21 Works

Data from: Stronger spatial genetic structure in recolonized areas than in refugia in the European beech

Guillaume De Lafontaine, Alexis Ducousso, Sophie Lefèvre, Elodie Magnanou & Rémy J. Petit
Extant rear-edge populations located in former glacial refugia remain understudied despite their high conservation value. These populations should have experienced strong genetic drift due to their small size and long isolation. Moreover, the prolonged action of isolation-by-distance in refugial areas should result in stronger regional spatial genetic structure than in recolonized areas, but empirical tests of this prediction are scarce. To fill this gap, we first used a set of 16 microsatellite markers to investigate...

Data from: Androgenesis is a maternal trait in the invasive ant Wasmannia auropunctata

Olivier Rey, Benoit Facon, Julien Foucaud, Anne Loiseau & Arnaud Estoup
Androgenesis is the production of an offspring containing exclusively the nuclear genome of the fathering male, via the maternal eggs. This unusual mating system is generally considered as a male trait, giving to androgenetic males a substantial fitness advantage over their sexually reproducing relatives. We here provide the first empirical study of the evolutionary outcomes of androgenesis in a haplo-diploid organism: the invasive ant Wasmannia auropunctata. Some of the populations of this species have a...

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: 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: Phenotypic and genotypic convergences are influenced by historical contingency and environment in yeast

Aymé Spor, Daniel J. Kvitek, Thibault Nidelet, Juliette Martin, Judith Legrand, Christine Dillmann, Aurélie Bourgais, Dominique De Vienne, Gavin Sherlock & Delphine Sicard
Different organisms have independently and recurrently evolved similar phenotypic traits at different points throughout history. This phenotypic convergence may be caused by genotypic convergence and in addition, constrained by historical contingency. To investigate how convergence may be driven by selection in a particular environment and constrained by history, we analyzed nine life-history traits and four metabolic traits during an experimental evolution of six yeast strains in four different environments. In each of the environments, the...

Data from: Unveiling the diet of elusive rainforest herbivores in next generation sequencing era? The tapir as a case study

Fabrice Hibert, Pierre Taberlet, Jérôme Chave, Caroline Scotti-Saintagne, Daniel Sabatier & Cécile Richard-Hansen
Characterizing the trophic relationships between large herbivores and the outstanding plant diversity in rainforest is a major challenge because of their elusiveness. This is crucial to understand the role of these herbivores in the functioning of the rainforest ecosystems. We tested a non-invasive approach based on the high-throughput sequencing of environmental samples using small plant plastid sequences (the trnL P6 loop) and ribosomal ITS1 primers, referred to as DNA metabarcoding, to investigate the diet of...

Data from: Phylogenetic affiliation of SSU rRNA genes generated by massively parallel sequencing: new insights into the freshwater protist diversity

Najwa Taib, Jean-François Mangot, Isabelle Domaizon, Gisèle Bronner & Didier Debroas
Recent advances in next-generation sequencing (NGS) technologies spur progress in determining the microbial diversity in various ecosystems by highlighting, for example, the rare biosphere. Currently, high-throughput pyrotag sequencing of PCR-amplified SSU rRNA gene regions is mainly used to characterize bacterial and archaeal communities, and rarely to characterize protist communities. In addition, although taxonomic assessment through phylogeny is considered as the most robust approach, similarity and probabilistic approaches remain the most commonly used for taxonomic affiliation....

Data from: Genetic signature of a range expansion and leap-frog event after the recent invasion of Europe by the grapevine downy mildew pathogen Plasmopara viticola

Michael C. Fontaine, Frederic Austerlitz, Tatiana Giraud, Frederic Labbé, Daciana Papura, Sylvie Richard-Cervera & Francois Delmotte
Biologic invasions can have important ecological, economic and social consequences, particularly when they involve the introduction and spread of plant invasive pathogens, as they can threaten natural ecosystems and jeopardize the production of human food. Examples include the grapevine downy mildew, caused by the oomycete Plasmopara viticola, an invasive species native to North America, introduced into Europe in the 1870s. We investigated the introduction and spread of this invasive pathogen, by analysing its genetic structure...

Data from: Melanin-based coloration of sneaker male Atlantic salmon is linked to viability and emergence timing of their offspring

Lucas Marie-Orleach, Jean-Marc Roussel, Jérôme Bugeon, Julien Tremblay, Dominique Ombredane & Guillaume Evanno
The ‘good genes’ hypothesis of sexual selection predicts that male ornaments are favoured by female mate choice because male ornament reveals genetic quality. In species with different male reproductive tactics, variation in genetic quality among ‘sneaking’ males has rarely been investigated, as usually ‘sneakers’ are thought not to be chosen by females. Here we focused on the alternative reproductive tactic in Atlantic salmon (Salmo salar Linnaeus, 1758) to test whether the skin colour of sneakers...

Data from: Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach

Jeanne Tonnabel, Isabelle Olivieri, Agnès Mignot, Tony Rebelo, Fabienne Justy, Sylvain Santoni, Stéfanie Caroli, Laure Sauné, Olivier Bouchez, Emmanuel J. P. Douzery, Emmanuel J.P. Douzery & Anthony Rebelo
Despite the recent advances in generating molecular data, reconstructing species-level phylogenies for non-models groups remains a challenge. The use of a number of independent genes is required to resolve phylogenetic relationships, especially for groups displaying low polymorphism. In such cases, low-copy nuclear exons and non-coding regions, such as 3′ untranslated regions (3′-UTRs) or introns, constitute a potentially interesting source of nuclear DNA variation. Here, we present a methodology meant to identify new nuclear orthologous markers...

Data from: Migration and dispersal may drive to high genetic variation and significant genetic mixing: the case of two agriculturally important, continental hoverflies (Episyrphus balteatus and Sphaerophoria scripta)

Lucie Raymond, Manuel Plantegenest & Aude Vialatte
Population structure of pests and beneficial species is an important issue when designing management strategies to optimize ecosystem services. In this study, we investigated for the first time the population structure at a continental scale of two migratory species of hoverflies providing both pest regulation and pollination services [Episyrphus balteatus and Sphaerophoria scripta (Diptera: Syrphidae)]. To achieve this objective, we used two sets of 12 species-specific microsatellite markers on a large-scale sampling from all over...

Data from: High genetic diversity and distinctiveness of rear-edge climate relicts maintained by ancient tetraploidisation for Alnus glutinosa

Olivier Lepais, Serge D. Muller, Samia Ben Saad-Limam, Mohamed Benslama, Laila Rhazi, Djamila Belouahem-Abed, Amina Daoud-Bouattour, Amor Mokhtar Gammar, Zeineb Ghrabi-Gammar & Cécile Fanny Emilie Bacles
Populations located at the rear-edge of a species’ distribution may have disproportionate ecological and evolutionary importance for biodiversity conservation in a changing global environment. Yet genetic studies of such populations remain rare. This study investigates the evolutionary history of North-African low latitude marginal populations of Alnus glutinosa Gaertn., a European tree species that plays a significant ecological role as a keystone of riparian ecosystems. We genotyped 551 adults from 19 populations located across North Africa...

Data from: Inferring the contribution of sexual reproduction, migration and off-season survival to the temporal maintenance of microbial populations: a case study on the wheat fungal pathogen Puccinia striiformis f.sp. tritici

Sajid Ali, Pierre Gladieux, Hidayatur Rahman, Muhammad Shahab Saqib, Muhammad Fiaz, Habib Ahmed, Marc Leconte, Angélique Gautier, Annemarie Fejer Justesen, Mogens Støvring Hovmøller, Jérôme Enjalbert & Claude De Vallavieille-Pope
Understanding the mode of temporal maintenance of plant pathogens is an important domain of microbial ecology research. Due to the inconspicuous nature of microbes, their temporal maintenance cannot be studied directly through tracking individuals and their progeny. Here, we suggest a series of population genetic analyses on molecular marker variation in temporally-spaced samples to infer about the relative contribution of sexual reproduction, off-season survival and migration in the temporal maintenance of pathogen populations. We used...

Data from: Divergent evolutionary processes associated with colonization of offshore islands

Natália Martínková, Ross Barnett, Thomas Cucchi, Rahel Struchen, Marine Pascal, Michel Pascal, Martin C. Fischer, Thomas Higham, Selina Brace, Simon Y. W. Ho, Jean-Pierre Quéré, Paul O'Higgins, Laurent Excoffier, Gerald Heckel, A. Rus Hoelzel, Keith M. Dobney & Jeremy B. Searle
Oceanic islands have been a test ground for evolutionary theory, but here, we focus on the possibilities for evolutionary study created by offshore islands. These can be colonized through various means and by a wide range of species, including those with low dispersal capabilities. We use morphology, modern and ancient sequences of cytochrome b (cytb) and microsatellite genotypes to examine colonization history and evolutionary change associated with occupation of the Orkney archipelago by the common...

Data from: A virus responds instantly to the presence of the vector on the host and forms transmission morphs

Alexandre Martinière, Aurélie Bak, Jean-Luc Macia, Nicole Lautredou, Daniel Gargani, Juliette Doumayrou, Elisa Garzo, Aranzazu Moreno, Alberto Fereres, Stéphane Blanc & Martin Drucker
Many plant and animal viruses are spread by insect vectors. Cauliflower mosaic virus (CaMV) is aphid-transmitted, with the virus being taken up from specialized transmission bodies (TB) formed within infected plant cells. However, the precise events during TB-mediated virus acquisition by aphids are unknown. Here, we show that TBs react instantly to the presence of the vector by ultra-rapid and reversible redistribution of their key components onto microtubules throughout the cell. Enhancing or inhibiting this...

Data from: Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms

Lenaïg Kermarrec, Alain Franc, Frédéric Rimet, Philippe Chaumeil, Jean-François Humbert, Agnès Bouchez & J. F. Humbert
The recent emergence of barcoding approaches coupled to those of Next Generation Sequencing (NGS) have raised new perspectives for studying environmental communities. In this framework, we tested the possibility to derive accurate inventories of diatom communities from pyrosequencing outputs with an available DNA reference library. We used three molecular markers targeting the nuclear, chloroplast and mitochondrial genomes (SSU rDNA, rbcL, and cox1), and three samples of a mock community composed of 30 known diatom strains...

Data from: Reduction of leaf area and symptom severity as proxies of disease-induced plant mortality: the example of the Cauliflower mosaic virus infecting two Brassicaceae hosts

Juliette Doumayrou, Sophie Leblaye, Rémy Froissart & Yannis Michalakis
Disease induced effects on host survival are important to understand the evolution of parasitic virulence and host resistance/tolerance. Unfortunately, experiments evaluating such effects are in most cases logistically demanding justifying the measurement of survival proxies. For plant hosts commonly used proxies are leaf area and the nature and severity of visual qualitative disease symptoms. In this study we tested whether these traits are indeed correlated to the host mortality rate induced by viral infection. We...

Data from: DNA barcoding reveals a largely unknown fauna of Gracillariidae leaf-mining moths in the Neotropics

D. C. Lees, A. Y. Kawahara, R. Rougerie, I. Ohshima, A. Kawakita, O. Bouteleux, J. De Prins & C. Lopez-Vaamonde
Higher taxa often show increasing species richness towards tropical low latitudes, a pattern known as the latitudinal biodiversity gradient (LBG). A rare reverse LBG (with greater richness towards temperate high latitudes) is exhibited by Gracillariidae leaf-mining moths, in which most described species occur in northern temperate areas. We carried out the first assessment of gracillariid species diversity in two Neotropical regions to test whether the relatively low tropical species diversity of this family is genuine...

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...

Registration Year

  • 2013

Resource Types

  • Dataset


  • French National Institute for Agricultural Research
  • French National Centre for Scientific Research
  • Joseph Fourier University
  • Royal Museum for Central Africa
  • University of Hassan II Casablanca
  • Swiss Institute of Bioinformatics
  • South African National Biodiversity Institute
  • Stanford University
  • Ecologie, Systématique et Evolution
  • Kyoto Prefectural University