A5011691995- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Genetic diversity and population structure
- Chromosomal and Genetic Variations
- RNA and protein synthesis mechanisms
- Protist diversity and phylogeny
- Legume Nitrogen Fixing Symbiosis
- Genome Rearrangement Algorithms
- Insect symbiosis and bacterial influences
- Bacterial Genetics and Biotechnology
- Bacteriophages and microbial interactions
- Evolution and Paleontology Studies
- Photosynthetic Processes and Mechanisms
- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
- Plant tissue culture and regeneration
- Machine Learning in Bioinformatics
- Nematode management and characterization studies
- French Urban and Social Studies
- Genetics, Bioinformatics, and Biomedical Research
- Legionella and Acanthamoeba research
- Plant Diversity and Evolution
- Evolution and Genetic Dynamics
- Insect behavior and control techniques
- Algal biology and biofuel production
Centre National de la Recherche Scientifique
2015-2024
Université Claude Bernard Lyon 1
2015-2024
Laboratoire de Biométrie et Biologie Evolutive
2015-2024
Science for Life Laboratory
2014
Stockholm University
2014
Eötvös Loránd University
2014
Centre de Recherche en Informatique
2013
Centre National pour la Recherche Scientifique et Technique (CNRST)
2013
Université de Montréal
2013
Université de Montpellier
2013
The duplication of entire genomes has long been recognized as having great potential for evolutionary novelties, but the mechanisms underlying their resolution through gene loss are poorly understood. Here we show that in unicellular eukaryote Paramecium tetraurelia, a ciliate, most nearly 40,000 genes arose at least three successive whole-genome duplications. Phylogenetic analysis indicates recent coincides with an explosion speciation events gave rise to P. aurelia complex 15 sibling...
The rapid increase in published genomic sequences for bacteria presents the first opportunity to reconstruct evolutionary events on scale of entire genomes. However, extensive lateral gene transfer (LGT) may thwart this goal by preventing establishment organismal relationships based individual phylogenies. group which cases LGT are most frequently documented and greatest density complete genome is available γ-Proteobacteria, an ecologically diverse ancient including free-living species as...
Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival soil, the other concert with host plant speciation adaptation. Actinobacteria from genus Frankia are facultative symbionts N 2 -fixing root nodules on diverse globally distributed angiosperms “actinorhizal” symbioses. Three closely related clades sp. strains recognized; members each clade infect a subset among eight angiosperm families. We...
Explaining the diversity of gene repertoires has been a major problem in modern evolutionary biology. In eukaryotes, this is believed to result mainly from duplication and loss, but prokaryotes, lateral transfer (LGT) can also contribute substantially genome contents. To determine histories inventories, we conducted an exhaustive analysis phylogenies for all families widely sampled group, γ-Proteobacteria. We show that, although these bacterial genomes display striking differences...
Comparisons of gene trees and species are key to understanding major processes genome evolution such as duplication loss. Because current methods reconstruct phylogenies fail model the two-way dependency between tree, they often misrepresent histories. We present a new probabilistic jointly infer rooted for dozens genomes thousands families. use simulations show that this method accurately infers tree trees, is robust misspecification models sequence family evolution, provides precise...
The characterization of functional elements in genomes relies on the identification footprints natural selection. In this quest, taking into account neutral evolutionary processes such as mutation and genetic drift is crucial because these forces can generate patterns that may obscure or mimic signatures mammals, probably many eukaryotes, another confounding factor called GC-Biased Gene Conversion (gBGC) has been documented. This mechanism generates identical to what expected under selection...
Gene trees record the combination of gene-level events, such as duplication, transfer and loss (DTL), species-level speciation extinction. tree-species tree reconciliation methods model these processes by drawing gene into species using a series events. The reconstruction based on sequence alone almost always involves choosing between statistically equivalent or weakly distinguishable relationships that could be much better resolved putative tree. To exploit this potential for accurate...
Gene acquisition is an ongoing process in many bacterial genomes, contributing to adaptation and ecological diversification. Lateral gene transfer considered the primary explanation for discordance among phylogenies as obstacle reconstructing tree of life. We measured extent phylogenetic conflict alien-gene within quartets sequenced genomes. Although comparisons complete inventories indicate appreciable gain loss genes, orthologs available reconstruction are consistent with a single tree.
Differences in gene repertoire among bacterial genomes are usually ascribed to loss or lateral transfer from unrelated cellular organisms. However, most bacteria contain large numbers of ORFans, that is, annotated genes restricted a particular genome and possess no known homologs. The uniqueness ORFans within has precluded the use comparative approach examine their function evolution. by identifying sequences unique monophyletic groups at increasing phylogenetic depths, we can make direct...
Incongruence between gene trees is the main challenge faced by phylogeneticists in genomic era. can occur for artefactual reasons, when we fail to recover correct trees, or biological true are actually distinct from each other, and species tree. Horizontal transfers (HGTs) genomes an important process of bacterial evolution resulting a substantial amount phylogenetic conflicts trees. We argue that (bacterial) tree still meaningful scientific concept even case HGTs, reconstructing it valid...
The timing of the evolution microbial life has largely remained elusive due to scarcity prokaryotic fossil record and confounding effects exchange genes among possibly distant species. history gene transfer events, however, is not a series individual oddities; it records which lineages were concurrent thus provides information on species diversification. Here, we use probabilistic model genome that accounts for differences between phylogenies tree as duplication, transfer, loss events...
Abstract Background Comparative genomics is a central step in many sequence analysis studies, from gene annotation and the identification of new functional regions genomes, to study evolutionary processes at molecular level (speciation, single or whole genome duplications, etc.) phylogenetics. In that context, databases providing users high quality homologous families alignments as well phylogenetic trees based on state art algorithms are becoming indispensable. Methods We developed an...
The phylogeny of the class Actinobacteria remains controversial, essentially because it is very sensitive to choice dataset and phylogenetic methods. We used a test proposed recently, based on complete genome data, which chooses among candidate species phylogenies number lateral gene transfers (LGT) needed explain diversity histories trees for set genomes. 100 completely sequenced genomes representing 35 families 17 orders evaluated eight different hypotheses their phylogeny, including one...
In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along phylogeny traced by ancestors extant species. presence lateral gene transfer, however, this may not be case, because species lineage from which a was transferred gone extinct or been sampled. Because it feasible specify reconstruct complete all species, we must describe genes outside represented modeling speciation dynamics that gave rise phylogeny. We demonstrate if number sampled small...
Lateral gene transfer (LGT), the acquisition of genes from other species, is a major evolutionary force. However, its success as an adaptive process makes reconstruction history life intricate puzzle: If no has remained unaffected during course life's evolution, how can one rely on molecular markers to reconstruct relationships among species? Here, we take completely different look at LGT and impact for life. Rather than trying remove effect in phylogenies, ignoring result most information...
The definition of bacterial species is based on genomic similarities, giving rise to the operational concept species, but reasons occurrence differentiated remain largely unknown. We used Agrobacterium tumefaciens complex and particularly presently called genomovar G8, which includes sequenced strain C58, test hypothesis having specific ecological adaptations possibly involved in speciation process. analyzed gene repertoire G8 identify potential adaptive genes. By hybridizing 25 strains A....
Although the role of lateral gene transfer is well recognized in evolution bacteria, it generally assumed that has had less influence among eukaryotes. To explore this hypothesis, we compare dynamics genome two groups organisms: cyanobacteria and fungi. Ancestral genomes are inferred both clades using types methods: first, Count, a tree unaware method models duplications, gains losses to explain observed numbers genes present genome; second, ALE, more recent tree-aware reconciles trees with...
Laterally transferred genes have often been identified on the basis of compositional features that distinguish them from ancestral in genome. These are usually A+T-rich, arguing either there is a bias towards acquiring donor organisms having low G+C contents or acquired similar genomic base compositions go undetected these analyses.By examining genome closely related, fully sequenced bacteria, we uncovered confined to single and examined sequence genes. The analysis shows few transfer events...