115 Works

Data from: Comparison of pollen gene flow among four European beech (Fagus sylvatica L.) populations characterized by different management regimes

Andrea Piotti, Stefano Leonardi, Joukje Buiteveld, Thomas Geburek, Sophie Gerber, Koen Kramer, Cristina Vettori & Giovanni G. Vendramin
The study of dispersal capability of a species can provide essential information for the management and conservation of its genetic variability. Comparison of gene flow rates among populations characterized by different management and evolutionary histories allows one to decipher the role of factors such as isolation and tree density on gene movements. We used two paternity analysis approaches and different strategies to handle possible presence of genotyping errors to obtain robust estimates of pollen flow...

Data from: Outlier loci highlight the direction of introgression in oaks

Erwan Guichoux, Pauline Garnier-Gere, Lélia Lagache, Tiange Lang, Christophe Boury & Rémy J. Petit
Loci considered to be under selection are generally avoided in attempts to infer past demographic processes as they do not fit neutral model assumptions. However, opportunities to better reconstruct some aspects of past demography might thus be missed. Here we examined genetic differentiation between two sympatric European oak species with contrasting ecological dynamics (Quercus robur and Q. petraea) with both outlier (i.e. loci possibly affected by divergent selection between species or by hitchhiking effects with...

Data from: Genetic differentiation of the pine processionary moth at the southern edge of its range: contrasting patterns between mitochondrial and nuclear markers

Mhamed El Mokhefi, Carole Kerdelhué, Christian Burban, Andrea Battisti, Gahdab Chakali & Mauro Simonato
The pine processionary moth (Thaumetopoea pityocampa) is an important pest of coniferous forests at the southern edge of its range in Maghreb. Based on mitochondrial markers, a strong genetic differentiation was previously found in this species between western (pityocampa clade) and eastern Maghreb populations (ENA clade), with the contact zone between the clades located in Algeria. We focused on the moth range in Algeria, using both mitochondrial (a 648 bp fragment of the tRNA-cox2) and...

Data from: Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers

Sanna Olsson, Pedro Seoane Zonjic, Rocío Bautista, M. Gonzalo Claros, Santiago C. González-Martínez, Ivan Scotti, Caroline Scotti-Saintagne, Olivier J. Hardy & Myriam Heuertz
Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L.f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome...

Data from: Avian pest control in vineyards is driven by interactions between bird functional diversity and landscape heterogeneity

Luc Barbaro, Adrien Rusch, Evalyne W. Muiruri, Bastien Gravellier, Denis Thiery & Bastien Castagneyrol
Insectivorous birds are increasingly recognized for the crucial pest control services they provide to agroecosystems. While both the foraging activity and functional diversity of birds are enhanced by multiscale habitat heterogeneity, little is known about how these relationships may influence avian top-down control of insects. Specifically, interactive effects of bird community structure and habitat heterogeneity on pest control across spatial scales have rarely been explored. We sampled bird communities and measured avian predation on plasticine...

Data from: Loss of connectivity among island-dwelling Peary caribou following sea ice decline

Deborah A. Jenkins, Nicolas Lecomte, James A. Schaefer, Steffen M. Olsen, Didier Swingedouw, Steeve D. Côté, Loïc Pellissier & Glenn Yannic
Global warming threatens to reduce population connectivity for terrestrial wildlife through significant and rapid changes to sea ice. Using genetic fingerprinting, we contrasted extant connectivity in island-dwelling Peary caribou in northern Canada with continental-migratory caribou. We next examined if sea-ice contractions in the last decades modulated population connectivity and explored the possible impact of future climate change on long-term connectivity among island caribou. We found a strong correlation between genetic and geodesic distances for both...

Data from: Grape moth density in Bordeaux vineyards depends on local habitat management despite effects of landscape heterogeneity on their biological control

Adrien Rusch, Lionel Delbac & Denis Thiéry
1. Biological control of crop pests is a major ecosystem service affected by several variables acting at multiple spatial scales. Among these variables, heterogeneity at the habitat and landscape scales are known key drivers of trophic interactions and pest density in agroecosystems. However, studies that try to disentangle their relative effects in perennial cropping systems are scarce and nothing is known about their impacts on insect pest density and pesticide applications. 2. We examined the...

Data from: Latitudinal variation in plant chemical defences drives latitudinal patterns of leaf herbivory

Xoaquón Moreira, Bastien Castagneyrol, Luis Abdala-Roberts, Jorge C. Berny-Mier Y Terán, Bart G. H. Timmermans, Hans Henrik Kehlet Bruun, Felisa Covelo, Gaétan Glauser, Sergio Rasmann, Ayco J. M. Tack & Hans Henrik Bruun
A long-standing paradigm in ecology holds that herbivore pressure and thus plant defences increase towards lower latitudes. However, recent work has challenged this prediction where studies have found no relationship or opposite trends where herbivory or plant defences increase at higher latitudes. Here we tested for latitudinal variation in herbivory, chemical defences (phenolic compounds), and nutritional traits (phosphorus and nitrogen) in leaves of a long-lived tree species, the English oak Quercus robur. We further investigated...

Data from: Comparative assessment of SSR and SNP markers for inferring the population genetic structure of the common fungus Armillaria cepistipes

Tetyana Tsykun, Christian Rellstab, Cyril Dutech, György Sipos & Simone Prospero
During the last years, simple sequence repeats (SSRs, also known as microsatellites) and single-nucleotide polymorphisms (SNPs) have become the most popular molecular markers for describing neutral genetic variation in populations of a wide range of organisms. However, only a limited number of studies has focused on comparing the performance of these two types of markers for describing the underlying genetic structure of wild populations. Moreover, none of these studies targeted fungi, the group of organisms...

Data from: Pharmacological characterisation of S 47445, a novel positive allosteric modulator of AMPA receptors

Sylvie Bretin, Caroline Louis, Laure Seguin, Stéphanie Wagner, Jean-Yves Thomas, Sylvie Challal, Nathalie Rogez, Karine Albinet, Fabrice Iop, Nadège Villain, Sonia Bertrand, Ali Krazem, Daniel Bérachochéa, Stéphanie Billiald, Charles Tordjman, Alex Cordi, Daniel Bertrand, Pierre Lestage & Laurence Danober
S 47445 is a novel positive allosteric modulator of alpha-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) receptors (AMPA-PAM). S 47445 enhanced glutamate’s action at AMPA receptors on human and rat receptors and was inactive at NMDA and kainate receptors. Potentiation did not differ among the different AMPA receptors subtypes (GluA1/2/4 flip and flop variants) (EC50 between 2.5–5.4 μM), except a higher EC50 value for GluA4 flop (0.7 μM) and a greater amount of potentiation on GluA1 flop. A low...

Data from: The balance of canopy and soil effects determines intraspecific differences in foundation species’ effects on associated plants

Nuria Pistón, Richard Michalet, Christian Schöb, Petr Macek, Cris Armas & Francisco I. Pugnaire
1. The impact of plant-plant interactions on species diversity patterns has been broadly addressed in stressful environments, such as alpine ecosystems, where foundation species promote species richness by creating habitat for other species. However, foundation species with contrasting phenotypes might modify the microhabitat differently, which would alter the subordinate community composition, and coincide with distinct feedback effects of those subordinate species on the foundation species. However, the precise interaction mechanisms that facilitate species are not...

Data from: Functional limb muscle innervation prior to cholinergic transmitter specification during early metamorphosis in Xenopus

François M. Lambert, Laura Cardoit, Elric Courty, Marion Bougerol, Muriel Thoby-Brisson, John Simmers, Hervé Tostivint, Didier Le Ray & Francois M Lambert
In vertebrates, functional motoneurons are defined as differentiated neurons that are connected to a central premotor network and activate peripheral muscle using acetylcholine. Generally, motoneurons and muscles develop simultaneously during embryogenesis. However, during Xenopus metamorphosis, developing limb motoneurons must reach their target muscles through the already established larval cholinergic axial neuromuscular system. Here, we demonstrate that at metamorphosis onset, spinal neurons retrogradely labeled from the emerging hindlimbs initially express neither choline acetyltransferase nor vesicular acetylcholine...

Data from: Inferring selection in instances of long‐range colonization: the Aleppo pine (Pinus halepensis) in the Mediterranean Basin

Rose Ruiz Daniels, Richard S. Taylor, María Jesús Serra-Varela, Giovanni G. Vendramin, Santiago C. González-Martínez & Delphine Grivet
Teasing apart the effects of natural selection and demography on current allele frequencies is challenging, due to both processes leaving a similar molecular footprint. In particular, when attempting to identify selection in species that have undergone a recent range expansion, the increase of genetic drift at the edges of range expansions (“allele surfing”) can be a confounded factor. To address this potential issue, we first assess the long-range colonisation history of the Aleppo pine across...

Data from: Entropic bonding of the type 1 pilus from experiment and simulation

Fabiano Corsetti, Alvaro Alonso-Caballero, Simon Poly, Raul Perez-Jimenez & Emilio Artacho
The type 1 pilus is a bacterial filament consisting of a long coiled proteic chain of subunits joined together by non-covalent bonding between complementing β-strands. Its strength and structural stability are critical for its anchoring function in uropathogenic Escherichia coli bacteria. The pulling and unravelling of the FimG subunit of the pilus was recently studied by atomic force microscopy (AFM) experiments and steered molecular dynamics (SMD) simulations [A. Alonso-Caballero et al., Nature Commun. 9, 2758...

Shift from short-term competition to facilitation with drought stress is due to a decrease in long-term facilitation

Ghassen Chaieb, Xiangtai Wang, Chedly Abdelly & Richard Michalet
Disentangling short- and long-term neighbour effects, using both removal and observational methods within a single experiment, has strongly improved our understanding of the driving mechanisms of plant-plant interactions. However, there has been no attempt to assess two important underlying processes of their changes along gradients, environmental-severity (changes in target performance without neighbours) and neighbour-traits (changes in performance with neighbours) effects, the former previously shown in alpine communities to be involved in competition and the latter...

Crop diversity benefits carabid and pollinator communities in landscapes with semi-natural habitats

Guillermo Aguilera Núñez, Tomas Roslin, Kirsten Miller, Giovanni Tamburini, Klaus Birkhofer, Berta Caballero-Lopez, Sandra Lindström, Erik Öckinger, , Adrien Rusch, Henrik Smith & Riccardo Bommarco
1. In agricultural landscapes, arthropods provide essential ecosystem services such as biological pest control and pollination. Intensified crop management practices and homogenization of landscapes have led to declines among such organisms. Semi-natural habitats, associated with high numbers of these organisms, are increasingly lost from agricultural landscapes but diversification by increasing crop diversity has been proposed as a way to reverse observed arthropod declines and thus restore ecosystem services. However, whether or not an increase in...

How does increasing mast seeding frequency affect population dynamics of seed consumers? Wild boar as a case study

Laura Touzot, Eliane Schermer, Samuel Venner, Sylvain Delzon, Cyril Rousset, Eric Baubet, Jean-Michel Gaillard & Marlène Gamelon
Mast seeding in temperate oak populations shapes the dynamics of seed consumers and numerous communities. Mast seeding responds positively to warm spring temperatures and is therefore expected to increase under global warming. We investigated the potential effects of changes in oak mast seeding on wild boar population dynamics, a widespread and abundant consumer species. Using long-term monitoring data, we showed that abundant acorn production enhances the proportion of breeding females. With a body mass-structured population...

Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection

Lucie Tamisier, Annelies Haegeman, Yoika Foucart, Nicolas Fouillien, Maher Al Rwahnih, Nihal Buzkan, Thierry Candresse, Michela Chiumenti, Kris De Jonghe, Marie Lefebvre, Paolo Margaria, Jean Sébastien Reynard, Kristian Stevens, Denis Kutnjak & Sébastien Massart
In the last decade, High-Throughput Sequencing (HTS) has revolutionized biology and medicine. This technology allows the sequencing of huge amount of DNA and RNA fragments at a very low price. In medicine, HTS tests for disease diagnostics are already brought into routine practice. However, the adoption in plant health diagnostics is still limited. One of the main bottlenecks is the lack of expertise and consensus on the standardization of the data analysis. The Plant Health...

High variation in hydraulic efficiency but not xylem safety between roots and branches in four temperate broad-leaved tree species

Torben Lübbe, Laurent J. Lamarque, Sylvain Delzon, José M. Torres-Ruiz, Régis Burlett, Christoph Leuschner & Bernhard Schuldt
Xylem hydraulic safety and efficiency are key traits determining tree fitness in a warmer and drier world. While numerous plant hydraulic studies have focused on branches, our understanding of root hydraulic functioning remains limited, although roots control water uptake, influence stomatal regulation and have commonly been considered as the most vulnerable organ along the hydraulic pathway. We investigated 11 traits related to xylem safety and efficiency along the hydraulic pathway in four temperate broad-leaved tree...

Additional file 1 of CSPG4 expression in soft tissue sarcomas is associated with poor prognosis and low cytotoxic immune response

Laurys Boudin, A de Nonneville, Pascal Finetti, Léna Mescam, A Le Cesne, Antoine Italiano, Jean-Yves Blay, Daniel Birnbaum, Emilie Mamessier & François Bertucci
Additional file 1: Table S1. (File format .xls). List of soft tissue sarcoma data sets included.

Additional file 13 of CSPG4 expression in soft tissue sarcomas is associated with poor prognosis and low cytotoxic immune response

Laurys Boudin, A de Nonneville, Pascal Finetti, Léna Mescam, A Le Cesne, Antoine Italiano, Jean-Yves Blay, Daniel Birnbaum, Emilie Mamessier & François Bertucci
Additional file 13: Table S8. (File format .xls). Expression data of each tumor normalised and used for the paper.

Additional file 13 of CSPG4 expression in soft tissue sarcomas is associated with poor prognosis and low cytotoxic immune response

Laurys Boudin, A de Nonneville, Pascal Finetti, Léna Mescam, A Le Cesne, Antoine Italiano, Jean-Yves Blay, Daniel Birnbaum, Emilie Mamessier & François Bertucci
Additional file 13: Table S8. (File format .xls). Expression data of each tumor normalised and used for the paper.

Additional file 1 of CSPG4 expression in soft tissue sarcomas is associated with poor prognosis and low cytotoxic immune response

Laurys Boudin, A de Nonneville, Pascal Finetti, Léna Mescam, A Le Cesne, Antoine Italiano, Jean-Yves Blay, Daniel Birnbaum, Emilie Mamessier & François Bertucci
Additional file 1: Table S1. (File format .xls). List of soft tissue sarcoma data sets included.

Data from: Fine-scale environmental control of hybridization in oaks

Lélia Lagache, Etienne K. Klein, Erwan Guichoux & Rémy J. Petit
Natural hybridization is attracting much interest in modern speciation and conservation biology studies, but the underlying mechanisms remain poorly understood. In particular, it is unclear why environmental changes often increase hybridization rates. To study this question, we surveyed mating events in a mixed oak stand and developed a spatially-explicit individual-based hybridization model. This model, where hybridization is frequency dependent, pollen is non-limiting and which allows immigrant pollen to compete with local pollen, takes into account...

Data from: Disentangling the genetic origins of a plant pathogen during disease spread using an original molecular epidemiology approach

Constance Xhaard, Benoît Barrès, Axelle Andrieux, Lydia Bousset, Fabien Halkett & Pascal Frey
The advent of molecular epidemiology has greatly improved our ability to identify population sources and track pathogen movement. Yet the wide spatial and temporal scales usually considered are useful only to infer historical migration pathways. In this study, Bayesian genetic assignments and a landscape epidemiology approach were combined to unravel genetic origin and annual spread during a single epidemic of a plant pathogen: the poplar rust fungus Melampsora larici-populina. The study focused on a particular...

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