20 Works

Data from: Diet quality in a wild grazer declines under the threat of an ambush predator

Florian Barnier, Marion Valeix, Patrick Duncan, Simon Chamaillé-Jammes, Philippe Barre, Andrew J. Loveridge, David W. Macdonald, Hervé Fritz & S. Chamaille-Jammes
Predators influence prey populations not only through predation itself, but also indirectly through prompting changes in prey behaviour. The behavioural adjustments of prey to predation risk may carry nutritional costs, but this has seldom been studied in the wild in large mammals. Here, we studied the effects of an ambush predator, the African lion (Panthera leo), on the diet quality of plains zebras (Equus quagga) in Hwange National Park, Zimbabwe. We combined information on movements...

Data from: Development of genomic resources for Nothofagus species using next-generation sequencing data

Veronica Andrea El Mujtar, Leonardo Ariel Gallo, Lang Tiange & Pauline Garnier-Gere
Using next-generation sequencing, we developed the first whole-genome resources for two hybridizing Nothofagus species of the Patagonian forests that crucially lack genomic data, despite their ecological and industrial value. A de novo assembly strategy combining base quality control and optimization of the putative chloroplast gene map yielded ~32 000 contigs from 43% of the reads produced. With 12.5% of assembled reads, we covered ~96% of the chloroplast genome and ~70% of the mitochondrial gene content,...

Data from: Development of SNP genotyping arrays in two shellfish species

Sylvie Lapègue, Estelle Harrang, Serge Heurtebise, Emilie Flahauw, Cécile Donnadieu, Philippe Gayral, Marion Ballenghien, Lucie Genestout, Laetitia Barbotte, Rachid Mahla, Pierrick Haffray & Christophe Klopp
Use of SNPs has been favored due to their abundance in plant and animal genomes, accompanied by the falling cost and rising throughput capacity for detection and genotyping. Here, we present in vitro (obtained from targeted sequencing) and in silico discovery of SNPs, and the design of medium-throughput genotyping arrays for two oyster species, the Pacific oyster, Crassostrea gigas, and European flat oyster, Ostrea edulis. Two sets of 384 SNP markers were designed for two...

Data from: Postglacial climate changes and rise of three ecotypes of harbor porpoises, Phocoena phocoena, in western Palearctic waters

Michaël C. Fontaine, Kathleen Roland, Isabelle Calves, Frederic Austerlitz, Friso P. Palstra, Krystal A. Tolley, Sean Ryan, Marisa Ferreira, Thierry Jauniaux, Angela Llavona, Bayram Öztürk, Ayaka A. Öztürk, Vincent Ridoux, Emer Rogan, Ursula Siebert, Marina Sequeira, Gísli A. Vikingsson, Asunción Borrell, Johan R. Michaux & Alex Aguilar
Despite no obvious barriers to gene flow in the marine realm, environmental variation and ecological specializations can lead to genetic differentiation in highly mobile predators. Here, we investigated the genetic structure of the harbor porpoise over the entire species distribution range in western Palearctic waters. Combined analyses of ten microsatellite loci and a 5,085 bases-pairs portion of the mitochondrial genome revealed the existence of three ecotypes, equally divergent at the mitochondrial genome, distributed in the...

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: Linking niche theory to ecological impacts of successful invaders: insights from resource fluctuation-specialist herbivore interactions

Cindy Gidoin, Lionel Roques & Thomas Boivin
1. Theories of species coexistence and invasion ecology are fundamentally connected and provide a common theoretical framework for studying the mechanisms underlying successful invasions and their ecological impacts. Temporal fluctuations in resource availability and differences in life-history traits between invasive and resident species are considered as likely drivers of the dynamics of invaded communities. Current critical issues in invasion ecology thus relate to the extent to which such mechanisms influence coexistence between invasive and resident...

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: Fitness cost due to herbicide resistance may trigger genetic background evolution

Henri Darmency, Yosra Menchari, Valérie Le Corre & Christophe Délye
This paper investigates the possible existence of mechanisms counterbalancing the negative pleiotropic effects on development and reproduction that are conferred by alleles responsible for herbicide resistance in the weed Alopecurus myosuroides. We considered three herbicide-resistant, mutant acetyl-CoA carboxylase (ACCase) alleles: Leu1781, Asn2041 and Gly2078 found in eight resistant populations. Of these, Gly2078 is the only allele with a known fitness cost. We compared plants homozygous for wild-type ACCase alleles that were siblings of plants carrying...

Data from: The population biology of fungal invasions

Pierre Gladieux, Alice Feurtey, Michael E. Hood, Alodie Snirc, Joanne Clavel, Cyril Dutech, Melanie Roy & Tatiana Giraud
Fungal invasions are increasingly recognized as a significant component of global changes, threatening ecosystem health and damaging food production. Invasive fungi also provide excellent models to evaluate the generality of results based on other eukaryotes. We first consider here the reasons why fungal invasions have long been overlooked: they tend to be inconspicuous, and inappropriate methods have been used for species recognition. We then review the information available on the patterns and mechanisms of fungal...

Data from: Extending the use of ecological models without sacrificing details: a generic and parsimonious meta-modelling approach

Guillaume Marie & Guillaume Simioni
Process-based models (PBMs, see table 1 for a list of abbreviations) are essential tools to assess ecosystem response to climate change, land use changes, extreme weather patterns, or other environmental disturbances. PBMs allow to deal with the high level of interactions and feedbacks which are intrinsic to ecological processes, but their complexity comes at the cost of computation time and memory. Because of that, there is a trade-off between the resolution satisfactory to describe ecological...

Data from: Root community traits along a land use gradient: evidence of a community-level economics spectrum

Iván Prieto, Catherine Roumet, Remi Cardinael, Christian Dupraz, Christophe Jourdan, John H. Kim, Jean Luc Maeght, Zhun Mao, Alain Pierret, Noelia Portillo, Olivier Roupsard, Chantanousone Thammahacksa & Alexia Stokes
1. There is a fundamental trade-off between leaf traits associated with either resource acquisition or resource conservation. This gradient of trait variation, called the economics spectrum also applies to fine roots but whether it is consistent for coarse roots or at the plant community level remains untested. 2. We measured a set of morphological and chemical root traits at a community level (functional parameters; FP) in 20 plant communities located along land-use intensity gradients and...

Data from: Patterns of selection on Plasmodium falciparum erythrocyte binding antigens after the colonisation of the New World

Erhan Yalcindag, Virginie Rougeron, Eric Elguero, Céline Arnathau, Patrick Durand, Sylvain Brisse, Laure Diancourt, Agnes Aubouy, Pierre Becquart, Umberto D'Alessandro, Didier Fontenille, Dionicia Gamboa, Amanda Maestre, Didier Ménard, Lise Musset, Oscar Noya, Vincent Veron, Albina Wide, Bernard Carme, Eric Legrand, Christine Chevillon, Francisco J. Ayala, François Renaud & Franck Prugnolle
Pathogens, which have recently colonized a new host species or new populations of the same host, are interesting models for understanding how populations may evolve in response to novel environments. During its colonization of South America from Africa Plasmodium falciparum, the main agent of malaria, has been exposed to new conditions in distinctive new human populations (Amerindian and populations of mixed origins), that likely exerted new selective pressures on the parasite's genome. Among the genes...

Data from: Environmental DNA surveillance for invertebrate species: advantages and technical limitations to detect invasive crayfish Procambarus clarkii in freshwater ponds

Anne Tréguier, Jean-Marc Paillisson, Tony Dejean, Alice Valentini, Martin A. Schlaepfer & Jean-Marc Roussel
1. The introduction of non-native species is a major threat to biodiversity. While eradication programs of well-established invaders are costly and hazardous for non-target species, the early detection of a non-native species at low density is critical for preventing biological invasions in recipient ecosystems. Recent studies reveal that environmental DNA (eDNA) is a powerful tool for detecting target species in aquatic ecosystems, but these studies focus mostly on fish and amphibians. 2. We examine the...

Data from: Genetic and phenotypic changes in an Atlantic salmon population supplemented with non-local individuals: a longitudinal study over 21 years

Sabrina Le Cam, Charles Perrier, Anne-Laure Besnard, Louis Bernatchez, Guillaume Evanno & A.-L. Besnard
While introductions and supplementations using non-native and potentially domesticated individuals may have dramatic evolutionary effects on wild populations, few studies documented the evolution of genetic diversity and life-history traits in supplemented populations. Here, we investigated year-to-year changes from 1989 to 2009 in genetic admixture at 15 microsatellite loci and in phenotypic traits in an Atlantic salmon (Salmo salar) population stocked during the first decade of this period with two genetically and phenotypically distinct source populations....

Data from: Detecting short spatial scale local adaptation and epistatic selection in climate-related candidate genes in European beech (Fagus sylvatica) populations

Katalin Csilléry, Hadrien Lalagüe, Giovanni G. Vendramin, Santiago C. González-Martínez, Bruno Fady & Sylvie Oddou-Muratorio
Detecting signatures of selection in tree populations threatened by climate change is currently a major research priority. Here, we investigated the signature of local adaptation over a short spatial scale using 96 European beech (Fagus sylvatica L.) individuals originating from two pairs of populations on the northern and southern slopes of Mont Ventoux (south-eastern France). We performed both single and multilocus analysis of selection based on 53 climate-related candidate genes containing 546 SNPs. FST outlier...

Data from: Host range expansion of native insects to exotic trees increases with area of introduction and presence of congeneric native trees

Manuela Branco, Eckehard G. Brockerhoff, Bastien Castagneyrol, Christophe Orazio & Hervé Jactel
1. Exotic tree species are widely used in forest plantations for their often high productivity and performance compared to native trees. However, these advantages may be compromised by herbivore damage. 2. A list of European insect species that have expanded their host range to one of 28 exotic tree species introduced to Europe was compiled from a systematic literature review. The number of successful expansions was analysed using three predictors: (1) phylogenetic relatedness between exotic...

Data from: Cheaper isn’t always worse: more protective isolates of a defensive symbiont are less costly to the aphid host

Luis Cayetano, Lukas Rothacher, Jean-Christophe Simon, Christoph Vorburger & J.-C. Simon
Defences against parasites are typically associated with costs to the host that contribute to the maintenance of variation in resistance. This also applies to the defence provided by the facultative bacterial endosymbiont Hamiltonella defensa, which protects its aphid hosts against parasitoid wasps while imposing life-history costs. To investigate the cost–benefit relationship within protected hosts, we introduced multiple isolates of H. defensa to the same genetic backgrounds of black bean aphids, Aphis fabae, and we quantified...

Data from: Genetic diversity and population structure of wild/weedy eggplant (Solanum insanum L., Solanaceae) in southern India: implications for conservation

Evans Mutegi, Allison A. Snow, Rajkumar Mathu, Remy Pasquest, Hopeland Ponniah, Marie-Christine Daunay, Priya Davidar & Muthu Rajkumar
Mutegi et al eggplant SSR dataAn excel file with microsatellite data for the 10 natural populations of wild/weedy eggplant (S. insanum) and the 3 cultivar populations studied. A sheet with metadata to describe the fields is included.Mutegi et al Eggplant data1.xlsx

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...

Data from: Genomic regions repeatedly involved in divergence among plant-specialized pea aphid biotypes

Pierre Nouhaud, Jean Peccoud, Frédérique Mahéo, Lucie Mieuzet, Julie Jaquiéry & Jean-Christophe Simon
Understanding the genetic bases of biological diversification is a long-standing goal in evolutionary biology. Here we investigate whether replicated cases of adaptive divergence involve the same genomic regions in the pea aphid, Acyrthosiphon pisum, a large complex of genetically differentiated biotypes, each specialized on different species of legumes. A previous study identified genomic regions putatively involved in host-plant adaptation and/or reproductive isolation by performing a hierarchical genome scan in three biotypes. This led to the...

Registration Year

  • 2014

Resource Types

  • Dataset


  • French National Institute for Agricultural Research
  • French National Centre for Scientific Research
  • University of Montpellier
  • University of Paris-Sud
  • Ecologie des Forêts Méditerranéennes
  • Paul Sabatier University
  • University of Bordeaux
  • Swiss Federal Institute of Technology in Zurich
  • Centre de Biologie et de Gestion des Populations
  • Centre de Coopération Internationale en Recherche Agronomique pour le Développement