55 Works

Database PCA: A middle Pleistocene Homo from Nesher Ramla, Israel

Hila May, Israel Hershkovitz, Rachel Sarig, Ariel Pokhojaev, Dominique Grimaud-Hervé, Emiliano Bruner, Cinzia Fornai, Rolf Quam, Juan-Luis Arsuaga, Viktoria A. Krenn, Maria Martinón-Torres, José María Bermúdez De Castro, Laura Martín-Francés, Viviane Slon, Lou Albessard-Ball, Amélie Vialet, Tim Schüler, Giorgio Manzi, Antonio Profico, Fabio Di Vincenzo, Gerhard W. Weber & Yossi Zaidner
It has long been believed that Neanderthals originated and flourished on the European continent. However, recent morphological and genetic studies have suggested that they may have received a genetic contribution from a yet unknown non-European group. Here we report on the recent discovery of archaic Homo fossils from the site of Nesher Ramla, Israel, which we dated to 140,000 to 120,000 years ago. Comprehensive qualitative and quantitative analyses of the parietal bones, mandible, and lower...

Data from: Genetic architecture of sensory exploitation: QTL mapping of female and male receiver traits in an acoustic moth

Sylvain Alem, Réjane Streiff, Brigitte Courtois, Saliha Zenboudji, Denis Limousin & Michael D. Greenfield
The evolution of extravagant sexual traits by sensory exploitation occurs if males incidentally evolve features that stimulate females owing to a pre-existing environmental response that arose in the context of natural selection. The sensory exploitation process is thus expected to leave a specific genetic imprint, a pleiotropic control of the original environmental response and the novel sexual response in females. However, females may be subsequently selected to improve their discrimination of environmental and sexual stimuli....

Data from: Axial symptoms predict mortality in patients with Parkinson disease with subthalamic stimulation

Brian Lau, Niklaus Meier, Giulia Serra, Virginie Czernecki, Michael Schuepbach, Soledad Navarro, Philippe Cornu, David Grabli, Yves Agid, Marie Vidailhet, Carine Karachi & Marie-Laure Welter
Objective: To characterize how disease progression is associated with mortality in a large cohort of PD patients with long-term follow-up after STN-DBS. Methods: Motor and cognitive disabilities were assessed before, and 1, 2, 5 and 10 years after STN-DBS in 143 consecutive PD patients. We measured motor symptoms Off and On levodopa and STN-DBS, and recorded causes of death. We used linear mixed-models to characterize symptom progression, including interactions between treatment conditions and time to...

Data from: Genetic variation in aggregation behaviour and interacting phenotypes in Drosophila

Anne Sophie Philippe, Raphael Jeanson, Cristian Pasquaretta, Francois Rebaudo, Cedric Sueur & Frederic Mery
Aggregation behaviour is the tendency for animals to group together which may have important consequences on individual fitness. We used a combination of experimental and simulation approaches to study how genetic variation and social environment interact to influence aggregation dynamics in Drosophila. To do this, we use two different natural lines of Drosophila that arise from a polymorphism in the foraging gene (“rovers” and “sitters”). We placed groups of flies in a heated arena. Flies...

Data from: The demographic history of populations experiencing asymmetric gene flow: combining simulated and empirical data.

Ivan Paz Viñas, Erwan Quéméré, Lounès Chikhi, Géraldine Loot & Simon Blanchet
Population structure can significantly affect genetic-based demographic inferences, generating spurious bottleneck-like signals. Previous studies have typically assumed island or stepping-stone models, which are characterized by symmetric gene flow. However, many organisms are characterized by asymmetric gene flow. Here, we combined simulated and empirical data to test whether asymmetric gene flow affects the inference of past demographic changes. Through the analysis of simulated genetic data with three methods (i.e. bottleneck, M-ratio and msvar), we demonstrated that...

Data from: A genetic polymorphism affecting reliance on personal versus public information in a spatial learning task in Drosophila melanogaster

Julien Foucaud, Anne-Sophie Philippe, Celine Moreno & Frederic Mery
Organisms that face behavioural challenges can use different types of information to guide their decisions. First, they can use the personal information they sample in their environment. Second, they can use the inadvertent social information provided by the behaviour of conspecifics or heterospecifics (i.e. public information). Currently, little is known about the interaction between genetic variation and the use of personal versus public information in natural populations. Here, we investigated whether a natural genetic polymorphism...

Data from: How social network structure affects decision-making in Drosophila melanogaster

Cristian Pasquaretta, Marine Battesti, Elizabeth Klenschi, Christophe A. H. Bousquet, Cedric Sueur & Frederic Mery
Animals use a number of different mechanisms to acquire crucial information. During social encounters animals can pass information from one to another but, ideally, they would only use information that benefits survival and reproduction. Therefore, individuals need to be able to determine the value of the information they receive. One cue can come from the behaviour of other individuals that are already using the information. Here we study how individual decision-making is influenced by the...

Data from: Detection of invasive mosquito vectors using environmental DNA (eDNA) from water samples

Judith Schneider, Alice Valentini, Tony Dejean, Fabrizio Montarsi, Pierre Taberlet, Olivier Glaizot & Luca Fumagalli
Repeated introductions and spread of invasive mosquito species (IMS) have been recorded on a large scale these last decades worldwide. In this context, members of the mosquito genus Aedes can present serious risks to public health as they have or may develop vector competence for various viral diseases. While the Tiger mosquito (Aedes albopictus) is a well-known vector for e.g. dengue and chikungunya viruses, the Asian bush mosquito (Ae. j. japonicus) and Ae. koreicus have...

Data from: Ecology of information: social transmission dynamics within groups of non-social insects

Marine Battesti, Cristian Pasquaretta, Celine Moreno, Serafino Teseo, Dominique Joly, Elizabeth Klensch, Odile Petit, Cedric Sueur & Frederic Mery
While many studies focus on how animals use public information, the dynamics of information spread and maintenance within groups, i.e. the ‘ecology of information’, have received little attention. Here we use fruitflies trained to lay eggs on specific substrates to implement information into groups containing both trained and untrained individuals. We quantify inter-individual interactions and then measure the spread of oviposition preference with behavioural tests. Untrained individuals increase their interactive approaches in the presence of...

Acoustic data in four species of macaques

Nancy Rebout, Bernard Thierry, Alban Lemasson, Micheletta Jérôme & Roberto Cozzolino
We provide comparative data on vocal signals in adult females of four species of macaque : Tonkean macaques (Macaca tonkeana), crested macaques (M. nigra), Japanese macaques (M. fuscata), and rhesus macaques (M. mulatta). We distinguished three social contexts: agonistic, affiliative and neutral. The agonistic context included aggression (supplantation, lunge, chase, slap, grab, bite, facial threat display) and response to aggression (aggression, avoidance, flight, crouch, submissive facial displays). The affiliative context included affiliative behaviours (approach, sitting...

Flow cytometry data: healthy donor bone marrow taken during hip surgery

Jessica Timms, James Opzoomer, Kevin Blighe, Thanos Mourikis, Nicolas Chapuis, Richard Bekoe, Sedigeh Kareemaghay, Paola Nocerino, Benedetta Apollonio, Alan Ramsay, Mahvash Tavassoli, Claire Harrison, Francesca Ciccarelli, Peter Parker, Michaela Fontenay, Paul Barber, James Arnold & Shahram Kordasti
High dimensional cytometry is an innovative tool for immune monitoring in health and disease, it has provided novel insight into the underlying biology as well as biomarkers for a variety of diseases. However, the analysis of large multiparametric datasets usually requires specialist computational knowledge. Here we describe ImmunoCluster (https://github.com/kordastilab/ImmunoCluster) an R package for immune profiling cellular heterogeneity in high dimensional liquid and imaging mass cytometry, and flow cytometry data, designed to facilitate computational analysis by...

Imaging mass cytometry data: Diffuse large B-cell lymphoma lymph node section

Jessica Timms, James Opzoomer, Kevin Blighe, Thanos Mourikis, Nicolas Chapuis, Richard Bekoe, Sedigeh Kareemaghay, Paola Nocerino, Benedetta Apollonio, Alan Ramsay, Mahvash Tavassoli, Claire Harrison, Francesca Ciccarelli, Peter Parker, Michaela Fontenay, Paul Barber, James Arnold & Shahram Kordasti
High dimensional cytometry is an innovative tool for immune monitoring in health and disease, it has provided novel insight into the underlying biology as well as biomarkers for a variety of diseases. However, the analysis of large multiparametric datasets usually requires specialist computational knowledge. Here we describe ImmunoCluster (https://github.com/kordastilab/ImmunoCluster) an R package for immune profiling cellular heterogeneity in high dimensional liquid and imaging mass cytometry, and flow cytometry data, designed to facilitate computational analysis by...

Metagenomic bins and biosynthetic gene clusters in gut bacteria of turtle ants

Christophe Duplais
Cephalotes are herbivorous ants (>115 species) feeding on low-nitrogen food sources and they rely on gut symbionts to supplement their diet in nutrients by recycling nitrogen food waste into amino acids. These conserved gut symbionts, composed of five bacterial orders, have been studied previously for their primary nitrogen metabolism, however little is known about their ability to biosynthesize specialized metabolites which can play a role in bacterial interactions between communities living in close proximity in...

NMR spectra of Cephalotes ants gut and cuticle

Christophe Duplais
Across the evolutionary history of insects, the shift from nitrogen-rich carnivore/omnivore diets to nitrogen-poor herbivorous diets was made possible through symbiosis with microbes. The herbivorous turtle ants Cephalotes possess a conserved gut microbiome which enriches the nutrient composition by recycling nitrogen-rich metabolic waste to increase the production of amino acids. This enrichment is assumed to benefit the host, but we do not know to what extent. To gain insights into nitrogen assimilation in the ant...

The ULR-repro3 GPS data reanalysis solution (aka ULR7a)

Mederic Gravelle, Guy Woppelmann, Kevin Gobron, Zuheir Altamimi, Mikaël Guichard, Thomas Herring & Paul Rebischung
The ULR analysis center has participated in the third reprocessing campaign (repro3) of the International GNSS Service (IGS). Its ULR-repro3 solution (aka ULR7) included 601 stations for which the GNSS data available between 2000.0 and 2021.0 was reprocessed using the models and corrections adopted by the IGS for repro3. The main steps and features of ULR-repro3 reanalysis are as follows. First, daily GNSS solutions were computed using a free-network weighted least squares adjustment strategy. That...

Data from: Plasmid and clonal interference during post-horizontal gene transfer evolution

Stephanie Bedhomme, Danilo Perez-Pantoja & Ignacio G. Bravo
Plasmids are nucleic acid molecules that can drive their own replication in a living cell. They can be transmitted horizontally and can thrive in the host cell to high copy numbers. Plasmid replication and gene expression consume cellular resources and cells carrying plasmids incur fitness costs. But many plasmids carry genes that can be beneficial under certain conditions, allowing the cell to endure in the presence of antibiotics, toxins, competitors or parasites. Horizontal transfer of...

Data from: A new method for estimating locomotion type in large ground birds

Delphine Angst, Eric Buffetaut, Christophe Lecuyer & Romain Amiot
Estimating the locomotion type of fossil ground birds is necessary for a better understanding of their ecology. Until now, only one method has allowed us to estimate the locomotion of fossil ground birds, but its application is complicated in the majority of fossil cases because it requires data from the three bones from the same hindlimb of one individual. Here, we propose a new method using only the maximum length and minimum width of the...

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: Geographically distinct patterns of reproductive isolation and hybridisation in two sympatric species of the Jaera albifrons complex (marine isopods)

Ambre Ribardière, Claire Daguin-Thiébaut, Céline Houbin, Jérôme Coudret, Caroline Broudin, Olivier Timsit & Thomas Broquet
Sympatric species that in some populations hybridize and in other populations remain reproductively isolated open interesting research possibilities for the study of hybridization and speciation. Here we test for such a situation in two littoral isopods (Jaera albifrons and J. praehirsuta) that occur in mixed populations and where past morphological descriptions suggested that the two species are generally reproductively isolated except in rare populations where hybridization may be happening. Using field surveys and microsatellite genetic...

Data from: Background selection in partially selfing populations

Denis Roze
Self-fertilizing species often present lower levels of neutral polymorphism than their outcrossing relatives. Indeed, selfing automatically increases the rate of coalescence per generation, but also enhances the effects of background selection and genetic hitchhiking by reducing the efficiency of recombination. Approximations for the effect of background selection in partially selfing populations have been derived previously assuming tight linkage between deleterious alleles and neutral loci. However, loosely linked deleterious mutations may have important effects on neutral...

Data from: Evolutionary analysis of Old World arenaviruses reveals a major adaptive contribution of the viral polymerase

Chiara Pontremoli, Diego Forni, Rachele Cagliani, Uberto Pozzoli, Stefania Riva, Ignacio G. Bravo, Mario Clerici & Manuela Sironi
The Old World (OW) arenavirus complex includes several species of rodent-borne viruses, some of which (i.e., Lassa virus, LASV and Lymphocytic choriomeningitis virus, LCMV) cause human diseases. Most LCMV and LASV infections are caused by rodent-to-human transmissions. Thus, viral evolution is largely determined by events that occur in the wildlife reservoirs. We used a set of human- and rodent-derived viral sequences to investigate the evolutionary history underlying OW arenavirus speciation, as well as the more...

Data from: Characterizing and comparing the seasonality of influenza-like illnesses and invasive pneumococcal diseases using seasonal waveforms

Matthieu Domenech De Cellès, Helene Arduin, Emmanuelle Varon, Cécile Souty, Pierre-Yves Boëlle, Daniel Lévy-Bruhl, Sylvie Van Der Werf, Jean-Claude Soulary, Didier Guillemot, Laurence Watier & Lulla Opatowski
The seasonalities of influenza-like illnesses (ILIs) and invasive pneumococcal diseases (IPDs) remain incompletely understood. Experimental evidence indicates that influenza-virus infection predisposes to pneumococcal disease, so that a correspondence in the seasonal patterns of ILIs and IPDs might exist at the population level. We developed a method to characterize seasonality by means of easily interpretable summary statistics of seasonal shape—or seasonal waveforms. Non-linear mixed-effects models were used to estimate those waveforms based on weekly case reports...

Data from: Sexual harassment induces a temporary fitness cost but does not constrain the acquisition of environmental information in fruit flies

Serafino Teseo, Liisa Veerus, Celine Moreno & Frédéric Mery
Across animals, sexual harassment induces fitness costs for females and males. However, little is known about the cognitive costs involved, i.e. whether it constrains learning processes, which could ultimately affect an individual's fitness. Here we evaluate the acquisition of environmental information in groups of fruit flies challenged with various levels of male sexual harassment. We show that, although high sexual harassment induces a temporary fitness cost for females, all fly groups of both sexes exhibit...

Tree phenology - observer intercalibration and individual tree phenological scoring

Nicolas Delpierre, Isabelle Chuine & Eleanor Cole
We report data documenting (1) the dynamics of budburst and leaf senescence in three European natural forest tree populations over the period od 2012-2015 and (2) the variability among phenological observers as documented from seven observer inter-calibration experiments conducted in France over 2007-2017 for both the budburst and leaf senescence period.

Data from: Can the genomics of ecological speciation be predicted across the divergence continuum from host races to species? A case study in Rhagoletis

Meredith M. Doellman, Peter J. Meyers, Gregory J. Ragland, Glen R. Hood, Scott P. Egan, Thomas H. Q. Powell, Patrik Nosil & Jeffrey L. Feder
Studies assessing the predictability of evolution typically focus on short-term adaptation within populations or the repeatability of change among lineages. A missing consideration in speciation research is to determine whether natural selection predictably transforms standing genetic variation within populations into differences between species. Here, we test whether host-related selection on diapause timing anticipates genome-wide differentiation during ecological speciation by comparing ancestral hawthorn and newly formed apple-infesting host races of Rhagoletis pomonella to their sibling species...

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