190 Works

Simultaneous genotyping of snails and infecting trematode parasites using high-throughput amplicon sequencing.

Cyril Hammoud, Stephen Mulero, Bert Van Bocxlaer, Jérôme Boissier, Dirk Verschuren, Christian Albrecht & Tine Huyse
Several methodological issues currently hamper the study of entire trematode communities within populations of their intermediate snail hosts. Here we develop a new workflow using high-throughput amplicon sequencing to simultaneously genotype snail hosts and their infecting trematode parasites. We designed primers to amplify 4 snail and 5 trematode markers in a single multiplex PCR. While also applicable to other genera, we focused on medically and economically important snail genera within the Superorder Hygrophila and targeted...

Data from: Alternative food sources interfere with removal of a fungal amphibian pathogen by zooplankton

Arne Deknock, Frank Pasmans, Robby Van Leeuwenberg, Sarah Van Praet, Stijn Bruneel, Luc Lens, Siska Croubels, An Martel & Peter Goethals
1. While the amphibian disease chytridiomycosis is causing ongoing population declines and biodiversity losses around the globe, efficient mitigation strategies are lacking. The free-living zoospores of the causative agents of this disease, the chytrid pathogens Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal), are a potential food source for filter-feeding micropredators as part of the aquatic food web. While consumption of zoospores can lower environmental pathogen loads, alternative food sources may interfere with pathogen removal rates....

Nematodes community composition and environmental parameters, Eastern Antarctic Peninsula

Gabriella Panto, Francesca Pasotti, Lara Macheriotou & Ann Vanreusel
This study provides a snapshot of the largely understudied meiobenthic and nematode communities in the Prince Gustav Channel and Duse Bay. We compared five stations sampled at different water depths along the shelf and investigated their meiobenthic community structure. We approached nematode biodiversity comparing traditional taxonomic identification and high throughput sequencing (HTS), with the use of Amplicon Sequence Variants (ASVs). Additionally, we characterized the environment by primary production proxies, grain size and seasonal ice conditions....

Caulerpa-associated bacterial 16S rRNA in response to environmental stress

Kathryn Morrissey
This dataset contains data from algal-associated bacteria from the green macroalgae, Caulerpa, from the paper " Morrissey, K.L. et al. (2021) Impacts of environmental stress on resistance and resilience of algal-associated bacterial communities. Ecology and Evolution". The experiment investigates the effects of a factorial combination of nutrient and temperature stress on the bacterial communities. We have also assessed the resistance and resilience of the algal-associated microbiota to environmental stress, using community dissimilarity metrics. Bacteria were...

Data from: A brief history and popularity of methods and tools used to estimate micro-evolutionary forces

Jonathan Kidner, Panagiotis Theodorou, Martin Husemann, Jan Engler & Martin Taubert
Population genetics is a field of research that predates the current generations of sequencing technology. Those approaches, that were established before massively parallel sequencing methods, have been adapted to these new marker systems (in some cases involving the development of new methods) that allow genome-wide estimates of the four major micro-evolutionary forces – mutation, gene flow, genetic drift and selection. Nevertheless, classic population genetic markers are still commonly used and a plethora of analysis methods...

Saturated solute transport micro-CT dataset in Savonnières limestone

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

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...

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: 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: 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: 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: 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: Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass

José L. Blanco-Pastor, Philippe Barre, Thomas Keep, Thomas Ledauphin, Abraham Escobar-Gutiérrez, Anna Maria Roschanski, Evelyn Willner, Klaus Dehmer, Matthew Hegarty, Hilde Muylle, Elisabeth Veeckman, Klaas Vandepoele, Tom Ruttink, Isabel Roldán-Ruiz, Stéphanie Manel & Jean-Paul Sampoux
Germplasm from perennial ryegrass (Lolium perenne L.) natural populations is useful for breeding because of its adaptation to a wide range of climates. Climate-adaptive genes can be detected from associations between genotype, phenotype and climate but an integrated framework for the analysis of these three sources of information is lacking. We used two approaches to identify adaptive loci in perennial ryegrass and their effect on phenotypic traits. First, we combined Genome-Environment Association (GEA) and GWAS...

Species-specific effects of thermal stress on the expression of genetic variation across a diverse group of plant and animal taxa under experimental conditions

Klaus Fischer, Jürgen Kreyling, Michaël Beaulieu, Ilka Beil, Manuela Bog, Dries Bonte, Stefanie Holm, Sabine Knoblauch, Dustin Koch, Lena Muffler, Pierick Mouginot, Maria Paulinich, J.F. Scheepens, Raijana Schiemann, Jonas Schmeddes, Martin Schnittler, Gabriele Uhl, Marieke Van Der Maaten-Theunissen, Julia M. Weier, Martin Wilmking, Robert Weigel & Phillip Gienapp
Assessing the genetic adaptive potential of populations and species is essential for better understanding evolutionary processes. However, the expression of genetic variation may depend on environmental conditions, which may speed up or slow down evolutionary responses. Thus, the same selection pressure may lead to different responses. Against this background, we here investigate the effects of thermal stress on genetic variation, mainly under controlled laboratory conditions. We estimated additive genetic variance (VA), narrow-sense heritability (h2), and...

Forest microclimate dynamics drive plant responses to warming

Florian Zellweger, Pieter De Frenne & David Coomes
Climate warming is causing a shift in biological communities in favor of warm-affinity species (i.e., thermophilisation). However, species responses often lag behind climate warming and local microclimates modulated by vegetation and topography are usually ignored. Here we analyze multidecadal understorey microclimate dynamics in European forests and show that thermophilisation and the climatic lag in forest plant communities are primarily controlled by microclimate. Increasing tree canopy cover reduces warming rates inside forests, but loss of canopy...

A metacommunity approach for detecting species influenced by mass effect

Thibault Leboucher, Juliette Tison-Rosebery, William R. Budnick, Aurélien Jamoneau, Wim Vyverman, Janne Soininen, Sébastien Boutry & Sophia I. Passy
1. Mass effect, allowing species to persist in unfavourable habitats, and dispersal limitation, preventing species from reaching favourable habitats, are the two major dispersal processes. While dispersal limitation can be detected by experimental or modeling techniques, mass effect is more challenging to evaluate, which hampers our ability to disentangle the influence of the environment vs. dispersal on species distribution. This is undesirable for biomonitoring programs built on known species-environment relationships. 2. We developed an approach...

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...

Chytrid Fungi and Nitrile Gloves Research Data

Valarie Thomas, Pascale Van Rooij, Celine Meerpoel, Gwij Stegen, Jella Wauters, Lynn Vanhaecke, An Martel & Frank Pasmans
To prevent transmission of the pathogenic chytrid fungi Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal), hygiene protocols prescribe the single use of disposable gloves for handling amphibians. We discovered that rinse water from nitrile gloves instantly kills 99% of Bd and Bsal zoospores. Transmission experiments using midwife toads (Alytes obstetricans) and Bd, and Alpine newts (Ichthyosaura alpestris) and Bsal, show that the use of the same pair of gloves for 2 subsequent individuals does not...

Because You Had a Bad Day: General and Daily Relations between Reactive Temperament, Emotion Regulation, and Depressive Symptoms in Youth

Marie-Lotte Van Beveren, Sofie Kuppens, Benjamin Hankin & Caroline Braet
Negative emotionality (NE) and positive emotionality (PE) have repeatedly shown to act as vulnerability factors for youth depression. Less research examined the mechanisms through which these reactive temperament traits may differently confer vulnerability to depression. Based on recent integrated models of depression proposing emotion regulation as a key underlying mechanism, the current study aimed to clarify the general and day-to-day relations among temperament, emotion regulation strategies, and depressive symptoms in Dutch-speaking youth (35% boys; M_age...

A preliminary field trial to compare control techniques for invasive Berberis aquifolium in Belgian coastal dunes

Tim Adriaens, Pieter Verschelde, Emma Cartuyvels, Bram D'hondt, Edward Vercruysse, Wouter Van Gompel, Evy Dewulf & Sam Provoost
Non-native Berberis aquifolium is notoriously invasive in Belgian coastal dunes. With its strong clonal growth through suckers, this evergreen shrub outcompetes native species and affects dune succession. To prevent further secondary spread and mitigate its impact, there was an urgent need for knowledge on the effectiveness of control measures, both at the plant and habitat level. Here, we report on a first control experiment. Individual B. aquifolium clones were subjected to one of four treatments...

Data from: Induced phenological avoidance: a neglected defense mechanism against seed predation in plants

Bram Sercu, Iris Moeneclaey, Dries Bonte & Lander Baeten
1. Flowering phenology is an important life history trait affecting plant reproductive performance and is influenced by various abiotic and biotic factors. Pre-dispersal seed predation and pollination are expected to impose counteracting selection pressure on flowering phenology, with pre-dispersal seed predation expected to favor off-peak flowering and pollination to favor synchronous flowering. 2. Here we studied the effect of pre-dispersal seed predation by the beetle Byturus ochraceus, a specialist seed herbivore, on the flowering phenology...

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: 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,...

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: 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...

Registration Year

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  • 2012

Resource Types

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  • Ghent University
  • KU Leuven
  • Research Institute for Nature and Forest
  • University of Antwerp
  • French National Centre for Scientific Research
  • Royal Belgian Institute of Natural Sciences
  • Swedish University of Agricultural Sciences
  • Swiss Federal Institute for Forest, Snow and Landscape Research
  • University of Zurich
  • University of Groningen