A5054940859- Genetic diversity and population structure
- Evolution and Genetic Dynamics
- Plant and animal studies
- Chromosomal and Genetic Variations
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Plant Reproductive Biology
- Genetic and phenotypic traits in livestock
- Ecology and Vegetation Dynamics Studies
- RNA and protein synthesis mechanisms
- Plant Taxonomy and Phylogenetics
- Wheat and Barley Genetics and Pathology
- Evolution and Paleontology Studies
- Genetics and Plant Breeding
- CRISPR and Genetic Engineering
- Insect and Arachnid Ecology and Behavior
- Botany and Plant Ecology Studies
- Physiological and biochemical adaptations
- Genetic and Environmental Crop Studies
- Mitochondrial Function and Pathology
- Plant Virus Research Studies
- Plant Disease Resistance and Genetics
- Evolutionary Game Theory and Cooperation
- Mathematical and Theoretical Epidemiology and Ecology Models
- Aquatic Invertebrate Ecology and Behavior
Centre National de la Recherche Scientifique
2015-2024
Uppsala University
2015-2024
Ecosystèmes, Biodiversité, Evolution
2016-2024
Université de Rennes
2017-2024
Science for Life Laboratory
2015-2024
Institut de Biologia Evolutiva
2015-2023
Czech Academy of Sciences, Biology Centre
2015-2023
Swedish University of Agricultural Sciences
2023
Centre National pour la Recherche Scientifique et Technique (CNRST)
2018-2022
Université de Montpellier
2010-2019
Within-species genetic diversity is thought to reflect population size, history, ecology, and ability adapt. Using a comprehensive collection of polymorphism data sets covering approximately 3000 animal species, we show that the widely used mitochondrial DNA (mtDNA) marker does not species abundance or ecology: mtDNA higher in invertebrates than vertebrates, marine terrestrial small large organisms. Nuclear loci, contrast, fit these intuitive expectations. The unexpected distribution...
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...
Several demographic and selective events occurred during the domestication of wheat from allotetraploid wild emmer (Triticum turgidum ssp. dicoccoides). Cultivated has since been affected by other historical events. We analyzed nucleotide diversity at 21 loci in a sample 101 individuals representing 4 taxa corresponding to representative steps recent evolution (wild, domesticated, cultivated durum, bread wheats) unravel evolutionary history wheats quantify its impact on genetic diversity....
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...
A central question in evolutionary biology is why some species have more genetic diversity than others and a no less important selection efficacy varies among species. Although these questions started to be tackled animals, they not been addressed the same extent plants. Here, we estimated nucleotide at synonymous, πS, nonsynonymous sites, πN, measure of selection, ratio πN/πS, 34 animal 28 plant using full genome data. We then evaluated relationship with effective population size,...
Abstract Accumulation of deleterious mutations has important consequences for the evolution mating systems and persistence small populations. It is well established that consanguineous can purge a part mutation load lethal also be purged in However, efficiency purging natural populations, due to either or reduced population size, been questioned. Consequences size are often equated under “inbreeding” because both increase homozygosity, selection though more efficient against homozygous...
A fundamental challenge in population genetics and molecular evolution is to understand the forces shaping patterns of genetic diversity within among species. Among them, mating systems are thought have important influences on genome evolution. Selfing expected reduce effective size, N e , recombination rates, directly leading reduced polymorphism increased linkage disequilibrium compared with outcrossing. Increased isolation between populations also results from selfing or indirectly...
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...
The distribution of fitness effects (DFE) encompasses the fraction deleterious, neutral, and beneficial mutations. It conditions evolutionary trajectory populations, as well rate adaptive molecular evolution (α). Inferring DFE α from patterns polymorphism, given through site frequency spectrum (SFS) divergence data, has been a longstanding goal genetics. A widespread assumption shared by previous inference methods is that mutations only contribute negligibly to polymorphism data. Hence,...
Evolution of selfing from outcrossing recurrently occurred in many lineages, especially flowering plants. induces dramatic changes the population genetics functioning but its consequences on dynamics adaptation have been overlooked. We studied a simple one-locus model where experiences an environmental change at given time. first determined effect mating system genetic bases and speed adaptation, focusing dominance beneficial mutations respective part standing variation new mutations. Then,...
The identification of loci influenced by positive selection is a major goal evolutionary genetics. A popular approach to perform scans alignments on genome-wide scale in order find regions evolving at accelerated rates particular branch phylogenetic tree. However, not the only process that can lead evolution. Notably, GC-biased gene conversion (gBGC) recombination-associated results biased fixation G and C nucleotides. This potentially generate bursts nucleotide substitutions within hotspots...
Much evidence indicates that GC-biased gene conversion (gBGC) has a major impact on the evolution of mammalian genomes. However, detailed quantification process is still lacking. The strength gBGC can be measured from analysis derived allele frequency spectra (DAF), but this approach sensitive to number confounding factors. In particular, we show by simulations inference pervasively affected polymorphism polarization errors and spatial heterogeneity in strength. We propose new general method...
Selection on codon usage bias is well documented in a number of microorganisms. Whether also generally shaped by natural selection large organisms, despite their relatively small effective population size (Ne), unclear. In animals, the genetics has only been studied handful model organisms so far, and can be affected confounding, nonadaptive processes such as GC-biased gene conversion experimental artefacts. Using transcriptomics data, we analyzed relationship between usage, expression,...
Meiotic recombination is a fundamental cellular process, with important consequences for evolution and genome integrity. However, we know little about how rates vary across the genomes of most species molecular evolutionary determinants this variation. The honeybee, Apis mellifera, has extremely high meiotic recombination, although causes are unclear. Here use patterns linkage disequilibrium in whole resequencing data from 30 diploid honeybees to construct fine-scale map crossing over...
Cultivated wheats are derived from an intricate history of three genomes, A, B, and D, present in both diploid polyploid species. It was recently proposed that the D genome originated ancient hybridization between A B lineages. However, this result has been questioned, a robust phylogeny wheat relatives is still lacking. Using transcriptome data all species new methodological approach, our comprehensive phylogenomic analysis revealed more than half descend event but with complex scenario...
During meiosis, crossover rates are not randomly distributed along the chromosome and their location may have a strong impact on functioning evolution of genome. To date, broad diversity recombination landscapes among plants has rarely been investigated formal comparative genomic approach is still needed to characterize assess determinants species chromosomes. We gathered genetic maps genomes for 57 flowering plant species, corresponding 665 chromosomes, which we estimated large-scale...
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,...
Mating systems are thought to play a key role in molecular evolution through their effects on effective population size (N(e)) and recombination rate. Because of reduced N(e), selection self-fertilizing species is supposed be less efficient, allowing fixation weakly deleterious alleles or lowering adaptation, which may jeopardize long-term evolution. Relaxed pressures selfers should detectable at the level analyses ratio nonsynonymous synonymous divergence, D(n)/D(s), polymorphism,...
Abstract Background A large number of bioinformatics applications in the fields bio-sequence analysis, molecular evolution and population genetics typically share input/ouput methods, data storage requirements analysis algorithms. Such common features may be conveniently bundled into re-usable libraries, which enable rapid development new methods robust applications. Results We present Bio++, a set Object Oriented libraries written C++. Available components include classes for handling...