26 Works

Data from: Disentangling the pathways of land use impacts on the functional structure of fish assemblages in Amazon streams

Rafael P. Leitão, Jansen Zuanon, David Mouillot, Cecília G. Leal, Robert M. Hughes, Philip R. Kaufmann, Sébastien Villéger, Paulo S. Pompeu, Daniele Kasper, Felipe R. De Paula, Silvio F. B. Ferraz & Toby A. Gardner
Agricultural land use is a primary driver of environmental impacts on streams. However, the causal processes that shape these impacts operate through multiple pathways and at several spatial scales. This complexity undermines the development of more effective management approaches, and illustrates the need for more in-depth studies to assess the mechanisms that determine changes in stream biodiversity. Here we present results of the most comprehensive multi-scale assessment of the biological condition of streams in the...

Data from: The fitness effect of mutations across environments: Fisher’s geometrical model with multiple optima

Guillaume Martin & Thomas Lenormand
When are mutations beneficial in one environment and deleterious in another? More generally, what is the relationship between mutation effects across environments? These questions are crucial to predict adaptation in heterogeneous conditions in a broad sense. Empirical evidence documents various patterns of fitness effects across environments but we still lack a framework to analyse these multivariate data. In this paper, we extend Fisher’s geometrical model to multiple environments determining distinct peaks. We derive the fitness...

Data from: Nesting sites of giant honey bees modulated by landscape patterns

Charlotte Pavageau, Cédric Gaucherel, Claude Garcia & Jaboury Ghazoul
1. The composition of agro-ecological landscapes is thought to have important implications for the production of major crops through its effects on pollinator abundance and behaviour. 2. We explored the roles of land cover and land cover heterogeneity on bee nest distribution for Apis dorsata, a key species for coffee pollination, in a complex agroforest landscape. We emphasized scaling and non-uniform effects by combining two different approaches of spatial analysis, the point-pattern analysis and surface-pattern...

Data from: A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes

Timothée Bonnet, Raphaël Leblois, Francois Rousset & Pierre-André Crochet
Hybridization is increasingly recognized as a significant evolutionary process, in particular because it can lead to introgression of genes from one species to another. A striking pattern of discordance in the amount of introgression between mitochondrial and nuclear markers exists such that substantial mitochondrial introgression is often found in combination with no or little nuclear introgression. Multiple mechanisms have been proposed to explain this discordance, including positive selection for introgressing mitochondrial variants, several types of...

Data from: Are pollinators the agents of selection on flower colour and size in irises?

Daniel Souto-Vilarósa, Ana Vuleta, Sanja Manitašević Jovanović, Sanja Budečević, Hui Wang, Yuval Sapir & Eric Imbert
Plant-pollinator interactions are believed to play a major role in the evolution of floral traits. Flower colour and flower size are important for attracting pollinators, directly influencing reproduction, and thus expected to be under pollinator-mediated selection. Pollinator-mediated selection is also proposed to play a role in maintaining flower colour polymorphism within populations. However, pigment concentrations, and thus flower colour, are also under selective pressures independent of pollinators. We quantified phenotypic pollinator-mediated selection on flower colour...

Data from: Great tits and the city: distribution of genomic diversity and gene-environment associations along an urbanization gradient

Charles Perrier, Ana Lozano Del Campo, Marta Szulkin, Virginie Demeyrier, Arnaud Gregoire & Anne Charmantier
Urbanization is a growing concern challenging the evolutionary potential of wild populations by reducing genetic diversity and imposing new selection regimes affecting many key fitness traits. However, genomic footprints of urbanization have received little attention so far. Using RAD sequencing, we investigated the genome-wide effects of urbanization on neutral and adaptive genomic diversity in 140 adult great tits Parus major collected in locations with contrasted urbanization levels (from a natural forest to highly urbanized areas...

Data from: Demonstrating multiple benefits from periodically harvested fisheries closures

Jordan S. Goetze, Joachim Claudet, Fraser Januchowski-Hartley, Timothy J. Langlois, Shaun K. Wilson, Crow White, Rebecca Weeks & Stacy D. Jupiter
1.Periodically harvested closures (PHCs) are one of the most common forms of fisheries management in Melanesia, demonstrating multiple objectives, including sustaining fish stocks and increasing catch efficiency to support small-scale fisheries. No studies have comprehensively assessed their ability to provide short-term fisheries benefits across the entire harvest regime. 2.We present a novel analytical framework to guide a meta-analysis and assist future research in conceptualizing and assessing the potential of PHCs to deliver benefits for multiple...

Data from: Mapping and explaining wolf recolonization in France using dynamic occupancy models and opportunistic data

Julie Louvrier, Christophe Duchamp, Valentin Lauret, Eric Marboutin, Sarah Cubaynes, Rémi Choquet, Christian Miquel & Olivier Gimenez
While large carnivores are recovering in Europe, assessing their distributions can help to predict and mitigate conflicts with human activities. Because they are highly mobile, elusive and live at very low density, modeling their distributions presents several challenges due to i) their imperfect detectability, ii) their dynamic ranges over time and iii) their monitoring at large scales consisting mainly of opportunistic data without a formal measure of the sampling effort. Here, we focused on wolves...

Data from: Adaptation costs to constant and alternating polluted environments

Morgan Dutilleul, Denis Reale, Benoit Goussen, Catherine Lecomte, Simon Galas & Jean-Marc Bonzom
Some populations quickly adapt to strong and novel selection pressures caused by anthropogenic stressors. However, this short-term evolutionary response to novel and harsh environmental conditions may lead to adaptation costs, and evaluating these costs is important if we want to understand the evolution of resistance to anthropogenic stressors. In this experimental evolution study, we exposed Caenorhabditis elegans populations to uranium (U populations), salt (NaCl populations), alternating uranium/salt treatments (U/NaCl populations), and to a control environment...

Data from: Aggression supersedes individual oxygen demand to drive group air-breathing in a social catfish

Shaun S. Killen, Andrew J. Esbaugh, Nicolas Martins, F. Tadeau Rantin, David J. McKenzie, Nicolas F. Martins & F. Tadeu Rantin
1) Group-living is widespread among animals and comes with numerous costs and benefits. To date, research examining group-living has focused on trade-offs surrounding foraging, while other forms of resource acquisition have been largely overlooked. 2) Air breathing has evolved in many fish lineages, allowing animals to obtain oxygen in hypoxic aquatic environments. Breathing air increases the threat of predation, so some species perform group air breathing, to reduce individual risk. Within species, air breathing can...

Data from: Shared evolutionary origin of MHC polymorphism in sympatric lemurs

Eva Kaesler, Peter M. Kappeler, Markus Brameier, Janina Demeler, Cornelia Kraus, Josué H. Rakotoniaina, Anni M. Hämäläinen & Elise Huchard
Genes of the Major Histocompatibility Complex (MHC) play a central role in adaptive immune responses of vertebrates. They exhibit remarkable polymorphism, often crossing species boundaries with similar alleles or allelic motifs shared across species. This pattern may reflect parallel parasite-mediated selective pressures, either favouring the long maintenance of ancestral MHC allelic lineages across successive speciation events by balancing selection (‘trans-species polymorphism’), or alternatively favouring the independent emergence of functionally similar alleles post-speciation via convergent evolution....

Data from: Vegetation recovery in tidal marshes reveals critical slowing down under increased inundation

Jim Van Belzen, Johan Van De Koppel, Matthew L. Kirwan, Daphne Van Der Wal, Peter M. J. Herman, Vasilis Dakos, Sonia Kéfi, Marten Scheffer, Glenn R. Guntenspergen & Tjeerd J. Bouma
A declining rate of recovery following disturbance has been proposed as an important early warning for impending tipping points in complex systems. Despite extensive theoretical and laboratory studies, this ‘critical slowing down’ remains largely untested in the complex settings of real-world ecosystems. Here, we provide both observational and experimental support of critical slowing down along natural stress gradients in tidal marsh ecosystems. Time series of aerial images of European marsh development reveal a consistent lengthening...

Data from: Shifts in plant functional strategies over the course of wheat domestication

Agathe Roucou, Cyrille Violle, Florian Fort, Pierre Roumet, Martin Escarnot, Denis Vile & Martin Ecarnot
1. Human selection, changes in environmental conditions and management practices drove the phenotypic trajectory of crops during domestication. The characterization of the crop domestication syndrome lies mostly on reproductive characters. However, biophysical and ecophysiological constraints during vegetative growth are also at play and can strongly impact crop phenotypes. It has been argued that a broadened examination of crop phenotypes through a functional trait-based lens should improve our understanding of the domestication syndrome. 2. We used...

Data from: Large-scale genetic panmixia in the blue shark (Prionace glauca): a single worldwide population, or a genetic lag-time effect of the “grey zone” of differentiation?

Diane Bailleul, Alicia Mackenzie, Olivier Sacchi, François Poisson, Nicolas Bierne & Sophie Arnaud-Haond
The blue shark Prionace glauca, among the most common and widely studied pelagic sharks, is a top predator, exhibiting the widest distribution range. However, little is known about its population structure and spatial dynamics. With an estimated removal of 10 to 20 million individuals per year by fisheries, the species is classified as “Near Threatened” by International Union for Conservation of Nature. We lack the knowledge to forecast the long-term consequences of such a huge...

Data from: Genomic signatures of adaptation to wine biological aging conditions in biofilm-forming flor yeasts

Anna-Lisa Coi, Frederic Bigey, Sandrine Mallet, Souhir Marsit, Giacomo Zara, Pierre Gladieux, Virginie Galeote, Marilena Budroni, Sylvie Dequin, Jean-Luc Legras & A. L. Coi
The molecular and evolutionary processes underlying fungal domestication remain largely unknown despite the importance of fungi to bioindustry and for comparative adaptation genomics in eukaryotes. Wine fermentation and biological aging are performed by strains of S. cerevisiae with, respectively, pelagic fermentative growth on glucose, and biofilm aerobic growth utilizing ethanol. Here, we use environmental samples of wine and flor yeasts to investigate the genomic basis of yeast adaptation to contrasted anthropogenic environments. Phylogenetic inference and...

Data from: Impact of disease on the survival of three commercially fished species

John M. Hoenig, Maya L. Groner, Matthew W. Smith, Wolfgang K. Vogelbein, David M. Taylor, , John T. Swenarton, David T. Gauthier, Philip Sadler, Mark A. Matsche, Ashley N. Haines, Hamish J. Small, Roger Pradel, Rémi Choquet & Jeffrey D. Shields
Recent increases in emergent infectious diseases have raised concerns about the population stability of some marine species. The complexity and expense of studying diseases in marine systems often dictate that conservation and management decisions are made without quantitative data on population-level impacts of disease. Mark-recapture is a powerful, underutilized, tool for calculating impacts of disease on population size and structure, even in the absence of etiological information. We applied logistic regression models to mark-recapture data...

Data from: The ace-1 locus is amplified in all resistant Anopheles gambiae mosquitoes: fitness consequences of homogeneous and heterogeneous duplications.

Benoît S. Assogba, Pascal Milesi, Luc S. Djogbénou, Arnaud Berthomieu, Patrick Makoundou, Lamine S. Baba-Moussa, Anna-Sophie Fiston-Lavier, Khalid Belkir, Pierrick Labbé, Mylène Weill & Khalid Belkhir
Gene copy-number variations are widespread in natural populations, but investigating their phenotypic consequences requires contemporary duplications under selection. Such duplications have been found at the ace-1 locus (encoding the organophosphate and carbamate insecticides’ target) in the mosquito Anopheles gambiae (the major malaria vector); recent studies have revealed their intriguing complexity, consistent with the involvement of various numbers and types (susceptible or resistant to insecticide) of copies. We used an integrative approach, from genome to phenotype...

Data from: Frugivory-related traits promote speciation of tropical palms

Renske E. Onstein, William J. Baker, Thomas L. P. Couvreur, Søren Faurby, Jens-Christian Svenning & W. Daniel Kissling
Animal-mediated seed dispersal by frugivorous birds and mammals is central to the ecology and functioning of ecosystems, but whether and how frugivory-related traits have affected plant speciation remains little explored. Fruit size is directly linked to plant dispersal capacity and therefore influences gene flow and genetic divergence of plant populations. Using a global species-level phylogeny with comprehensive data on fruit sizes and plant species distributions, we test whether fruit size has affected speciation rates of...

Data from: Entangled fates of holobiont genomes during invasion: nested bacterial and host diversities in Caulerpa taxifolia

Sophie Arnaud-Haond, Tania Aires, Rui Candeias, Sara J. L. Teixeira, Carlos M. Duarte, Myriam Valero & Ester A. Serrão
Successful prevention and mitigation of biological invasions requires retracing the initial steps of introduction, as well as understanding key elements enhancing the adaptability of invasive species. We studied the genetic diversity of the green alga Caulerpa taxifolia and its associated bacterial communities in several areas around the world. The striking congruence of α and ß diversity of the algal genome and endophytic communities reveals a tight association, supporting the holobiont concept as best describing the...

Data from: Human management and hybridization shape treegourd fruits in the Brazilian Amazon Basin

Priscila Ambrosio Moreira, Cédric Mariac, Leila Zekraoui, Marie Couderc, Doriane Picanco Rodrigues, Charles R. Clement & Yves Vigouroux
Local people's perceptions of cultivated and wild agrobiodiversity, as well as their management of hybridization are still understudied in Amazonia. Here we analyze domesticated treegourd (Crescentia cujete), whose versatile fruits have technological, symbolic and medicinal uses. A wild relative (C. amazonica) of the cultivated species grows spontaneously in Amazonian flooded forests. We demonstrated, using whole chloroplast sequences and nuclear microsatellites, that the two species are strongly differentiated. Nonetheless, they hybridize readily throughout Amazonia and the...

Data from: Using sensitivity analysis to identify key factors for the propagation of a plant epidemic

Loup Rimbaud, Claude Bruchou, Sylvie Dallot, David R.J. Pleydell, Emmanuel Jacquot, Samuel Soubeyrand, Gaël Thébaud & David R. J. Pleydell
Identifying the key factors underlying the spread of a disease is an essential but challenging prerequisite to design management strategies. To tackle this issue, we propose an approach based on sensitivity analyses of a spatiotemporal stochastic model simulating the spread of a plant epidemic. This work is motivated by the spread of sharka, caused by Plum pox virus, in a real landscape. We first carried out a broad-range sensitivity analysis, ignoring any prior information on...

Data from: Influence of the geography of speciation on current patterns of coral reef fish biodiversity across the Indo-Pacific

Théo Gaboriau, Fabien Leprieur, David Mouillot & Nicolas Hubert
The role of speciation processes in shaping current biodiversity patterns represents a major scientific question for ecologists and biogeographers. Hence, numerous methods have been developed to determine the geography of speciation based on co-occurrence between sister-species. Most of these methods rely on the correlation between divergence time and several metrics based on the geographic ranges of sister-taxa (i.e. overlap, asymmetry). The relationship between divergence time and these metrics has scarcely been examined in a spatial...

Data from: Does water shortage generate water stress? An ecohydrological approach across Mediterranean plant communities

Karim Barkaoui, Marie-Laure Navas, Catherine Roumet, Pablo Cruz & Florence Volaire
The interactions between hydrological and ecological processes are key issues to improve our predictions of ecosystem responses to increasing droughts. However, predicting the dynamics and the impacts of vegetation water stress remains challenging because of complex ecohydrological feedbacks. The ecohydrological optimality approach proposes that functional adjustments within plant communities may buffer the increase in vegetation water stress despite local water shortage. This study aimed to test whether vegetation water stress may be invariant across contrasting...

Data from: Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow

Mark Ravinet, Rui Faria, Roger K. Butlin, Juan Galindo, Nicolas Bierne, Marina Rafajlović, Mohamed A. F. Noor, Bernhard Mehlig & Anja M. Westram
Speciation, the evolution of reproductive isolation amongst populations, is continuous, complex, and involves multiple, interacting barriers. Until it is complete, the effects of this process vary along the genome and can lead to a heterogeneous genomic landscape with peaks and troughs of differentiation and divergence. When gene flow occurs during speciation, barriers restricting migration locally in the genome lead to patterns of heterogeneity. However, genomic heterogeneity can also be produced or modified by variation in...

Data from: Evolutionary rescue and local adaptation under different rates of temperature increase: a combined analysis of changes in phenotype expression and genotype frequency in Paramecium microcosms

Joshua Killeen, Claire Gougat-Barbera, Sascha Krenek & Oliver Kaltz
Evolutionary Rescue (ER) occurs when populations, which have declined due to rapid environmental change, recover through genetic adaptation. The success of this process and the evolutionary trajectory of the population strongly depend on the rate of environmental change. Here we investigated how different rates of temperature increase (from 23°C to 32°C) affect population persistence and evolutionary change in experimental microcosms of the protozoan Paramecium caudatum. Consistent with theory on ER, we found that those populations...

Registration Year

  • 2017

Resource Types

  • Dataset


  • University of Montpellier
  • French National Centre for Scientific Research
  • James Cook University
  • Centre de Coopération Internationale en Recherche Agronomique pour le Développement
  • Biology and Genetics of Plant-Pathogen Interactions
  • University of Gothenburg
  • College of William & Mary
  • Montpellier SupAgro
  • French Research Institute for Exploitation of the Sea
  • Wageningen University & Research