39 Works

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: Dynamic transmission, host quality and population structure in a multi-host parasite of bumble bees

Mario Xavier Ruiz-González, John Bryden, Yannick Moret, Christine Reber-Funk, Paul Schmid-Hempel & Mark J. F. Brown
The evolutionary ecology of multi-host parasites is predicted to depend upon patterns of host quality and the dynamics of transmission networks. Depending upon the differences in host quality and transmission asymmetries, as well as the balance between intra- and inter-specific transmission, the evolution of specialist or generalist strategies is predicted. Using a trypanosome parasite of bumble bees we ask how host quality and transmission networks relate to parasite population structure across host species, and thus...

Data from: New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems

Laura S. Epp, Sanne Boessenkool, Eva P. Bellemain, James Haile, Alfonso Esposito, Tiayyba Riaz, Christer Erséus, Vladimir I. Gusarov, Mary E. Edwards, Arild Johnsen, Hans K. Stenøien, Kristian Hassel, Håvard Kauserud, Nigel G. Yoccoz, Kari Anne Bråthen, Eske Willerslev, Pierre Taberlet, Eric Coissac & Christian Brochmann
Metabarcoding approaches use total and typically degraded DNA from environmental samples to analyse biotic assemblages and can potentially be carried out for any kinds of organisms in an ecosystem. These analyses rely on specific markers, here called metabarcodes, which should be optimized for taxonomic resolution, minimal bias in amplification of the target organism group and short sequence length. Using bioinformatic tools, we developed metabarcodes for several groups of organisms: fungi, bryophytes, enchytraeids, beetles and birds....

Data from: Artificial selection on allometry: change in elevation but not slope

Camilla K. Egset, Thomas F. Hansen, Arnaud Le Rouzic, Geir H. Bolstad, Gunilla Rosenqvist & Christophe Pélabon
To what extent within-species (static) allometries constitute a constraint on evolution is the subject of a long-standing debate in evolutionary biology. A prerequisite for the constraint hypothesis is that static allometries are hard to change. Several studies have attempted to test this hypothesis with artificial-selection experiments, but their results remain inconclusive due to various methodological issues. Here, we present results from an experiment in which we selected independently on the slope and the elevation of...

Data from: Adaptive radiation driven by the interplay of eco-evolutionary and landscape dynamics

Robin Aguilée, David Claessen & Amaury Lambert
We investigate an individual-based model of adaptive radiation based on the biogeographical changes of the Great African Lakes where cichlid fishes radiated. In our model, the landscape consists of a mosaic of three habitat types which may or may not be separated by geographic barriers. We study the effect of the alternation between allopatry and sympatry called landscape dynamics. We show that landscape dynamics can generate a significantly higher diversity than allopatric or sympatric speciation...

Data from: Pairing context determines condition-dependence of song rate in a monogamous passerine bird

Morgan David, Yannick Auclair, Sasha R. X. Dall & Frank Cézilly
Condition-dependence of male ornaments is thought to provide honest signals on which females can base their sexual choice for genetic quality. Recent studies show that condition-dependence patterns can vary within populations. Although long-term association is thought to promote honest signalling, no study has explored the influence of pairing context on the condition-dependence of male ornaments. In this study, we assessed the influence of natural variation in body condition on song rate in zebra finches (Taeniopygia...

Data from: Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load

Sébastien Wielgoss, Jeffrey E. Barrick, Olivier Tenaillon, Michael J. Wiser, W. James Dittmar, Stéphane Cruveiller, Béatrice Chane-Woon-Ming, Claudine Médigue, Richard E. Lenski & Dominique Schneider
Mutations are the ultimate source of heritable variation for evolution. Understanding how mutation rates themselves evolve is thus essential for quantitatively understanding many evolutionary processes. According to theory, mutation rates should be minimized for well-adapted populations living in stable environments, whereas hypermutators may evolve if conditions change. However, the long-term fate of hypermutators is unknown. Using a phylogenomic approach, we found that an adapting Escherichia coli population that first evolved a mutT hypermutator phenotype was...

Data from: Intergametophytic selfing and microgeographic genetic structure shape populations of the intertidal red seaweed Chondrus crispus

Stacy A. Krueger-Hadfield, Denis Roze, Stephane Mauger & Myriam Valero
Understanding how abiotic factors influence the spatial distribution of genetic variation provides insight into microevolutionary processes. The intertidal seascape is characterized by highly heterogeneous habitats which probably influence the partitioning of genetic variation at very small scales. The effects of tidal height on genetic variation in both the haploid (gametophytes) and diploid (tetrasporophytes) stages of the red alga Chondrus crispus were studied. Fronds were sampled every 25 cm within a 5 m × 5 m...

Data from: Stretched to the limit; can a short pelagic larval duration connect adult populations of an Indo-Pacific diadromous fish (Kuhlia rupestris)?

Pierre Feutry, Alan Vergnes, Damien Broderick, Josie Lambourdière, Philippe Keith & Jennifer R. Ovenden
Freshwater species on tropical islands face localized extinction and the loss of genetic diversity. Their habitats can be ephemeral due to variability in freshwater run-off and erosion. Even worse, anthropogenic effects on these ecosystems are intense. Most of these species are amphidromous or catadromous (i.e. their life cycle includes a marine larval phase), which buffers them against many of these effects. A long pelagic larval duration (PLD) was thought to be critical to ensure the...

Data from: Genetic polymorphism in dopamine receptor D4 is associated with early body condition in a large population of greater flamingos, Phoenicopterus roseus

Mark A. F. Gillingham, Arnaud Béchet, Julia Geraci, Remi Wattier, Christine Dubreuil & Frank Cezilly
Body condition is an important determinant of fitness in many natural populations. However, as for many fitness traits, the underlying genes that regulate body condition remain elusive. The dopamine receptor D4 gene (DRD4) is a promising candidate as dopamine is known to play an important role in the regulation of food intake and the metabolism of both glucose and lipids in vertebrates. In this study we take advantage of a large dataset of greater flamingos,...

Data from: Testing the influence of family structure and outbreeding depression on heterozygosity-fitness correlations in small populations

Helene Jourdan-Pineau, Joy Folly, Pierre-André Crochet & Patrice David
Theory predicts that positive Heterozygosity-Fitness Correlations (HFC) arise as a consequence of inbreeding, which is often assumed to have a strong impact in small, fragmented populations. Yet according to empirical data, HFC in such populations seem highly variable and impredictible. We here discuss two overlooked phenomena that may contribute to this variation. First, in a small population, each generation may consist of a few families. This generates random correlations between particular alleles and fitness (AFC,...

Data from: Kin selection, not group augmentation, predicts helping in an obligate cooperatively breeding bird

Lucy E. Browning, Samantha C. Patrick, Lee A. Rollins, Simon C. Griffith & Andrew F. Russell
Kin selection theory has been the central model for understanding the evolution of cooperative breeding, where non-breeders help bear the cost of rearing young. Recently the dominance of this idea has been questioned; particularly in obligate cooperative breeders where breeding without help is uncommon and seldom successful. In such systems, the direct benefits gained through augmenting current group size have been hypothesised to provide a tractable alternative (or addition) to kin selection. However, clear empirical...

Data from: The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

Angelique D'Hont, France Denoeud, Jean-Marc Aury, Franc-Christophe Baurens, Françoise Carreel, Olivier Garsmeur, Benjamin Noel, Stéphanie Bocs, Gaëtan Droc, Mathieu Rouard, Corinne Da Silva, Jabbari Kamel, Céline Cardi, Julie Poulain, Marlène Souquet, Karine Labadie, Cyril Jourda, Juliette Lengellé, Marguerite Rodier-Goud, Adriana Alberti, Maria Bernard, Margot Correa, Saravanaraj Ayyampalayam, Michael R. McKain, Jim Leebens-Mack … & Patrick Wincker
Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries1. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations2, and selection of diploid...

Data from: Genetic drift and collective dispersal can result in chaotic genetic patchiness

Thomas Broquet, Frédérique Viard & Jonathan M. Yearsley
Chaotic genetic patchiness denotes unexpected patterns of genetic differentiation that are observed at a fine scale and are not stable in time. These patterns have been described in marine species with free-living larvae, but are unexpected because they occur at a scale below the dispersal range of pelagic larvae. At the scale where most larvae are immigrants, theory predicts spatially homogeneous, temporally stable genetic variation. Empirical studies have suggested that genetic drift interacts with complex...

Data from: Mature male parr contribution to the effective size of an anadromous Atlantic salmon (Salmo salar) population over 30 years

Devon L. Johnstone, Michael F. O'Connell, Friso P. Palstra & Daniel E. Ruzzante
We describe temporal changes in the genetic composition of a small anadromous Atlantic salmon (Salmo salar) population from South Newfoundland, an area where salmon populations are considered threatened (COSEWIC 2010). We examined the genetic variability (13 microsatellite loci) in 869 out-migrating smolt and post-spawning kelt samples, collected from 1985 to 2011 for a total of 22 annual collections and a 30 year span of assigned cohorts. We estimated the annual effective number of breeders (Nb)...

Data from: Global genetic analysis reveals the putative native source of the invasive termite, Reticulitermes flavipes, in France

Elfie Perdereau, Anne-Geneviève Bagnères-Urbany, Stephanie Bankhead-Dronnet, Simon Dupont, Marie Zimmermann, Edward L. Vargo & Franck Dedeine
Biological invasions are recognized as a major threat to both natural and managed ecosystems. Phylogeographic and population genetic analyses can provide information about the geographical origins and patterns of introduction and explain the causes and mechanisms by which introduced species have become successful invaders. Reticulitermes flavipes is a North American subterranean termite that has been introduced into several areas, including France where introduced populations have become invasive. To identify likely source populations in the USA...

Data from: Are species’ responses to global change predicted by past niche evolution?

Sébastien Lavergne, Margaret E. K. Evans, Ian J. Burfield, Frederic Jiguet & Wilfried Thuiller
Predicting how and when adaptive evolution might rescue species from global change, and integrating this process into tools of biodiversity forecasting, has now become an urgent task. Here we explored whether recent population trends of species can be explained by their past rate of niche evolution, which can be inferred from increasingly available phylogenetic and niche data. We examined the assemblage of 409 European bird species for which estimates of demographic trends between 1970 and...

Data from: Direct genetic evidence for reproductive philopatry and associated fine-scale migrations in female blacktip reef sharks (Carcharhinus melanopterus) in French Polynesia.

Johann Mourier & Serge Planes
Conservation of top predators has been emphasised as essential in an ecosystem due to their role in trophic chain regulation. Optimization of conservation strategies for these endangered marine top predators requires direct estimates of breeding patterns and connectivity, which are essential to understand their population dynamics. While there have been some attempts to investigate breeding patterns of reef sharks from litter reconstruction using molecular analyses, direct fine-scale migrations of female sharks for parturition as well...

Data from: Testing and quantifying phylogenetic signals and homoplasy in morphometric data

Christian Peter Klingenberg & Nelly A. Gidaszewski
The relationship between morphometrics and phylogenetic analysis has long been controversial. Here we propose an approach that is based on mapping morphometric traits onto phylogenies derived from other data and thus avoids the pitfalls encountered by previous studies. This method treats shape as a single, multidimensional character. We propose a test for the presence of a phylogenetic signal in morphometric data, which simulates the null hypothesis of the complete absence of phylogenetic structure by permutation...

Data from: The distribution of mutational fitness effects of phage ϕX174 on different hosts

Pedro F. Vale, Marc Choisy, Rémy Froissart, Rafael Sanjuán & Sylvain Gandon
Adaptation depends greatly on the distribution of mutation fitness effects (DMFE), but the phenotypic expression of mutations is often environment-dependent. The environments of multi-host pathogens are mostly governed by their hosts and therefore measuring the DMFE on multiple hosts can inform on the likelihood of short-term establishment and longer-term adaptation of emerging pathogens. We explored this by measuring the growth rate of 36 mutants of the lytic bacteriophage ϕX174 on two host backgrounds, Escherichia coli...

Data from: Genome scans reveal candidate regions involved in the adaptation to host plant in the pea aphid complex

Julie Jaquiéry, Solenn Stoeckel, Pierre Nouhaud, Lucie Mieuzet, Frédérique Mahéo, Fabrice Legeai, Nina Bernard, Antoine Bonvoisin, Renaud Vitalis & Jean-Christophe Simon
A major goal in evolutionary biology is to uncover the genetic basis of adaptation. Divergent selection exerted on ecological traits may result in adaptive population differentiation and reproductive isolation and affect differentially the level of genetic divergence along the genome. Genome-wide scan of large sets of individuals from multiple populations is a powerful approach to identify loci or genomic regions under ecologically divergent selection. Here, we focused on the pea aphid, a species complex of...

Data from: Microsatellite length variation in candidate genes correlates with habitat in the gilthead sea bream Sparus aurata

Lamya Chaoui, Pierre-Alexandre Gagnaire, Bruno Guinand, Jean-Pierre Quignard, Costas Tsigenopoulos, M. Hichem Kara & Francois Bonhomme
The genetic basis and evolutionary implications of local adaptation in high gene flow marine organisms are still poorly understood. In several Mediterranean fish species, alternative migration patterns exist between individuals entering coastal lagoons that offer favorable conditions for growth and those staying in the sea where environmental conditions are less subject to rapid and stressful change. Whether these coexisting strategies are phenotypically plastic or include a role for local adaptation through differential survival needs to...

Data from: Translocation of wild populations: conservation implications for the genetic diversity of the black-lipped pearl oyster Pinctada margaritifera

Sarah Lemer & Serge Planes
Translocation has been widely studied as a tool for conservation management to restore or enhance degraded populations. On the contrary few studies have been conducted on translocation for commercial purposes. In this study we evaluate the genetic consequences of translocation of wild individuals of Pinctada margaritifera on farmed and adjacent wild populations. We tested the hypotheses that translocations would induce high genetic heterogeneity in farmed populations and this heterogeneity would then leak into the adjacent...

Data from: Ergosterol biosynthesis: a fungal pathway for life on land?

Sebastien Dupont, Guillaume Lemetais, Thierry Ferreira, Philippe Cayot, Patrick Gervais & Laurent Beney
Sterols, essential lipids of most eukaryotic cells, ensure important structural and signaling functions. The selection pressure which has led to different dominant sterols in the three eukaryotic kingdoms remains unknown. Here we investigated the influence of the progression in the different steps of the ergosterol biosynthetic pathway (EBP) on the yeast resistance to transitions from aqueous to aerial media, typical perturbations of the higher fungi habitats. Five mutants of the EBP (ergΔ), accumulating different sterol...

Data from: Forecasting changes in population genetic structure of alpine plants in response to global warming

Flora Jay, Stéphanie Manel, Nadir Alvarez, Eric Y. Durand, Wilfried Thuiller, Rolf Holderegger, Pierre Taberlet & Olivier François
Species range shifts in response to climate and land use change are commonly forecasted with species distribution models based on species occurrence or abundance data. Although appealing, these models ignore the genetic structure of species, and the fact that different populations might respond in different ways due to adaptation to their environment. Here, we introduced ancestry distribution models, i.e., statistical models of the spatial distribution of ancestry proportions, for forecasting intra-specific changes based on genetic...

Registration Year

  • 2012

Resource Types

  • Dataset


  • French National Centre for Scientific Research
  • University of Oslo
  • Centre d'Ecologie Fonctionnelle et Evolutive
  • Natural History Museum
  • University of Lausanne
  • University of California, Berkeley
  • Dalhousie University
  • University of Southampton
  • French National Institute for Agricultural Research
  • University of Paris-Sud