87 Works

Changes in plant species richness due to land use and nitrogen deposition across the globe

Juan Gallego-Zamorano, Mark Huijbregts & Aafke Schipper
Data and scripts corresponding to the article "Combined effects of land use and nitrogen deposition on plant species richness worldwide". In the article, we quantified the combined effects of land use and nitrogen deposition on terrestrial plant species richness at a 0.25º spatial resolution across the globe. We first determined the proportional changes in plant species richness for different land-use types and N deposition values through meta-analyses of local monitoring data obtained from the literature....

Data from: Thermal limits in native and alien freshwater peracarid Crustacea: the role of habitat use and oxygen limitation

Wilco C.E.P. Verberk, Rob S.E.W. Leuven, Gerard Van Der Velde & Friederike Gabel
1. In order to predict which species can successfully cope with global warming and how other environmental stressors modulate their vulnerability to climate related environmental factors, an understanding of the ecophysiology underpinning thermal limits is essential for both conservation biology a nd invasion biology. 2. Heat tolerance and the extent to which heat tolerance differed with oxygen availability were examined for four native and four alien freshwater peracarid crustacean species, with differences in habitat use...

Data from: Corrections for rooting volume and plant size reveal negative effects of neighbour presence on root allocation in pea

Bin J. W. Chen, Heinjo J. During, Peter J. Vermeulen, Hans De Kroon, Hendrik Poorter & Niels P. R. Anten
Plants are able to detect the presence of their neighbours belowground. The associated root responses may affect plant performance, plant-plant interactions and community dynamics, but the extent and direction of these responses is heavily debated. Some studies suggest that plants will over-proliferate roots in response to neighbours at the expense of reproduction, which was framed as a “tragedy of the commons”. Others proposed an “ideal free distribution” hypothesis, stating that plants produce roots simply as...

Data from: Peatland vascular plant functional types affect methane dynamics by altering microbial community structure

Bjorn J. M. Robroek, Vincent E. J. Jassey, Martine A. R. Kox, Roeland L. Berendsen, Robert T. E. Mills, Lauric Cécillon, Jéremy Puissant, Marion Meima–Franke, Peter A. H. M. Bakker, Paul L. E. Bodelier & Marion Meima-Franke
1. Peatlands are natural sources of atmospheric methane (CH4), an important greenhouse gas. It is established that peatland methane dynamics are controlled by both biotic and abiotic conditions, yet the interactive effect of these drivers is less studied and consequently poorly understood. 2. Climate change affects the distribution of vascular plant functional types (PFTs) in peatlands. By removing specific PFTs, we assessed their effects on peat organic matter chemistry, microbial community composition and on potential...

Data from: A quantitative theory of gamma synchronization in macaque V1

Eric Lowet, Mark Jonathan Roberts, Alina Peter, Bart Gips & Peter De Weerd
Gamma-band synchronization coordinates brief periods of excitability in oscillating neuronal populations to optimize information transmission during sensation and cognition. Commonly, a stable, shared frequency over time is considered a condition for functional neural synchronization. Here, we demonstrate the opposite: instantaneous frequency modulations are critical to regulate phase relations and synchronization. In monkey visual area V1, nearby local populations driven by different visual stimulation showed different gamma frequencies. When similar enough, these frequencies continually attracted and...

Data from: Are acute and acclimated thermal effects on metabolic rate modulated by cell size? A comparison between diploid and triploid zebrafish larvae

Adam Hermaniuk, Iris L.E. Van De Pol & Wilco Verberk
Being composed of small cells may carry energetic costs related to maintaining ionic gradients across cell membranes as well as benefits related to diffusive oxygen uptake. Here we test the hypothesis that these costs and benefits of cell size in ectotherms are temperature dependent. To study the consequences of cell size for whole-organism metabolic rate we compared diploid and triploid zebrafish larvae differing in cell size. A fully factorial design was applied combining three different...

Data from: Warming and eutrophication interactively drive changes in the methane-oxidizing community of shallow lakes

Thomas P.A. Nijman, Thomas A. Davidson, Stefan T.J. Weideveld, Joachim Audet, Chiara Esposito, Eti E. Levi, Adrian Ho, Leon P.M. Lamers, Erik Jeppesen & Annelies J. Veraart
Freshwater ecosystems are the largest natural source of the greenhouse gas methane (CH4), with shallow lakes a particular hot spot. Eutrophication and warming generally increase lake CH4 emissions but their impacts on the sole biological methane sink - methane oxidation - and methane-oxidizer community dynamics are poorly understood. We used the world’s longest-running freshwater climate-change mesocosm experiment to determine how methane-oxidizing bacterial (MOB) abundance and composition, and methane oxidation potential in the sediment respond to...

Data from: How habitat-modifying organisms structure the food web of two coastal ecosystems

Els M. Van Der Zee, Christine Angelini, Laura L. Govers, Marjolijn J. A. Christianen, Andrew H. Altieri, Karin J. Van Der Reijden, Brian R. Silliman, Johan Van De Koppel, Matthijs Van Der Geest, Jan A. Van Gils, Henk W. Van Der Veer, Theunis Piersma, Peter C. De Ruiter, Han Olff & Tjisse Van Der Heide
The diversity and structure of ecosystems has been found to depend both on trophic interactions in food webs and on other species interactions such as habitat modification and mutualism that form non-trophic interaction networks. However, quantification of the dependencies between these two main interaction networks has remained elusive. In this study, we assessed how habitat-modifying organisms affect basic food web properties by conducting in-depth empirical investigations of two ecosystems: North American temperate fringing marshes and...

Data from: Transgenerational effects of mild heat in Arabidopsis thaliana show strong genotype specificity that is explained by climate at origin

Maartje P. Groot, Alexander Kubisch, N. Joop Ouborg, Joern Pagel, Karl J. Schmid, Philippine Vergeer & Christian Lampei
Transgenerational environmental effects can trigger strong phenotypic variation. However, it is unclear how cues from different preceding generations interact. Also, little is known about genetic variation for these life-history-traits. Here we present effects of grandparental and parental mild heat, and their combination, on four traits of the third-generation phenotype of 14 Arabidopsis thaliana genotypes. We tested for correlations of these effects with climate and constructed a conceptual model to identify the environmental conditions that favour...

Data from: Mutation in the intracellular chloride channel CLCC1 associated with autosomal recessive retinitis pigmentosa

Lin Li, Xiaodong Jiao, Ilaria D’Atri, Fumihito Ono, Ralph Nelson, Chi-Chao Chan, Naoki Nakaya, Zhiwei Ma, Yan Ma, Xiaoying Cai, Longhua Zhang, Siying Lin, Abdul Hameed, Barry A. Chioza, Holly Hardy, Gavin Arno, Sarah Hull, Muhammad Imran Khan, James Fasham, V. Gaurav Harlalka, Michel Michaelides, Anthony T. Moore, Zeynep Hande Coban Akdemir, Shalini Jhangiani, James R. Lupski … & Frans P. M. Cremers
We identified a homozygous missense alteration (c.75C>A, p.D25E) in CLCC1, encoding a presumptive intracellular chloride channel highly expressed in the retina, associated with autosomal recessive retinitis pigmentosa (arRP) in eight consanguineous families of Pakistani descent. The p.D25E alteration decreased CLCC1 channel function accompanied by accumulation of mutant protein in granules within the ER lumen, while siRNA knockdown of CLCC1 mRNA induced apoptosis in cultured ARPE-19 cells. TALEN KO in zebrafish was lethal 11 days post...

Data from: Niche differentiation and expansion of plant species are associated with mycorrhizal symbiosis

Maret Gerz, C. Guillermo Bueno, Wim A. Ozinga, Martin Zobel & Mari Moora
Mycorrhizal symbiosis is a widespread association between plant roots and mycorrhizal fungi, which is thought to contribute to plant niche differentiation and expansion. However, this has so far not been explicitly tested. To address the effect of mycorrhizal symbiosis on plants’ realized niches, we addressed how mycorrhizal status (i.e. the frequency of occurrence of mycorrhizal symbiosis), flexibility (i.e. the ability to grow both with and without mycorrhizal symbiosis) and type of a plant species affect...

Data from: Coverage of the 2011 Q fever vaccination campaign in the Netherlands, using retrospective population-based prevalence estimation of cardiovascular risk-conditions for chronic Q fever

Patricia E. Vermeer-De Bondt, Teske Schoffelen, Ann M. Vanrolleghem, Leslie D. Isken, Marcel Van Deuren, Miriam C. J. M. Sturkenboom & Aura Timen
Background: In 2011, a unique Q fever vaccination campaign targeted people at risk for chronic Q fever in the southeast of the Netherlands. General practitioners referred patients with defined cardiovascular risk-conditions (age >15 years). Prevalence rates of those risk-conditions were lacking, standing in the way of adequate planning and coverage estimation. We aimed to obtain prevalence rates retrospectively in order to estimate coverage of the Q fever vaccination campaign. Methods: With broad search terms for...

Data from: Intergenerational environmental effects: functional signals in offspring transcriptomes and metabolomes after parental jasmonic acid treatment in apomictic dandelion

Koen J. F. Verhoeven, Eline H. Verbon, Thomas P. Van Gurp, Carla Oplaat, Julie Ferreira De Carvalho, Alison M. Morse, Mark Stahl, Mirka Macel & Lauren M. McIntyre
Parental environments can influence offspring traits. However, the magnitude of the impact of parental environments on offspring molecular phenotypes is poorly understood. Here, we test the direct effects and intergenerational effects of jasmonic acid (JA) treatment, which is involved in herbivory-induced defense signaling, on transcriptomes and metabolomes in apomictic common dandelion (Taraxacum officinale). In a full factorial crossed design with parental and offspring JA and control treatments, we performed leaf RNA-seq gene expression analysis, LC-MS...

Data from: Functional antibodies against Plasmodium falciparum sporozoites are associated with a longer time to qPCR-detected infection among schoolchildren in Burkina Faso

Aissata Barry, Marije C. Behet, Issa Nébié, Kjerstin Lanke, Lynn Grignard, Alphonse Ouedraogo, Issiaka Soulama, Chris Drakeley, Robert Sauerwein, Judith M. Bolscher, Koen J. Dechering, Teun Bousema, Alfred B. Tiono & Bronner P. Gonçalves
Background: Individuals living in malaria-endemic regions develop naturally acquired immunity against severe malarial disease, but it is unclear whether immunity that affects the establishment of infections develops following continuous natural exposure. Methods: We cleared schoolchildren in Burkina Faso of possible sub-patent infections and examined them weekly for incident infections by PCR. Plasma samples collected at enrolment were used to quantify antibodies to the pre-eryhrocytic-stage antigens circumsporozoite protein (CSP) and liver stage antigen. Sporozoite gliding inhibition...

Data from: Plant traits and plant biogeography control the biotic resistance provided by generalist herbivores

Bart M. C. Grutters, Yvonne O. A. Roijendijk, Wilco C. E. P. Verberk & Elisabeth S. Bakker
Globalization and climate change trigger species invasions and range shifts, which reshuffle communities at an exceptional rate and expose plant migrants to unfamiliar herbivores. Dominant hypotheses to predict plant success are based on evolutionary novelty: either herbivores are maladapted to consume novel plants (enemy release hypothesis), or novel plants are maladapted to deter herbivores (biotic resistance hypothesis). Since novelty can work both ways, it fails to consistently predict when herbivores will consume novel over non-novel...

Data from: Effects of multi-generational stress exposure and offspring environment on the expression and persistence of transgenerational effects in Arabidopsis thaliana

Maartje P. Groot, Rik Kooke, Nieke Knoben, Philippine Vergeer, Joost J. B. Keurentjes, N. Joop Ouborg, Koen Verhoeven & Koen J. F. Verhoeven
Plant phenotypes can be affected by environments experienced by their parents. Parental environmental effects are reported for the first offspring generation and some studies showed persisting environmental effects in second and further offspring generations. However, the expression of these transgenerational effects proved context-dependent and their reproducibility can be low. Here we study the context-dependency of transgenerational effects by evaluating parental and transgenerational effects under a range of parental induction and offspring evaluation conditions. We systematically...

Data from: The impact of hotspot-targeted interventions on malaria transmission in Rachuonyo south district in the western Kenyan highlands: a cluster-randomized controlled trial

Teun Bousema, Gillian Stresman, Amrish Y. Baidjoe, John Bradley, Philip Knight, William Stone, Victor Osoti, Euniah Makori, Chrispin Owaga, Wycliffe Odongo, Pauline China, Shehu Shagari, Ogobara K. Doumbo, Robert W. Sauerwein, Simon Kariuki, Chris Drakeley, Jennifer Stevenson & Jonathan Cox
Background: Malaria transmission is highly heterogeneous, generating malaria hotspots that can fuel malaria transmission across a wider area. Targeting hotspots may represent an efficacious strategy for reducing malaria transmission. We determined the impact of interventions targeted to serologically defined malaria hotspots on malaria transmission both inside hotspots and in surrounding communities. Methods and Findings: Twenty-seven serologically defined malaria hotspots were detected in a survey conducted from 24 June to 31 July 2011 that included 17,503...

Data from: Local soil legacy effects in a multi-species grassland community are underlain by root foraging and soil nutrient availability

, Nyncke J. Hoekstra, Cornelis A.M. Wagemaker, Hannie De Caluwe, Annemiek E. Smit-Tiekstra, Eric J.W. Visser & Hans De Kroon
1. Plant soil legacies consisting of species-specific microbial communities are hypothesized to play a critical, structuring role in plant species co-existence processes. Plant species are thought to perform worse on soil conditioned by the same species compared to soil of other species, which serves as a self-limitation mechanism and averts mono-dominance of strong competitors. Here we test in a multi-species community setting, whether root colonisation and resource utilisation of soil patches with distinct soil legacies,...

Data from: Spatiotemporal variation in disturbance impacts derived from simultaneous tracking of aircraft and shorebirds

Henk-Jan Van Der Kolk, Andrew Allen, Bruno Ens, Kees Oosterbeek, Eelke Jongejans & Martijn Van De Pol
1. Assessing impacts of disturbance over large areas and long time periods is crucial for nature management, but also challenging since impacts depend on both wildlife responses to disturbance and on the spatiotemporal distribution of disturbance sources. Combined tracking of animals and disturbance sources enables quantification of wildlife responses as a function of the distance to a disturbance source. We provide a framework to derive such distance-response curves and combine those with disturbance source presence...

Apparent breeding success drives long-term population dynamics of a migratory swan

Rascha Nuijten, Stefan Vriend, Kevin Wood, Trinus Haitjema, Eileen Rees, Eelke Jongejans & Bart Nolet
The ability of a species to adapt to environmental change is ultimately reflected in its vital rates – i.e., survival and reproductive success of individuals. Together, vital rates determine trends in numbers, commonly monitored using counts of species abundance. Rapid changes in abundance can give rise to concern, leading to calls for research into the biological mechanisms underlying variations in demography. For the NW European population of Bewick’s swan (Cygnus columbianus bewickii), there have been...

Human-induced reduction in mammalian movements impacts seed dispersal in the tropics

Marlee Tucker, Michela Busana, Mark Huijbregts & Adam Ford
Seed dispersal is a key process affecting the structure, composition and spatial dynamics of plant populations. Numerous plant species in the tropics rely upon animals to disperse their seeds. Humans have altered mammalian movements, which will likely affect seed dispersal distances (SDD). Altered SDD may have a range of consequences for plant communities including reduced seedling recruitment and plant biomass, seed trait homogenization, altered gene flow and a reduced capacity to respond to environmental changes....

Data for: Environmental and anthropogenic constraints on animal space use drive extinction risk worldwide

Myriam R. Hirt, Andrew D. Barnes, Alessandro Gentile, Laura J. Pollock, Benjamin Rosenbaum, Wilfried Thuiller, Marlee A. Tucker & Ulrich Brose
Animals require a certain amount of habitat to persist and thrive, and habitat loss is one of the most critical drivers of global biodiversity decline. While habitat requirements have been predicted by relationships between species traits and home range size, little is known about constraints imposed by environmental conditions and human impacts on a global scale. Our meta-analysis of 395 vertebrate species shows that global climate gradients in temperature and precipitation exert indirect effects via...

Spitzer-IRS spectra associated with the IDEOS project

Henrik Spoon, Antonio Hernán-Caballero, David Rupke, Rens Waters, Vianney Lebouteiller, Alexander Tielens, Thomas Loredo, Yubo Su & Vince Viola

Data from: Unravelling the immune signature of Plasmodium falciparum transmission-reducing immunity

Will J. R. Stone, Joseph J. Campo, André Lin Ouédraogo, Lisette Meerstein-Kessel, Isabelle Morlais, Dari Da, Anna Cohuet, Sandrine Nsango, Colin J. Sutherland, Marga Van De Vegte-Bolmer, Rianne Siebelink-Stoter, Geert-Jan Van Gemert, Wouter Graumans, Kjerstin Lanke, Adam D. Shandling, Jozelyn V. Pablo, Andy A. Teng, Sophie Jones, Roos M. De Jong, Amanda Fabra-García, John Bradley, Will Roeffen, Edwin Lasonder, Giuliana Gremo, Evelin Schwarzer … & Matthijs M. Jore
Infection with Plasmodium can elicit antibodies that inhibit parasite survival in the mosquito, when they are ingested in an infectious blood meal. Here, we determine the transmission-reducing activity (TRA) of naturally acquired antibodies from 648 malaria-exposed individuals using lab-based mosquito-feeding assays. Transmission inhibition is significantly associated with antibody responses to Pfs48/45, Pfs230, and to 43 novel gametocyte proteins assessed by protein microarray. In field-based mosquito-feeding assays the likelihood and rate of mosquito infection are significantly...

Data from: A family-based study into penetrance in facioscapulohumeral muscular dystrophy type 1

Mariëlle Wohlgemuth, Richard J. Lemmers, Marianne Jonker, Ely Van Der Kooi, Corinne G. Horlings, Baziel G. Van Engelen, Silvere M. Van Der Maarel, George W. Padberg & Nicol C. Voermans
Objective: An observational cross-sectional study was conducted in a national facioscapulohumeral muscular dystrophy (FSHD) expertise center to estimate the penetrance of FSHD1 and to evaluate phenotype–genotype correlations. Methods: Ten FSHD1 probands carrying 4–9 D4Z4 unit alleles and 140 relatives were examined. All 150 participants were genetically characterized, including D4Z4 methylation levels in the mutation carriers. Mutation carriers were classified as (1) symptomatic: with symptoms of muscle weakness on history and muscle FSHD signs on examination;...

Registration Year

  • 2022
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  • 2013

Resource Types

  • Dataset


  • Radboud University Nijmegen
  • Nederlands Instituut voor Ecologie
  • Royal Netherlands Institute for Sea Research
  • Utrecht University
  • London School of Hygiene & Tropical Medicine
  • Dutch Centre for Field Ornithology
  • University of Florida
  • Wageningen University & Research
  • Duke University
  • University of Queensland