19 Works

Data from: Predicting the ancestral character changes in a tree is typically easier than predicting the root state

Olivier Gascuel & Mike Steel
Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed for this purpose. Theoretical results are available that show that when the substitution rate become too large, reconstructing the ancestral state at the tree root is no longer feasible. Here, we also study the reconstruction of the ancestral changes that occurred along the tree edges. We show...

Data from: Host-parasite network structure is associated with community-level immunogenetic diversity

Shai Pilosof, Miguel A. Fortuna, Jean-François Cosson, Maxime Galan, Chaisiri Kittipong, Alexis Ribas, Eran Segal, Boris R. Krasnov, Serge Morand & Jordi Bascompte
Genes of the major histocompatibility complex (MHC) encode proteins that recognize foreign antigens and are thus crucial for immune response. In a population of a single host species, parasite-mediated selection drives MHC allelic diversity. However, in a community-wide context, species interactions may modulate selection regimes because the prevalence of a given parasite in a given host may depend on its prevalence in other hosts. By combining network analysis with immunogenetics, we show that host species...

Data from: Congruent signals of population history but radically different patterns of genetic diversity between mitochondrial and nuclear markers in a mountain lizard

Anne-Laure Ferchaud, Rémy Eudeline, Véronique Arnal, Marc Cheylan, Gilles Pottier, Raphaël Leblois & Pierre-Andre Crochet
Historical factors, current population size, population connectivity and selective processes at linked loci contribute to shaping contemporary patterns of neutral genetic diversity. It is now widely acknowledged that nuclear and mitochondrial markers react differently to current demography as well as to past history, so the use of both types of markers is often advocated to gain insight on both historical and contemporary processes. We used 12 microsatellite loci genotyped in 13 populations of a mountain...

Data from: Development of SNP genotyping arrays in two shellfish species

Sylvie Lapègue, Estelle Harrang, Serge Heurtebise, Emilie Flahauw, Cécile Donnadieu, Philippe Gayral, Marion Ballenghien, Lucie Genestout, Laetitia Barbotte, Rachid Mahla, Pierrick Haffray & Christophe Klopp
Use of SNPs has been favored due to their abundance in plant and animal genomes, accompanied by the falling cost and rising throughput capacity for detection and genotyping. Here, we present in vitro (obtained from targeted sequencing) and in silico discovery of SNPs, and the design of medium-throughput genotyping arrays for two oyster species, the Pacific oyster, Crassostrea gigas, and European flat oyster, Ostrea edulis. Two sets of 384 SNP markers were designed for two...

Data from: Mitochondrial DNA as a tool for reconstructing past life-history traits in mammals

Emeric Figuet, Jonathan Romiguier, Julien Y. Dutheil & Nicolas Galtier
Reconstructing the ancestral characteristics of species is a major goal in evolutionary and comparative biology. Unfortunately, fossils are not always available and sufficiently informative, and phylogenetic methods based on models of character evolution can be unsatisfactory. Genomic data offer a new opportunity to estimate ancestral character states, through: (i) the correlation between DNA evolutionary processes and species life-history traits, and (ii) available reliable methods for ancestral sequence inference. Here we assess the relevance of mitochondrial...

Data from: Genetic structure and diversity of the endangered fir tree of Lebanon (Abies cilicica Carr.): implications for conservation

Lara Awad, Bruno Fady, Carla Khater, Anne Roig & Rachid Cheddadi
The threatened conifer Abies cilicica currently persists in Lebanon in geographically isolated forest patches. The impact of demographic and evolutionary processes on population genetic diversity and structure were assessed using 10 nuclear microsatellite loci. All remnant 15 local populations revealed a low genetic variation but a high recent effective population size. FST-based measures of population genetic differentiation revealed a low spatial genetic structure, but Bayesian analysis of population structure identified a significant Northeast-Southwest population structure....

Data from: Do North Atlantic Eels show parallel patterns of spatially varying selection?

Malene G. Ulrik, José Martín Pujolar, Anne-Laure Ferchaud, Magnus W. Jacobsen, Thomas D. Als, Pierre Alexandre Gagnaire, Jane Frydenberg, Peder K. Bøcher, Bjarni Jónsson, Louis Bernatchez & Michael M. Hansen
Background: The two North Atlantic eel species, the European and the American eel, represent an ideal system in which to study parallel selection patterns due to their sister species status and the presence of ongoing gene flow. A panel of 80 coding-gene SNPs previously analyzed in American eel was used to genotype European eel individuals (glass eels) from 8 sampling locations across the species distribution. We tested for single-generation signatures of spatially varying selection in...

Data from: Vertically transmitted symbiont reduces host fitness along temperature gradient

Eike Dusi, Sascha Krenek, Martina Schrallhammer, René Sachse, Gisep Rauch, Oliver Kaltz, Thomas Berendonk & T. U. Berendonk
Parasites with exclusive vertical transmission from host parent to offspring are an evolutionary puzzle. With parasite fitness entirely linked to host reproduction, any fitness cost for infected hosts risks their selective elimination. Environmental conditions likely influence parasite impact, and thereby the success of purely vertical transmission strategies. We tested for temperature-dependent virulence of Caedibacter taeniospiralis, a vertically transmitted bacterial symbiont of the protozoan Paramecium tetraurelia. We compared growth of infected and cured host populations at...

Data from: Evidence for adaptation from standing genetic variation on an antimicrobial peptide gene in the mussel Mytilus edulis

Célia C. Gosset, Joana Do Nascimento, Marie-Thérèse Augé & Nicolas Bierne
Genome scans of population differentiation identify candidate loci for adaptation but provide little information on how selection has influenced the genetic structure of these loci. Following a genome scan, we investigated the nature of the selection responsible for the outlying differentiation observed between populations of the marine mussel Mytilus edulis at a leucine/arginine polymorphism (L31R) in the antimicrobial peptide MGD2. We analysed DNA sequence polymorphisms, allele frequencies and population differentiation of polymorphisms closely linked to...

Data from: Pine afforestation decreases the long-term performance of understory shrubs in a semiarid Mediterranean ecosystem: a stable isotope approach.

Cristina Moreno-Gutiérrez, Giovanna Battipaglia, Paolo Cherubini, Antonio Delgado Huertas & José Ignacio Querejeta
1. Plant–plant interactions shape the structure and composition of plant communities, but shifts in interaction outcomes might occur in the face of ongoing climate change. 2. We assessed the influence of Pinus halepensis plantations on the long-term ecophysiological performance of understorey vegetation, by conducting a retrospective comparison (1989–2007) of growth-ring widths, δ13C and δ18O between Rhamnus lycioides shrubs from two contrasting vegetation types: P. halepensis plantations vs. open woodlands. We also measured the leaf δ13C,...

Data from: Decomposing changes in phylogenetic and functional diversity over space and time

Loïc Chalmandrier, Tamara Münkemüller, Vincent Devictor, Sébastien Lavergne & Wilfried Thuiller
1. The α, β, γ diversity decomposition methodology is commonly used to investigate changes in diversity over space or time but rarely conjointly. However, with the ever-increasing availability of large-scale biodiversity monitoring data, there is a need for a sound methodology capable of simultaneously accounting for spatial and temporal changes in diversity. 2. Using the properties of Chao's index, we adapted Rao's framework of diversity decomposition between orthogonal dimensions to a multiplicative α, β, γ...

Data from: The early spread and epidemic ignition of HIV-1 in human populations

Nuno R. Faria, Andrew Rambaut, Marc A. Suchard, Guy Baele, Trevor Bedford, Melissa J. Ward, Andrew J. Tatem, João D. Sousa, Nimalan Arinaminpathy, Jacques Pépin, David Posada, Martine Peeters, Oliver P. Pybus & Philippe Lemey
Thirty years after the discovery of HIV-1, the early transmission, dissemination and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M...

Data from: Bushmeat genetics: setting up a reference framework for the DNA-typing of African forest bushmeat

Philippe Gaubert, Flobert Njiokou, Ayodeji Olayemi, Paolo Pagani, Sylvain Dufour, Emmanuel Danquah, Mac Elikem K. Nutsuakor, Gabriel Ngua, Alain-Didier Missoup, Pablo A. Tedesco, Rémy Dernat & Agostinho Antunes
The bushmeat trade in tropical Africa represents illegal, unsustainable off-takes of millions of tons of wild game – mostly mammals – per year. We sequenced four mitochondrial gene fragments (cyt b, COI, 12S, 16S) in >300 bushmeat items representing nine mammalian orders and 59 morphological species from five western and central African countries (Guinea, Ghana, Nigeria, Cameroon and Equatorial Guinea). Our objectives were to assess the efficiency of cross-species PCR amplification and to evaluate the...

Data from: Density- and trait-mediated effects of a parasite and a predator in a tri-trophic food web

Aabir Banerji, Alison B. Duncan, Joanne S. Griffin, Stuart Humphries, Owen L. Petchey & Oliver Kaltz
1. Despite growing interest in ecological consequences of parasitism in food webs, relatively little is known about effects of parasites on long-term population dynamics of non-host species or about whether such effects are density- or trait- mediated. 2. We studied a tri-trophic food chain comprised of: (i) a bacterial basal resource (Serratia fonticola), (ii) an intermediate consumer (Paramecium caudatum), (iii) a top predator (Didinium nasutum), and (iv) a parasite of the intermediate consumer (Holospora undulata)....

Data from: Root community traits along a land use gradient: evidence of a community-level economics spectrum

Iván Prieto, Catherine Roumet, Remi Cardinael, Christian Dupraz, Christophe Jourdan, John H. Kim, Jean Luc Maeght, Zhun Mao, Alain Pierret, Noelia Portillo, Olivier Roupsard, Chantanousone Thammahacksa & Alexia Stokes
1. There is a fundamental trade-off between leaf traits associated with either resource acquisition or resource conservation. This gradient of trait variation, called the economics spectrum also applies to fine roots but whether it is consistent for coarse roots or at the plant community level remains untested. 2. We measured a set of morphological and chemical root traits at a community level (functional parameters; FP) in 20 plant communities located along land-use intensity gradients and...

Data from: Patterns of selection on Plasmodium falciparum erythrocyte binding antigens after the colonisation of the New World

Erhan Yalcindag, Virginie Rougeron, Eric Elguero, Céline Arnathau, Patrick Durand, Sylvain Brisse, Laure Diancourt, Agnes Aubouy, Pierre Becquart, Umberto D'Alessandro, Didier Fontenille, Dionicia Gamboa, Amanda Maestre, Didier Ménard, Lise Musset, Oscar Noya, Vincent Veron, Albina Wide, Bernard Carme, Eric Legrand, Christine Chevillon, Francisco J. Ayala, François Renaud & Franck Prugnolle
Pathogens, which have recently colonized a new host species or new populations of the same host, are interesting models for understanding how populations may evolve in response to novel environments. During its colonization of South America from Africa Plasmodium falciparum, the main agent of malaria, has been exposed to new conditions in distinctive new human populations (Amerindian and populations of mixed origins), that likely exerted new selective pressures on the parasite's genome. Among the genes...

Data from: Gene-dosage effects on fitness in recent adaptive duplications: ace-1 in the mosquito Culex pipiens

Pierrick Labbé, Pascal Milesi, André Yébakima, Nicole Pasteur, Mylène Weill & Thomas Lenormand
Gene duplications have long been advocated to contribute to the evolution of new functions. The role of selection in their early spread is more controversial. Unless duplications are favored for a direct benefit of increased expression, they are likely detrimental. In this paper, we investigated the case of duplications favored because they combine already functionally divergent alleles. Their gene-dosage/fitness relations are poorly known, because selection may operate on both overall expression and duplicates relative dosage....

Data from: Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family

Pierre-Jean G. Malé, Léa Bardon, Guillaume Besnard, Eric Coissac, Frédéric Delsuc, Julien Engel, Emeline Lhuillier, Caroline Scotti-Saintagne, Alexandra Tinaut & Jérôme Chave
Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high-copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid...

Data from: Stability of the gorilla microbiome despite simian immunodeficiency virus infection

Andrew H. Moeller, Martine Peeters, Ahidjo Ayouba, Eitel Mpoudi Ngole, Amadine Esteban, Beatrice H. Hahn & Howard Ochman
Simian immunodeficiency viruses (SIVs) have been discovered in over 45 primate species; however, the pathogenic potential of most SIV strains remains unknown due to difficulties inherent in observing wild populations. Because those SIV infections that are pathogenic have been shown to induce changes in the host's gut microbiome, monitoring the microbiota present in faecal samples can provide a noninvasive means for studying the effects of SIV infection on the health of wild-living primates. Here, we...

Registration Year

  • 2014
    19

Resource Types

  • Dataset
    19

Affiliations

  • University of Montpellier
    19
  • French National Centre for Scientific Research
    4
  • French National Institute for Agricultural Research
    3
  • Aarhus University
    2
  • Paul Sabatier University
    2
  • Centre de Biologie et de Gestion des Populations
    2
  • Fred Hutchinson Cancer Research Center
    1
  • Centre d'Ecologie Fonctionnelle et Evolutive
    1
  • French Poultry and Aquaculture Breeders Association
    1
  • University of Pennsylvania
    1