87 Works

Data from: Finding candidate genes under positive selection in non-model species: examples of genes involved in host specialization in pathogens

Gabriela Aguileta, Juliette Lengelle, Sylvain Marthey, Hélène Chiapello, François Rodolphe, Annie Gendrault, Roxana Yockteng, Elodie Vercken, Benjamin Devier, Michael Fontaine, Patrick Wincker, Carole Dossat, Corinne Cruaud, Arnaud Couloux & Tatiana Giraud
Numerous genes in diverse organisms have been shown to be under positive selection, especially genes involved in reproduction, adaptation to contrasting environments, hybrid inviability, and host-pathogen interactions. Looking for genes under positive selection in pathogens has been a priority in efforts to investigate coevolution dynamics and to develop vaccines or drugs. To elucidate the functions involved in host specialization, here we aimed at identifying candidate sequences that could have evolved under positive selection among closely...

Data from: Genetic diversity of oilseed rape fields and feral populations in the context of coexistence with GM crops

Diane Bailleul, Sébastien Ollier & Jane Lecomte
Despite growing concern about transgenes escaping from fields, few studies have analysed the genetic diversity of crops in an agroecosystem over several years. Accurate information about the dynamics and relationship of the genetic diversity of crops in an agroecosystem is essential for risk assessment and policies concerning the containment of genetically modified crops and their coexistence with crops grown by conventional practices. Here, we analysed the genetic diversity of oilseed rape plants from fields and...

Data from: Association mapping for phenology and plant architecture in maize shows higher power for developmental traits compared with growth influenced traits

Sophie Bouchet, Pascal Bertin, Thomas Presterl, Philippe Jamin, Denis Coubriche, Brigitte Gouesnard, Jacques Laborde & Alain Charcosset
Plant architecture, phenology and yield components of cultivated plants have repeatedly been shaped by selection to meet human needs and adaptation to different environments. Here we assessed the genetic architecture of 24 correlated maize traits that interact during plant cycle. Overall, 336 lines were phenotyped in a network of 9 trials and genotyped with 50K single-nucleotide polymorphisms. Phenology was the main factor of differentiation between genetic groups. Then yield components distinguished dents from lower yielding...

Data from: Evolutionary radiations of Proteaceae are triggered by the interaction between traits and climates in open habitats

Renske E. Onstein, Gregory J. Jordan, Hervé Sauquet, Peter H. Weston, Yanis Bouchenak-Khelladi, Ian J. Wright, Raymond J. Carpenter & H. Peter Linder
Aim: Ecologically driven diversification can create spectacular diversity in both species numbers and form. However, the prediction that the match between intrinsic (e.g. functional trait) and extrinsic (e.g. climatic niche) variables may lead to evolutionary radiation has not been critically tested. Here, we test this hypothesis in the Southern Hemisphere plant family Proteaceae, which shows a spectacular diversity in open mediterranean shrublands in the Southwest Australian Floristic Region (SWAFR) and the Cape Floristic Region (CFR)....

Data from: Comparing van Oosterhout and Chybicki-Burczyk methods of estimating null allele frequencies for inbred populations

Pascal Campagne, Peter E. Smouse, Georges Varouchas, Jean-Francois Silvain, Bruno Le Rü, J.-F. Silvain & B. Leru
In spite of the usefulness of codominant markers in population genetics, the existence of null alleles raises challenging estimation issues in natural populations that are characterized by positive inbreeding coefficients (F > 0). Disregarding the possibility of F > 0 in a population will generally lead to overestimates of null allele frequencies. Conversely, estimates of inbreeding coefficients (F) may be strongly biased upwards (excess homozygotes), in the presence of nontrivial frequencies of null alleles. An...

Data from: Why do mixotrophic plants stay green? A comparison between green and achlorophyllous orchid individuals in situ

Melanie Roy, Cedric Gonneau, Alain Rocheteau, Daniel Berveiller, Jean-Claude Thomas, Claire Damesin, Marc André Selosse & M.-A. Selosse
Some forest plants adapt to shade by mixotrophy, i.e., they obtain carbon both from photosynthesis and from their root mycorrhizal fungi. Fully achlorophyllous species using exclusively fungal carbon (the so-called mycoheterotrophic plants) have repeatedly evolved from such mixotrophic ancestors. However, adaptations for this evolutionary transition, and the reasons why it has happened a limited number of times, remain unknown. We investigated this using achlorophyllous variants (i.e., albinos) spontaneously occurring in Cephalanthera damasonium, a mixotrophic orchid....

3D models of planetary bodies

Frederic Schmidt, Gaspard Salomon & Laurent Daumas
Current technology allows us to print various object in 3D for teaching and education purposes, including for the visually disabled [1]. The use of 3D printer for planetary science has been perceived since the premises of this industrial revolution [2]. In parallel several services and web-services have been developed to help the users to create their own model [3]. We propose here a database of ready-to-use 3D model of planetary bodies at full scale.

Exploring the effects of trifluoromethyl group in the design of organocatalysts, enzyme inhibitors and in the conformational control of saturated nitrogen-containing heterocycles

Volodymyr Sukach, Sergii Melnykov, Sylvain Bertho & Pascal Retailleau

Data from: Dearth of polymorphism associated with a sustained response to selection for flowering time in maize

Eleonore Durand, Maud I. Tenaillon, Xavier Raffoux, Stéphanie Thépot, Matthieu Falque, Philippe Jamin, Aurélie Bourgais, Adrienne Ressayre & Christine Dillmann
Background: Long term selection experiments bring unique insights on the genetic architecture of quantitative traits and their evolvability. Indeed, they are utilized to (i) monitor changes in allele frequencies and assess the effects of genomic regions involved traits determinism; (ii) evaluate the role of standing variation versus new mutations during adaptation; (iii) investigate the contribution of non allelic interactions. Here we describe genetic and phenotypic evolution of two independent Divergent Selection Experiments (DSEs) for flowering...

Data from: Inference of domestication history and differentiation between early- and late-flowering varieties in pearl millet

Yann Dussert, Alodie Snirc & Thierry Robert
Pearl millet (Pennisetum glaucum) is a staple crop in Sahelian Africa. Farmers usually grow varieties with different cycle lengths and complementary functions in Sahelian agrosystems. Both the level of genetic differentiation of these varieties and the domestication history of pearl millet have been poorly studied. We investigated the neutral genetic diversity and population genetic structure of early- and late-flowering domesticated and wild pearl millet populations using 18 microsatellite loci and 8 nucleotide sequences. Strikingly, early-...

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: Escape from predators and genetic variance in birds

Yiting Jiang & Anders Pape Møller
Predation is a common cause of death in numerous organisms, and a host of anti-predator defenses have evolved. Such defenses often have a genetic background as shown by significant heritability and micro-evolutionary responses towards weaker defenses in the absence of predators. Flight initiation distance (FID) is the distance at which an individual animal takes flight when approached by a human, and hence it reflects the life history compromise between risk of predation and the benefits...

Data from: Tillage and herbicide reduction mitigate the gap between conventional and organic farming effects on foraging activity of insectivorous bats

Kévin Barré, Isabelle Le Viol, Romain Julliard, François Chiron & Christian Kerbiriou
The increased use of pesticides and tillage intensification is known to negatively affect biodiversity. Changes in these agricultural practices such as herbicide and tillage reduction have variable effects among taxa, especially at the top of the trophic network including insectivorous bats. Very few studies compared the effects of agricultural practices on such taxa, and overall, only as a comparison of conventional versus organic farming without accurately accounting for underlying practices, especially in conventional where many...

Data from: Historical mutation rates predict susceptibility to radiation in Chernobyl birds

Anders P Møller, Johannes Erritzøe, Filiz Karadas & Timothy A Mousseau
Extreme environmental perturbations are rare, but may have important evolutionary consequences. Responses to current perturbations may provide important information about the ability of living organisms to cope with similar conditions in the evolutionary past. Radioactive contamination from Chernobyl constitutes one such extreme perturbation, with significant but highly variable impact on local population density and mutation rates of different species of animals and plants. We explicitly tested the hypothesis that species with strong impacts of radiation...

Data from: Multiple components of environmental change drive populations of breeding waders in seminatural grasslands

Karsten Laursen, Javier Balbontín, Ole Thorup, Henrik Haaning Nielsen, Tommy Asferg & Anders Pape Møller
Environments are rapidly changing due to climate change, land-use, intensive agriculture and the impact of hunting on predator populations. Here we analysed long-term data recorded during 1928-2014 on the size of breeding populations of waders at two large nature reserves in Denmark, Vejlerne and Tipperne, to determine the effects of components of environmental change on breeding populations of waders. Waders are closely associated with coastal marshes and meadows, and such habitats have been reduced extensively...

Data from: A nonrandom subset of olfactory genes is associated with host preference in the fruit fly Drosophila orena

Aaron A. Comeault, Antonio Serrato-Capuchina, David A. Turissini, Patrick J. McLaughlin, Jean R. David & Daniel R. Matute
Specialization onto different host plants has been hypothesized to be a major driver of diversification in insects, and traits controlling olfaction have been shown to play a fundamental role in host preferences. A diverse set of olfactory genes control olfactory traits in insects, and it remains unclear whether specialization onto different hosts is likely to involve a nonrandom subset of these genes. Here, we test the role of olfactory genes in a novel case of...

Data from: Virtual patients and sensitivity analysis of the Guyton model of blood pressure regulation: towards individualized models of whole-body physiology

Robert Moss, Thibault Grosse, Ivanny Marchant, Nathalie Lassau, François Gueyffier & S. Randall Thomas
Mathematical models that integrate multi-scale physiological data can offer insight into physiological and pathophysiological function, and may eventually assist in individualized predictive medicine. We present a methodology for performing systematic analyses of multi-parameter interactions in such complex, multi-scale models. Human physiology models are often based on or inspired by Arthur Guyton’s whole-body circulatory regulation model. Despite the significance of this model, it has not been the subject of a systematic and comprehensive sensitivity study. Therefore,...

Data from: Sibling competition arena: selfing and a competition arena can combine to constitute a barrier to gene flow in sympatry

Amanda Kyle Gibson, Michael E. Hood & Tatiana Giraud
Closely-related species coexisting in sympatry provide critical insight into the mechanisms underlying speciation and the maintenance of genetic divergence. Selfing may promote reproductive isolation by facilitating local adaptation, causing reduced hybrid fitness in parental environments. Here, we propose a novel mechanism by which selfing can further impair interspecific gene flow: selfing may act to ensure that non-hybrid progeny systematically co-occur whenever hybrid genotypes are produced. Under a competition arena, the fitness differentials between non-hybrid and...

Data from: Should the WHO growth charts be used in France?

Pauline Scherdel, Jérémie Botton, Marie-Françoise Rolland-Cachera, Juliane Léger, Fabienne Pelé, Pierre Yves Ancel, Chantal Simon, Katia Castetbon, Benoit Salanave, Hélène Thibault, Sandrine Lioret, Sandrine Péneau, Gaelle Gusto, Marie-Aline Charles & Barbara Heude
Background: Growth charts are an essential clinical tool for evaluating a child's health and development. The current French reference curves, published in 1979, have recently been challenged by the 2006 World Health Organization (WHO) growth charts. Objective: To evaluate and compare the growth of French children who were born between 1981 and 2007, with the WHO growth charts and the French reference curves currently used. Design: Anthropometric measurements from French children, who participated in 12...

Data from: Local dynamics of a fast evolving sex-ratio system in Drosophila simulans

Héloïse Bastide, Pierre R. Gérard, David Ogereau, Michel Cazemajor & Catherine Montchamp-Moreau
By distorting Mendelian transmission to their own advantage, X-linked meiotic drive elements can rapidly spread in natural populations, generating a sex-ratio bias. One expected consequence is the triggering of a coevolutionary arms race between the sex chromosome that carries the distorter and suppressors counteracting its effect. Such an arms race has been theoretically and experimentally established, and can have many evolutionary consequences. However, its dynamics in contemporary populations is still poorly documented. Here, we investigate...

Data from: High-throughput sequencing of Bacillus anthracis in France: investigating genome diversity and population structure using whole-genome SNP discovery

Guillaume Girault, Yann Blouin, Gilles Vergnaud & Sylviane Derzelle
Background: Single nucleotide polymorphisms (SNPs) are ideal signatures for subtyping monomorphic pathogens such as Bacillus anthracis. Here we report the use of next-generation sequencing technology to investigate the historical, geographic and genetic diversity of Bacillus anthracis in France. 122 strains isolated over a 50-years period throughout the country were whole-genome sequenced and comparative analyses were carried out with a focus on SNPs discovery to discriminate regional sub-groups of strains.Results: A total of 1581 chromosomal SNPs...

Data from: Migratory connectivity and effects of winter temperatures on migratory behaviour of the European robin Erithacus rubecula: a continent-wide analysis

Roberto Ambrosini, José Cuervo, Chris Du Feu, Wolfgang Fiedler, Musitelli Federica, Diego Rubolini, Beatrice Sicurella, Fernando Spina, Nicola Saino, Anders Møller & Federica Musitelli
1. Many partially migratory species show phenotypically divergent populations in terms of migratory behaviour, with climate hypothesized to be a major driver of such variability through its differential effects on sedentary and migratory individuals. 2. Based on long-term (1947–2011) bird ringing data, we analysed phenotypic differentiation of migratory behaviour among populations of the European robin Erithacus rubecula across Europe. 3. We showed that clusters of populations sharing breeding and wintering ranges varied from partial (British...

Data from: Migration patterns and changes in population biology associated with the worldwide spread of the oilseed rape pathogen Leptosphaeria maculans

Azita Dilmaghani, Pierre Gladieux, Lilian Gout, Tatiana Giraud, Patrick C. Brunner, Anna Stachowiak, Marie-Hélène Balesdent & Thierry Rouxel
Pathogen introductions into novel areas can lead to the emergence of new fungal diseases of plants. Understanding the origin, introduction pathways, possible changes in reproductive system and population size of fungal pathogens is essential in devising an integrated strategy for the control of these diseases. We used minisatellite markers to infer the worldwide invasion history of the fungal plant pathogen Leptosphaeria maculans, which causes stem canker (blackleg) of oilseed and vegetable brassicas. Clustering analyses partitioned...

Data from: Independent domestications of cultivated tree peonies from different wild peony species

Jun-Hui Yuan, Amandine Cornille, Tatiana Giraud, Fang-Yun Cheng & Yong-Hong Hu
An understanding of plant domestication history provides insights into general mechanisms of plant adaptation and diversification and can guide breeding programs that aim to improve cultivated species. Cultivated tree peonies (genus Paeonia L.) are among the most popular ornamental plants in the world, yet the history of their domestication is still unresolved. Here, we explored whether the domestication in China of historically cultivated peonies, i.e., the common and flare cultivated tree peonies, was a single...

Data from: Barriers to gene flow in the marine environment: insights from two common intertidal limpet species of the Atlantic and Mediterranean

Alexandra Sá Pinto, Madalena Simas Branco, Paulo Barros Alexandrino, Michaël C. Fontaine & Stuart J. E. Baird
Knowledge of the scale of dispersal and the mechanisms governing gene flow in marine environments remains fragmentary despite being essential for understanding evolution of marine biota and to design management plans. We use the limpets Patella ulyssiponensis and Patella rustica as models for identifying factors affecting gene flow in marine organisms across the North-East Atlantic and the Mediterranean Sea. A set of allozyme loci and a fragment of the mitochondrial gene cytochrome C oxidase subunit...

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  • University of Paris-Sud
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