maximum-likelihood techniques. These approaches have been effectively employed to estimate how speciation and extinction rates vary with key abiotic variables, such as temperature and sea level, and we...

Data from: Relatedness with plant species in native community influences ecological consequences of range expansions

Kadri Koorem, Olga Kostenko, L. Basten Snoek, Carolin Weser, Kelly S. Ramirez, Rutger A. Wilschut & Wim H. Van Der Putten
Global warming is enabling many plant species to expand their range to higher latitudes and altitudes, where they may suffer less from natural aboveground and belowground enemies. Reduced control by natural enemies can enable climate warming-induced range expanders to get an advantage in competition with natives and become disproportionally abundant in their new range. However, so far studies have examined individual growth of range expanders, which have common congeneric plant species in their new range....

Data from: Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of South America

Michael D. Pirie, Paul J.M. Maas, Rutger A. Wilschut, Heleen Melchers-Sharrott & Lars W. Chatrou
Much of the immense present day biological diversity of Neotropical rainforests originated from the Miocene onwards, a period of geological and ecological upheaval in South America. We assess the impact of the Andean orogeny, drainage of lake Pebas, and closure of the Panama Isthmus on two clades of tropical trees (Cremastosperma, c. 31 spp.; and Mosannona, c. 14 spp.; both Annonaceae). Phylogenetic inference revealed similar patterns of geographically restricted clades and molecular dating showed diversifications...

Data from: Demonstrating multiple benefits from periodically harvested fisheries closures

Jordan S. Goetze, Joachim Claudet, Fraser Januchowski-Hartley, Timothy J. Langlois, Shaun K. Wilson, Crow White, Rebecca Weeks & Stacy D. Jupiter
1.Periodically harvested closures (PHCs) are one of the most common forms of fisheries management in Melanesia, demonstrating multiple objectives, including sustaining fish stocks and increasing catch efficiency to support small-scale fisheries. No studies have comprehensively assessed their ability to provide short-term fisheries benefits across the entire harvest regime. 2.We present a novel analytical framework to guide a meta-analysis and assist future research in conceptualizing and assessing the potential of PHCs to deliver benefits for multiple...

Data from: Intestinal Ralstonia pickettii augments glucose intolerance in obesity

Shanthadevi Udayappan, Petia Kovatcheva-Datchary, Guido Bakker, Stefan Havik, Hilde Herrema, Patrice Cani, Kristien Bouter, Clara Belzer, Julia J. Witjes, Anne Vrieze, Eleonore Susanne Victoria De Sonnaville, Alice Chaplin, Daniel Van Raalte, Steven Aalvink, Geesje Dallinga-Thie, Hans Heilig, Goran Bergstrom, Suzan Van Der Meij, Bart Van Wagensveld, Joost Hoekstra, Frits Holleman, Erik Stroes, Albert Groen, Fredrik Backhed, Willem De Vos … & Daniel H. Van Raalte
An altered intestinal microbiota composition has been implicated in the pathogenesis of metabolic disease including obesity and type 2 diabetes mellitus (T2DM). Low grade inflammation, potentially initiated by the intestinal microbiota, has been suggested to be a driving force in the development of insulin resistance in obesity. Here, we report that bacterial DNA is present in mesenteric adipose tissue of obese but otherwise healthy human subjects. Pyrosequencing of bacterial 16S rRNA genes revealed that DNA...

Data from: Plant community evenness responds to spatial plant-soil feedback heterogeneity primarily through the diversity of soil conditioning

E. R. Jasper Wubs & Martijn T. Bezemer
1.Plant-soil feedback (PSF) has been identified as a key driver of local plant diversity and evenness in competitive communities. However, while it has been shown that spatial PSF heterogeneity can alter plant performance and competitive interactions, there is no proof of principle that spatial PSF heterogeneity enhances community diversity. 2.Using a grassland model system we separated two aspects of spatial heterogeneity: the number of species conditioning the soil and spatial distribution of the PSFs. 3.Our...

Data from: Belowground complementarity effects in a grassland biodiversity experiment are related to deep-rooting species

Natalie J. Oram, Janneke M. Ravenek, Kathryn E. Barry, Alexandra Weigelt, Hongmei Chen, Arthur Gessler, Annette Gockele, Hans De Kroon, Jan Willem Van Der Paauw, Michael Scherer-Lorenzen, Annemiek Smit-Tiekstra, Jasper Van Ruijven & Liesje Mommer
1. Belowground resource partitioning is often proposed as the underlying mechanism for the positive relationship between plant species richness and productivity. For example, if species have different root distributions, a mixture of plant species may be able to use the available resources more completely than the individual species in a monoculture. However, there is little experimental evidence for differentiation in vertical root distributions among species and its contribution to biodiversity effects. 2. We determined species-specific...

Data from: What are the prospects for citizen science in agriculture? Evidence from three continents on motivation and mobile telephone use of resource-poor farmers

Eskender Beza, Jonathan Steinke, Jacob Van Etten, Pytrik Reidsma, Carlo Fadda, Sarika Mittra, Prem Mathur & Lammert Kooistra
As the sustainability of agricultural citizen science projects depends on volunteer farmers who contribute their time, energy and skills, understanding their motivation is important to attract and retain participants in citizen science projects. The objectives of this study were to assess 1) farmers' motivations to participate as citizen scientists and 2) farmers' mobile telephone usage. Building on motivational factors identified from previous citizen science studies, a questionnaire based methodology was developed which allowed the analysis...

Data from: Cascading effects of predator activity on tick-borne disease risk

Tim R. Hofmeester, Patrick A. Jansen, Hendrikus J. Wijnen, Elena C. Coipan, Manoj Fonville, Herbert H.T. Prins, Hein Sprong, Sip E. Van Wieren, Herbert H. T. Prins & Sipke E. Van Wieren
Predators and competitors of vertebrates can in theory reduce the density of infected nymphs (DIN)—an often-used measure of tick-borne disease risk—by lowering the density of reservoir-competent hosts and/or the tick burden on reservoir-competent hosts. We investigated this possible indirect effect of predators by comparing data from 20 forest plots across the Netherlands that varied in predator abundance. In each plot, we measured the density of questing Ixodes ricinus nymphs (DON), DIN for three pathogens, rodent...

Data from: A general model for estimating macroevolutionary landscapes

Florian C. Boucher, Vincent Démery, Elena Conti, Luke J. Harmon & Josef Uyeda
The evolution of quantitative characters over long timescales is often studied using stochastic diffusion models. The current toolbox available to students of macroevolution is however limited to two main models: Brownian motion and the Ornstein-Uhlenbeck process, plus some of their extensions. Here we present a very general model for inferring the dynamics of quantitative characters evolving under both random diffusion and deterministic forces of any possible shape and strength, which can accommodate interesting evolutionary scenarios...

Registration Year

  • 2017
    59

Resource Types

  • Dataset
    59

Affiliations

  • Wageningen University & Research
    59
  • Nederlands Instituut voor Ecologie
    11
  • Swedish University of Agricultural Sciences
    6
  • Radboud University Nijmegen
    3
  • French National Centre for Scientific Research
    3
  • University of Helsinki
    3
  • Max Planck Institute for Ornithology
    2
  • University of Groningen
    2
  • University of California, Berkeley
    2
  • National Institute for Public Health and the Environment
    2