50 Works

Data from: Unequal contribution of widespread and narrow-ranged species to botanical diversity patterns

Andre S. J. Van Proosdij, Niels Raes, Jan J. Wieringa & Marc S. M. Sosef
In conservation studies, solely widespread species are often used as indicators of diversity patterns, but narrow-ranged species can show different patterns. Here, we assess how well subsets of narrow-ranged, widespread or randomly selected plant species represent patterns of species richness and weighted endemism in Gabon, tropical Africa. Specifically, we assess the effect of using different definitions of widespread and narrow-ranged and of the information content of the subsets. Finally, we test if narrow-ranged species are...

Data from: Spatial patterns of self-recruitment of a coral reef fish in relation to island-scale retention mechanisms

Ricardo Beldade, Sally J. Holbrook, Russell J. Schmitt, Serge Planes & Giacomo Bernardi
Oceanographic features influence the transport and delivery of marine larvae, and physical retention mechanisms, such as eddies, can enhance self-recruitment (i.e. the return of larvae to their natal population). Knowledge of exact locations of hatching (origin) and settlement (arrival) of larvae of reef animals provides a means to compare observed patterns of self-recruitment ‘connectivity’ with those expected from water circulation patterns. Using parentage inference based on multiple sampling years in Moorea, French Polynesia, we describe...

Data from: Cascading effects of defaunation on the coexistence of two specialized insect seed predators

Guille Peguero, Helene C. Muller-Landau, Patrick A. Jansen & S. Joseph Wright
Identification of the mechanisms enabling stable coexistence of species with similar resource requirements is a central challenge in ecology. Such coexistence can be facilitated by species at higher trophic levels through complex multi-trophic interactions, a mechanism that could be compromised by ongoing defaunation. We investigated cascading effects of defaunation on Pachymerus cardo and Speciomerus giganteus, the specialized insect seed predators of the Neotropical palm Attalea butyracea, testing the hypothesis that vertebrate frugivores and granivores facilitate...

Data from: Genetic variation of loci potentially under selection confounds species-genetic diversity correlations in a fragmented habitat

Angeline Bertin, Nicolas Gouin, Alex Baumel, Ernesto Gianoli, Juan Serratosa, Rodomiro Osorio & Stéphanie Manel
Positive species-genetic diversity correlations (SGDCs) are often thought to result from the parallel influence of neutral processes on genetic and species diversity. Yet, confounding effects of non-neutral mechanisms have not been explored. Here, we investigate the impact of non-neutral genetic diversity on SGDCs in high Andean wetlands. We compare correlations between plant species diversity (SD) and genetic diversity (GD) calculated with and without loci potentially under selection (outlier loci). The study system includes 2188 specimens...

Data from: Modification of plant-induced responses by an insect ecosystem engineer influences the colonization behaviour of subsequent shelter-users

Akane Uesugi, Kimberly Morrell, Erik H. Poelman, Ciska E. Raaijmakers & André Kessler
Herbivores that modify plant morphology, such as gall forming insects, can disproportionately impact arthropod community on their host plants by providing novel habitats and shelters from biotic and abiotic stresses. These ecosystem engineers could also modify plant chemical properties, but how such changes in plant quality affect the behaviour of subsequent colonizers has rarely been investigated. We explored how an initial infestation of the tall goldenrod (Solidago altissima) by an ecosystem engineer, the rosette gall-midge...

Data from: Adaptation to abiotic conditions drives local adaptation in bacteria and viruses coevolving in heterogeneous environments

Florien A. Gorter, Pauline D. Scanlan & Angus Buckling
Parasite local adaptation, the greater performance of parasites on their local compared with foreign hosts, has important consequences for the maintenance of diversity and epidemiology. While the abiotic environment may significantly affect local adaptation, most studies to date have failed either to incorporate the effects of the abiotic environment, or to separate them from those of the biotic environment. Here, we tease apart biotic and abiotic components of local adaptation using the bacterium Pseudomonas fluorescens...

Data from: Fine-scale spatial genetic structure in the frankincense tree Boswellia papyrifera (Del.) Hochst. and implications for conservation

A. B. Addisalem, Jérôme Duminil, Doret Wouters, Frans Bongers & Marinus J. M. Smulders
The fine-scale genetic structure and how it varies between generations depends on the spatial scale of gene dispersal and other fundamental aspects of species’ biology, such as the mating system. Such knowledge is crucial for the design of genetic conservation strategies. This is particularly relevant for species that are increasingly fragmented such as Boswellia papyrifera. This species occurs in dry tropical forests from Ethiopia, Eritrea and Sudan and is an important source of frankincense, a...

Data from: Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing

Nathalie Smitz, Pim Van Hooft, Rasmus Heller, Daniel Cornélis, Philippe Chardonnet, Robert Kraus, Ben J. Greyling, Richard Crooijmans, Martien Groenen, Johan Michaux & Ben Greyling
This study aimed to develop a set of SNP markers with high resolution and accuracy within the African buffalo. Such a set can be used, among others, to depict subtle population genetic structure for a better understanding of buffalo population dynamics. In total, 18.5 million DNA sequences of 76 bp were generated by next generation sequencing on an Illumina Genome Analyzer II from a reduced representation library using DNA from a panel of 13 African...

Data from: De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens

Daniel Blande, Pauliina Halimaa, Arja I. Tervahauta, Mark G. M. Aarts & Sirpa O. Kärenlampi
Noccaea caerulescens of the Brassicaceae family has become the key model plant among the metal hyperaccumulator plants. Populations/accessions of N. caerulescens from geographic locations with different soil metal concentrations differ in their ability to hyperaccumulate and hypertolerate metals. Comparison of transcriptomes in several accessions provides candidates for detailed exploration of the mechanisms of metal accumulation and tolerance and local adaptation. This can have implications in the development of plants for phytoremediation and improved mineral nutrition....

Data from: Species interactions increase the temporal stability of community productivity in Pinus sylvestris-Fagus sylvatica mixtures across Europe

Miren Del Río, Hans Pretzsch, Ricardo Ruiz-Peinado, Evy Ampoorter, Peter Annighöfer, Ignacio Barbeito, Kamil Bielak, Gediminas Brazaitis, Lluis Coll, Lars össler, Marek Fabrika, David I. Forrester, Michael Heym, Václav Hurt, Viktor Kurylyak, Magnus Löf, Fabio Lombardi, Ekaterina Makrickiene, Bratislav Matovic, Frits Mohren, Renzo Motta, Jan Den Ouden, Maciej Pach, Quentin Ponette, Gerhard Schütze … & Lars Drössler
1.There is increasing evidence that species diversity enhances the temporal stability of community productivity in different ecosystems, although its effect at population and tree levels seems to be negative or neutral. Asynchrony in species responses to environmental conditions was found to be one of the main drivers of this stabilizing process. However, the effect of species mixing on the stability of productivity, and the relative importance of the associated mechanisms, remain poorly understood in forest...

Data from: Compatible and incompatible pathogen-plant interactions differentially affect plant volatile emissions and the attraction of parasitoid wasps

Camille Ponzio, Berhane T. Weldegergis, Marcel Dicke & Rieta Gols
The effects of multiple insect attacks on herbivore-induced plant volatiles and carnivorous arthropods are increasingly studied. Phytopathogens also represent an important threat to plants, and plant defense strategies against pathogens and insects are strongly interconnected, yet the potential impact of pathogens on insect-induced volatiles has been largely overlooked, and degree of pathogenicity rarely considered. We investigated how pathogen challenge, with virulent and avirulent strains of Xanthomonas campestris either alone or with simultaneous Pieris brassicae caterpillar...

Data from: Aboveground mammal and invertebrate exclusions cause consistent changes in soil food webs of two subalpine grassland types, but mechanisms are system-specific

Martijn L. Vandegehuchte, Wim H. Van Der Putten, Henk Duyts, Martin Schütz & Anita C. Risch
Ungulates, smaller mammals, and invertebrates can each affect soil biota through their influence on vegetation and soil characteristics. However, direct and indirect effects of the aboveground biota on soil food webs remain to be unraveled. We assessed effects of progressively excluding aboveground large-, medium- and small-sized mammals as well as invertebrates on soil nematode diversity and feeding type abundances in two subalpine grassland types: short- and tall-grass vegetation. We explored pathways that link exclusions of...

Data from: Faunal community consequence of interspecific bark trait dissimilarity in early-stage decomposing logs

Juan Zuo, Matty Berg, Roy Klein, Jasper Nusselder, Gert Neurink, Orsi Decker, Mariet M. Hefting, Ute Sass-Klaassen, Richard S. P. Van Logtestijn, Leo Goudzwaard, Jurgen Van Hal, Frank J. Sterck, Lourens Poorter, Johannes H. C. Cornelissen & Matty P. Berg
Dead tree trunks have significant ecosystem functions related to biodiversity and biogeochemical cycles. When lying on the soil surface, they are colonized by an array of invertebrate fauna, but what determines their community composition is still unclear. We apply community assembly theory to colonization of tree logs by invertebrates. During early decomposition, the attached bark is critically important as an environment filter for community assembly through habitat provision. Specifically, we hypothesized that the more dissimilar...

Data from: Plant quantity affects development and survival of a gregarious insect herbivore and its endoparasitoid wasp

Minghui Fei, Rieta Gols, Feng Zhu & Jeffrey A. Harvey
Virtually all studies of plant-herbivore-natural enemy interactions focus on plant quality as the major constraint on development and survival. However, for many gregarious feeding insect herbivores that feed on small or ephemeral plants, the quantity of resources is much more limiting, yet this area has received virtually no attention. Here, in both lab and semi-field experiments using tents containing variably sized clusters of food plants, we studied the effects of periodic food deprivation in a...

Data from: Modeling winter moth Operophtera brumata egg phenology: nonlinear effects of temperature and developmental stage on developmental rate

Lucia Salis, Marjolein Lof, Margriet Van Asch & Marcel E. Visser
Understanding the relationship between an insect's developmental rate and temperature is crucial to forecast insect phenology under climate change. In the winter moth Operophtera brumata timing of egg-hatching has severe fitness consequences on growth and reproduction as egg-hatching has to match bud burst of the host tree. In the winter moth, as in many insect species, egg development is strongly affected by ambient temperatures. Here we use laboratory experiments to show for the first time...

Data from: Does biomass growth increase in the largest trees? Flaws, fallacies and alternative analyses

Douglas Sheil, Chris S. Eastaugh, Mart Vlam, Pieter A. Zuidema, Peter Groenendijk, Peter Van Der Sleen, Alex Jay & Jerome Vanclay
The long-standing view that biomass growth in trees typically follows a rise-and-fall unimodal pattern has been challenged by studies concluding that biomass growth increases with size even among the largest stems in both closed forests and in open competition-free environments. We highlight challenges and pitfalls that influence such interpretations. The ability to observe and calibrate biomass change in large stems requires adequate data regarding these specific stems. Data checking and control procedures can bias estimates...

Data from: Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle

Maulik R. Upadhyay, Wei Chen, Johannes A. Lenstra, C. R. J. Goderie, David E. MacHugh, Stephen D. E. Park, David A. Magee, Donato Matassino, Ferdinando Ciani, Hendrik-Jan Megens, J. A. M. Van Arendonk, Martien A. M. Groenen, European Cattle Genetic Diversity Consortium & Richard P. M. A. Crooijmans
The domestication of taurine cattle initiated ~10 000 years ago in the Near East from a wild aurochs (Bos primigenius) population followed by their dispersal through migration of agriculturalists to Europe. Although gene flow from wild aurochs still present at the time of this early dispersion is still debated, some of the extant primitive cattle populations are believed to possess the aurochs-like primitive features. In this study, we use genome-wide single nucleotide polymorphisms to assess...

Data from: DISCOMARK: nuclear marker discovery from orthologous sequences using draft genome data

Sereina Rutschmann, Harald Detering, Sabrina Simon, Jakob Fredslund & Michael T. Monaghan
High-throughput sequencing has laid the foundation for fast and cost-effective development of phylogenetic markers. Here we present the program discomark, which streamlines the development of nuclear DNA (nDNA) markers from whole-genome (or whole-transcriptome) sequencing data, combining local alignment, alignment trimming, reference mapping and primer design based on multiple sequence alignments to design primer pairs from input orthologous sequences. To demonstrate the suitability of discomark, we designed markers for two groups of species, one consisting of...

Data from: Distribution of the invasive Caprella mutica Schurin, 1935 and native Caprella linearis (Linnaeus, 1767) on artificial hard substrates in the North Sea: separation by habitat

Joop W.P. Coolen, Wouter Lengkeek, Steven Degraer, Francis Kerckhof, Roger J. Kirkwood, Han J. Lindeboom & Han Lindeboom
Studying offshore natural and artificial hard substrates in the southern North Sea (51ºN–57ºN/1ºW–9ºE), the invasive introduced Japanese skeleton shrimp Caprella mutica Schurin, 1935 was found to co-exist with the native Caprella linearis (Linnaeus, 1767) only on near-shore locations that had an intertidal zone (e.g., wind farm foundations). In contrast, on far offshore and strictly subtidal locations, such as shipwrecks and rocky reefs, only C. linearis was found. Based on these exploratory observations, we hypothesised that...

Data from: Mek1 down regulates Rad51 activity during yeast meiosis by phosphorylation of Hed1

Tracy L. Callender, Raphaelle Laureau, Lihong Wan, Xiangyu Chen, Rima Sandhu, Saif Laljee, Sai Zhou, Ray T. Suhandynata, Evelyn Prugar, William A. Gaines, YoungHo Kwon, G. Valentin Börner, Alain Nicolas, Aaron M. Neiman & Nancy M. Hollingsworth
During meiosis, programmed double strand breaks (DSBs) are repaired preferentially between homologs to generate crossovers that promote proper chromosome segregation at Meiosis I. In many organisms, there are two strand exchange proteins, Rad51 and the meiosis-specific Dmc1, required for interhomolog (IH) bias. This bias requires the presence, but not the strand exchange activity of Rad51, while Dmc1 is responsible for the bulk of meiotic recombination. How these activities are regulated is less well established. In...

Data from: Endure and call for help: strategies of black mustard plants to deal with a specialised caterpillar

Dani Lucas-Barbosa, Marcel Dicke, Twan Kranenburg, Yavanna Aartsma, Teris A. Van Beek, Martinus E. Huigens & Joop J. A. Van Loon
Plants have evolved inducible resistance and tolerance mechanisms against insect herbivores. Resistance mechanisms that affect herbivorous insects directly can be effective against generalist herbivores, but will not deter specialist herbivores from attacking the plant. Tolerance mechanisms and indirect plant resistance are more likely effective strategies used by plants when dealing with specialist herbivores. However, inducible indirect resistance and tolerance mechanisms have rarely been investigated within the same study system. We studied multiple tolerance mechanisms and...

Data from: Can above-ground ecosystem services compensate for reduced fertilizer input and soil organic matter in annual crops?

Stijn Van Gils, Wim H. Van Der Putten & David Kleijn
Above-ground and below-ground environmental conditions influence crop yield by pollination, pest pressure, and resource supply. However, little is known about how interactions between these factors contribute to yield. Here, we used oilseed rape Brassica napus to test their effects on crop yield. We exposed potted plants to all combinations of high and low levels of soil organic matter (SOM) and fertilizer supply, and placed all treatments at a variety of field sites representing a gradient...

Data from: Conservative species drive biomass productivity in tropical dry forests

Jamir A. Prado Junior, Ivan Schiavini, Vagner S. Vale, Carolina S. Arantes, Masha T. Van Der Sande, Madelon Lohbeck, Lourens Poorter & Jamir A. Prado-Junior
1. Forests account for a substantial part of the terrestrial biomass storage and productivity. To better understand forest productivity we need to disentangle the processes underlying net biomass change. 2. We tested how above-ground net biomass change and its underlying biomass dynamics (biomass recruitment, growth, and mortality) can be explained by four alterative and contested hypotheses; the soil fertility, biomass ratio, niche complementarity and vegetation quantity hypotheses. 3. Above-ground biomass dynamics were evaluated over a...

Data from: Experimental evolution to increase the efficacy of the entomopathogenic fungus Beauveria bassiana against malaria mosquitoes: effects on mycelial growth and virulence

Claudio A. Valero-Jiménez, Jan A. L. Van Kan, Constantianus J. M. Koenraadt, Bas J. Zwaan & Sijmen E. Schoustra
Entomopathogenic fungi such as Beauveria bassiana are currently considered as a potential control agent for malaria mosquitoes. The success of such strategies depends among others on the efficacy of the fungus to kill its hosts. As B. bassiana can use various resources for growth and reproduction, increasing the dependency on mosquitoes as a nutritional source may be instrumental for reaching this goal. Passage of entomopathogenic fungi through an insect host has been shown to increase...

Data from: Above and belowground responses of four tundra plant functional types to deep soil heating and surface soil fertilization

Peng Wang, Juul Limpens, Liesje Mommer, Jasper Van Ruijven, Ake L. Nauta, Frank Berendse, Gabriela Schaepman-Strub, Daan Blok, Trofim C. Maximov, Monique M. P. D. Heijmans & Monique M.P.D. Heijmans
1.Climate warming is faster in the Arctic than the global average. Nutrient availability in the tundra soil is expected to increase by climate warming through 1) accelerated nutrient mobilization in the surface soil layers, and 2) increased thawing depths during the growing season which increases accessibility of nutrients in the deeper soil layers. Both processes may initiate shifts in tundra vegetation composition. It is important to understand the effects of these two processes on tundra...

Registration Year

  • 2016

Resource Types

  • Dataset


  • Wageningen University & Research
  • Nederlands Instituut voor Ecologie
  • VU University Amsterdam
  • University of Novi Sad
  • Lund University
  • University of Groningen
  • PSL Research University
  • United States Department of Agriculture
  • University of Sao Paulo
  • Utrecht University