120 Works

Data from: Costs of CRISPR-Cas mediated resistance in Streptococcus thermophilus

Pedro F. Vale, Guillaume Lafforgue, François Gatchitch, Rozenn Gardan, Sylvain Moineau & Sylvain Gandon
CRISPR-Cas is a form of adaptive sequence-specific immunity in microbes. This system offers unique opportunities for the study of coevolution between bacteria and their viral pathogens, bacteriophages. A full understanding of the coevolutionary dynamics of CRISPR-Cas requires knowing the magnitude of the cost of resisting infection. Here, using the gram-positive bacterium Streptococcus thermophilus and its associated virulent phage 2972, a well-established model system harbouring at least two type II functional CRISPR-Cas systems, we obtained different...

Data from: Assessing bundles of ecosystem services from regional to landscape scale: insights from the French Alps

Emilie Crouzat, Maud Mouchet, Francis Turkelboom, Coline Byczek, Jeroen Meersmans, Frederic Berger, Pieter Johannes Verkerk & Sandra Lavorel
1. Assessments of ecosystem services (ES) and biodiversity (hereafter ecological parameters) provide a comprehensive view of the links between landscapes, ecosystem functioning and human well-being. The investigation of consistent associations between ecological parameters, called bundles, and of their links to landscape composition and structure is essential to inform management and policy, yet it is still in its infancy. 2. We mapped over the French Alps an unprecedented array of 18 ecological parameters (16 ES and...

Data from: The building of a biodiversity hotspot across a land-bridge in the Mediterranean

Rafael Molina-Venegas, Abelardo Aparicio, Sébastien Lavergne & Juan Arroyo
Many of the macroevolutionary processes that have shaped present-day phylogenetic patterns were caused by geological events such as plate tectonics and temporary land-bridges. The study of spatial patterns of phylogenetic diversity can provide insights into these past events. Here we focus on a western Mediterranean biodiversity hotspot located in the southern Iberian Peninsula and northwest Africa, two regions that are separated by the Strait of Gibraltar. We explore the spatial structure of the phylogenetic relationships...

Data from: Fine-scale genetic structure reflects sex-specific dispersal strategies in a population of sociable weavers (Philetairus socius)

René E. Van Dijk, Rita Covas, Claire Doutrelant, Claire N. Spottiswoode & Ben J. Hatchwell
Dispersal is a critical driver of gene flow, with important consequences for population genetic structure, social interactions and other biological processes. Limited dispersal may result in kin-structured populations in which kin selection may operate, but it may also increase the risk of kin competition and inbreeding. Here, we use a combination of long-term field data and molecular genetics to examine dispersal patterns and their consequences for the population genetics of a highly social bird, the...

Data from: Quantification of correlational selection on thermal physiology, thermoregulatory behavior and energy metabolism in lizards

Paulina Artacho, Julia Saravia, Beatriz Decencière Ferrandière, Samuel Perret & Jean-François Le Galliard
Phenotypic selection is widely accepted as the primary cause of adaptive evolution in natural populations, but selection on complex functional properties linking physiology, behavior, and morphology has been rarely quantified. In ectotherms, correlational selection on thermal physiology, thermoregulatory behavior, and energy metabolism is of special interest because of their potential coadaptation. We quantified phenotypic selection on thermal sensitivity of locomotor performance (sprint speed), thermal preferences, and resting metabolic rate in captive populations of an ectothermic...

Data from: Within-individual plasticity explains age-related decrease in stress response in a short-lived bird

Ádám Z. Lendvai, Mathieu Giraudeau, Veronika Bókony, Frédéric Angelier & Olivier Chastel
A crucial problem for every organism is how to allocate energy between competing life-history components. The optimal allocation decision is often state-dependent and mediated by hormones. Here, we investigated how age, a major state variable affects individuals' hormonal response to a standardized stressor: a trait that may reflect allocation between self-maintenance and reproduction. We caught free-living house sparrows and measured their hormonal (corticosterone) response to capture stress in consecutive years. Using a long-term ringing dataset,...

Data from: The red coral (Corallium rubrum) transcriptome: a new resource for population genetics and local adaptation studies

Marine Pratlong, Anne Haguenauer, Olivier Chabrol, Christophe Klopp, Pierre Pontarotti & Didier Aurelle
The question of species survival and evolution in heterogeneous environments has long been a subject for study. Indeed, it is often difficult to identify the molecular basis of adaptation to contrasted environments, and nongenetic effects increase the difficulty to disentangle fixed effects, such as genetic adaptation, from variable effects, such as individual phenotypic plasticity, in adaptation. Nevertheless, this question is also of great importance for understanding the evolution of species in a context of climate...

Data from: \"De novo assembly transcriptome for the rostrum dace (Leuciscus burdigalensis, Cyprinidae: fish) naturally infected by a copepod ectoparasite\" in Genomic Resources Notes accepted 1 December 2014 to 31 January 2015

Olivier Rey, Géraldine Loot, Olivier Bouchez, Simon Blanchet, Maria Jose Ruiz-Lopez, Nelson Ting, Paul D. Etter, Eric A. Johnson, Tony L. Goldberg, Colin A. Chapman, James H. Jones, Patrick A. Omeja & William M. Switzer
The emergence of pathogens represents substantial threats to public health, livestock, domesticated animals, and biodiversity. How wild populations respond to emerging pathogens has generated a lot of interest in the last two decades. With the recent advent of high-throughput sequencing technologies it is now possible to develop large transcriptomic resources for non-model organisms, hence allowing new research avenues on the immune responses of hosts from a large taxonomic spectra. We here focused on a wild...

Data from: Neural modularity helps organisms evolve to learn new skills without forgetting old

Kai Olav Ellefsen, Jean-Baptiste Mouret & Jeff Clune
A long-standing goal in artificial intelligence is creating agents that can learn a variety of different skills for different problems. In the artificial intelligence subfield of neural networks, a barrier to that goal is that when agents learn a new skill they typically do so by losing previously acquired skills, a problem called catastrophic forgetting. That occurs because, to learn the new task, neural learning algorithms change connections that encode previously acquired skills. How networks...

Data from: High genetic variation in resting stage production in a metapopulation: is there evidence for local adaptation?

Anne Carole Roulin, Mahendra Mariadassou, Matthew D. Hall, Jean-Claude Walser, Christoph Haag & Dieter Ebert
Local adaptation is a key process for the maintenance of genetic diversity and population diversification. A better understanding of the mechanisms that allow (or prevent) local adaptation constitutes a key in apprehending how and at what spatial scale it occurs. The production of resting stages is found in many taxa and reflects an adaptation to outlast adverse environmental conditions. Daphnia magna (Crustacea) can alternate between asexual and sexual reproduction, the latter being linked to dormancy,...

Data from: Population genomic footprints of fine-scale differentiation between habitats in Mediterranean blue tits

Marta Szulkin, Pierre-Alexandre Gagnaire, Nicolas Bierne, Anne Charmantier & P.-A. Gagnaire
Linking population genetic variation to the spatial heterogeneity of the environment is of fundamental interest to evolutionary biology and ecology, in particular when phenotypic differences between populations are observed at biologically small spatial scales. Here, we applied restriction-site associated DNA sequencing (RAD-Seq) to test whether phenotypically differentiated populations of wild blue tits (Cyanistes caeruleus) breeding in a highly heterogeneous environment exhibit genetic structure related to habitat type. Using 12106 SNPs in 197 individuals from deciduous...

Data from: Investigating the genetic architecture of conditional strategies using the environmental threshold model

Bruno Buzatto, Mathieu Buoro, Wade Hazel, Joseph Tomkins, Bruno A. Buzatto, Joseph L. Tomkins & Wade N. Hazel
The threshold expression of dichotomous phenotypes that are environmentally cued or induced comprise the vast majority of phenotypic dimorphisms in color, morphology, behavior, and life history. Modeled as conditional strategies under the framework of evolutionary game theory, the quantitative genetic basis of these traits is a challenge to estimate. The challenge exists firstly because the phenotypic expression of the trait is dichotomous and secondly because the apparent environmental cue is separate from the biological signal...

Data from: Protein expression parallels thermal tolerance and ecologic changes in the diversification of a diving beetle species complex

Amparo Hidalgo-Galiana, Marta Monge, David G. Biron, Francesc Canals, Ignacio Ribera & Alexandra Cieslak
Physiological changes associated with evolutionary and ecological processes such as diversification, range expansion or speciation are still incompletely understood, especially for non-model species. Here we study differences in protein expression in response to temperature in a western Mediterranean diving beetle species complex, using two-dimensional differential gel electrophoresis with one Moroccan and one Iberian population each of Agabus ramblae and Agabus brunneus. We identified proteins with significant expression differences after thermal treatments comparing them with a...

Data from: Plant–plant interactions as a mechanism structuring plant diversity in a Mediterranean semi-arid ecosystem

Antonio I. Arroyo, Yolanda Pueyo, Hugo Saiz & Concepción L. Alados
Plant–plant interactions are among the fundamental processes that shape structure and functioning of arid and semi-arid plant communities. Despite the large amount of studies that have assessed the relationship between plant–plant interactions (i.e., facilitation and competition) and diversity, often researchers forget a third kind of interaction, known as allelopathy. We examined the effect of plant–plant interactions of three dominant species: the perennial grass Lygeum spartum, the allelopathic dwarf shrub Artemisia herba-alba, and the nurse shrub...

Data from: Antagonistic effect of helpers on breeding male and female survival in a cooperatively breeding bird

Matthieu Paquet, Claire Doutrelant, Ben J. Hatchwell, Claire N. Spottiswoode & Rita Covas
1. Cooperatively breeding species are typically long lived and hence, according to theory, are expected to maximize their lifetime reproductive success through maximizing survival. Under these circumstances, the presence of helpers could be used to lighten the effort of current reproduction for parents to achieve higher survival. 2. In addition, individuals of different sexes and ages may follow different strategies, but whether male and female breeders and individuals of different ages benefit differently from the...

Data from: Heterozygote advantage at MHC DRB may influence response to infectious disease epizootics

Amy J. Osborne, John Pearson, Sandra S. Negro, B. Louise Chilvers, Martin A. Kennedy & Neil J. Gemmell
The effect of MHC polymorphism on individual fitness variation in the wild remains equivocal; however, much evidence suggests that heterozygote advantage is a major determinant. To understand the contribution of MHC polymorphism to individual disease resistance or susceptibility in natural populations, we investigated two MHC class II B loci, DQB and DRB, in the New Zealand sea lion (NZSL, Phocarctos hookeri). The NZSL is a threatened species which is unusually susceptible to death by bacterial...

Data from: Tracking marine mammals in 3D using electronic tag data

Christophe Laplanche, Tiago A. Marques & Len Thomas
1. Information about at-depth behaviour of marine mammals is fundamental yet very hard to obtain from direct visual observation. Animal-borne multisensor electronic tags provide a unique window of observation into such behaviours. 2. Electronic tag sensors allow the estimation of the animal's 3-dimensional (3D) orientation, depth and speed. Using tag flow noise level to provide an estimate of animal speed, we extend existing approaches of 3D track reconstruction by allowing the direction of movement to...

Data from: Impacts and recovery from Severe Tropical Cyclone Yasi on the Great Barrier Reef

Roger J. Beeden, Jeffrey Maynard, Marjetta Puotinen, Paul Marshall, Jen Dryden, Jeremy Goldberg, Gareth Williams & Roger Beeden
Full recovery of coral reefs from tropical cyclone (TC) damage can take decades, making cyclones a major driver of habitat condition where they occur regularly. Since 1985, 44 TCs generated gale force winds (≥17 metres/second) within the Great Barrier Reef Marine Park (GBRMP). Of the hurricane strength TCs (≥H1—Saffir Simpson scale; ≥ category 3 Australian scale), TC Yasi (February, 2011) was the largest. In the weeks after TC Yasi crossed the GBRMP, participating researchers, managers...

Data from: Assessing the distribution of disease-bearing rodents in human-modified tropical landscapes

Serge Morand, Frédéric Bordes, Kim Blasdell, Shai Pilosof, Jean-François Cornu, Kittipong Chaisiri, Yannick Chaval, Jean-François Cosson, Julien Claude, Tristan Feyfant, Vincent Herbreteau, Stéphane Dupuy & Annelise Tran
1. We tested how habitat structure and fragmentation affect the spatial distribution of common murine rodents inhabiting human-dominated landscapes in southeast Asia. The spatial distribution patterns observed for each rodent species were then used to assess how changes in habitat structure may potentially affect the risk of several major rodent-borne diseases. 2. For this analysis, we used an extensive geo-referenced database containing details of rodents trapped from seven sites in Thailand, Cambodia and Lao PDR....

Data from: An experimental test of density-dependent selection on temperament traits of activity, boldness and sociability

Jean-François Le Galliard, Matthieu Paquet, Marianne Mugabo & J.-F. Le Galliard
Temperament traits are seen in many animal species, and recent evolutionary models predict that they could be maintained by heterogeneous selection. We tested this prediction by examining density-dependent selection in juvenile common lizards Zootoca viviparascored for activity, boldness and sociability at birth and at the age of 1 year. We measured three key life-history traits (juvenile survival, body growth rate and reproduction) and quantified selection in experimental populations at five density levels ranging from low...

Data from: Developmental plasticity affects sexual size dimorphism in an anole lizard

Camille Bonneaud, Erin Marnocha, Anthony Herrel, Bieke Vanhooydonck, Duncan J. Irschick & Thomas B. Smith
While developmental plasticity has been shown to contribute to sexual size dimorphism (SSD) in laboratory studies, its role in shaping SSD variation in wild vertebrate populations is unclear. Here we use a field study and a laboratory experiment to show that resource availability influences the degree of SSD among insular populations of Anolis sagrei lizards in the Bahamas. Total amounts of food biomass explained variation in male, but not female, body size on six Bahamian...

Data from: Social learning and the replication process: an experimental investigation

Maxime Derex, Romain Feron, Bernard Godelle & Michel Raymond
Human cultural traits typically result from a gradual process that has been described as analogous to biological evolution. This observation has led pioneering scholars to draw inspiration from population genetics to develop a rigorous and successful theoretical framework of cultural evolution. Social learning, the mechanism allowing information to be transmitted between individuals, has thus been described as a simple replication mechanism. Although useful, the extent to which this idealization appropriately describes the actual social learning...

Data from: Re-growing a tropical dry forest: functional plant trait composition and community assembly during succession

Vanessa Buzzard, Catherine M. Hulshof, Trevor Birt, Cyrille Violle & Brian J. Enquist
A longstanding goal of ecology and conservation biology is to understand the environmental and biological controls of forest succession. However, the patterns and mechanisms that guide successional trajectories, especially within tropical forests, remain unclear. We collected leaf functional trait and abiotic data across a 110-year chronosequence within a tropical dry forest in Costa Rica. Focusing on six key leaf functional traits related to resource acquisition and competition, along with measures of forest stand structure, we...

Data from: Testing for Depéret’s rule (body size increase) in mammals using combined extinct and extant data

Folmer Bokma, Marc Godinot, Olivier Maridet, Sandrine Ladevèze, Loïc Costeur, Floréal Solé, Emmanuel Gheerbrant, Stéphane Peigné, Florian Jacques & Michel Laurin
Whether or not evolutionary lineages in general show a tendency to increase in body size has often been discussed. This tendency has been dubbed “Cope's rule” but because Cope never hypothesized it, we suggest renaming it after Depéret, who formulated it clearly in 1907. Depéret's rule has traditionally been studied using fossil data, but more recently a number of studies have used present-day species. While several paleontological studies of Cenozoic placental mammals have found support...

Data from: An integrated assessment model of seabird population dynamics: can individual heterogeneity in susceptibility to fishing explain abundance trends in Crozet wandering albatross?

Geoffrey N. Tuck, Robin B. Thomson, Christophe Barbraud, Karine Delord, Maite Louzao, Miguel Herrera & Henri Weimerskirch
1. Seabirds have been incidentally caught in distant-water longline fleets operating in the Southern Ocean since at least the 1970s, and breeding numbers for some populations have shown marked trends of decline and recovery concomitant with longline fishing effort within their distributions. However, lacking is an understanding of how forms of among-individual heterogeneity may interact with fisheries bycatch and influence population dynamics. 2. We develop a model that uses comprehensive data on the spatial and...

Registration Year

  • 2015

Resource Types

  • Dataset


  • French National Centre for Scientific Research
  • French National Institute for Agricultural Research
  • University of Toulouse
  • University of Montpellier
  • Centre d'Ecologie Fonctionnelle et Evolutive
  • University of Cambridge
  • Uppsala University
  • Ghent University
  • Stanford University
  • Université Paul-Valéry Montpellier