174 Works

Data from: Rapid divergence of genome architectures following the origin of an ectomycorrhizal symbiosis in the genus Amanita

Jaqueline Hess, Inger Skrede, Maryam Chaib De Mares, Matthieu Hainaut, Bernard Henrissat & Anne Pringle
Fungi are evolutionary shape shifters and adapt quickly to new environments. Ectomycorrhizal (EM) symbioses are mutualistic associations between fungi and plants and have evolved repeatedly and independently across the fungal tree of life, suggesting lineages frequently reconfigure genome content to take advantage of open ecological niches. To date analyses of genomic mechanisms facilitating EM symbioses have involved comparisons of distantly related species, but here, we use the genomes of three EM and two asymbiotic (AS)...

Data from: Effects of two grass species on the composition of soil fungal communities

Bello Mouhamadou, Jeremy Puissant, Emanuelle Personeni, Marie Desclos-Theveniau, Eva M. Kastl, Michael Schloter, Lucie Zinger, Julien Roy, Sandra Lavorel & Roberto A. Geremia
Many studies have shown effects of plants species on fungal communities, but these are often confounded with soil effects. Thus, the specific role of plant species in structuring rhizospheric and soil fungal communities is poorly described. Our study used microcosms in which plants were grown under artificial conditions to bridge this gap. Two perennial grasses dominating subalpine grasslands, Festuca paniculata and Dactylis glomerata, were grown at two levels of fertilization on standard soil. Fungal communities...

Data from: Virus adaptation to quantitative plant resistance: erosion or breakdown?

J. Montarry, E. Cartier, M. Jacquemond, A. Palloix & B. Moury
Adaptation of populations to new environments is frequently costly due to trade-offs between life history traits, and consequently, parasites are expected to be locally adapted to sympatric hosts. Also, during adaptation to the host, an increase of parasite fitness could have direct consequences on its aggressiveness (i.e. the quantity of damages caused to the host by the virus). These two phenomena have been observed in the context of pathogen adaptation to host qualitative and monogenic...

Data from: Plant functional groups mediate drought resistance and recovery in a multi-site grassland experiment

Kathleen A. Mackie, Michaela Zeiter, Juliette M.G. Bloor, Andreas Stampfli & Juliette M. G. Bloor
1. Climate change predictions suggest that summer droughts will become more intense and recurrent in Europe. While drought-induced reductions in grassland primary productivity are well documented, the drivers behind drought resistance (the capacity to withstand change) and recovery (the capacity for recovery of function) of above- and belowground biomass remain poorly understood. 2. Across eight grasslands differing in plant community productivity (CP) we investigated the effects of summer drought on plant and soil microbial variables,...

Data from: Leaf-cutter ants engineer large nitrous oxide hot spots in tropical forests

Fiona M. Soper, Benjamin W. Sullivan, Brooke B. Osborne, Alanna N. Shaw, Laurent Philippot & Cory C. Cleveland
Though tropical forest ecosystems are among the largest natural sources of the potent greenhouse gas nitrous oxide (N2O), the spatial distribution of emissions across landscapes is often poorly resolved. Leaf-cutter ants (LCA, Atta and Acromyrmex, Myrmicinae) are dominant herbivores throughout Central and South America and influence multiple aspects of forest structure and function. In particular, their foraging creates spatial heterogeneity by concentrating large quantities of organic matter (including nitrogen, N) from the surrounding canopy into...

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: The red coral (Corallium rubrum) transcriptome: a new resource for population genetics and local adaptation studies

Marine Pratlong, Anne Haguenauer, Olivier Chabrol, Christophe Klopp, Pierre Pontarotti & Didier Aurelle
The question of species survival and evolution in heterogeneous environments has long been a subject for study. Indeed, it is often difficult to identify the molecular basis of adaptation to contrasted environments, and nongenetic effects increase the difficulty to disentangle fixed effects, such as genetic adaptation, from variable effects, such as individual phenotypic plasticity, in adaptation. Nevertheless, this question is also of great importance for understanding the evolution of species in a context of climate...

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: 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: 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: Genome scan reveals selection acting on genes linked to stress response in wild pearl millet

Cécile Berthouly-Salazar, Anne-Céline Thuillet, Bénédicte Rhoné, Cédric Mariac, Issaka Salia Ousseini, Marie Couderc, Maud I. Tenaillon & Yves Vigouroux
Uncovering genomic regions involved in adaption is a major goal in evolutionary biology. High-throughput sequencing now makes it possible to tackle this challenge in nonmodel species. Yet, despite the increasing number of methods targeted to specifically detect genomic footprints of selection, the complex demography of natural populations often causes high rates of false positive in gene discoveries. The aim of this study was to identify climate adaptations in wild pearl millet populations, Cenchrus americanus ssp....

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: Patterns of MHC-dependent mate selection in humans and non-human primates: a meta-analysis

Jamie Winternitz, Jessica Abbate, Elise Huchard, Jan Havlíček & Laszlo Z. Garamszegi
Genes of the major histocompatibility complex (MHC) in vertebrates are integral for effective adaptive immune response and are associated with sexual selection. Evidence from a range of vertebrates supports MHC-based preference for diverse and dissimilar mating partners, but evidence from human mate choice studies has been disparate and controversial. Methodologies and sampling peculiarities specific to human studies make it difficult to know whether wide discrepancies in results among human populations are real or artefact. To...

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: 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: 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: Facilitation promotes invasions in plant-associated microbial communities

Mei Li, Zhong Wei, Jianing Wang, Alexandre Jousset, Ville-Petri Friman, Yangchun Xu, Qirong Shen & Thomas Pommier
While several studies have established a positive correlation between community diversity and invasion resistance, it is less clear how species interactions within resident communities shape this process. Here, we experimentally tested how antagonistic and facilitative pairwise interactions within resident model microbial communities predict invasion by the plant–pathogenic bacterium Ralstonia solanacearum. We found that facilitative resident community interactions promoted and antagonistic interactions suppressed invasions both in the lab and in the tomato plant rhizosphere. Crucially, pairwise...

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: 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: 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: 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: 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: High genetic variation in resting stage production in a metapopulation: is there evidence for local adaptation?

Anne Carole Roulin, Mahendra Mariadassou, Matthew D. Hall, Jean-Claude Walser, Christoph Haag & Dieter Ebert
Local adaptation is a key process for the maintenance of genetic diversity and population diversification. A better understanding of the mechanisms that allow (or prevent) local adaptation constitutes a key in apprehending how and at what spatial scale it occurs. The production of resting stages is found in many taxa and reflects an adaptation to outlast adverse environmental conditions. Daphnia magna (Crustacea) can alternate between asexual and sexual reproduction, the latter being linked to dormancy,...

Data from: Fungal disease incidence along tree diversity gradients depends on latitude in European forests

Diem Nguyen, Bastien Castagneyrol, Helge Bruelheide, Filippo Bussotti, Virginie Guyot, Hervé Jactel, Bogdan Jaroszewicz, Fernando Valladares, Jan Stenlid & Johanna Boberg
European forests host a diversity of tree species that are increasingly threatened by fungal pathogens, which may have cascading consequences for forest ecosystems and their functioning. Previous experimental studies suggest that foliar and root pathogen abundance and disease severity decrease with increasing tree species diversity, but evidences from natural forests are rare. Here, we tested whether foliar fungal disease incidence was negatively affected by tree species diversity in different forest types across Europe. We measured...

Data from: Low reproductive isolation and highly variable levels of gene flow reveal limited progress toward speciation between European river and brook lampreys

Quentin Rougemont, Arnaud Gaigher, Emilien Lasne, Jessica Côte, Maïra Coke, Anne-Laure Besnard, Sophie Launey & Guillaume Evanno
Ecologically based divergent selection is a factor that could drive reproductive isolation even in the presence of gene flow. Population pairs arrayed along a continuum of divergence provide a good opportunity to address this issue. Here we used a combination of mating trials, experimental crosses and population genetics analyses to investigate the evolution of reproductive isolation between two closely related species of lampreys with distinct life histories. We used microsatellite markers to genotype over 1000...

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