25 Works

Reciprocal cybrids reveal how organellar genomes affect plant phenotypes

Tom Theeuwen, Pádraic Flood, Korbinian Schneeberger, Paul Keizer, Willem Kruijer, Edouard Severing, Evangelos Kouklas, Jos Hageman, Raúl Wijfjes, Vanessa Calvo-Baltanas, Frank Becker, Sabine Schnabel, Leo Willems, Wilco Ligterink, Jeroen Van Arkel, Roland Mumm, José Gualberto, Linda Savage, David Kramer, Joost Keurentjes, Fred Van Eeuwijk, Maarten Koornneef, Jeremy Harbinson, Mark Aarts & Erik Wijnker
Assessing the impact of variation in chloroplast and mitochondrial DNA (collectively termed the plasmotype) on plant phenotypes is challenging due to the difficulty in separating their effect from nuclear derived variation (the nucleotype). Haploid inducer lines can be used as efficient plasmotype donors to generate new plasmotype-nucleotype combinations (cybrids). We generated a panel comprising all possible cybrids of seven Arabidopsis thaliana accessions and extensively phenotyped these lines for 1859 phenotypes under stable and fluctuating conditions....

Data from: Warming enhances sedimentation and decomposition of organic carbon in shallow macrophyte-dominated systems with zero net effect on carbon burial

Mandy Velthuis, Sarian Kosten, Ralf Aben, Garabet Kazanjian, Sabine Hilt, Edwin T. H. M. Peeters, Ellen Van Donk & Elisabeth S. Bakker
Temperatures have been rising throughout recent decades and are predicted to rise further in the coming century. Global warming affects carbon cycling in freshwater ecosystems, which both emit and bury substantial amounts of carbon on a global scale. Currently, most studies focus on the effect of warming on overall carbon emissions from freshwater ecosystems, while net effects on carbon budgets may strongly depend on burial in sediments. Here, we tested whether year‐round warming increases the...

Data from: Coasting in live-bearing fish: the drag penalty of being pregnant

Elsa M. Quicazan-Rubio, Johan L. Van Leeuwen, Klaas Van Manen, Mike Fleuren, Bart J. A. Pollux & Eize J. Stamhuis
Swimming performance of pregnant live-bearing fish is presumably constrained by the additional drag associated with the reproductive burden. Yet, it is still unclear how and to what extent the reproductive investment affects body drag of the females. We examined the effect of different levels of reproductive investment on body drag. The biggest measured increase in body volume due to pregnancy was about 43%, linked to a wetted area increase of about 16% and 69% for...

Immuno-competence data

Asmoro Lelono, Diana Robledo-Ruiz, Tom Berghof, Henk Parmentier, Bernd Riestra & Ton Groothuis
The exposure of yolk androgens can positively stimulate chick growth and competitive ability but may negatively affect immunity. It has been hypothesized that only chicks from immunologically superior fathers can bear the cost of prenatal exposure to high androgen levels. To test this hypothesis we paired roosters from two selection lines, one up- and one down-selected for natural antibodies, with hens from a control line. We measured yolk testosterone and androstenedione levels, and we injected...

The percentage of total agricultural area under maize, rice, wheat, vegetables, pulses and fruit production, by country, subject to water scarcity in 2050 as estimated from a multi-model ensemble

N. Fitton, P. Alexander, N. Arnell, B. Bajzelj, K. Calvin, J. Doelman, J.S. Gerber, P. Havlik, T. Hasegawa, M. Herrero, T. Krisztin, H. Van Meijl, T. Powell, R. Sands, E. Stehfest, P.C. West & P. Smith
Projections of global changes in water scarcity with the current extent of maize, rice, wheat, vegetables, pulses and fruit production commodities were combined to identify the potential country level vulnerabilities of cropland land to water scarcity in 2050. The data relate to an analysis of the impact changes in water availability will have on maize, rice, wheat, vegetables, pulses and fruit production commodities availability in 2050.

Data from: Stiffness gradients facilitate ovipositor bending and spatial probing control in a parasitic wasp

Uroš Cerkvenik, Johan L. Van Leeuwen, Alexander Kovalev, Stanislav N. Gorb, Yoko Matsumura & Sander W. S. Gussekloo
Many parasitic wasps use slender and steerable ovipositors to lay eggs in hosts hidden in substrates, but it is currently unknown how steering is achieved. The ovipositors generally consist of three longitudinally connected elements, one dorsal and two ventral valves that can slide along each other. For the parasitic wasp Diachasmimorpha longicaudata, it has been shown that protraction of the ventral valves causes incurving of the ventral valves towards the dorsal one, which results in...

Transparent experiments: releasing data from mechanical tests on three dimensional hydrogel sphere packings

Jonathan Barés, Nicolas Brodu, Hu Zheng & Joshua Dijksman
We describe here experiments on the mechanics of hydrogel particle packings from the Behringer lab, performed between 2012 and 2015. These experiments quantify the evolution of all contact forces inside soft particle packings exposed to compression, shear, and the intrusion of a large intruder. The experimental set-ups and processes are presented and the data are concomitantly published in a repository.

No evidence for an adaptive role of early molt into breeding plumage in a female fairy-wren

Sergio Nolazco, Michelle L. Hall, Sjouke A. Kingma, Kaspar Delhey & Anne Peters
The evolution of ornaments as sexually selected signals is well understood in males, but female ornamentation remains understudied. Fairy-wrens offer an excellent model system, given their complex social structure and mating systems, and the diversity of female ornamentation. We investigated whether early molt into ornamental breeding plumage plays an adaptive role in females of the monogamous purple-crowned fairy-wren Malurus coronatus, the only fairy-wren known to have female seasonal plumage. Using six years of monitoring, we...

Data from: Old World and New World Phasmatodea: phylogenomics resolve the evolutionary history of stick and leaf insects

Sabrina Simon, Harald Letsch, Sarah Bank, Thomas R. Buckley, Alexander Donath, Shanlin Liu, Ryuichiro Machida, Karen Meusemann, Bernhard Misof, Lars Podsiadlowski, Xin Zhou, Benjamin Wipfler & Sven Bradler
Phasmatodea comprises over 3,000 extant species and stands out as one of the last remaining insect orders for which a robust, higher-level phylogenetic hypothesis is lacking. New research suggests that the extant diversity is the result of a surprisingly recent and rapid radiation that has been difficult to resolve with standard Sanger sequence data. In order to resolve the early branching events of stick and leaf insects, we analyzed transcriptomes from 61 species, including 38...

Data from: Genetic diversity of Nile tilapia (Oreochromis niloticus) throughout West Africa

Curtis Lind, Seth Agyakwah, Felix Attipoe, Christopher Nugent, Richard Crooijmans & Aboubacar Toguyeni
Nile tilapia (Oreochromis niloticus) is a globally significant aquaculture species rapidly gaining status as a farmed commodity. In West Africa, wild Nile tilapia genetic resources are abundant yet knowledge of fine-scale population structure and patterns of natural genetic variation are limited. Coinciding with this is a burgeoning growth in tilapia aquaculture in Ghana and other countries within the region underpinned by locally available genetic resources. Using 192 single nucleotide polymorphism (SNP) markers this study conducted...

Future of the human climate niche

Chi Xu, Timothy Kohler, Timothy Lenton, Jens-Christian Svenning & Marten Scheffer
All species have an environmental niche, and despite technological advances, humans are unlikely to be an exception. Here, we demonstrate that for millennia, human populations have resided in the same narrow part of the climatic envelope available on the globe, characterized by a major mode around ∼11 °C to 15 °C mean annual temperature (MAT). Supporting the fundamental nature of this temperature niche, current production of crops and livestock is largely limited to the same...

Data from: Effects of landscape complexity on pollinators are moderated by pollinators’ association with mass-flowering crops

Thijs Fijen, Jeroen Scheper, Bastiaen Boekelo, Ivo Raemakers & David Kleijn
Conserving and restoring semi-natural habitat, i.e. enhancing landscape complexity, is one of the main strategies to mitigate pollinator decline in agricultural landscapes. However, we still have limited understanding of how landscape complexity shapes pollinator communities in both crop and non-crop habitat, and whether pollinator responses to landscape complexity vary with their association with mass-flowering crops. Here, we surveyed pollinator communities on mass-flowering leek crops and in nearby semi-natural habitat in landscapes of varying complexity. Surveys...

Data from: Disturbance regulates the density–body mass relationship of soil fauna

Frank Van Langevelde, Vincent Comor, Steven De Bie, Herbert Prins & Madhav Thakur
Theory on the density-body mass (DBM) relationship predicts that the density of animal species decreases by the power of −0.75 per unit increase in their body mass, or by the power of −1 when taxa across trophic levels are studied. This relationship is, however, largely debated as the slope often deviates from the theoretical predictions. Here, we tested the ability of the DBM relationship to reflect changes in the structure of communities subjected to an...

Data from: Combined transcriptome and metabolome analysis identifies defence responses in spider-mite infested pepper

Yuanyuan Zhang, Harro J. Bouwmeester & Iris F. Kappers
Plants regulate responses towards herbivory through fine-tuning of defence-related hormone production, expression of defence genes and production of secondary metabolites. Jasmonic acid (JA) plays a key role in plant-herbivorous arthropod interactions. To understand how pepper responds to herbivory, leaf transcriptomes and metabolomes of two genotypes different in their susceptibility to spider mites, were studied. Mites induced both JA and salicylic acid (SA) signalling. However, mite infestation and exogenous JA resulted in distinct transcriptome profiles. Compared...

Data from: A standardized assessment of forest mammal communities reveals consistent functional composition and vulnerability across the tropics

Francesco Rovero, Jorge Ahumada, Patrick Jansen, Douglas Sheil, Patricia Alvarez, Kelly Boekee, Santiago Espinosa, Marcela Lima, Emanuel Martin, Timothy O’Brien, Julia Salvador, Fernanda Santos, Melissa Rosa, Alexander Zvoleff, Chris Sutherland & Simone Tenan
Understanding global diversity patterns has benefitted from a focus on functional traits and how they relate to variation in environmental conditions among assemblages. Distant communities in similar environments often share characteristics, and for tropical forest mammals, this functional trait convergence has been demonstrated at coarse scales (110-200 km resolution), but less is known about how these patterns manifest at fine scales, where local processes (e.g., habitat features and anthropogenic activities) and biotic interactions occur. Here,...

Genomic relatedness and diversity of Swedish native cattle breeds

Maulik Upadhyay, Susanne Eriksson, Sofia Mikko, Erling Strandberg, Hans Stålhammar, Martien AM Groenen, Richard PMA Crooijmans, Göran Andersson & Anna M Johansson
Background Native cattle breeds are important genetic resources given their adaptation to the local environment in which they are bred. However, the widespread use of commercial cattle breeds has resulted in a marked reduction in population size of several native cattle breeds worldwide. Therefore, conservation management of native cattle breeds requires urgent attention to avoid their extinction. To this end, we genotyped nine Swedish native cattle breeds with genome-wide 150K single nucleotide polymorphisms (SNPs) to...

Data from: Soil functional responses to drought under range-expanding and native plant communities

Marta Manrubia, Wim Van Der Putten, Carolin Weser, Freddy Ten Hooven, Henk Martens, Pella Brinkman, Stefan Geisen, Kelly Ramirez & Ciska Veen
1. Current climate warming enables plant species and soil organisms to expand their range to higher latitudes and altitudes. At the same time, climate change increases the incidence of extreme weather events such as drought. While it is expected that plants and soil organisms originating from the south are better able to cope with drought, little is known about the consequences of their range shifts on soil functioning under drought events. 2. Here, we test...

Distinct genomic signals of lifespan and life history evolution in response to postponed reproduction and larval diet in Drosophila

Katja Hoedjes, Joost Van Den Heuvel, Martin Kapun, Laurent Keller, Thomas Flatt & Bas Zwaan
Reproduction and diet are two major factors controlling the physiology of aging and life history, but how they interact to affect the evolution of longevity is unknown. Moreover, while studies of large-effect mutants suggest an important role of nutrient sensing pathways in regulating aging, the genetic basis of evolutionary changes in lifespan remains poorly understood. To address these questions, we analyzed the genomes of experimentally evolved Drosophila melanogaster populations subjected to a factorial combination of...

Data from: Establishment of wildflower fields in poor quality landscapes enhances micro-parasite prevalence in wild bumble bees

Niels Piot, Ivan Meeus, David Kleijn, Jeroen Scheper, Theo Linders & Guy Smagghe
The current worldwide pollinator decline is caused by the interplay of different drivers. Several strategies have been undertaken to counteract or halt this decline, one of which is the implementation of wildflower fields. These supplementary flowers provide extra food resources and have proven their success in increasing pollinator biodiversity and abundance. Yet such landscape alterations could also alter the host–pathogen dynamics of pollinators, which could affect the populations. In this study, we investigated the influence...

Data from: Relevance of heterokaryosis for adaptation and azole-resistance development in Aspergillus fumigatus

Jianhua Zhang, Eveline E. Snelders, Bas J. Zwaan, Sijmen E. Schoustra, Ed J. Kuijper, Maiken C. Arendrup, Willem J.G. Melchers, Paul E. Verweij, Alfons J.M. Debets & Alfons J. M. Debets
Aspergillus fumigatus causes a range of diseases in humans, some of which are characterized by fungal persistence. A. fumigatus, being a generalist saprotroph, may initially establish lung colonisation due to its physiological versatility and subsequently adapt through genetic changes to the human lung environment and antifungal treatments. Human lung-adapted genotypes can arise by spontaneous mutation and/or recombination and subsequent selection of the fittest genotypes. Sexual and asexual spores are considered crucial contributors to the genetic...

Data from: Genetic differences among Cedrela odorata sites in Bolivia provide limited potential for fine-scale timber tracing

Kathelyn Paredes-Villanueva, G. Arjen De Groot, Ivo Laros, Jan Bovenschen, Frans Bongers & Pieter A. Zuidema
Illegal trade of tropical timber leads to biodiversity and economic losses worldwide. There is a need for forensic tools that allow tracing the origin of timber and verifying compliance with international and national regulations. We evaluated the potential for genetic tracing of Cedrela odorata, one of the most traded neotropical timbers, within Bolivia. Using a set of seven microsatellites (SSRs), we studied the spatial distribution and genetic diversity and tested whether populations show sufficient genetic...

Data from: An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea)

Dominic A. Evangelista, Benjamin Wipfler, Olivier Béthoux, Alexander Donath, Mari Fujita, Manpreet K. Kohli, Frédéric Legendre, Shanlin Liu, Ryuichiro Machida, Berhard Misof, Ralph Peters, Lars Podsiadlowski, Jes Rust, Kai Schuette, Ward Tollenaar, Jessica L. Ware, Torsten Wappler, Xin Zhou, Karen Meusemann & Sabrina Simon
READMEREADME of Supplementary Archives and included files of Evangelista et al. 2019Evangelista_et_al_README_DRYAD.pdfSupplementary Archive 1Files included in Supplementary Archive 1, see Evangelista_et_al_README_DRYAD.pdfSupplementary_Archive_1.zipSupplementary Archive 2Files included in Supplementary Archive 2, see Evangelista_et_al_README_DRYAD.pdfSupplementary_Archive_2.zip

Data from: Mechanics of composite hydrogels approaching phase separation

Xiufeng Li, Wolf Rombouts, Jasper Van Der Gucht, Renko De Vries & Joshua A. Dijksman
For polymer-particle composites, limited thermodynamic compatibility of polymers and particles often leads to poor dispersal and agglomeration of the particles in the matrix, which negatively impacts the mechanics of composites. To study the impact of particle compatibility in polymer matrices on the mechanical properties of composites, we here study composite silica- protein based hydrogels. The polymer used is a previously studied telechelic protein-based polymer with end groups that form triple helices, and the particles are...

Data from: Equivalence analysis to support environmental safety assessment: using nontarget organism count data from field trials with cisgenically modified potato

Hilko Van Der Voet, Paul W. Goedhart, Jenny Lazebnik, Geert J. T. Kessel, Ewen Mullins, Joop J. A. Van Loon & Salvatore Arpaia
This paper considers the statistical analysis of entomological count data from field experiments with genetically modified (GM) plants. Such trials are carried out to assess environmental safety. Potential effects on nontarget organisms (NTOs), as indicators of biodiversity, are investigated. The European Food Safety Authority (EFSA) gives broad guidance on the environmental risk assessment (ERA) of GM plants. Field experiments must contain suitable comparator crops as a benchmark for the assessment of designated endpoints. In this...

Data from: Superfetation reduces the negative effects of pregnancy on the fast-start escape performance in live-bearing fish

Mike Fleuren, Johan Van Leeuwen & Bart Pollux
Superfetation, the ability to simultaneously carry multiple litters of different developmental stages in utero, is a reproductive strategy that evolved repeatedly in viviparous animal lineages. The evolution of superfetation is hypothesized to reduce the reproductive burden and, consequently, improve the locomotor performance of the female during pregnancy. Here, we apply new computer-vision based techniques to study changes in body shape and three-dimensional fast-start escape performance during pregnancy in three livebearing fishes (family Poeciliidae) that exhibit...

Registration Year

  • 2019

Resource Types

  • Dataset


  • Wageningen University & Research
  • Nederlands Instituut voor Ecologie
  • Zoological Research Museum Alexander Koenig
  • University of Groningen
  • University of Tsukuba
  • Commonwealth Scientific and Industrial Research Organisation
  • University of Exeter
  • China Agricultural University
  • Autonomous University of San Luis Potosí
  • University of Massachusetts Amherst