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: Evidence for water-mediated mechanisms in coral–algal interactions

Hendrikje Jorissen, Christina Skinner, Ronald Osinga, Dirk De Beer & Maggy M. Nugues
Although many coral reefs have shifted from coral-to-algal dominance, the consequence of such a transition for coral–algal interactions and their underlying mechanisms remain poorly understood. At the microscale, it is unclear how diffusive boundary layers (DBLs) and surface oxygen concentrations at the coral–algal interface vary with algal competitors and competitiveness. Using field observations and microsensor measurements in a flow chamber, we show that coral (massive Porites) interfaces with thick turf algae, macroalgae, and cyanobacteria, which...

Data from: Drosophila clock is required in brain pacemaker neurons to prevent premature locomotor aging independently of its circadian function

Alexandra Vaccaro, Abdul-Raouf Issa, Laurent Seugnet, Serge Birman & André Klarsfeld
Circadian clocks control many self-sustained rhythms in physiology and behavior with approximately 24-hour periodicity. In many organisms, oxidative stress and aging negatively impact the circadian system and sleep. Conversely, loss of the clock decreases resistance to oxidative stress, and may reduce lifespan and speed up brain aging and neurodegeneration. Here we examined the effects of clock disruptions on locomotor aging and longevity in Drosophila. We found that lifespan was similarly reduced in three arrhythmic mutants...

Data from: The origin of floral organ identity quartets

Philip Ruelens, Zhicheng Zhang, Hilda Van Mourik, Steven Maere, Kerstin Kaufmann & Koen Geuten
The origin of flowers has puzzled plant biologists ever since Darwin referred to their sudden appearance in the fossil record as an abominable mystery. Flowers are considered to be an assembly of protective, attractive and reproductive male and female leaf-like organs. Their origin cannot be understood by a morphological comparison to gymnosperms, their closest relatives, which develop separate male or female cones. Despite these morphological differences, gymnosperms and angiosperms possess a similar genetic toolbox consisting...

Data from: Diminishing-returns epistasis among random beneficial mutations in a multicellular fungus

Sijmen Schoustra, Sungmin Hwang, Joachim Krug, J. Arjan G.M. De Visser & J. Arjan G. M. De Visser
Adaptive evolution ultimately is fuelled by mutations generating novel genetic variation. Non-additivity of fitness effects of mutations (called epistasis) may affect the dynamics and repeatability of adaptation. However, understanding the importance and implications of epistasis is hampered by the observation of substantial variation in patterns of epistasis across empirical studies. Interestingly, some recent studies report increasingly smaller benefits of beneficial mutations once genotypes become better adapted (called diminishing-returns epistasis) in unicellular microbes and single genes....

Data from: Origins of food crops connect countries worldwide

Colin K. Khoury, Harold A. Achicanoy, Anne D. Bjorkman, Carlos Navarro-Racines, Luigi Guarino, Ximena Flores-Palacios, Johannes M. M. Engels, John H. Wiersema, Hannes Dempewolf, Steven Sotelo, Julian Ramírez-Villegas, Nora P. Castañeda Álvarez, Cary Fowler, Andy Jarvis, Loren H. Rieseberg & Paul C. Struik
Research into the origins of food plants has led to the recognition that specific geographical regions around the world have been of particular importance to the development of agricultural crops. Yet the relative contributions of these different regions in the context of current food systems have not been quantified. Here we determine the origins (‘primary regions of diversity’) of the crops comprising the food supplies and agricultural production of countries worldwide. We estimate the degree...

Data from: The genome of the yellow potato cyst nematode Globodera rostochiensis reveals insights into the basis of parasitism and virulence

Sebastian Eves-Van Den Akker, Dominik Laetsch, Peter Thorpe, Catherine Lilley, Etienne Danchin, Martine Da Rocha, Corinne Rancurel, Nancy Holroyd, James Cotton, Amir Szitenberg, Eric Grenier, Josselin Montarry, Benjamin Mimee, Marc-Olivier Duceppe, Ian Boyes, Jessica Marvin, Laura Jones, Hazijah Yusup, Joël Lafond-Lapalme, Magali Esquibet, Michael Sabeh, Michael Rott, Hein Overmars, Anna Finkers-Tomczak, Geert Smant … & John Jones
Background: The yellow potato cyst nematode Globodera rostochiensis is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes effectors from pharyngeal glands, some of which were acquired by horizontal gene transfer, to manipulate host processes and promote parasitism. G. rostochiensis is classified into pathotypes with different plant resistance-breaking phenotypes. Results: We generate a high-quality genome assembly for G. rostochiensis pathotype Ro1, identify putative effectors and horizontal gene transfer events, map gene expression...

Data from: Rapid multiple-level coevolution in experimental populations of yeast killer and non-killer strains

Magdalena Pieczynska, Dominika Wloch-Salamon, Ryszard Korona, J. Arjan G.M. De Visser, Magdalena D. Pieczynska & J. Arjan G. M. De Visser
Coevolution between different biological entities is considered an important evolutionary mechanism at all levels of biological organization. Here we provide evidence for coevolution of a yeast killer strain (K) carrying cytoplasmic dsRNA viruses coding for anti-competitor toxins and an isogenic toxin-sensitive strain (S) during 500 generations of laboratory propagation. Signatures of coevolution developed at two levels. One of them was coadaptation of K and S. Killing ability of K first increased quickly and was followed...

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...

Registration Year

  • 2016
    50

Resource Types

  • Dataset
    50

Affiliations

  • Wageningen University & Research
    50
  • Nederlands Instituut voor Ecologie
    14
  • VU University Amsterdam
    2
  • University of Novi Sad
    2
  • Lund University
    2
  • University of Groningen
    2
  • PSL Research University
    2
  • United States Department of Agriculture
    2
  • University of Sao Paulo
    2
  • Utrecht University
    2