175 Works

Data from: Polymorphism pattern at a Miniature Inverted-repeat Transposable Element locus downstream of the domestication gene Teosinte-branched1 in wild and domesticated pearl millet

Yann Dussert, Marie-Stanislas Remigereau, Michael C. Fontaine, Alodie Snirc, Ghayas Lakis, Solenn Stoeckel, Thierry Langin, Aboubakry Sarr, Thierry Robert & M.-S. Remigereau
Unraveling the mechanisms involved in adaptation to understand plant morphological evolution is a challenging goal. For crop species, identification of molecular causal polymorphisms involved in domestication traits are central to this issue. Pearl millet, a domesticated grass mostly found in semi-arid areas of Africa and India, is an interesting model to address this topic: the domesticated form shares common derived phenotypes with some other cereals such as a decreased ability to develop basal and axillary...

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: Fungal adaptation to contemporary fungicide applications: the case of Botrytis cinerea populations from Champagne vineyards (France)

Anne-Sophie Walker, Virginie Ravigné, Adrien Rieux, S. Ali, F. Carpentier, Elisabeth Fournier, V. Ravigne & A.-S. Walker
In addition to being one of the most acute problems impeding chemical control of fungal diseases, the evolution of fungicide resistance is an emblematic case of local adaptation to spatially heterogeneous and temporally variable selection pressures. Here we dissected the adaptation of Botrytis cinerea (the causal agent of grey mould) populations on grapes to several fungicides. We carried out a 2-year survey (four collection dates) on three treated/untreated pairs of plots from vineyards in Champagne...

Data from: Host specialization involving attraction, avoidance and performance, in two phytophagous moth species

Marion Orsucci, Philippe Audiot, Alexandra Pommier, Christophe Raynaud, Béatrice Ramora, Anne Zanetto, Denis Bourguet & Réjane Streiff
Host specialization plays a key role in the extreme diversification of phytophagous insects. Whereas proximate mechanisms of specialization have been studied extensively, their consequences for species divergence remain unclear. Preference for, and performance on hosts are thought to be a major source of divergence in phytophagous insects. We assessed these major components of specialization in two moth species, the European corn borer (ECB) and the Adzuki bean borer (ABB), by testing their oviposition behaviour in...

Data from: Cytonuclear discordance among the Southeast Asian Black rats (Rattus rattus complex)

Marie Pagès, Eric Bazin, Maxime Galan, Yannick Chaval, Julien Claude, Vincent Herbreteau, Johan Michaux, Sylvain Piry, Serge Morand & Jean-François Cosson
Black rats are major invasive vertebrate pests with severe ecological, economic and health impacts. Remarkably, their evolutionary history has received little attention, and there is no firm agreement on how many species should be recognized within the black rat complex. This species complex is native to India and Southeast Asia. According to current taxonomic classification, there are three taxa living in sympatry in several parts of Thailand, Cambodia and Lao People's Democratic Republic, where this...

Data from: Sylleptic branching in winter-headed apple (Malus × domestica) trees: accession-dependent responses and their relationships with other tree architectural characteristics

Stijn Vanderzande, Niek Hias, Daniel Edge-Garza, Evelyne Costes, Mark W. Davey & Johan Keulemans
Well-feathered apple trees are essential for commercial orchards to optimize yields. However, most cultivars do not form these sylleptic branches readily in commercial nurseries due to high apical dominance. Several treatments exist to promote their formation in the nurseries, one of which is heading. However, not all cultivars are expected to react similarly to these treatments. We studied the branching response of 155 genotypes following heading and its relation to other architectural traits as a...

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: Tree, sex and size: ecological determinants of male versus female fecundity in three Fagus sylvatica stands

Sylvie Oddou-Muratorio, Julie Gauzere, Aurore Bontemps, Jean-François Rey & Etienne K. Klein
Inter-individual variation in fecundities has major consequences on population evolutionary potential, through genetic drift and selection. Using two spatially explicit mating models that analyze the genotypes of seeds and seedlings, we investigated the variation of male and female fecundities within and among three European beech (Fagus sylvatica) stands situated along an elevational gradient. Female and male individual fecundity distributions were both skewed in this monoecious species, and we found a higher variance in female as...

Data from: Colonization of the Mediterranean Basin by the vector biting midge species Culicoides imicola: an old story

Stephanie Jacquet, Claire Garros, Eric Lombaert, Catherine Walton, Johana Restrepo, Xavier Allene, Thierry Baldet, Catherine Cetre-Sossah, Alexandra Chaskopoulou, Jean-Claude Delecolle, Amelie Desvars, Mouloud Djerbal, Moussa Fall, Laetitia Gardes, Michel De Garine-Wichatitsky, Maria Goffredo, Yuval Gottlieb, Assane Gueye Fall, Muo Kasina, Karien Labuschagne, Youssef Lhor, Javier Lucientes, Thibaud Martin, Bruno Mathieu, Miguel Miranda … & J.-C. Delecolle
Understanding the demographic history and genetic make-up of colonizing species is critical for inferring population sources and colonization routes. This is of main interest for designing accurate control measures in areas newly colonized by vector species of economically important pathogens. The biting midge Culicoides imicola is a major vector of orbiviruses to livestock. Historically, the distribution of this species was limited to the Afrotropical region. Entomological surveys first revealed the presence of C. imicola in...

Data from: Biological traits, rather than environment, shape detection curves of large vertebrates in neotropical rainforests

Thomas Denis, Cécile Richard-Hansen, Olivier Brunaux, Marie-Pierre Etienne, Stéphane Guitet & Bruno Hérault
Line transect surveys are widely used in neotropical rainforests to estimate the population abundance of medium- and large-sized vertebrates. The use of indices such as Encounter Rate has been criticized because the probability of animal detection may fluctuate due to the heterogeneity of environmental conditions among sites. In addition, the morphological and behavioral characteristics (biological traits) of species affect their detectability. In this study, we compared the extent to which environmental conditions and species’ biological...

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: Forest management adaptation to climate change: a Cornelian dilemma between drought resistance and soil macro-detritivore functional diversity

Ludovic Henneron, Michaël Aubert, Fabrice Bureau, Yann Dumas, François Ningre, Sandrine Perret, Claudine Richter, Philippe Balandier & Matthieu Chauvat
1. Global warming induces new constraints on forest ecosystems and requires forest management adaptation. The reduction in stand density is currently debated as a potential tool to face increasing summer drought risk by improving forest resistance to climate change-induced tree mortality. However, few studies have yet assessed the impacts of this management change on soil biodiversity. 2. We conducted a large-scale, multi-site assessment of the response of soil macro-detritivore assemblages and soil functioning to experimental...

Data from: Inferences on population history of a seed chalcid wasp: invasion success despite a severe founder effect from an unexpected source population

Marie-Anne Auger-Rozenberg, Thomas Boivin, Emmanuelle Magnoux, Claudine Courtin, Alain Roques & Carole Kerdelhué
Most invasive species established in Europe originate from either Asia or North America, but little is currently known about the potential of the Anatolian Peninsula (Asia Minor) and/or the Near East to constitute invasion sources. Mediterranean forests are generally fragile ecosystems that can be threatened by invasive organisms coming from different regions of the Mediterranean Basin, but for which historical data are difficult to gather and the phylogeographic patterns are still poorly understood for most...

Data from: It’s all about connections: hubs and invasion in habitat networks

Thibaut Morel-Journel, Claire Rais Assa, Ludovic Mailleret & Elodie Vercken
During the early stages of invasion, the interaction between the features of the invaded landscape, notably its spatial structure, and the internal dynamics of an introduced population, has a crucial impact on establishment and spread. By approximating introduction areas as networks of patches linked by dispersal, we characterized their spatial structure with specific metrics and tested their impact on two essential steps of the invasion process: establishment and spread. By combining simulations with experimental introductions...

Data from: Digging through model complexity: using hierarchical models to uncover evolutionary processes in the wild

Mathieu Buoro, Etienne Prévost & Olivier Gimenez
The growing interest for studying questions in the wild requires acknowledging that eco-evolutionary processes are complex, hierarchically structured and often partially observed or with measurement error. These issues have long been ignored in evolutionary biology, which might have led to flawed inference when addressing evolutionary questions. Hierarchical modelling (HM) has been proposed as a generic statistical framework to deal with complexity in ecological data and account for uncertainty. However, to date, HM has seldom been...

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: Phenotypic selection and covariation in the life‐history traits of elephant seals: heavier offspring gain a double selective advantage

W. Chris Oosthuizen, Res Altwegg, Marie Nevoux, Marthán N. Bester, P.J. Nico De Bruyn & P. J. Nico De Bruyn
Early developmental conditions contribute to individual heterogeneity of both phenotypic traits and fitness components, ultimately affecting population dynamics. Although the demographic consequences of ontogenic growth are best quantified using an integrated measure of fitness, most analyses to date have instead studied individual fitness components in isolation. Here, wWe estimated phenotypic selection on weaning mass in female southern elephant seals (Mirounga leonina) by analyzing individual-based data collected between 1986 and 2016 with capture-recapture and matrix projection...

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: 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: Are generalist Aphidiinae (Hym. Braconidae) mostly cryptic species complexes?

Stéphane A. P. Derocles, Manuel Plantegenest, Jean-Yves Rasplus, Alexia Marie, Darren M. Evans, David H. Lunt & Anne Le Ralec
Aphidiinae are mostly composed of specialist parasitoids and the few species described as generalist are suspected to be composed of cryptic specialists, almost indistinguishable based on morphological characteristics. The use of molecular markers has proven to be a useful tool for revealing cryptic species complexes and here we use seven mitochondrial and nuclear gene fragments to study possible genetic differentiation among seven Aphidiinae generalists. Maximum likelihood (ML) trees and Bayesian Poisson tree processes (bPTP) models...

Data from: Extracellular DNA extraction is a fast, cheap and reliable alternative for multi-taxa surveys based on soil DNA

Lucie Zinger, Jérôme Chave, Eric Coissac, Amaia Iribar, Eliane Louisanna, Sophie Manzi, Vincent Schilling, Heidy Schimann, Guilhem Sommeria-Klein & Pierre Taberlet
DNA metabarcoding on soil samples is increasingly used for large-scale and multi-taxa biodiversity studies. However, DNA extraction may be a major bottleneck for such wide uses. It should be cost/time effective and allow dealing with large sample volumes so as to maximise the representativeness of both micro- and macro-organisms diversity. Here, we compared the performances of a fast and cheap extracellular DNA extraction protocol with a total DNA extraction method in retrieving bacterial, eukaryotic and...

Data from: Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes

Quentin Rougemont, Pierre-Alexandre Gagnaire, Charles Perrier, Clémence Genthon, Anne-Laure Besnard, Sophie Launey & Guillaume Evanno
Understanding the evolutionary mechanisms generating parallel genomic divergence patterns among replicate ecotype pairs remains an important challenge in speciation research. We investigated the genomic divergence between the anadromous parasitic river lamprey (Lampetra fluviatilis) and the freshwater-resident nonparasitic brook lamprey (Lampetra planeri) in nine population pairs displaying variable levels of geographic connectivity. We genotyped 338 individuals with RAD sequencing and inferred the demographic divergence history of each population pair using a diffusion approximation method. Divergence patterns...

Data from: Automixis in Artemia: solving a century-old controversy

Odrade Nougué, Nicolas O. Rode, Roula Zahab, Adeline Ségard, Luis-Miguel Chevin, Christoph R. Haag, Thomas Lenormand & R. Jabbour-Zahab
Parthenogenesis (reproduction through unfertilized eggs) encompasses a variety of reproduction modes with (automixis) or without (apomixis) meiosis. Different modes of automixis have very different genetic and evolutionary consequences but can be particularly difficult to tease apart. In this paper, we propose a new method to discriminate different types of automixis from population-level genetic data. We apply this method to diploid Artemia parthenogenetica, a crustacean whose reproductive mode remains controversial despite a century of intensive cytogenetic...

Data from: Integrating encounter theory with decision analysis to evaluate collision risk and determine optimal protection zones for wildlife

Bradley J. Udell, Julien Martin, , Mathieu Bonneau, Holly Edwards, Timothy A. Gowan, Stacie K. Hardy, Eliezer Gurarie, Charles Calleson, Charles J. Deutsch, Robert J. Fletcher & Charles S. Calleson
1. Better understanding human-wildlife interactions and their links with management can help improve the design of wildlife protection zones. One important example is the problem of wildlife collisions with vehicles or human-built structures (e.g. power lines, wind farms). In fact, collisions between marine wildlife and watercraft are among the major threats faced by several endangered species of marine mammals. Natural resource managers are therefore interested in finding cost-effective solutions to mitigate these threats. 2. We...

Data from: A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird

Yann X.C. Bourgeois, Boris Delahaie, Mathieu Gautier, Emeline Lhuillier, Pierre-Jean G. Malé, Joris A.M. Bertrand, Josselin Cornuault, Kazumasa Wakamatsu, Olivier Bouchez, Claire Mould, Jade Bruxaux, Hélène Holota, Borja Mila, Christophe Thébaud, Joris A. M. Bertrand & Yann X. C. Bourgeois
Understanding the mechanisms responsible for phenotypic diversification within and among species ultimately rests with linking naturally occurring mutations to functionally and ecologically significant traits. Colour polymorphisms are of great interest in this context because discrete colour patterns within a population are often controlled by just a few genes in a common environment. We investigated how and why phenotypic diversity arose and persists in the Zosterops borbonicus white-eye of Reunion (Mascarene archipelago), a colour polymorphic songbird...

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