Jean‐François Flot
A5090803386- Genomics and Phylogenetic Studies
- Subterranean biodiversity and taxonomy
- Coral and Marine Ecosystems Studies
- Genetic diversity and population structure
- Environmental DNA in Biodiversity Studies
- Aquatic Invertebrate Ecology and Behavior
- Protist diversity and phylogeny
- Parasite Biology and Host Interactions
- Ichthyology and Marine Biology
- Evolution and Genetic Dynamics
- Marine Biology and Ecology Research
- Identification and Quantification in Food
- Microbial Community Ecology and Physiology
- Marine and coastal plant biology
- Chromosomal and Genetic Variations
- Molecular Biology Techniques and Applications
- Marine Ecology and Invasive Species
- Nematode management and characterization studies
- Species Distribution and Climate Change
- Gene expression and cancer classification
- Plant and animal studies
- RNA and protein synthesis mechanisms
- Insect symbiosis and bacterial influences
- Marine Sponges and Natural Products
- Invertebrate Taxonomy and Ecology
Université Libre de Bruxelles
2016-2025
Institute of Bioinformatics
2021-2025
Museo Nacional de Ciencias Naturales
2023
Emil Racovita Institute of Speleology
2022
Romanian Institute of Science and Technology
2022
University Library in Bratislava
2022
3E (Belgium)
2020
ORCID
2020
Leefmilieu Brussel
2018
State of The Art
2017
The program phase is widely used for Bayesian inference of haplotypes from diploid genotypes; however, manually creating input files sequence alignments an error-prone and time-consuming process, especially when dealing with numerous variable sites and/or individuals. Here, a web tool called seqphase presented that generates fasta converts output back into fasta. During the production file, several consistency checks are performed on dataset suitable command line options to be actual data...
The duplication of genes can occur through various mechanisms and is thought to make a major contribution the evolutionary diversification organisms. There increasing evidence for large-scale in some chelicerate lineages including two rounds whole genome (WGD) horseshoe crabs. To investigate this further, we sequenced analyzed common house spider Parasteatoda tepidariorum. We found pervasive both coding non-coding spider, clusters Hox genes. Analysis synteny conservation across P....
The genome of the asexual rotifer Adineta vaga lacks homologous chromosomes; instead, its allelic regions are rearranged and sometimes found on same chromosome in a palindromic fashion, structure reminiscent primate Y other mitotic lineages such as cancer cells. Bdelloid rotifers thought to have persisted diversified asexually for millions years, which is odd because loss sexual reproduction widely considered be an evolutionary dead end metazoans. suspicion remained that they might engage...
Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate genomes representing global biodiversity. These provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses population functional genomics, are expected revolutionize conservation genomics.
Molecular approaches to species delimitation are increasingly used ascertain the number of in a sample prior taxonomic, ecological or physiological studies. Although multilocus gaining fast popularity, single-gene methods still predominate literature. However, available simulation benchmarks these focus exclusively on species-poor samples and/or tree-based approaches: as result, travellers land single-locus lack comprehensive "hitchhiker's guide" highlighting sweet spots and dangers their...
Root-knot nematodes (genus Meloidogyne) exhibit a diversity of reproductive modes ranging from obligatory sexual to fully asexual reproduction. Intriguingly, the most widespread and devastating species global agriculture are those that reproduce asexually, without meiosis. To disentangle this surprising parasitic success despite absence sex genetic exchanges, we have sequenced assembled genomes three ameiotic Meloidogyne. We compared them relatives able perform meiosis show Meloidogyne...
Genomic analyses of microbial populations in their natural environment remain limited by the difficulty to assemble full genomes individual species. Consequently, chromosome organization microorganisms has been investigated a few model species, but extent which features described can be generalized other taxa remains unknown. Using controlled mixes bacterial and yeast we developed meta3C, metagenomic conformation capture approach that allows characterizing average within mix organisms. Not...
The protection, preservation and restoration of aquatic ecosystems their functions are global importance. For European states it became legally binding mainly through the EU-Water Framework Directive (WFD). In order to assess ecological status a given water body, biodiversity data obtained compared reference body. quantified mismatch determines extent potential management actions. current approach assessment is based on morpho-taxonomy. This has many drawbacks such as being time consuming,...
Abstract Closing gaps in draft genome assemblies can be costly and time-consuming, published genomes are therefore often left ‘unfinished.’ Here we show that genome-wide chromosome conformation capture (3C) data used to overcome these limitations, present a computational approach rooted polymer physics determines the most likely structure using chromosomal contact data. This algorithm—named GRAAL—generates high-quality of which repeated duplicated regions accurately represented offers direct...
Stony corals form the foundation of coral reef ecosystems. Their phylogeny is characterized by a deep evolutionary divergence that separates into robust and complex clade dating back to at least 245 mya. However, genomic consequences clade-specific evolution remain unexplored. In this study we have produced genome coral, Stylophora pistillata, compared it available Acropora digitifera. We conducted fine-scale gene-based analysis focusing on ortholog groups. Among core set conserved proteins,...
Usual methods for inferring species boundaries from molecular sequence data rely either on gene trees or population genetic analyses. Another way of delimiting species, based a view as "fields recombination" (FFRs) characterized by mutual allelic exclusivity, was suggested in 1995 Doyle. Here we propose to use haplowebs (haplotype networks with additional connections between haplotypes found co-occurring heterozygous individuals) visualize and delineate single-locus FFRs (sl-FFRs)....
Most single-locus molecular approaches to species delimitation available date have been designed and tested on data sets comprising at least tens of species, whereas the opposite case (species-poor for which hypothesis that all individuals are conspecific cannot by rejected beforehand) has rarely focus such attempts. Here we compare performance barcode gap detection, haplowebs generalized mixed Yule–coalescent (GMYC) models delineate chimpanzees bonobos using nuclear sequence markers, then...
Niphargus dancaui sp. nov., previously referred to as cf. stygius, was sampled from various groundwater sites in and near the town of Mangalia (SE Romania) described with Movile Cave (a sulfidic, chemoautotrophically based ecosystem) type locality. A short comparison stygius specimens Slovenia made, together a morphological analysis interpopulational variability. Males N. nov. were relatively large (17 mm), long antennae, pereiopods uropod III. Females slightly smaller, shorter...
Scleractinian corals of the genus Pocillopora (Lamarck, 1816) are notoriously difficult to identify morphologically with considerable debate on degree which phenotypic plasticity, introgressive hybridization and incomplete lineage sorting obscure well-defined taxonomic lineages. Here, we used RAD-seq resolve phylogenetic relationships among seven species represented by 15 coral holobiont metagenomic libraries. We found strong concordance between datasets, reads that mapped damicornis...
Ecologists increasingly rely on molecular delimitation methods (MMs) to identify species boundaries, thereby potentially increasing the number of putative because presence morphologically cryptic species. It has been argued that could challenge our understanding what determine large‐scale biodiversity patterns which have traditionally documented from morphology alone. Here, we used and three MMs derive four different sets among European groundwater crustaceans. Then, regression models...
Abstract The discovery of multi-species synchronous spawning scleractinian corals on the Great Barrier Reef in 1980s stimulated an extraordinary effort to document times other parts globe. Unfortunately, most these data remain unpublished which limits our understanding regional and global reproductive patterns. Coral Spawning Database (CSD) collates much disparate into a single place. CSD includes 6178 observations (3085 were unpublished) time or day for over 300 species 61 genera from 101...
A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction have information available. In 2018, scientists across the world united under Earth BioGenome Project (EBP), aiming produce high-quality reference genomes containing ~1.5 million recognized species. As European node EBP, Reference Genome Atlas (ERGA) sought implement new decentralised, equitable and inclusive model for producing genomes. For this, ERGA launched...
Abstract For diploid organisms, haplotype determination usually requires sequencing cloned polymerase chain reaction (PCR) products or comparing the genotypes of several individuals. We found out that phase could be reconstructed from direct mixed PCR by combining for each individual complementary information contained in its forward and reverse chromatograms, provided these had different lengths. When applied to internal transcribed spacer 2 (ITS2) corals genus Pocillopora , this new method...