175 Works

Data from: Quantifying temporal isolation: a modelling approach assessing the effect of flowering time differences on crop-to-weed pollen flow in sunflower

Marie Roumet, Adeline Cayre, Muriel Latreille & Marie-Hélène Muller
Flowering time divergence can be a crucial component of reproductive isolation between sympatric populations but few studies have quantified its actual contribution to the reduction of gene flow. In this study, we aimed at estimating pollen-mediated gene flow between cultivated sunflower and a weedy conspecific sunflower population growing in the same field, and at quantifying how it is affected by the weeds’ flowering time. For that purpose, we extended an existing mating model by including...

Data from: Investigation of the geographic scale of adaptive phenological variation and its underlying genetics in Arabidopsis thaliana

Benjamin Brachi, Romain Villoutreix, Nathalie Faure, Nina-Coralie Hautekèete, Yves Piquot, Maxime Pauwels, Dominique Roby, Joel Cuguen, Joy Bergelson & Fabrice Roux
Despite the increasing number of genomic tools, identifying the genetics underlying adaptive complex traits remains challenging in the model species Arabidopsis thaliana. This is due, at least in part, to the lack of data on the geographical scale of adaptive phenotypic variation. The aims of this study were (i) to tease apart the historical roles of adaptive and nonselective processes in shaping phenological variation in A. thaliana in France and (ii) to gain insights into...

Data from: Familiarity to a feed additive modulates its effects on brain responses in reward and memory regions in the pig model

David Val-Laillet, Paul Meurice & Caroline Clouard
Brain responses to feed flavors with or without a feed additive (FA) were investigated in piglets familiarized or not with this FA. Sixteen piglets were allocated to 2 dietary treatments from weaning until d 37: the naive group (NAI) received a standard control feed and the familiarized group (FAM) received the same feed added with a FA mainly made of orange extracts. Animals were subjected to a feed transition at d 16 post-weaning, and to...

Data from: Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish

Stefan Dennenmoser, Fritz J. Sedlazeck, Michael C. Schatz, Janine Altmüller, Matthias Zytnicki & Arne W. Nolte
Hybridization can induce transposons to jump into new genomic positions, which may result in their accumulation across the genome. Alternatively, transposon copy numbers may increase through non-allelic (ectopic) homologous recombination in highly repetitive regions of the genome. The relative contribution of transposition bursts versus recombination-based mechanisms to evolutionary processes remains unclear because studies on transposon dynamics in natural systems are rare. We assessed the genome-wide distribution of transposon insertions in a young hybrid lineage (“invasive...

Data from: Combining GWAS and RNA-seq approaches for detection of the causal mutation for hereditary junctional epidermolysis bullosa in sheep

Aroa Suárez-Vega, Beatriz Gutiérrez-Gil, Julio Benavides, Valentín Perez, Gwenola Tosser-Klopp, Christophe Klopp, Stephen J. Keennel & Juan José Arranz
In this study, we demonstrate the use of a genome-wide association mapping together with RNA-seq in a reduced number of samples, as an efficient approach to detect the causal mutation for a Mendelian disease. Junctional epidermolysis bullosa is a recessive genodermatosis that manifests with neonatal mechanical fragility of the skin, blistering confined to the lamina lucida of the basement membrane and severe alteration of the hemidesmosomal junctions. In Spanish Churra sheep, junctional epidermolysis bullosa (JEB)...

Data from: Globally, functional traits are weak predictors of juvenile tree growth, and we do not know why

C. E. Timothy Paine, Lucy Amissah, Harald Auge, Christopher Baraloto, Martin Baruffol, Nils Bourland, Helge Bruelheide, Kasso Daïnou, Roland C. De Gouvenain, Jean-Louis Doucet, Susan Doust, Paul V. A. Fine, Claire Fortunel, Josephine Haase, Karen D. Holl, Hervé Jactel, Xuefei Li, Kaoru Kitajima, Julia Koricheva, Cristina Martínez-Garza, Christian Messier, Alain Paquette, Christopher Philipson, Daniel Piotto, Lourens Poorter … & Andy Hector
1. Plant functional traits, in particular specific leaf area (SLA), wood density and seed mass, are often good predictors of individual tree growth rates within communities. Individuals and species with high SLA, low wood density and small seeds tend to have faster growth rates. 2. If community-level relationships between traits and growth have general predictive value, then similar relationships should also be observed in analyses that integrate across taxa, biogeographic regions and environments. Such global...

Data from: A molecular phylogeny and revised higher-level classification for the leaf-mining moth family Gracillariidae and its implications for larval host-use evolution

Akito Y. Kawahara, David Plotkin, Issei Ohshima, Carlos Lopez-Vaamonde, Peter R. Houlihan, Jesse W. Breinholt, Atsushi Kawakita, Lei Xiao, Jerome C. Regier, Donald R. Davis, Tosio Kumata, Jay-Cheon Sohn, Jurate De Prins, Charles Mitter & JAE-CHEON SOHN
Gracillariidae are one of the most diverse families of internally feeding insects, and many species are economically important. Study of this family has been hampered by lack of a robust and comprehensive phylogeny. In the present paper, we sequenced up to 22 genes in 96 gracillariid species, representing all previously recognized subfamilies and genus groups, plus 20 outgroups representing other families and superfamilies. Following objective identification and removal of two rogue taxa, two datasets were...

Data from: The effects of climate change on a mega-diverse country: predicted shifts in mammalian species richness and turnover in continental Ecuador.

Paula Iturralde-Pólit, Olivier Dangles, Santiago F. Burneo & Christine N. Meynard
Ecuador is one of 17 nations with the greatest diversity in the world, sheltering lowland and mountain regions that are considered global biodiversity hotspots. While these regions are projected to be highly impacted by climate change, it is not clear what would be the consequences for faunal diversity and conservation. To address this issue, we used an ensemble of 8 species distribution models (SDM) to determine future shifts and identify areas of high changes in...

Data from: Species richness effects on grassland recovery from drought depend on community productivity in a multisite experiment

Juergen Kreyling, Jürgen Dengler, Julia Walter, Nikolay Velev, Emin Ugurlu, Desislava Sopotlieva, Johannes Ransijn, Catherine Picon-Cochard, Ivan Nijs, Pauline Hernandez, Behlül Güler, Philipp Von Gillhaussen, Hans J. De Boeck, Juliette M. G. Bloor, Sigi Berwaers, Carl Beierkuhnlein, Mohammed A. S. Arfin Khan, Iva Apostolova, Yasin Altan, Michaela Zeiter, Camilla Wellstein, Marcelo Sternberg, Andreas Stampfli, Giandiego Campetella, Sándor Bartha … & Juliette M.G. Bloor
Biodiversity can buffer ecosystem functioning against extreme climatic events, but few experiments have explicitly tested this. Here, we present the first multisite biodiversity × drought manipulation experiment to examine drought resistance and recovery at five temperate and Mediterranean grassland sites. Aboveground biomass production declined by 30% due to experimental drought (standardised local extremity by rainfall exclusion for 72–98 consecutive days). Species richness did not affect resistance but promoted recovery. Recovery was only positively affected by...

Data from: Partitioning genetic and species diversity refines our understanding of species-genetic diversity relationships

Vera W Pfeiffer, Brett M Ford, Johann Housset, Audrey McCombs, José L Blanco-Pastor, Nicolas Gouin, Stephanie Manel & Angéline Bertin
Illuminating the origin of species-genetic diversity correlations (SGDCs) is a challenging task that has sparked a lot of interest. Genetic and species diversity are comprised by components that respond differently to the same ecological processes. Thus, it can be useful to partition species and genetic diversity into their different components to infer the mechanisms behind SGDCs. In this study, we applied such an approach using a high-elevation Andean wetland system, where previous evidence identified neutral...

Data from: Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of single nucleotide polymorphisms

Elsa Quillery, Olivier Quenez, Pierre Peterlongo & Olivier Plantard
Assessing the genetic variability of the tick Ixodes ricinus - an important vector of pathogens in Europe - is an essential step for setting-up anti-tick control methods. Here, we report the first identification of a set of SNPs isolated from the genome of I. ricinus, carried out by applying a genomic complexity reduction step, followed by pyrosequencing and the use new bioinformatics tools. Almost 1.4 million reads (average length : 528 nt) were generated with...

Data from: \"De novo assembly transcriptome for the rostrum dace (Leuciscus burdigalensis, Cyprinidae: fish) naturally infected by a copepod ectoparasite\" in Genomic Resources Notes accepted 1 December 2014 to 31 January 2015

Olivier Rey, Géraldine Loot, Olivier Bouchez, Simon Blanchet, Maria Jose Ruiz-Lopez, Nelson Ting, Paul D. Etter, Eric A. Johnson, Tony L. Goldberg, Colin A. Chapman, James H. Jones, Patrick A. Omeja & William M. Switzer
The emergence of pathogens represents substantial threats to public health, livestock, domesticated animals, and biodiversity. How wild populations respond to emerging pathogens has generated a lot of interest in the last two decades. With the recent advent of high-throughput sequencing technologies it is now possible to develop large transcriptomic resources for non-model organisms, hence allowing new research avenues on the immune responses of hosts from a large taxonomic spectra. We here focused on a wild...

Data from: Estimation of the dispersal of a major pest of maize by cline analysis of a temporary contact zone between two invasive outbreaks

Gérald Bermond, Aurélie Blin, Elodie Vercken, Virginie Ravigné, Adrien Rieux, Sophie Mallez, Thibaut Morel-Journel, Thomas Guilllemaud & Thomas Guillemaud
Dispersal is a key factor in invasion, and in the persistence and evolution of species. Despite the importance of estimates of dispersal distance, dispersal measurement remains a real methodological challenge. In this study, we characterized dispersal by exploiting a specific case of biological invasion, in which multiple introductions in disconnected areas lead to secondary contact between two differentiated expanding outbreaks. By applying cline theory to this ecological setting, we estimated σ, the standard deviation of...

Data from: Adaptive admixture in the West African bovine hybrid zone: insight from the Borgou population

Laurence Flori, Sophie Thevenon, Guiguigbaza-Kossigan Dayo, Marcel Sénou, Souleymane Sylla, David Berthier, Katayou Moazami-Goudarzi, Mathieu Gautier & Katayoun Moazami-Goudarzi
Understanding the adaptive response to environmental fluctuations represents a central issue in evolutionary biology. Population admixture between divergent ancestries has often been considered as an efficient short-term adaptation strategy. Cattle populations from the West African Bos taurus x Bos indicus hybrid zone represent a valuable resource to characterize the effect of such adaptive admixture at the genome level. We here provide a detailed assessment of the global and local genome ancestries of the Borgou breed,...

Data from: Pulsed food resources, but not forest cover, determines lifetime reproductive success in a forest-dwelling rodent

Katrine S. Hoset, Alexandre Villers, Ralf Wistbacka & Vesa Selonen
1. The relative contributions of habitat and food availability on fitness may provide evidence for key habitat features needed to safeguard population persistence. However, defining habitat quality for a species can be a complex task, especially if knowledge on the relationship between individual performance and habitat quality is lacking. 2. Here, we determined the relative importance of availability of suitable forest habitat, body mass, and food from masting tree species on female lifetime reproductive success...

Data from: A comparison between transcriptome sequencing and 16S metagenomics for detection of bacterial pathogens in wildlife

Maria Razzauti, Maxime Galan, Maria Bernard, Sarah Maman, Christophe Klopp, Nathalie Charbonnel, Muriel Vayssier-Taussat, Marc Eloit & Jean-François Cosson
Background: Rodents are major reservoirs of pathogens responsible for numerous zoonotic diseases in humans and livestock. Assessing their microbial diversity at both the individual and population level is crucial for monitoring endemic infections and revealing microbial association patterns within reservoirs. Recently, NGS approaches have been employed to characterize microbial communities of different ecosystems. Yet, their relative efficacy has not been assessed. Here, we compared two NGS approaches, RNA-Sequencing (RNA-Seq) and 16S-metagenomics, assessing their ability to...

Data from: Stocking activities for the Arctic charr in Lake Geneva: genetic effects in space and time

Romain Savary, Christophe Dufresnes, Alexis Champigneulle, Arnaud Caudron, Sylvain Dubey, Nicolas Perrin & Luca Fumagalli
Artificial stocking practices are widely used by resource managers worldwide, in order to sustain fish populations exploited by both recreational and commercial activities, but their benefits are controversial. Former practices involved exotic strains, although current programs rather consider artificial breeding of local fishes (supportive breeding). Understanding the complex genetic effects of these management strategies is an important challenge with economic and conservation implications, especially in the context of population declines. In the present study, we...

Data from: Costs of CRISPR-Cas mediated resistance in Streptococcus thermophilus

Pedro F. Vale, Guillaume Lafforgue, François Gatchitch, Rozenn Gardan, Sylvain Moineau & Sylvain Gandon
CRISPR-Cas is a form of adaptive sequence-specific immunity in microbes. This system offers unique opportunities for the study of coevolution between bacteria and their viral pathogens, bacteriophages. A full understanding of the coevolutionary dynamics of CRISPR-Cas requires knowing the magnitude of the cost of resisting infection. Here, using the gram-positive bacterium Streptococcus thermophilus and its associated virulent phage 2972, a well-established model system harbouring at least two type II functional CRISPR-Cas systems, we obtained different...

Data from: Early Plasmodium-induced inflammation does not accelerate aging in mice

Cédric Lippens, Emmanuel Guivier, Sarah E. Reece, Aidan J. O'Donnell, Stephane Cornet, Bruno Faivre & Gabriele Sorci
Aging is associated with a decline of performance leading to reduced reproductive output and survival. While the antagonistic pleiotropy theory of aging has attracted considerable attention, the molecular/physiological functions underlying the early-life benefits/late-life costs paradigm remain elusive. We tested the hypothesis that while early activation of the inflammatory response confers benefits in terms of protection against infection, it also incurs costs in terms of reduced reproductive output at old age, and shortened longevity. We infected...

Data from: Escape of spring frost and disease through phenological variations in oak populations along elevation gradients

Cécile Françoise Dantec, Hugo Ducasse, Xavier Capdevielle, Olivier Fabreguettes, Sylvain Delzon & Marie-Laure Desprez-Loustau
1. The timing of tree flushing follows strong phenotypic and genetic clines across environmental gradients. It may be seen as an adaptive response to abiotic (escape of spring frost and maximizing growing season length) and biotic (escape of pest and disease) hazards. However, few studies have investigated jointly both types of hazards. 2. We assessed exposure to both abiotic (spring frost) and biotic (powdery mildew) hazards within and between sessile oak populations along elevation gradients,...

Data from: A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting

Elisabeth Fitzek, Adline Delcamp, Erwan Guichouc, Marlene Hahn, Matthew Lobdell, Andrew L. Hipp & Erwan Guichoux
DNA barcoding has proved difficult in a number of woody plant genera, including the ecologically important oak genus Quercus. In this study, we utilized restriction-site associated DNA sequencing (RAD-seq) to develop an economical single-nucleotide polymorphism (SNP) DNA barcoding system that suffices to distinguish eight common, sympatric eastern North American white oak species. Two de novo clustering pipelines, PyRAD and Stacks, were used in combination with post-clustering bioinformatic tools to generate a list of 291 potential...

Data from: Insular woody daisies (Argyranthemum , Asteraceae) are more resistant to drought-induced hydraulic failure than their herbaceous relatives

Larissa C. Doria, Diego S. Podadera, Marcelino Del Arco, Thibaud Chauvin, Erik Smets, Sylvain Delzon & Frederic Lens
1. Insular woodiness refers to the evolutionary transition from herbaceousness towards derived woodiness on (sub)tropical islands, and leads to island floras that have a higher proportion of woody species compared to floras of nearby continents. 2. Several hypotheses have tried to explain insular woodiness since Darwin’s original observations, but experimental evidence why plants became woody on islands is scarce at best. 3. Here, we combine experimental measurements of hydraulic failure in stems (as a proxy...

Data from: Temporal population genetics of time travelling insects: a long term longitudinal study in a seed-specialized wasp

Marie Suez, Cindy Gidoin, François Lefèvre, Jean-Noël Candau, Alain Chalon & Thomas Boivin
Many animal species experiencing spatial or interannual fluctuations of their environment are capable of prolonged diapause, a kind of dormancy that extends over more than one year. Such a prolonged diapause is commonly perceived as a temporal demographic refuge in stochastic environments, but empirical evidence is still lacking of its consequences on temporal population genetic structures. In this long-term study, we investigated how a particular pattern of prolonged diapause may influence the temporal population genetics...

Data from: The roots of the drought: hydrology and water uptake strategies mediate forest-wide demographic response to precipitation

Rutuja Chitra-Tarak, Laurent Ruiz, H. S. Dattaraja, M. S. Mohan Kumar, Jean Riotte, H. S. Suresh, Sean M. McMahon & Raman Sukumar
Drought-induced tree mortality is expected to increase globally due to climate change, with profound implications for forest composition, function and global climate feedbacks. How drought is experienced by different species is thought to depend fundamentally on where they access water vertically below ground, but this remains untracked so far due to the difficulty of measuring water availability at depths at which plants access water (few to several tens of meters), the broad temporal scales at...

Data from: Short-term variations in gene flow related to cyclic density fluctuations in the common vole

Bertrand Gauffre, Karine Berthier, Pablo Inchausti, Yannick Chaval, Jean-François Cosson & Vincent Bretagnolle
In highly fluctuating populations with complex social systems genetic patterns are likely to vary in space and time due to demographic and behavioural processes. Cyclic rodents are extreme examples of demographically instable populations that often exhibit strong social organisation. In such populations, kin structure and spacing behaviour may vary with density fluctuations and impact both the composition and spatial structure of genetic diversity. In this study, we analysed the multiannual genetic structure of a cyclic...

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