14 Works

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: Environmental effects on the detection of adaptation

Sara Magalhães, Elodie Blanchet, Martijn Egas & Isabelle Olivieri
Detecting adaptation involves comparing the performance of populations evolving in different environments. This detection may be confounded by effects due to the environment experienced by organisms prior to the test. We tested whether such confounding effects occur, using spider-mite selection lines on two novel hosts and one ancestral host, after 15 generations of selection. Mites were either sampled directly from the selection lines, or subjected to a common juvenile or to a common maternal environment,...

Data from: Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

France Denoeud, Simon Henriet, Sutada Mungpakdee, Jean-Marc Aury, Corinne Da Silva, Henner Brinkmann, Jana Mikhaleva, Lisbeth C. Olsen, Claire Jubin, Cristian Cañestro, Jean-Marie Bouquet, Gemma Danks, Julie Poulain, Coen Campsteijn, Marcin Adamski, Ismael Cross, Fekadu Yadetie, Matthieu Muffato, Alexandra Louis, Stephen Butcher, Georgia Tsagkogeorga, Anke Konrad, Sarabdeep Singh, Marit F. Jensen, Evelyne Huynh Cong … & Daniel Chourrout
Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on...

Data from: Gene flow among wild and domesticated almond species: insights from chloroplast and nuclear markers

Malou Delplancke
Hybridization has played a central role in the evolutionary history of domesticated plants. Notably, several breeding programs relying on gene introgression from the wild compartment have been performed in fruit tree species within the genus Prunus but few studies investigated spontaneous gene flow among wild and domesticated Prunus species. Consequently, a comprehensive understanding of genetic relationships and levels of gene flow between domesticated and wild Prunus species is needed. Combining nuclear and chloroplastic microsatellites, we...

Data from: Phylogenetic analyses of mitochondrial and nuclear data in haematophagous flies support the paraphyly of the genus Stomoxys (Diptera: Muscidae)

Najla Dsouli, Frédéric Delsuc, Johan Michaux, Eric De Stordeur, Arnaud Couloux, Michel Veuille & Gérard Duvallet
The genus Stomoxys Geoffroy (Diptera; Muscidae) contains species of parasitic flies that are of medical and economic importance. We conducted a phylogenetic analysis including 10 representative species of the genus including multiple exemplars, together with the closely related genera Prostomoxys Zumpt, Haematobosca Bezzi, and Haematobia Lepeletier & Serville. Phylogenetic relationships were inferred using maximum likelihood and Bayesian methods from DNA fragments from the cytochrome c oxidase subunit I (COI, 753 bp) and cytochrome b (CytB,...

Data from: Accelerated evolutionary rate of housekeeping genes in tunicates

Georgia Tsagkogeorga, Xavier Turon, Nicolas Galtier, Emmanuel J. P. Douzery & Frédéric Delsuc
Phylogenomics has recently revealed that tunicates represent the sister-group of vertebrates in the newly defined clade Olfactores. However, phylogenomic and comparative genomic studies have also suggested that tunicates are characterized by an elevated rate of molecular evolution and a high degree of genomic divergence. Despite the recurrent interest in the group, the picture of tunicate peculiar evolutionary dynamics is still fragmentary, as it mainly lies in studies focusing on only a few model species. In...

Data from: Phylogenetic signal in module composition and species connectivity in compartmentalized host-parasite networks

Boris R. Krasnov, Miguel A. Fortuna, David Mouillot, Irina S. Khokhlova, Georgy I. Shenbrot & Robert Poulin
Across different taxa, networks of mutualistic or antagonistic interactions show consistent architecture. Most networks are modular, with modules being distinct species subsets connected mainly with each other and having few connections to other modules. We investigate the phylogenetic relatedness of species within modules and whether a phylogenetic signal is detectable in the within- and among module connectivity of species using 27 mammal-flea networks from the Palaearctic. In the 24 networks that were modular, closely-related hosts...

Data from: Ecomorphological diversification among South American spiny rats (Rodentia, Echimyidae): a phylogenetic and chronological approach.

Thomas Galewski, Jean-François Mauffrey, Yuri L. R. Leite, James L. Patton, Emmanuel J. P. Douzery & Emmanuel J.P. Douzery
The phylogeny of South American spiny rats (Rodentia; Echimyidae) was studied using the exon 28 of the von Willebrand Factor nuclear gene (vWF). Sequences were analysed separately and in combination with a mitochondrial dataset (cyt b, 12S and 16S rRNAs) used in previous publications. The basal polytomy of echimyids was partially resolved and unexpected intergeneric clades were recovered. Thus, the intimate nested position of Myocastor within echimyids is evidenced. A well-supported clade is identified, including...

Data from: Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations.

Emmanuel J. P. Douzery, Frédéric Delsuc, Michael J. Stanhope & Dorothée Huchon
Reconstructing the chronology of mammalian evolution is a debated issue between molecule- and fossil-based inferences. A methodological limitation of molecules is the evolutionary rate variation among lineages, precluding the application of the global molecular clock. We considered 2422 first and second codon positions of the combined ADRA2B, IRBP, and vWF nuclear genes for a well-documented set of placentals including an extensive sampling of rodents. Using seven independent calibration points and a maximum-likelihood framework, we evaluated...

Data from: Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA.

Pierre-Henri Fabre, Andrew Rodrigues, Emmanuel J. P. Douzery, P-.H. Fabre & E.J.P. Douzery
Here, we present a new primate phylogeny inferred from molecular supermatrix analyses of size 42 kb containing 70% of missing data, and representing 75% of primate species diversity. The supermatrix was analysed using a gene-partitioned maximum likelihood approach to obtain an exhaustive molecular phylogenetic framework. All clades recovered from recent molecular works were upheld in our analyses demonstrating that the presence of missing data did not bias our supermatrix inference. The resulting phylogenetic tree was...

Data from: New DNA data from a Transthyretin nuclear intron suggest an Oligocene to Miocene diversification of living South America opossums (Marsupialia: Didelphidae).

Cynthia C. Steiner, Marie-Ka Tilak, Emmanuel J. P. Douzery, François M. Catzeflis & Emmanuel J.P. Douzery
Phylogenetic relationships of 19 species of didelphid marsupials were studied using two nuclear markers, the non-coding transthyretin intron 1 (TTR) and the coding interphotoreceptor retinoid binding protein exon 1 (IRBP), and two mitochondrial genes, the protein-coding cytochrome b (cyt-b) and the structural 12S ribosomal DNA (12S rDNA). Evolutionary dynamics of these four markers were compared to each other, revealing the appropriate properties presented by TTR intron 1 together with its well supported and resolved phylogenetic...

Data from: Reverse evolution: selection against costly resistance in disease-free microcosm populations of Paramecium caudatum

Alison B Duncan, Simon Fellous & Oliver Kaltz
Evolutionary costs of parasite resistance arise if genes conferring resistance reduce fitness in the absence of parasites. Thus, parasite-mediated selection may lead to increased resistance and a correlated decrease in fitness, whereas relaxed parasite-mediated selection may lead to reverse evolution of increased fitness and a correlated decrease in resistance. We tested this idea in experimental populations of the protozoan Paramecium caudatum and the parasitic bacterium Holospora undulata. After 8 years, resistance to infection and asexual...

Data from: Diversification in temporally heterogeneous environments: effect of the grain in experimental bacterial populations.

Patrick A Venail, Nicolas Mouquet, Oliver Kaltz, Isabelle Olivieri & Thomas Pommier
Although theory established the necessary conditions for diversification in temporally heterogeneous environments, empirical evidence remains controversial. One possible explanation is the difficulty of designing experiments including the relevant range of temporal grains and the appropriate environmental tradeoffs. Here, we experimentally explore the impact of the grain on the diversification of the bacterium Pseudomonas fluorescens SBW25 in a temporally fluctuating environment by including twenty different pairs of environments and four temporal grains. In general, higher levels...

Data from: Molecular phylogenetics unveils the ancient evolutionary origins of the enigmatic fairy armadillos

Frédéric Delsuc, Mariella Superina, Marie-Ka Tilak-Jean, Emmanuel J. P. Douzery, Alexandre Hassanin, Marie-Ka Tilak & Emmanuel J.P. Douzery
Fairy armadillos or pichiciegos (Xenarthra, Dasypodidae) are among the most elusive mammals. Due to their subterranean and nocturnal lifestyle, their basic biology and evolutionary history remain virtually unknown. Two distinct species with allopatric distributions are recognized: Chlamyphorus truncatus is restricted to central Argentina, while Calyptophractus retusus occurs in the Gran Chaco of Argentina, Paraguay, and Bolivia. To test their monophyly and resolve their phylogenetic affinities within armadillos, we obtained sequence data from modern and museum...

Registration Year

  • 2011

Resource Types

  • Dataset


  • University of Montpellier
  • French National Centre for Scientific Research
  • Centre de Recherches de Jouy-en-Josas
  • Princeton University
  • École Normale Supérieure Paris-Saclay
  • University of California System
  • University of Wyoming
  • University of Montreal
  • University of Otago
  • Genoscope