23 Works

Data from: A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate

Thomas Bataillon, Nicolas Galtier, Aurelien Bernard, Nicolai Cryer, Nicolas Faivre, Sylvain Santoni, Dany Severac, Theis N. Mikkelsen, Klaus S. Larsen, Claus Beier, Jesper G. Sørensen, Martin Holmstrup, Bodil Ehlers, Bodil K. Ehlers & Teis N. Mikkelsen
Whether species can respond evolutionarily to current climate change is crucial for the persistence of many species. Yet, very few studies have examined genetic responses to climate change in manipulated experiments carried out in natural field conditions. We examined the evolutionary response to climate change in a common annelid worm using a controlled replicated experiment where climatic conditions were manipulated in a natural setting. Analyzing the transcribed genome of 15 local populations, we found that...

Data from: Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact

Alan Le Moan, Pierre-Alexandre Gagnaire, Francois Bonhomme & P.-A. Gagnaire
Ecophenotypic differentiation among replicate ecotype pairs within a species complex is often attributed to independent outcomes of parallel divergence driven by adaptation to similar environmental contrasts. However, the extent to which parallel phenotypic and genetic divergence patterns have emerged independently is increasingly questioned by population genomic studies. Here, we document the extent of genetic differentiation within and among two geographic replicates of the coastal and marine ecotypes of the European anchovy (Engraulis encrasicolus) gathered from...

Data from: The summary-likelihood method and its implementation in the Infusion package

Francois Rousset, Alexandre Gouy, Camille Martinez-Almoyna & Alexandre Courtiol
In recent years, simulation methods such as approximate Bayesian computation have extensively been used to infer parameters of population genetic models where the likelihood is intractable. We describe an alternative approach, summary likelihood, that provides a likelihood-based analysis of the information retained in the summary statistics whose distribution is simulated. We provide an automated implementation as a standard R package, Infusion, and we test the method, in particular for a scenario of inference of population-size...

Data from: Fisher’s geometrical model and the mutational patterns of antibiotic resistance across dose gradients

Noémie Harmand, Romain Gallet, Roula Jabbour-Zahab, Guillaume Martin & Thomas Lenormand
Fisher's geometrical model (FGM) has been widely used to depict the fitness effects of mutations. It is a general model with few underlying assumptions that gives a large and comprehensive view of adaptive processes. It is thus attractive in several situations, e.g. adaptation to antibiotics, but comes with limitations, so that more mechanistic approaches are often preferred to interpret experimental data. It might be possible however to extend FGM assumptions to better account for mutational...

Data from: Adaptive evolution and segregating load contribute to the genomic landscape of divergence in two tree species connected by episodic gene flow

Camille Christe, Kai N. Stölting, Margot Paris, Christelle Fraїsse, Nicolas Bierne & Christian Lexer
Speciation often involves repeated episodes of genetic contact between divergent populations before reproductive isolation (RI) is complete. Whole-genome sequencing (WGS) holds great promise for unravelling the genomic bases of speciation. We have studied two ecologically divergent, hybridizing species of the ‘model tree’ genus Populus (poplars, aspens, cottonwoods), Populus alba and P. tremula, using >8.6 million single nucleotide polymorphisms (SNPs) from WGS of population pools. We used the genomic data to (i) scan these species’ genomes...

Data from: Immigration of susceptible hosts triggers the evolution of alternative parasite defence strategies

Hélène Chabas, Van Houte Stineke, Molin Hoyland-Kroghsbo Nina, Buckling Angus, Westra R. Edze, Nina Molin Høyland-Kroghsbo, Angus Buckling, Stineke Van Houte & Edze R. Westra
Migration of hosts and parasites can have a profound impact on host–parasite ecological and evolutionary interactions. Using the bacterium Pseudomonas aeruginosa UCBPP-PA14 and its phage DMS3vir, we here show that immigration of naive hosts into coevolving populations of hosts and parasites can influence the mechanistic basis underlying host defence evolution. Specifically, we found that at high levels of bacterial immigration, bacteria switched from clustered regularly interspaced short palindromic repeats (CRISPR-Cas) to surface modification-mediated defence. This...

Data from: Measuring and interpreting sexual selection metrics - evaluation and guidelines

Nils Anthes, Ines K. Häderer, Nico K. Michiels & Tim Janicke
(1) Routine assessments of overall sexual selection, including comparisons of its direction and intensity between sexes or species, rely on summary metrics that capture the essence of sexual selection. Nearly all currently employed metrics require population-wide estimates of individual mating success and reproductive success. The resulting sexual selection metrics, however, can heavily and systematically vary with the chosen approaches in terms of sampling, measurement, and analysis. (2) Our review illustrates this variation using the Bateman...

Data from: Hot spots become cold spots: coevolution in variable temperature environments

Alison B. Duncan, Eike Dusi, Franck Jacob, Johan Ramsayer, Michael E. Hochberg & Oliver Kaltz
Antagonistic coevolution between hosts and parasites is a key process in the genesis and maintenance of biological diversity. Whereas coevolutionary dynamics show distinct patterns under favourable environmental conditions, the effects of more realistic, variable conditions are largely unknown. We investigated the impact of a fluctuating environment on antagonistic coevolution in experimental microcosms of Pseudomonas fluorescens SBW25 and lytic phage SBWΦ2. High-frequency temperature fluctuations caused no deviations from typical coevolutionary arms-race dynamics. However, coevolution was stalled...

Data from: Relating fitness to long-term environmental variations in natura

Pascal Milesi, Thomas Lenormand, Christophe Lagneau, Mylène Weill & Pierrick Labbé
Quantifying links between ecological processes and adaptation dynamics in natura remains a crucial challenge. Many studies have documented the strength, form and direction of selection, and its variations in space and time, but only a few managed to link these variations to their proximal causes. This step is, however, crucial, if we are to understand how the variation in selective pressure affects adaptive allele dynamics in natural settings. We used data from a long-term survey...

Data from: Distinguishing contemporary hybridization from past introgression with postgenomic ancestry-informative SNPs in strongly differentiated Ciona species

Sarah Bouchemousse, Cathy Liautard-Haag, Nicolas Bierne & Frédérique Viard
Biological introductions bring into contact species that can still hybridize. The evolutionary outcomes of such secondary contacts may be diverse (e.g. adaptive introgression from or into the introduced species) but are not yet well examined in the wild. The recent secondary contact between the non-native sea squirt Ciona robusta (formerly known as C. intestinalis type A) and its native congener C. intestinalis (formerly known as C. intestinalis type B), in the Western English Channel, provides...

Data from: How the truffle got its mate: insights from genetic structure in spontaneous and planted Mediterranean populations of Tuber melanosporum

Elisa Taschen, François Rousset, Mathieu Sauve, Laure Benoit, Marie-Pierre Dubois, Franck Richard, Marc-André Selosse, M.-P. Dubois & M.-A. Selosse
The life cycles and dispersal of edible fungi are still poorly known, thus limiting our understanding of their evolution and domestication. The prized Tuber melanosporum produces fruitbodies (fleshy organs where meiospores mature) gathered in natural, spontaneously inoculated forests or harvested in plantations of nursery-inoculated trees. Yet, how fruitbodies are formed remains unclear, thus limiting yields, and how current domestication attempts affect population genetic structure is overlooked. Fruitbodies result from mating between two haploid individuals: the...

Data from: Phylogeography of the small Indian civet and origin of introductions to western Indian Ocean islands

Philippe Gaubert, Riddhi Patel, Geraldine Veron, Steve M. Goodman, Maraike Willsch, Raquel Vasconcelos, Andre Lourenço, Marie Sigaud, Fabienne Justy, Bheem Dutt Joshi, Joerns Fickel & Abdreas Wilting
The biogeographic dynamics affecting the Indian subcontinent, East and Southeast Asia during the Plio-Pleistocene has generated complex biodiversity patterns. We assessed the molecular biogeography of the small Indian civet (Viverricula indica) through mitogenome and cytochrome b + control region sequencing of 89 historical and modern samples to (i) establish a time-calibrated phylogeography across the species’ native range and (ii) test introduction scenarios to western Indian Ocean islands. Bayesian phylogenetic analyses identified three geographic lineages (East...

Data from: RClone: a package to identify MultiLocus Clonal Lineages and handle clonal datasets in R

Diane Bailleul, Solenn Stoeckel & Sophie Arnaud-Haond
Partially clonal species are common in the Tree of Life. And yet, population genetics models still mostly focus on the extremes: strictly sexual versus purely asexual reproduction. Here we present an R package built upon GenClone software including new functions and several improvements. The RClone package includes functions to handle clonal datasets, allowing (i) checking for dataset reliability to discriminate multi-locus genotypes (MLG), (ii) ascertainment of MLG and semi-automatic determination of clonal lineages (MLL), (iii)...

Data from: DNA metabarcoding of Amazonian ichthyoplankton swarms

Marie Eugenie Maggia, Yves Vigouroux, Jean François Renno, Fabrice Duponchelle, Erick Desmarais, Jesus Nunez, Carmen García-Dávila, Fernando M. Carvajal, Emmanuel Paradis, Jean Francois Martin & Cédric Mariac
Tropical rainforests harbor extraordinary biodiversity. The Amazon basin is thought to hold 30% of all river fish species in the world. Information about the ecology, reproduction, and recruitment of most species is still lacking, thus hampering fisheries management and successful conservation strategies. One of the key understudied issues in the study of population dynamics is recruitment. Fish larval ecology in tropical biomes is still in its infancy owing to identification difficulties. Molecular techniques are very...

Data from: Size evolution in microorganisms masks trade-offs predicted by the growth rate hypothesis

Isabelle Gounand, Tanguy Daufresne, Dominique Gravel, Corinne Bouvier, Thierry Bouvier, Marine Combe, Claire Gougat-Barbera, Franck Poly, Clara Torres-Barceló & Nicolas Mouquet
Adaptation to local resource availability depends on responses in growth rate and nutrient acquisition. The growth rate hypothesis (GRH) suggests that growing fast should impair competitive abilities for phosphorus and nitrogen due to high demand for biosynthesis. However, in microorganisms, size influences both growth and uptake rates, which may mask trade-offs and instead generate a positive relationship between these traits (size hypothesis, SH). Here, we evolved a gradient of maximum growth rate (μmax) from a...

Data from: Range expansion underlies historical introgressive hybridization in the Iberian hare

João P. Marques, Liliana Farelo, Joana Vilela, Dan Vanderpool, Paulo C. Alves, Jeffrey M. Good, Pierre Boursot & José Melo-Ferreira
Introgressive hybridization is an important and widespread evolutionary process, but the relative roles of neutral demography and natural selection in promoting massive introgression are difficult to assess and an important matter of debate. Hares from the Iberian Peninsula provide an appropriate system to study this question. In its northern range, the Iberian hare, Lepus granatensis, shows a northwards gradient of increasing mitochondrial DNA (mtDNA) introgression from the arctic/boreal L. timidus, which it presumably replaced after...

Data from: How structured is the entangled bank? The surprisingly simple organization of multiplex ecological networks leads to increased persistence and resilience

Sonia Kéfi, Vincent Miele, Evie A. Wieters, Sergio A. Navarrete & Eric L. Berlow
Species are linked to each other by a myriad of positive and negative interactions. This complex spectrum of interactions constitutes a network of links that mediates ecological communities’ response to perturbations, such as exploitation and climate change. In the last decades, there have been great advances in the study of intricate ecological networks. We have, nonetheless, lacked both the data and the tools to more rigorously understand the patterning of multiple interaction types between species...

Data from: Rare species contribute disproportionately to the functional structure of species assemblages

Rafael P. Leitão, Jansen Zuanon, Sebastien Villeger, Stephen E. Williams, Christopher Baraloto, Claire Fortunel, Fernando P. Mendonça & David Mouillot
There is broad consensus that the diversity of functional traits within species assemblages drives several ecological processes. It is also widely recognized that rare species are the first to go extinct following human-induced disturbances. Surprisingly, however, the functional importance of rare species is still poorly understood, particularly in tropical species-rich assemblages where the majority of species are rare and the rate of species extinction can be high. Here we investigated the consequences of local and...

Data from: An integrative framework of coexistence mechanisms in competitive metacommunities

Bertrand Fournier, Nicolas Mouquet, Mathew A. Leibold & Dominique Gravel
Species distribution in a metacommunity varies according to their traits, the distribution of environmental conditions and connectivity among localities. These ingredients contribute to coexistence across spatial scales via species sorting, patch dynamics, mass effects and neutral dynamics. These mechanisms however seldom act in isolation and the impact of landscape configuration on their relative importance remains poorly understood. We present a new model of metacommunity dynamics that simultaneously considers these four possible mechanisms over spatially explicit...

Data from: Body reserves mediate trade-offs between life history traits: new insights from small pelagic fish reproduction

Pablo Brosset, Josep Lloret, Marta Muñoz, Christian Fauvel, Elisabeth Van Beveren, Virginie Marques, Jean-Marc Fromentin, Frédéric Ménard & Claire Saraux
Limited resources in the environment prevent individuals from simultaneously maximizing all life-history traits, resulting in trade-offs. In particular, the cost of reproduction is well known to negatively affect energy investment in growth and maintenance. Here, we investigated these trade-offs during contrasting periods of high versus low fish size and body condition (before/after 2008) in the Gulf of Lions. Female reproductive allocation and performance in anchovy (Engraulis encrasicolus) and sardine (Sardina pilchardus) were examined based on...

Data from: Unexpected high vulnerability of functions in wilderness areas: evidence from coral reef fishes

Stephanie D'agata, Laurent Vigliola, Nickolas A.J. Graham, Laurent Wantiez, Valeriano Parravicini, Sébastien Villéger, Gérard Mou-Tham, Phillipe Frolla, Alan M. Friedlander, Michel Kulbicki, David Mouillot & Nicholas A. J. Graham
High species richness is thought to support the delivery of multiple ecosystem functions and services under changing environments. Yet, some species might perform unique functional roles while others are redundant. Thus, the benefits of high species richness in maintaining ecosystem functioning are uncertain if functions have little redundancy, potentially leading to high vulnerability of functions. We studied the natural propensity of assemblages to be functionally buffered against loss prior to fishing activities, using functional trait...

Data from: From randomness to traplining: a framework for the study of routine movement behavior

Louise Riotte-Lambert, Simon Benhamou & Simon Chamaillé-Jammes
Memory allows many animals to benefit from the spatial predictability of their environment by revisiting known profitable places. Travel route optimization or resource acquisition constraints usually lead to repeated sequences of visits, which may have major evolutionary and ecological implications. However, the study of this behavior has been impaired by a lack of concepts and methodologies. We here formally define routine movement behavior, provide an index that quantifies the degree of repetitiveness in movement sequences...

Data from: Sibship effects on dispersal behaviour in a preindustrial human population

Aïda Nitsch, Virpi Lummaa & Charlotte Faurie
Understanding dispersal behaviour and its determinants is critical for studies on life-history maximizing strategies. Although many studies have investigated the causes of dispersal, few have focused on the importance of sibship, despite that sibling interactions are predicted to lead to intrafamilial differences in dispersal patterns. Using a large demographic data set from pre-industrial Finland (n = 9000), we tested whether the sex-specific probability of dispersal depended on the presence of same-sex or opposite-sex elder siblings...

Registration Year

  • 2016
    23

Resource Types

  • Dataset
    23

Affiliations

  • University of Montpellier
    23
  • French National Centre for Scientific Research
    9
  • Sorbonne University
    3
  • University of Porto
    2
  • French Research Institute for Exploitation of the Sea
    2
  • James Cook University
    2
  • Leibniz Institute for Zoo and Wildlife Research
    2
  • Biology and Genetics of Plant-Pathogen Interactions
    1
  • University of Montana
    1
  • The University of Texas at Austin
    1