252 Works

Data from: WisecondorX: improved copy number detection for routine shallow whole-genome sequencing

Lennart Raman, Annelies Dheedene, Matthias De Smet, Jo Van Dorpe & Björn Menten
Shallow whole-genome sequencing to infer copy number alterations (CNAs) in the human genome is rapidly becoming the method par excellence for routine diagnostic use. Numerous tools exist to deduce aberrations from massive parallel sequencing data, yet most are optimized for research and often fail to redeem paramount needs in a clinical setting. Optimally, a read depth-based analytical software should be able to deal with single-end and low-coverage data—this to make sequencing costs feasible. Other important...

Data from: Spatially correlated extinctions select for less emigration but larger dispersal distances in the spider mite Tetranychus urticae

Emanuel A. Fronhofer, Jonas M. Stelz, Eva Lutz, Hans Joachim Poethke & Dries Bonte
Dispersal is a central process to almost all species on earth, as it connects spatially structured populations and thereby increases population persistence. Dispersal is subject to (rapid) evolution and local patch extinctions are an important selective force in this context. In contrast to the randomly distributed local extinctions considered in most theoretical studies, habitat fragmentation or other anthropogenic interventions will lead to spatially correlated extinction patterns. Under such conditions natural selection is thought to lead...

Data from: Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next generation sequencing

Gregory Neils Puncher, Alessia Cariani, Gregory E. Maes, Jeroen Van Houdt, Koen Herten, Rita Cannas, Naiara Rodriguez-Ezpeleta, Aitor Albaina, M. Andone Estonba, Molly Lutcavage, Alex Hanke, Jay Rooker, James S. Franks, Joseph M. Quattro, Gualtiero Basilone, Igaratza Fraile, Urtzi Laconcha, Nicolas Goñi, Ai Kimoto, A. David Macías, Francisco Alemany, Simeon Deguara, Salem W. Zgozi, Fulvio Garibaldi, Isik K. Oray … & Fausto Tinti
The Atlantic bluefin tuna is a highly migratory species emblematic of the challenges associated with shared fisheries management. In an effort to resolve the species’ stock dynamics, a genome-wide search for spatially informative single nucleotide polymorphisms (SNPs) was undertaken, by way of sequencing reduced representation libraries. An allele frequency approach to SNP discovery was used, combining the data of 555 larvae and young-of-the-year (LYOY) into pools representing major geographical areas and mapping against a newly...

Data from: Genetic patterns in Neotropical Magnolias (Magnoliaceae) using de novo developed microsatellite markers

Emily Veltjen, Pieter Asselman, Majela Hernández Rodríguez, Alejandro Palmarola Bejerano, Ernesto Testé Lozano, Luis Roberto González Torres, Paul Goetghebeur, Isabel Larridon & Marie-Stéphanie Samain
Conserving tree populations safeguards forests since they represent key elements of the ecosystem. The genetic characteristics underlying the evolutionary success of the tree growth form: high genetic diversity, extensive gene flow and strong species integrity, contribute to their survival in terms of adaptability. However, different biological and landscape contexts challenge these characteristics. This study employs 63 de novo developed microsatellite or SSR (Single Sequence Repeat) markers in different datasets of nine Neotropical Magnolia species. The...

Data from: An integrative approach to understanding the evolution and diversity of Copiapoa (Cactaceae), a threatened endemic Chilean genus from the Atacama Desert

Isabel Larridon, Helmut E. Walter, Pablo C. Guerrero, Milén Duarte, Mauricio A. Cisternas, Carol Peña Hernández, Kenneth Bauters, Pieter Asselman, Paul Goetghebeur & Marie-Stéphanie Samain
PREMISE OF THE STUDY: Species of the endemic Chilean cactus genus Copiapoa have cylindrical or (sub)globose stems that are solitary or form (large) clusters and typically yellow flowers. Many species are threatened with extinction. Despite being icons of the Atacama Desert and well loved by cactus enthusiasts, the evolution and diversity of Copiapoa has not yet been studied using a molecular approach. METHODS: Sequence data of three plastid DNA markers (rpl32-trnL, trnH-psbA, ycf1) of 39...

Data from: Mammalian herbivores affect leafhoppers associated with specific plant functional types at different timescales

Martijn L. Vandegehuchte, Valeria Trivellone, Martin Schütz, Jennifer Firn, Frederic De Schaetzen & Anita C. Risch
1. Theory predicts that mammalian herbivores affect the quantity and quality of plants on which they preferentially feed in the short term. In the longer term, they can promote either preferred or less preferred plants, depending on whether preferred plants are adapted or sensitive to grazing. Less clear are the short- and long-term responses of herbivorous insects to mammalian herbivory, and how these responses depend on the specific plants or plant functional types on which...

Data from: Epigenetic alterations and decreasing insecticide sensitivity of the Asian tiger mosquito Aedes albopictus

A. Oppold, A. Kreß, J. Vanden Bussche, J. B. Diogo, U. Kuch, J. Oehlmann, M. B. Vandegehuchte, R. Müller, M.B. Vandegehuchte & J.B. Diogo
A range of environmental factors, including chemicals, can affect epigenetic processes in organisms leading to variations in phenotype. Thus, epigenetics displays an important environmentally responsive element. The transgenerational impact of environmental stressors on DNA methylation and phenotype was the focus of this study. The influence of two known DNA methylation-changing agents, the phytoestrogen genistein and the fungicide vinclozolin, on the overall DNA methylation level in the Asian tiger mosquito Aedes albopictus was investigated. The experiment...

Data from: Maternal exposure to predator scents: offspring phenotypic adjustment and dispersal

Elvire Bestion, Aimeric Teyssier, Fabien Aubret, Jean Clobert & Julien Cote
Predation is a strong selective pressure generating morphological, physiological and behavioural responses in organisms. As predation risk is often higher during juvenile stages, antipredator defences expressed early in life are paramount to survival. Maternal effects are an efficient pathway to produce such defences. We investigated whether maternal exposure to predator cues during gestation affected juvenile morphology, behaviour and dispersal in common lizards (Zootoca vivipara). We exposed 21 gravid females to saurophagous snake cues for one...

Data from: The influence of balanced and imbalanced resource supply on biodiversity-functioning relationship across ecosystems

Aleksandra M. Lewandowska, Antje Biermann, Elizabeth T. Borer, Miguel A. Cebrian-Piqueras, Steven A. J. Declerck, Luc De Meester, Ellen Van Donk, Lars Gamfeldt, Daniel S. Gruner, Nicole Hagenah, W. Stanley Harpole, Kevin P. Kirkman, Christopher A. Klausmeier, Michael Kleyer, Johannes M. H. Knops, Pieter Lemmens, Eric M. Lind, Elena Litchman, Jasmin Mantilla-Contreras, Koen Martens, Sandra Meier, Vanessa Minden, Joslin L. Moore, Harry Olde Venterink, Eric W. Seabloom … & Helmut Hillebrand
Numerous studies show that increasing species richness leads to higher ecosystem productivity. This effect is often attributed to more efficient portioning of multiple resources in communities with higher numbers of competing species, indicating the role of resource supply and stoichiometry for biodiversity–ecosystem functioning relationships. Here, we merged theory on ecological stoichiometry with a framework of biodiversity–ecosystem functioning to understand how resource use transfers into primary production. We applied a structural equation model to define patterns...

Data from: microCT-based phenomics in the zebrafish skeleton reveals virtues of deep phenotyping in a distributed organ system

Matthew Hur, Charlotte A. Gistelinck, Philippe Huber, Jane Lee, Marjorie H. Thompson, Adrian T. Monstad-Rios, Claire J. Watson, Sarah K. McMenamin, Andy Willaert, David M. Parichy, Paul Coucke & Ronald Y. Kwon
Phenomics, which ideally involves in-depth phenotyping at the whole-organism scale, may enhance our functional understanding of genetic variation. Here, we demonstrate methods to profile hundreds of phenotypic measures comprised of morphological and densitometric traits at a large number of sites within the axial skeleton of adult zebrafish. We show the potential for vertebral patterns to confer heightened sensitivity, with similar specificity, in discriminating mutant populations compared to analyzing individual vertebrae in isolation. We identify phenotypes...

Data from: Using archived television video footage to quantify phenology responses to climate change

Pieter De Frenne, Lisa Van Langenhove, Alain Vandriessche, Cedric Bertrand, Kris Verheyen & Pieter Vangansbeke
Predicting how the timing of cyclic life‐history events, such as leafing and flowering, respond to climate change is of paramount importance due to the cascading impacts of vegetation phenology on species and ecosystem fitness. However, progress of this field is hampered by the relative scarcity, and geographic and phylogenetic bias, of long‐term phenology datasets. By taking advantage of archived television video footage, we here developed an innovative tool using previously unexploited records to build long‐term...

Data from: A prioritised list of invasive alien species to assist the effective implementation of EU legislation

Carles Carboneras, Piero Genovesi, Montserrat Vila, Tim Blackburn, Martina Carrete, Miguel Clavero, Bram D'hondt, Jorge F. Orueta, Belinda Gallardo, Pedro Geraldes, Pablo González-Moreno, Richard D. Gregory, Wolfgang Nentwig, Jean-Yves Paquet, Petr Pysek, Wolfgang Rabitsch, Iván Ramírez, Riccardo Scalera, Jose Tella, Paul Walton, Robin Wynde & Tim M. Blackburn
1. Effective prevention and control of invasive species generally relies on a comprehensive, coherent and representative list of species that enables resources to be used optimally. European Union (EU) Regulation 1143/2014 on invasive alien species (IAS) aims to control or eradicate priority species, and to manage pathways to prevent the introduction and establishment of new IAS; it applies to species considered of Union concern and subject to formal risk assessment. So far, 49 species have...

Data from: Genotypic diversity and differentiation among populations of two benthic freshwater diatoms as revealed by microsatellites

Pieter Vanormelingen, Katharine M. Evans, David G. Mann, Stacey Lance, Ann-Eline Debeer, Sofie D'Hondt, Tine Verstraete, Luc De Meester & Wim Vyverman
Given their large population sizes and presumed high dispersal capacity, protists are expected to exhibit homogeneous population structure over large spatial scales. On the other hand, the fragmented and short-lived nature of the lentic freshwater habitats that many protists inhabit promotes strong population differentiation. We used microsatellites in two benthic freshwater diatoms, Eunotia bilunaris ‘robust’ and Sellaphora capitata, sampled from within a pond and connected ponds, through isolated ponds from the same region to western...

Data from: Urbanization-driven changes in web-building and body size in an orb-web spider

Maxime Dahirel, Maarten De Cock, Pieter Vantieghem & Dries Bonte
1. In animals, behavioural responses may play an important role in determining population persistence in the face of environmental changes. Body size is a key trait central to many life history traits and behaviours. Correlations with body size may constrain behavioural variation in response to environmental changes, especially when size itself is influenced by environmental conditions. 2. Urbanization is an important human-induced rapid environmental change that imposes multiple selection pressures on both body size and...

Data from: Covert deformed wing virus infections have long-term deleterious effects on honeybee foraging and survival

Kristof Benaets, Anneleen Van Geystelen, Dries Cardoen, Lina De Smet, Dirk C. De Graaf, Liliane Schoofs, Maarten H.D. Larmuseau, Laura E. Brettell, Stephen J. Martin, Tom Wenseleers & Maarten H. D. Larmuseau
Several studies have suggested that covert stressors can contribute to bee colony declines. Here we provide a novel case study and show using radiofrequency identification tracking technology that covert deformed wing virus (DWV) infections in adult honeybee workers seriously impact long-term foraging and survival under natural foraging conditions. In particular, our experiments show that adult workers injected with low doses of DWV experienced increased mortality rates, that DWV caused workers to start foraging at a...

Data from: Genetic signature of population fragmentation varies with mobility in seven bird species of a fragmented Kenyan cloud forest

Tom Callens, Peter Galbusera, Erik Matthysen, Eric Y Durand, Mwangi Githiru, Jeroen R Huyghe & Luc Lens
Habitat fragmentation can restrict geneflow, reduce neighbourhood effective population size, and increase genetic drift and inbreeding in small, isolated habitat remnants. The extent to which habitat fragmentation leads to population fragmentation, however, differs among landscapes and taxa. Commonly, researchers use information on the current status of a species to predict population effects of habitat fragmentation. Such methods, however, do not convey information on species-specific responses to fragmentation. Here we compare levels of past population differentiation,...

Data from: Dispersal constraints for the conservation of the grassland herb Thymus pulegioides L. in a highly fragmented agricultural landscape

An Vanden Broeck, Tobias Ceulemans, Gunter Kathagen, Maurice Hoffmann, Olivier Honnay & Joachim Mergeay
Species-rich grassland communities are one of the most important habitats for biodiversity and of high conservation priority in Europe. Restoration actions are mainly focused on the improvement of abiotic conditions, such as nutrient depletion techniques, and are generally based on the assumption that the target community will re-establish at the restored site when the target species exist in the neighborhood. Information on the contemporary seed-dispersal range is therefore crucial to develop effective conservation measures. Here,...

Saturated solute transport micro-CT dataset in Savonnières limestone

Stefanie Van Offenwert, Tom Bultreys, Marijn Boone & Veerle Cnudde

Speech Disfluencies as Actual and Believed Cues to Deception: Individuality of Liars and the Collective of Listeners

Nette Vandenhouwe & Robert J. Hartsuiker
There is no consensus about the relationship between disfluencies and deception in speech production. However, it is well established that listeners believe deceptive speech to contain more disfluencies than truthful speech. Here, we used an interactive game to collect the speech of liars and the veracity decisions of listeners. Using Multivariate Pattern Analysis (MVPA), we determined the predictive value of speech disfluencies as both actual and believed cues to deception. We found that patterns of...

Disfluency patterns in Alzheimer’s disease and Frontotemporal lobar degeneration

Aurélie Pistono, Marie Rafiq, Jérémie Pariente & Mélanie Jucla

Nitrogen and brine injected into Estaillades carbonate - steady-state experiments

Catherine Spurin, Samuel Krevor, Martin Blunt & Tom Bultreys
This data is micro-CT images of the simultaneous injection of nitrogen and brine into a porous carbonate rock (Estaillades). The images were acquired during steady-state, which was deduced from a plateau in the differential pressure across the sample. The experiments were conducted in the capillary dominated regime (the total flow rate was kept constant, with the fractional flow (fw) changed in sequence 0.85fw, 0.7fw, 0.5fw, 0.25fw, 0.03fw, 0fw). There is the high Ca experiment where...

Time-Varying Effects of Oil Supply Shocks on the U.S. Economy

Baumeister Christiane & Gert Peersman
We use vector autoregressions with drifting coefficients and stochastic volatility to investigate how the dynamic effects of oil supply shocks on the U.S. economy have changed over time. We find a substantial decline in the short-run price elasticity of oil demand since the mid-eighties. This finding helps explain why an oil production shortfall of the same magnitude is associated with a stronger response of oil prices and more severe macroeconomic consequences over time, while an...

Data from: Low genetic diversity despite multiple introductions of the invasive plant species Impatiens glandulifera in Europe

Jenny Hagenblad, Jennifer Hülskötter, Kamal Prasad Acharya, Jörg Brunet, Olivier Chabrerie, Sara A. O. Cousins, Pervaiz A. Dar, Martin Diekmann, Pieter De Frenne, Martin Hermy, Aurélien Jamoneau, Annette Kolb, Isgard Lemke, Jan Plue, Zafar A. Reshi & Bente Jessen Graae
Background: Invasive species can be a major threat to native biodiversity and the number of invasive plant species is increasing across the globe. Population genetic studies of invasive species can provide key insights into their invasion history and ensuing evolution, but also for their control. Here we genetically characterise populations of Impatiens glandulifera, an invasive plant in Europe that can have a major impact on native plant communities. We compared populations from the species’ native...

Data from: Kinematics of chisel-tooth digging by African mole-rats

Sam Van Wassenbergh, Stef Heindryckx & Dominique Adriaens
Mole-rats are known to use their protruding, chisel-like incisors to dig underground networks of tunnels, but it remains unknown how these incisors are used to break and displace the soil. Theoretically, different excavation strategies can be used. Mole-rats could either use their head depressor muscles to power scooping motions of the upper incisors (by nose-down head rotations) or the lower incisors (by nose-up head rotations), or their jaw adductors to grab and break the soil...

Data from: Contributions of feather microstructure to eider down insulation properties

Liliana D'Alba, Thomas Holm Carlsen, Árni Ásgeirsson, Matthew D. Shawkey & Jon Einar Jonsson
Insulation is an essential component of nest structure that helps provide incubation requirements for birds. Many species of waterfowl breed in high latitudes where rapid heat loss can necessitate a high energetic input from parents and use down feathers to line their nests. Common eider Somateria mollissima nest down has exceptional insulating properties but the microstructural mechanisms behind the feather properties have not been thoroughly examined. Here, we hypothesized that insulating properties of nest down...

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