A5005797093- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- RNA and protein synthesis mechanisms
- Wildlife Ecology and Conservation
- Lepidoptera: Biology and Taxonomy
- Evolution and Genetic Dynamics
- Avian ecology and behavior
- Bird parasitology and diseases
- Mitochondrial Function and Pathology
- Plant and animal studies
- Evolution and Paleontology Studies
- Orthoptera Research and Taxonomy
- Identification and Quantification in Food
- Genetic and phenotypic traits in livestock
- Plant and Fungal Interactions Research
- Ecology and Vegetation Dynamics Studies
- Physiological and biochemical adaptations
- Wildlife-Road Interactions and Conservation
- Plant Virus Research Studies
- Species Distribution and Climate Change
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Animal Behavior and Reproduction
- Fish biology, ecology, and behavior
- Botany and Plant Ecology Studies
Université de Montpellier
2014-2025
Institut des Sciences de l'Evolution de Montpellier
2016-2025
Centre National de la Recherche Scientifique
2014-2025
Institut de Recherche pour le Développement
2016-2025
Institut Universitaire de France
2020-2025
École Pratique des Hautes Études
2016-2024
Délégation Paris 6
2024
Agropolis International
2014
Genetic Improvement and Adaptation of Mediterranean and Tropical Plants
2014
Uppsala University
2009-2013
To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis 48 species representing all orders Neoaves using phylogenomic methods created to handle data. We recovered highly resolved tree that confirms previously controversial sister or close relationships. identified first divergence in Neoaves, two groups named Passerea and Columbea, independent lineages diverse convergently evolved land water bird species. Among Passerea, infer common ancestor core...
Abstract Thanks to the development of high‐throughput sequencing technologies, target enrichment nuclear ultraconserved DNA elements (UCEs) now allows routine inference phylogenetic relationships from thousands genomic markers. Recently, it has been shown that mitochondrial (mtDNA) is frequently sequenced alongside targeted loci in such capture experiments. Despite its broad evolutionary interest, mtDNA rarely assembled and used conjunction with markers capture‐based studies. Here, we...
The genome of the zebra finch — a songbird and model for study vertebrate brain, behaviour evolution has been sequenced. Its comparison with chicken genome, only other bird available, shows that genes neural function implicated in cognitive processing song have rapidly evolving lineage. also vocal communication engages much brain transcriptome identifies potential integrator microRNA signals linked to communication. studying Comparison are Moreover, brain. is an important organism several...
Mitochondrial DNA (mtDNA) is the most popular marker of molecular diversity in animals, primarily because its elevated mutation rate. After >20 years intensive usage, extent mitochondrial evolutionary rate variations across species, their practical consequences on sequence analysis methods, and ultimate reasons for mtDNA hypermutability are still largely unresolved issues. Using an extensive cytochrome b data set, fossil data, taking advantage decoupled dynamics synonymous nonsynonymous...
It is commonly assumed that mitochondrial DNA (mtDNA) evolves at a faster rate than nuclear (nuDNA) in animals. This has contributed to the popularity of mtDNA as molecular marker evolutionary studies. Analyzing 121 multilocus data sets and four phylogenomic encompassing 4,676 species animals, we demonstrate ratio over mutation highly variable among animal taxa. In nonvertebrates, such insects arachnids, nuDNA varies between 2 6, whereas it above 20, on average, vertebrates scaled reptiles...
During the last ten years, major advances have been made in characterizing and understanding evolution of mitochondrial DNA, most popular marker molecular biodiversity. Several important results were recently reported using mammals as model organisms, including (i) absence relationship between DNA diversity life-history or ecological variables, (ii) prominent adaptive selection, contrary to what was found invertebrates, (iii) unexpectedly large variation neutral substitution rate among...
Efficient algorithms and programs for the analysis of ever-growing amount biological sequence data are strongly needed in genomics era. The pace at which new methodologies generated calls use pre-existing, optimized—yet extensible—code, typically distributed as libraries or packages. This motivated Bio++ project, aiming developing a set C++ analysis, phylogenetics, population genetics, molecular evolution. main attractiveness is extensibility reusability its components through...
In animals, the population genomic literature is dominated by two taxa, namely mammals and drosophilids, in which fully sequenced, well-annotated genomes have been available for years. Data from other metazoan phyla are scarce, probably because vast majority of living species still lack a closely related reference genome. Here we achieve de novo, reference-free analysis wild samples five non-model animal species, based on next-generation sequencing transcriptome data. We introduce pipe-line...
Abstract Background Obtaining a draft genome sequence of the zebra finch ( Taeniopygia guttata ), second bird to be sequenced, provides necessary resource for whole-genome comparative analysis gene evolution in non-mammalian vertebrate lineage. To analyze basic molecular evolutionary processes during avian evolution, and contrast these with situation mammals, we aligned protein-coding sequences 8,384 1:1 orthologs chicken, finch, lizard three mammalian species. Results We found clear...
According to current assemblies, avian genomes differ from those of the other lineages amniotes in 1) containing a lower number genes; 2) displaying high stability karyotype and recombination map; 3) lacking any correlation between evolutionary rates (dN/dS) life-history traits, unlike mammals nonavian reptiles. We question reality bird missing genes investigate whether insufficient representation gene content might have biased previous analyses. Mining RNAseq data, we show that vast...
Determining the evolutionary relationships among major lineages of extant birds has been one biggest challenges in systematic biology. To address this challenge, we assembled or collected genomes 48 avian species spanning most orders birds, including all Neognathae and two five Palaeognathae orders. We used these to construct a genome-scale phylogenetic tree perform comparative genomic analyses. Here present datasets associated with phylogenomic analyses, which include sequence alignment...
The nearly neutral theory of molecular evolution predicts that small populations should accumulate deleterious mutations at a faster rate than large populations. analysis nonsynonymous (dN) versus synonymous (dS) substitution rates in birds mammals, however, has provided contradictory results, questioning the generality theory. Here we analyzed impact life history traits, taken as proxies effective population size, on evolutionary and genetic processes amniotes, including so far neglected...
Abstract Evolutionary relationships have remained unresolved in many well-studied groups, even though advances next-generation sequencing and analysis, using approaches such as transcriptomics, anchored hybrid enrichment, or ultraconserved elements, brought systematics to the brink of whole genome phylogenomics. Recently, it has become possible sequence entire genomes numerous nonbiological models parallel at reasonable cost, particularly with shotgun sequencing. Here, we identify...
Whether adaptation is limited by the beneficial mutation supply a long-standing question of evolutionary genetics, which more generally related to determination adaptive substitution rate and its relationship with species effective population size (Ne) genetic diversity. Empirical evidence reported so far equivocal, some but not all studies supporting higher in large-Ne than small-Ne species. We gathered coding sequence polymorphism data estimated amino-acid ωa, 50 from ten distant groups...
Abstract The mega-diversity of herbivorous insects is attributed to their co-evolutionary associations with plants. Despite abundant studies on insect-plant interactions, we do not know whether host-plant shifts have impacted both genomic adaptation and species diversification over geological times. We show that the antagonistic interaction between swallowtail butterflies highly toxic birthworts began 55 million years ago in Beringia, followed by several major ancient shifts. This...
Abstract Mitochondrial DNA (mtDNA) is one of the most popular population genetic markers. Its relevance as an indicator size and history has recently been questioned by several large-scale studies in animals reporting evidence for recurrent adaptive evolution, at least invertebrates. Here we focus on mammals, a more restricted taxonomic group which issue mtDNA near neutrality crucial. By analyzing distribution diversity across species relating it to allozyme diversity, life-history traits,...
Resolving the phylogenetic relationships among birds is a classical problem in systematics, and this particularly so when it comes to understanding Neoaves. Previous inference of has been limited mitochondrial genomes or few nuclear genes. Here, we apply deep brain transcriptome sequencing nine bird species (several passerines, hummingbirds, dove, parrot, emu), using next-generation technology understand features evolution how affects inference, combine with data from two first generation...
The evolutionary rate of mitochondrial DNA (mtDNA) is highly variable across lineages in animals, and particularly mammals. This variation has been interpreted as reflecting variations metabolic rate: respiratory activity would tend to generate mutagenic agents, thus increasing the mutation rate. Here we review recent evidence suggesting that a direct, mechanical effect species on mtDNA unlikely. We suggest natural selection could act reduce (somatic) long-lived species, agreement with theory ageing.
Abstract The African cultivated rice ( Oryza glaberrima ) was domesticated in West Africa 3000 years ago. Although less than the Asian O. sativa ), landraces often display interesting adaptation to rustic environment (e.g. drought). Here, using RNA ‐seq technology, we were able compare more 12 000 transcripts between 9 glaberrima, 10 wild barthii and one meridionalis individuals. With a synonymous nucleotide diversity π s = 0.0006 per site, appears as least genetically diverse crop grass...
The nearly neutral theory of molecular evolution has been widely accepted as the guiding principle for understanding how selection affects gene sequence evolution. One its central predictions is that rate at which proteins evolve should negatively scale with effective population size (Ne). In contrast to expectation reduced selective constraint in mitochondrial genome following from lower Ne, we observe what can be interpreted opposite: a taxonomically diverse set organisms (birds, mammals,...
Abstract Mitochondrial DNA remains one of the most widely used molecular markers to reconstruct phylogeny and phylogeography closely related birds. It has been proposed that bird mitochondrial genomes evolve at a constant rate ~0.01 substitution per site million years, is they according strict clock. This clock often in studies dating. However, rates genome evolution vary among species correlate with life history traits such as body mass generation time. These correlations could cause...