A5023266894- Genetic diversity and population structure
- Evolution and Genetic Dynamics
- Genetic Mapping and Diversity in Plants and Animals
- Genetic and phenotypic traits in livestock
- Plant and animal studies
- Insect-Plant Interactions and Control
- Genetic Associations and Epidemiology
- Viral Infections and Vectors
- Chromosomal and Genetic Variations
- Forensic and Genetic Research
- Forest Insect Ecology and Management
- Gene expression and cancer classification
- Bayesian Methods and Mixture Models
- Nutrition, Genetics, and Disease
- Insect symbiosis and bacterial influences
- Insect behavior and control techniques
- Wheat and Barley Genetics and Pathology
- Fern and Epiphyte Biology
- Animal Ecology and Behavior Studies
- Metabolomics and Mass Spectrometry Studies
- Bioenergy crop production and management
- Insect Pest Control Strategies
- Heavy metals in environment
- Animal Genetics and Reproduction
- Insect Resistance and Genetics
Centre de Biologie et de Gestion des Populations
2014-2024
Agropolis International
2011-2024
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2020-2024
Université de Montpellier
2000-2023
Institut Agro Montpellier
2010-2023
Centre de Coopération Internationale en Recherche Agronomique pour le Développement
2010-2023
Institut de Recherche pour le Développement
2010-2023
L'Institut Agro
2023
Institut Montpelliérain Alexander Grothendieck
2016-2020
Centre Occitanie-Montpellier
2020
With the development of next-generation sequencing and genotyping approaches, large single nucleotide polymorphism haplotype datasets are becoming available in a growing number both model non-model species. Identifying genomic regions with unexpectedly high local homozygosity relatively to neutral expectation represents powerful strategy ascertain candidate genes responding natural or artificial selection. To facilitate genome-wide scans selection based on analysis long-range haplotypes, we...
Bottlenecks in population size can reduce fitness and evolutionary potential, yet introduced species often become invasive. This poses a dilemma referred to as the genetic paradox of invasion. Three characteristics must hold true for an be considered paradoxical this sense. First, it pass through bottleneck that reduces variation. Second, despite bottleneck, not succumb many problems associated with low Third, adapt novel environment. Some populations are they do combine these conditions. In...
Abstract Identifying genomic regions with unusually high local haplotype homozygosity represents a powerful strategy to characterize candidate genes responding natural or artificial positive selection. To that end, statistics measuring the extent of within (e.g. EHH , iHS ) and between (Rsb XP ‐ populations have been proposed in literature. The rehh package for r was previously developed facilitate genome‐wide scans selection, based on analysis long‐range haplotypes. However, its performance...
Abstract The advent of high throughput sequencing and genotyping technologies enables the comparison patterns polymorphisms at a very large number markers. While characterization genetic structure from individual data remains expensive for many nonmodel species, it has been shown that pools DNAs (Pool-seq) represents an attractive cost-effective alternative. However, analyzing sequence read counts DNA pool instead genotypes raises statistical challenges in deriving correct estimates...
Simulation-based methods such as approximate Bayesian computation (ABC) are well-adapted to the analysis of complex scenarios populations and species genetic history. In this context, supervised machine learning (SML) provide attractive statistical solutions conduct efficient inferences about scenario choice parameter estimation. The Random Forest methodology (RF) is a powerful ensemble SML algorithms used for classification or regression problems. allows conducting at low computational...
Abstract Population structure and history have similar effects on the genetic diversity at all neutral loci. However, some marker loci may also been strongly influenced by natural selection. Selection shapes in a locus-specific manner. If we could identify those that responded to selection during divergence of populations, then obtain better estimates parameters population excluding these Previous attempts were made outlier from distribution sample statistics under models history....
Recent papers have promoted the view that model-based methods in general, and those based on Approximate Bayesian Computation (ABC) particular, are flawed a number of ways, therefore inappropriate for analysis phylogeographic data. These further argue Nested Clade Phylogeographic Analysis (NCPA) offers best approach statistical phylogeography. In order to remove confusion misconceptions introduced by these papers, we justify explain reasoning behind inference. We ABC is statistically valid...
Abstract Reconstructing the demographic history of populations is a central issue in evolutionary biology. Using likelihood-based methods coupled with Monte Carlo simulations, it now possible to reconstruct past changes population size from genetic data. simulated data sets under various scenarios, we evaluate statistical performance Msvar, full-likelihood Bayesian method that infers change microsatellite Our simulation tests show Msvar very efficient at detecting declines and expansions,...
Understanding the drivers of speciation is critical to interpreting patterns biodiversity. The identification genetic changes underlying adaptation and reproductive isolation necessary link barriers gene flow causal origins divergence. Here, we present a novel approach genetics speciation, which should complement commonly used approaches quantitative trait locus mapping genome-wide scans for selection. We large-scale candidate by means sequence capture, applied identifying in pea aphid,...
By capturing various patterns of the structuring genetic variation across populations, f -statistics have proved highly effective for inference demographic history. Such statistics are defined as covariances SNP allele frequency differences among sets populations without requiring haplotype information and hence particularly relevant analysis pooled sequencing (Pool-Seq) data. We here propose a reinterpretation F (and D ) parameters in terms probability gene identity derive from this unified...
Understanding the demographic history of populations and species is a central issue in evolutionary biology molecular ecology. In this work, we develop maximum-likelihood method for inference past changes population size from microsatellite allelic data. Our based on importance sampling gene genealogies, extended new mutation models, notably generalized stepwise model (GSM). Using simulations, test its performance to detect characterize reductions size. First, estimation precision confidence...
Abstract The recent advent of high-throughput sequencing and genotyping technologies makes it possible to produce, easily cost effectively, large amounts detailed data on the genotype composition populations. Detecting locus-specific effects may help identify those genes that have been, or are currently, targeted by natural selection. How best these selected regions, loci, single nucleotides remains a challenging issue. Here, we introduce new model-based method, called SelEstim, distinguish...
Abstract Standard methods for inferring demographic parameters from genetic data are based mainly on one-locus theory. However, the association of genes at different loci (e.g., two-locus identity disequilibrium) may also contain some information about populations. In this article, we define one- and population structure as functions probabilities in state genes. Since these known an infinite island model, develop moment-based estimators effective size immigration rate parameters. We...
In many annual plant populations, seeds may be dormant for several seasons before they germinate. Here, we investigate the consequences of both conditional (dispersed cannot enter a stage) and unconditional seed dormancy on amount distribution neutral genetic diversity within among populations. We present joint demographic population genetics models single subdivided populations derive effective size differentiation at local metapopulation scales. suggest that Wahlund effect is unlikely to...
In the last two decades, mitochondrial DNA (mtDNA) and non-recombining portion of Y chromosome (NRY) have been extensively used in order to measure maternally paternally inherited genetic structure human populations, infer sex-specific demography history. Most studies converge towards notion that among women are genetically less structured than men. This has mainly explained by a higher migration rate women, due patrilocality, tendency for men stay their birthplace while move husband's...
Abstract To assess the effects of altitude on level and structure genetic diversity, a survey was conducted in 12 populations sessile oak ( Quercus petraea ) located between 130 1660 m two parallel valleys northern side Pyrenees Mountains. Genetic diversity monitored at 16 nuclear microsatellite loci 5 chloroplast DNA (cpDNA) markers. The cpDNA suggested that extant both shared same source from plain. There no visible trend along altitude, even if indirect estimates effective population...
Abstract A major goal in evolutionary biology is to uncover the genetic basis of adaptation. Divergent selection exerted on ecological traits may result adaptive population differentiation and reproductive isolation affect differentially level divergence along genome. Genome‐wide scan large sets individuals from multiple populations a powerful approach identify loci or genomic regions under ecologically divergent selection. Here, we focused pea aphid, species complex host races, explore...
Chromosomal polymorphisms, such as inversions, are presumably involved in the rapid adaptation of populations to local environmental conditions. Reduced recombination between alternative arrangements heterozygotes may protect sets locally adapted genes, promoting ecological divergence and potentially leading reproductive isolation speciation. Through a comparative analysis chromosomal inversions microsatellite marker we hereby present biological evidence that strengthens this view mosquito...
Estimating population parameters from polymorphism frequency data requires neutral genetic markers. Any departure neutrality may invalidate the inferences drawn such analyses. We recently discussed possibility of identifying markers that show deviation expectations in pairwise comparisons diverging populations. are now releasing a user-friendly software package implements all necessary steps to identify signature selection among molecular set data. This can be downloaded free charge at...
Pollution by heavy metals is one of the strongest environmental constraints in human-altered environments that only a handful species can cope with. Identifying genes conferring to those ability grow polluted areas first step towards global understanding evolutionary processes involved and will eventually improve phytoremediation practices. We used genome-scan approach detect loci under divergent selection among four populations Arabidopsis halleri growing on either or nonpolluted habitats....