75 Works

Data from: Tracking earthworm communities from soil DNA

Friederike Bienert, Sébastien De Danieli, Christian Miquel, Eric Coissac, Carole Poillot, Jean-Jacques Brun & Pierre Taberlet
Earthworms are known for their important role within the functioning of an ecosystem, and their diversity can be used as an indicator of ecosystem health. To date, earthworm diversity has been investigated through conventional extraction methods such as handsorting, soil washing or the application of a mustard solution. Such techniques are time-consuming and often difficult to apply. We showed that combining DNA metabarcoding and next generation sequencing facilitates the identification of earthworm species from soil...

Data from: Testicular melanization has evolved in birds with high mtDNA mutation rates

Ismael Galván, Anders P. Møller & Johannes Erritzøe
Melanin is mainly found in the integument of animals, but it also appears in several extracutaneous tissues. The presence of melanin in testes has been anecdotally reported in all vertebrate groups, but the causes and functions of this melanin remain unknown. Similar to other extracutaneous melanins, testicular melanin may protect male germ cells from oxidative stress. Given the high respiratory activity of spermatozoa, oxidative stress generated by mitochondrial dysfunction as a consequence of mtDNA mutations...

Data from: A new malaria agent in African hominids.

Benjamin Ollomo, Patrick Durand, Franck Prugnolle, Emmanuel J. P. Douzery, Céline Arnathau, Dieudonné Nkoghe, Eric Leroy & François Renaud
Plasmodium falciparum is the major human malaria agent responsible for 200 to 300 million infections and one to three million deaths annually, mainly among African infants. The origin and evolution of this pathogen within the human lineage is still unresolved. A single species, P. reichenowi, which infects chimpanzees, is known to be a close sister lineage of P. falciparum. Here we report the discovery of a new Plasmodium species infecting Hominids. This new species has...

Data from: Variation in patriline reproductive success during queen production in orphaned colonies of the thelytokous ant Cataglyphis cursor

Blandine Chéron, Thibaud Monnin, Pierre Fédérici & Claudie Doums
In genetically diverse insect societies (polygynous or polyandrous queens), the production of new queens can set the ground for competition among lineages. This competition can be very intense when workers can reproduce using thelytoky as worker patrilines that manage to produce new queens gain a huge benefit. Selection at the individual level might then lead to the evolution of cheating genotypes, i.e. genotypes that reproduce more than their fair share. We studied the variation in...

Data from: High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries

Thibaut Malausa, André Gilles, Emese Meglécz, Hélène Blanquart, Stéphanie Duthoy, Caroline Costedoat, Vincent Dubut, Nicolas Pech, Philippe Castagnone-Sereno, Christophe Délye, Nicolas Feau, Pascal Frey, Philippe Gauthier, Thomas Guillemaud, Laurent Hazard, Valérie Le Corre, Brigitte Lung-Escarmant, Pierre-Jean G Malé, Stéphanie Ferreira & Jean-François Martin
Microsatellites (or SSR: simple sequence repeat) are among the most frequently used DNA markers in many areas of research. The use of microsatellite markers is limited by the difficulties involved in their de novo isolation from species for which no genomic resources are available. We describe here a high-throughput method for isolating microsatellite markers based on coupling multiplex microsatellite enrichment and Next-Generation Sequencing on 454 GS-FLX Titanium platforms. The procedure was calibrated on a model...

Data from: Comparing the genetic architecture and potential response to selection of native and invasive populations of reed canary grass

Brittny Calsbeek, Manisha Patel, Sebastien Lavergne & Jane Molofsky
Evolutionary processes such as migration, genetic drift, and natural selection are thought to play a prominent role in species invasions into novel environments. However, few empirical studies have explored the mechanistic basis of invasion in an evolutionary framework. One promising tool for inferring evolutionarily important changes in introduced populations is the genetic variance-covariance matrix (G matrix). G matrix comparisons allow for the inference of changes in the genetic architecture of introduced populations relative to their...

Data from: Scale-specific sex-biased dispersal in the Valais shrew unveiled by genetic variation on the Y chromosome, autosomes, and mitochondrial DNA

Glenn Yannic, Patrick Basset, Lucie Büchi, Jacques Hausser & Thomas Broquet
We investigated sex-specificities in the evolutionary processes shaping Y chromosome, autosomes and mitochondrial DNA patterns of genetic structure in the Valais shrew (Sorex antinorii), a mountain dwelling species with a hierarchical distribution. Both hierarchical analyses of variance and isolation-by-distance analyses revealed patterns of population structure that were not consistent across maternal, paternal and bi-parentally inherited markers. Differentiation on a Y microsatellite was lower than expected from the comparison with autosomal microsatellites and mtDNA, and it...

Data from: A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability

Tina Jørgensen, James Haile, Per Möller, Andrei Andreev, Sanne Boessenkool, Morten Rasmussen, Frank Kienast, Eric Coissac, Pierre Taberlet, Christian Brochmann, Nancy H. Bigelow, Kenneth Andersen, Ludovic Orlando, M. Thomas P. Gilbert & Eske Willerslev
Although ancient DNA from sediments (sedaDNA) has been used to investigate past ecosystems, the approach has never been directly compared to the traditional methods of pollen and macrofossil analysis. We conducted a comparative survey of 18 ancient permafrost samples spanning the Late Pleistocene (46–12.5 thousand years ago), from the Taymyr Peninsula in northern Siberia. The results show that pollen, macrofossils and sedaDNA are complementary rather than overlapping, and in combination reveal more detailed information on...

Data from: Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA meta-barcoding

Tina Jørgensen, Kurt H Kjær, James Haile, Morten Rasmussen, Sanne Boessenkool, Kenneth Andersen, Eric Coissac, Pierre Taberlet, Christian Brochmann, Ludovic Orlando, M. Thomas P. Gilbert & Eske Willerslev
Nunataks are isolated bedrocks protruding through ice sheets. They vary in age, but represent island environments in “oceans” of ice through which organism dispersals and replacements can be studied over time. The J.A.D. Jensen’s Nunataks at the southern Greenland ice sheet are the most isolated nunataks on the northern hemisphere - some 30 km from the nearest biological source. They constitute around 2 km2 of ice-free land that was established in the early Holocene. We...

Data from: Testing gradual and speciational models of evolution in extant taxa: the example of ratites

Michel Laurin, Sander W.S. Gussekloo, David Marjanovic, Lucas Legendre & Jorge Cubo
Ever since Eldredge and Gould proposed their model of punctuated equilibria, evolutionary biologists have debated how often this model is the best description of nature and how important it is compared to the more gradual models of evolution expected from natural selection and the neo-Darwinian paradigm. Recently, Cubo proposed a method to test whether morphological data in extant ratites are more compatible with a gradual or with a speciational model (close to the punctuated equilibrium...

Data from: Effects of parasitic sex-ratio distorters on host genetic structure in the Armadillidium vulgare-Wolbachia association

Sébastien Verne, Monique Johnson, Didier Bouchon & Frédéric Grandjean
In the pill bug Armadillidium vulgare (Crustacea, Oniscidea) Wolbachia facilitates its spread through vertical transmission via the eggs by inducing feminization of genetic males. The spread of feminizing Wolbachia within and across populations is therefore expected to influence mtDNA genetic structure by hitchhiking. To test this hypothesis, we analysed nuclear and mtDNA genetic structure, and Wolbachia prevalence in 13 populations of the pill bug host. Wolbachia prevalence (ranging from 0 to 100% of sampled females)...

Data from: An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

Georgia Tsagkogeorga, Xavier Turon, Russell R. Hopcroft, Marie-Ka Tilak, Tamar Feldstein, Noa Shenkar, Yossi Loya, Dorothée Huchon, Emmanuel J. P. Douzery & Frédéric Delsuc
BACKGROUND: Tunicates have been recently revealed to be the closest living relatives of vertebrates. Yet, with more than 2500 described species, details of their evolutionary history are still obscure. From a molecular point of view, tunicate phylogenetic relationships have been mostly studied based on analyses of 18S rRNA sequences, which indicate several major clades at odds with the traditional class-level arrangements. Nonetheless, substantial uncertainty remains about the phylogenetic relationships and taxonomic status of key groups...

Data from: Sexual selection on song and cuticular hydrocarbons in two distinct populations of Drosophila montana

Paris Veltsos, Claude Wicker-Thomas, Roger K. Butlin, Anneli Hoikkala & Michael G. Ritchie
Sexual selection has the potential to contribute to population divergence and speciation. Most studies of sexual selection in Drosophila have concentrated on a single signaling modality, usually either courtship song or cuticular hydrocarbons (CHCs), which can act as contact pheromones. We have examined the relationship between both signal types and reproductive success using F1-3 offspring of wild-collected flies, raised in the lab. We used two populations of the Holarctic species Drosophila montana, that represent different...

Data from: Ecological speciation in dynamic landscapes

Robin Aguilée, Amaury Lambert & David Claessen
Although verbal theories of speciation consider landscape changes, ecological speciation is usually modeled in a fixed geographical arrangement. Yet landscape changes occur, at different spatio-temporal scales, due to geological, climatic or ecological processes, and these changes result in repeated divisions and reconnections of populations. We examine the effect of such landscape dynamics on speciation. We use a stochastic, sexual population model with polygenic inheritance, embedded in a landscape dynamics model (allopatry-sympatry oscillations). We show that,...

Data from: Differential selection between the sexes and selection for sex

Denis Roze & Sarah P. Otto
Anisogamy is known to generate an important cost for sexual reproduction (the famous "twofold cost of sex"). However, male-female differences may have other consequences on the evolution of sex, due to the fact that selective pressures may differ among the sexes. On the one hand, intralocus sexual conflict should favor asexual females, which can fix female-beneficial, male-detrimental alleles. On the other hand, it has been suggested repeatedly that sexual selection among males may help to...

Data from: Host and habitat specialization of avian malaria in Africa

Claire Loiseau, Ryan J. Harrigan, Alexandre Robert, Rauri C. K. Bowie, Henri A. Thomassen, Thomas B. Smith, Ravinder N. M. Sehgal, Claire Loiseau, Ryan J. Harrigan, Alexandre Robert, Rauri C. K. Bowie, Henri A. Thomassen, Thomas B. Smith & Ravinder N. M. Sehgal
Studies of both vertebrates and invertebrates have suggested that specialists, as compared to generalists, are likely to suffer more serious declines in response to environmental change. Less is known about the effects of environmental conditions on specialist vs. generalist parasites. Here, we study the evolutionary strategies of malaria parasites (Plasmodium spp.) among different bird host communities. We determined the parasite diversity and prevalence of avian malaria in three bird communities in the lowland forests in...

Data from: Reconstructing the origins of high-alpine niches and cushion life form in the genus Androsace s.l. (Primulaceae)

Florian Boucher, Wilfried Thuiller, Cristina Roquet, Rolland Douzet, Serge Aubert, Nadir Alvarez & Sébastien Lavergne
Relatively few species have been able to colonize extremely cold alpine environments. We investigate the role played by the cushion life form in the evolution of climatic niches in the plant genus Androsace s.l., which spreads across the mountain ranges of the Northern Hemisphere. Using robust methods that account for phylogenetic uncertainty, intraspecific variability of climatic requirements and different life history evolution scenarios, we show that climatic niches of Androsace s.l. exhibit low phylogenetic signal...

Data from: The coupling hypothesis: why genome scans may fail to map local adaptation genes

Nicolas Bierne, John Welch, Etienne Loire, François Bonhomme & Patrice David
Genomic scans of multiple populations often reveal marker loci with greatly increased differentiation between populations. Often this differentiation coincides in space with contrasts in ecological factors, forming a genetic–environment association (GEA). GEAs imply a role for local adaptation, and so it is tempting to conclude that the strongly differentiated markers are themselves under ecologically based divergent selection, or are closely linked to loci under such selection. Here, we highlight an alternative and neglected explanation: intrinsic...

Data from: Social organisation and genetic structure: insights from co-distributed bat populations

Stephen J. Rossiter, Akbar Zubaid, Adura Mohd-Adnan, Matthew J. Struebig, Thomas H. Kunz, Sucharita Gopal, Eric J. Petit & Tigga Kingston
The impact of ecology and social organisation on genetic structure at landscape spatial scales, where gene dynamics shape evolution as well as determine susceptibility to habitat fragmentation, is poorly understood. Attempts to assess these effects must take into account the potentially confounding effects of history. We used microsatellites to compare genetic structure in seven bat species with contrasting patterns of roosting ecology and social organisation, all of which are co-distributed in an ancient forest habitat...

Data from: Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay

Lucie Bittner, Angélique Gobet, Stéphane Audic, Sarah Romac, Elianne S. Egge, Sébastien Santini, Hiroyuki Ogata, Ian Probert, Bente Edvardsen & Colomban De Vargas
Haptophytes are a key phylum of marine protists, including ~300 described morphospecies and 80 morphogenera. We used 454 pyrosequencing on large subunit ribosomal DNA (LSU rDNA) fragments to assess the diversity from size-fractioned plankton samples collected in the Bay of Naples. One group-specific primer set targeting the LSU rDNA D1/D2 region was designed to amplify Haptophyte sequences from nucleic acid extracts (total DNA or RNA) of two size fractions (0.8–3 or 3–20 μm) and two...

Data from: Hybridization and barriers to gene flow in an island bird radiation

Ben H. Warren, Eldredge Bermingham, Yann Bourgeois, Laura K. Estep, Robert P. Prys-Jones, Dominique Strasberg & Christophe Thébaud
While reinforcement may play a role in all major modes of speciation, relatively little is known about the timescale over which species hybridize without evolving complete reproductive isolation. Birds have high potential for hybridization, and islands provide simple settings for uncovering speciation and hybridization patterns. Here we develop a phylogenetic hypothesis for a phenotypically-diverse radiation of finch-like weaver-birds (Foudia) endemic to the western Indian Ocean islands. We find that unlike Darwin’s finches, each island-endemic Foudia...

Data from: Ecology and life history affect different aspects of the population structure of 27 high-alpine plants

Patrick G. Meirmans, Jerome Goudet, IntraBioDiv Consortium & Oscar E. Gaggiotti
A plant species' genetic population structure is the result of a complex combination of its life history, ecological preferences, position in the ecosystem, and historical factors. As a result, many different statistical methods exist that measure different aspects of species’ genetic structure. However, little is known about how these methods are interrelated and how they are related to a species’ ecology and life history. In this study, we used the IntraBioDiv AFLP-dataset from 27 high-alpine...

Data from: Phenotypic plasticity allows the Mediterranean parsley frog Pelodytes punctatus to exploit two contrasted temporal niches under continuous gene flow

Hélène Jourdan-Pineau, Patrice David & Pierre-Andre Crochet
Environmental changes, such as climate change, lead to the opening of new niches. In such situations, species that adapt to new niches can survive and/or expand their ranges. However, gene flow can hamper genetic adaptation to new environments. Alternatively, recent models have highlighted the importance of phenotypic plasticity in tracking environmental change. In this study, we illustrate how plasticity allows an amphibian species to exploit two very different climatic niches under continuous gene flow. In...

Data from: Inter-island divergence within Drosophila mauritiana, a species of the D. simulans complex: past history and/or speciation in progress?

Delphine Legrand, Thomas Chenel, Cécile Campagne, Daniel Lachaise & Marie-Louise Cariou
Speciation with gene flow may be more common than generally thought making detailed understanding of the extent and pattern of genetic divergence between geographically isolated populations useful. Species of the Drosophila simulans complex provide a good model for speciation and evolutionary studies; understanding their population genetic structure will increase our understanding of the context in which speciation has occurred. Here we describe the genetic diversity and the genetic differentiation, at mitochondrial and nuclear loci, of...

Data from: Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan

Wasim Shehzad, Tiayyba Riaz, Christian Miquel, Carole Poillot, Safdar Shah, Eric Coissac, Pierre Taberlet, Muhammad Ali Nawaz & François Pompanon
Diet analysis is a prerequisite to fully understand the biology of a species and the functioning of ecosystems. For carnivores, traditional diet analyses mostly rely upon the morphological identification of undigested remains in the feces. Here, we developed a methodology for carnivore diet analyses based on next generation sequencing. We applied this approach to the analysis of the vertebrate component of leopard cat diet in two ecologically distinct regions in northern Pakistan. Despite being a...

Registration Year

  • 2011

Resource Types

  • Dataset


  • French National Centre for Scientific Research
  • University of Lausanne
  • University of Oslo
  • Spanish National Research Council
  • Natural History Museum
  • University of Alaska Fairbanks
  • Aix-Marseille University
  • Tel Aviv University
  • University of Montpellier
  • University of Jyväskylä