87 Works

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: Crop-to-wild gene flow and its fitness consequences for a wild fruit tree: towards a comprehensive conservation strategy of the wild apple in Europe

Alice Feurtey, Amandine Cornille, Jacqui A. Shykoff, Alodie Snirc & Tatiana Giraud
Crop-to-wild gene flow can reduce the fitness and genetic integrity of wild species. Malus sylvestris, the European crabapple fruit tree, in particular is threatened by the disappearance of its habitat and by gene flow from its domesticated relative, Malus domestica. With the aims of evaluating threats for M. sylvestris and of formulating recommendations for its conservation, we studied here, using microsatellite markers and growth experiments: i) hybridization rates in seeds and trees from a French...

Data from: Brain size and the risk of getting shot

Anders Pape Møller & Johannes Erritzøe
Hunting kills hundreds of millions of animals annually, potentially constituting an important selection pressure on hunted species. We hypothesized that hunted individuals differing from survivors by having better ability to distinguish between dangerous humans and other human beings would be at a selective advantage. We tested whether shot individual birds had smaller brains than survivors, under the assumption that individuals with larger brains had superior escape ability. We used a large database on birds from...

Data from: Brain regions associated with visual cues are important for bird migration

Orsolya Vincze, Csongor I. Vágási, Péter L. Pap, Gergely Osváth & Anders Pape Møller
Long-distance migratory birds have relatively smaller brains than short-distance migrants or residents. Here, we test whether reduction in brain size with migration distance can be generalized across the different brain regions suggested to play key roles in orientation during migration. Based on 152 bird species, belonging to 61 avian families from six continents, we show that the sizes of both the telencephalon and the whole brain decrease, and the relative size of the optic lobe...

Data from: A longitudinal study of age-related changes in Haemoproteus infection in a passerine bird

Alfonso Marzal, Javier Balbontín, Maribel Reviriego, Luz García-Longoria, Carmen Relinque, Ignacio G Hermosell, Sergio Magallanes, Cosme López-Calderón, Florentino De Lope & Anders Pape Moller
Blood parasites such as malaria and related haemosporidians commonly infect vertebrate species including birds. Understanding age-specific patterns of parasite infections is crucial for quantifying the fitness consequences of parasitism for hosts and for understanding parasite transmission dynamics. We analyzed longitudinal and cross-sectional infection data in house martins Delichon urbica, a migratory bird suffering from intense haemosporidian infection. We separated within- from among-individual effects of age on prevalence. Our results showed that the probability of blood...

Data from: Past and present dynamics of sorghum and pearl millet diversity in Mount Kenya region

Vanesse Labeyrie, Monique Deu, Yann Dussert, Bernard Rono, Françoise Lamy, Charles Marangu, Dan Kiambi, Caroline Calatayud, Geo Coppens D’Eeckenbrugge, Thierry Robert, Christian Leclerc & Geo Coppens D'Eeckenbrugge
Crop populations in smallholder farming systems are shaped by the interaction of biological, ecological and social processes, occurring on different spatiotemporal scales. Understanding these dynamics is fundamental for the conservation of crop genetic resources. In this paper we investigated the processes involved in sorghum and pearl millet diversity dynamics on Mount Kenya. Surveys were conducted in ten sites distributed along two elevation transects and occupied by six ethnolinguistic groups. Varieties of both species grown in...

Data from: Cortical recruitment determines learning dynamics and strategy

Sebastian Ceballo, Alexandre Kempf, Jacques Bourg, Zuzanna Piwkowska, Aurélie Daret, Pierre Pinson, Thomas Deneux, Simon Rumpel & Brice Bathellier
Salience is a broad and widely used concept in neuroscience whose neuronal correlates, however, remain elusive. In behavioral conditioning, salience is used to explain various effects, such as stimulus overshadowing, and refers to how fast and strongly a stimulus can be associated with a conditioned event. Here, we identify sounds of equal intensity and perceptual detectability, which due to their spectro-temporal content recruit different levels of population activity in mouse auditory cortex. When using these...

Data from: New physiological bench test reproducing noctural breathing pattern of patients with sleep disordered breathing

Petitjean Michel, Yann Rétory, Amélie Sagniez, Sébastien HARDY, François Cottin, Gabriel Roisman & Shuo Liu
Previous studies have shown that Automatic Positive Airway Pressure (APAP) devices display different behaviors when connected to a bench using theoretical respiratory cycle scripts. However, these scripts are limited and do not simulate physiological behavior during the night. Our aim was to develop a physiological bench that is able to simulate patient breathing airflow by integrating polygraph data. We developed an algorithm analyzing polygraph data and transformed this information into digital inputs required by the...

Data from: Conserved class of queen pheromones stops social insect workers from reproducing

Annette Van Oystaeyen, Ricardo Caliari Oliveira, Luke Holman, Jelle S. Van Zweden, Carmen Romero, Cintia A. Oi, Patrizia D'Ettorre, Mohammadreza Khalesi, Johan Billen, Felix Wäckers, Jocelyn G. Millar & Tom Wenseleers
A major evolutionary transition to eusociality with reproductive division of labor between queens and workers has arisen independently at least 10 times in the ants, bees, and wasps. Pheromones produced by queens are thought to play a key role in regulating this complex social system, but their evolutionary history remains unknown. Here, we identify the first sterility-inducing queen pheromones in a wasp, bumblebee, and desert ant and synthesize existing data on compounds that characterize female...

Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double stranded DNA viruses

Clement Gilbert, Elisabeth Herniou, Yannis Moreau, Nicolas Lévêque, Carine Meignin, Laurent Daeffler, Brian Federici, Richard Cordaux & Vincent Loiseau
Our knowledge of the diversity and frequency of genomic structural variation segregating in populations of large double stranded (ds) DNA viruses is limited. Here we sequenced the genome of a baculovirus (AcMNPV) purified from beet armyworm (Spodoptera exigua) larvae at depths >195,000X using both short-read (Illumina) and long-read (PacBio) technologies. Using a pipeline relying on hierarchical clustering of structural variants (SVs) detected in individual short- and long-reads by six variant callers, we identified a total...

Holocene extinctions of a top predator – effects of time, habitat area and habitat subdivision

Göran Englund, Gunnar Öhlund, Fredrik Olajos, Anders Finstad, Celine Bellard & Bernard Hugueny
1. Loss of habitat and changes in the spatial configuration of habitats are major drivers of species extinctions, but the response to these drivers differs between organisms. To advance theory on how extinction risk from different types of habitat alteration relate to species-specific traits, there is a need for studies on the long-term extinction dynamic of individual species. 2. The goal of this study was to quantify how habitat area and the spatial configuration of...

Data from: A novel phenotype combining primary ovarian insufficiency growth retardation and pilomatricomas with MCM8 mutation

Abdelkader Heddar, Dominique Beckers, Baptiste Fouquet, Dominique Roland & Micheline Misrahi
Context: Primary Ovarian insufficiency (POI) affects 1% of women under 40 years and leads most often to definitive infertility with adverse health outcomes. Very recently, genes involved in DNA repair have been shown to cause POI. Objective: To identify the cause of a familial POI in a consanguineous Turkish family. Design: Exome sequencing was performed in the proposita and her mother. Chromosomal breaks were studied in lymphoblastoid cell lines treated with Mitomycin (MMC). Setting and...

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....

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: Induction of sexual reproduction and genetic diversity in the cheese fungus Penicillium roqueforti

Jeanne Ropars, Manuela López-Villavicencio, Joëlle Dupont, Alodie Snirc, Guillaume Gillot, Monika Coton, Jean-Luc Jany, Emmanuel Coton & Tatiana Giraud
The emblematic fungus Penicillium roqueforti is used throughout the world as a starter culture in the production of blue-veined cheeses. Like other industrial filamentous fungi, P. roqueforti was thought to lack a sexual cycle. However, an ability to induce recombination is of great economic and fundamental importance, as it would make it possible to transform and improve industrial strains, promoting the creation of novel phenotypes and eliminating the deleterious mutations that accumulate during clonal propagation....

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: 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: 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: 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: Uropygial gland volume and malaria infection are related to survival in migratory house martins

Sergio Magallanes, Luz García-Longoria, Cosme López-Calderón, Maribel Reviriego, Florentino De Lope, Anders P. Moller & Alfonso Marzal
Pathogens such as bacteria, fungi and malaria and related haemosporidians provoke negative effects on the fitness of their hosts. Animals have developed a range of defensive mechanisms to resist or eliminate these parasitic infections and their negative fitness costs. The uropygial gland secretion has been proposed to act as defensive barrier of skin and plumage in the fight against bacteria and fungi, and may prevent birds from acquiring haemosporidian infections. Thus, the secretion of uropygial...

Data from: New insights into the history of domesticated and wild apricots and its contribution to Plum pox virus resistance

Stéphane Decroocq, Amandine Cornille, David Tricon, Sevda Babayeva, Aurélie Chague, Jean-Philippe Eyquard, Raul Karychev, Svetlana Dolgikh, Tatiana Kostritsyna, Shuo Liu, Weisheng Liu, Wenjuan Geng, Kang Liao, Bayram Asma, Zeynal Akparov, Tatiana Giraud, Veronique Decroocq & Bayram M. Asma
Studying domesticated species and their wild relatives allows understanding of the mechanisms of population divergence and adaptation, and identifying valuable genetic resources. Apricot is an important fruit in the Northern hemisphere, where it is threatened by the Plum pox virus (PPV), causing the sharka disease. The histories of apricot domestication and of its resistance to sharka are however still poorly understood. We used 18 microsatellite markers to genotype a collection of 230 wild trees from...

Data from: Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes

Sara Branco, Ke Bi, Hui-Ling Liao, Pierre Gladieux, Helene Badouin, Chris E. Ellison, Nhu H. Nguyen, Rytas Vilgalys, Kabir G. Peay, John W. Taylor, Thomas D. Bruns & Christopher E. Ellison
Recent advancements in sequencing technology allowed researchers to better address the patterns and mechanisms involved in microbial environmental adaptation at large spatial scales. Here we investigated the genomic basis of adaptation to climate at the continental scale in Suillus brevipes, an ectomycorrhizal fungus symbiotically associated with the roots of pine trees. We used genomic data from 55 individuals in seven locations across North America to perform genome scans to detect signatures of positive selection and...

Data from: Molecular evolution accompanying functional divergence of duplicated genes along the plant starch biosynthesis pathway

Odrade Nougué, Jonathan Corbi, Steven G. Ball, Domenica Manicacci & Maud I. Tenaillon
Background: Starch is the main source of carbon storage in the Archaeplastida. The Starch Biosynthesis Pathway (SBP) emerged from cytosolic glycogen metabolism shortly after plastid endosymbiosis and was redirected to the plastid stroma during the green lineage divergence. The SBP is a complex network of genes, most of which are members of large multigene families. While some gene duplications occurred in the Archaeplastida ancestor, most were generated during the SBP redirection process, and the remaining...

Data from: Arrival date and microorganisms in barn swallows

Zaid Al Rubaiee, H. Al Murayati & Anders Pape Moller
Migration between breeding sites and winter quarters constitute a major life history strategy in birds. The benefits of such migrations must at least equal the costs for such behavior to evolve and be maintained. We tested whether there was a relationship between abundance and diversity of microorganisms on nest lining feathers and timing of arrival by barn swallows Hirundo rustica. Nest lining feathers are chosen and transported by adult barn swallows to their nests just...

Data from: Anthropogenic and natural drivers of gene flow in a temperate wild fruit tree: a basis for conservation and breeding programs in apples

Amandine Cornille, Alice Feurtey, Uriel Gélin, Jeanne Ropars, Kristine Misvanderbrugge, Pierre Gladieux & Tatiana Giraud
Gene flow is an essential component of population adaptation and species evolution. Understanding of the natural and anthropogenic factors affecting gene flow is also critical for the development of appropriate management, breeding and conservation programs. Here, we explored the natural and anthropogenic factors impacting crop-to-wild and within wild gene flow in apples in Europe using an unprecedented dense sampling of 1,889 wild apple (Malus sylvestris) from European forests and 339 apple cultivars (Malus domestica). We...

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