A5057284934- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Evolution and Paleontology Studies
- Genome Rearrangement Algorithms
- Chromosomal and Genetic Variations
- Plant Diversity and Evolution
- Bioinformatics and Genomic Networks
- Plant and animal studies
- Algorithms and Data Compression
- Wildlife Ecology and Conservation
- Gene expression and cancer classification
- Constraint Satisfaction and Optimization
- Legume Nitrogen Fixing Symbiosis
- Genetic Mapping and Diversity in Plants and Animals
- Biomedical Text Mining and Ontologies
- Wildlife-Road Interactions and Conservation
- Plant and Fungal Species Descriptions
- Lepidoptera: Biology and Taxonomy
- Species Distribution and Climate Change
- Identification and Quantification in Food
- RNA and protein synthesis mechanisms
- Plant Taxonomy and Phylogenetics
- Wheat and Barley Genetics and Pathology
- Data Mining Algorithms and Applications
- Evolutionary Algorithms and Applications
Institut des Sciences de l'Evolution de Montpellier
2016-2025
Université de Montpellier
2015-2024
Centre National de la Recherche Scientifique
2015-2024
Institut de Recherche pour le Développement
2015-2024
École Pratique des Hautes Études
2015-2024
Institut Supérieur d'Études Maritimes
2024
Institut Montpelliérain Alexander Grothendieck
2015-2016
Genetic Improvement and Adaptation of Mediterranean and Tropical Plants
2016
University of Tübingen
2010-2011
Computer Algorithms for Medicine
2011
Dendroscope 3 is a new program for working with rooted phylogenetic trees and networks. It provides number of methods drawing comparing networks, computing them from trees. The can be used interactively or in command-line mode. written Java, use the software free, installers all major operating systems downloaded www.dendroscope.org. [Phylogenetic trees; networks; software.].
Phylogenetic inference from genome-wide data (phylogenomics) has revolutionized the study of evolution because it enables accounting for discordance among evolutionary histories across genome. To this end, summary methods have been developed to allow accurate and scalable species trees gene trees. However, most these methods, including widely used ASTRAL, can only handle single-copy do not attempt model duplication loss. As a result, phylogenomic studies focused on genes discarded large...
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...
The evolutionary history of a set species is usually described by rooted phylogenetic tree. Although it generally undisputed that bifurcating speciation events and descent with modifications are major forces evolution, there growing belief reticulate also have role to play. Phylogenetic networks provide an alternative trees may be more suitable for data sets where evolution involves significant amounts events, such as hybridization, horizontal gene transfer, or recombination. In this...
The impact of incomplete lineage sorting (ILS) on phylogenetic conflicts among genes, and the related issue whether to account for ILS in species tree reconstruction, are matters intense controversy. Here, focusing full-genome data placental mammals, we empirically test two assumptions underlying current usage tree-building methods that ILS. We show this set (i) distinct exons from a common gene do not share genealogy, (ii) is only minor determinant existing conflict. These results shed new...
In systematic biology, one is often faced with the task of comparing different phylogenetic trees, in particular multi-gene analysis or cospeciation studies. One approach to use a tanglegram which two rooted trees are drawn opposite each other, using auxiliary lines connect matching taxa. There an increasing interest networks represent evolutionary history, so as explicitly reticulate events, such horizontal gene transfer, hybridization reassortment. Thus, question arises how define and...
ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions nine ascidian species. It provides increased integration with external molecular taxonomy databases, better support epigenomics datasets, in particular RNA-seq, ChIP-seq SELEX-seq, features novel interactive interfaces existing datatypes. In particular, cross-species navigation...
: A gene tree-species tree reconciliation explains the evolution of a within species given model gene-family evolution. We describe ecceTERA, program that implements generic parsimony algorithm, which accounts for duplication, loss and transfer (DTL) as well speciation, involving sampled unsampled lineages, undated, fully dated or partially trees. The ecceTERA algorithm generalize improve upon most published DTL algorithms binary trees Moreover, can estimate accurate species-tree aware using...
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...
Abstract We present version 10 of OrthoMaM, a database orthologous mammalian markers. OrthoMaM is already 11 years old and since the outset it has kept on improving, providing alignments phylogenetic trees high-quality computed with state-of-the-art methods up-to-date data. The main contribution this increase in number taxa: 116 genomes for 14,509 one-to-one genes. This been made possible by combination genomic data deposited Ensembl complemented additional good-quality only available NCBI....
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...
Abstract Introgression is an important biological process affecting at least 10% of the extant species in animal kingdom. significantly impacts inference phylogenetic relationships where a strictly binary tree model cannot adequately explain reticulate net-like relationships. Here, we use phylogenomic approaches to understand patterns introgression along evolutionary history unique, nonmodel insect system: dragonflies and damselflies (Odonata). We demonstrate that pervasive force across...
Comparative genomic studies extensively rely on alignments of orthologous sequences. Yet, selecting, gathering, and aligning exons protein-coding sequences (CDS) that are relevant for a given evolutionary analysis can be difficult time-consuming task. In this context, we developed OrthoMaM, database ORTHOlogous MAmmalian Markers describing the dynamics genes in mammalian genomes using phylogenetic framework. Since its first release 2007, OrthoMaM has regularly evolved, not only to include...
Phylogenetic networks represent the evolution of organisms that have undergone reticulate events, such as recombination, hybrid speciation or lateral gene transfer. An important way to interpret a phylogenetic network is in terms trees it displays, which all possible histories characters carried by network. Interestingly, however, different may display exactly same set trees, an observation poses problem for reconstruction: from perspective many inference methods are indistinguishable. This...
Introgressive events (e.g., hybridization, gene flow, horizontal transfer) and incomplete lineage sorting of ancestral polymorphisms are a challenge for phylogenetic analyses since different genes may exhibit conflicting genealogical histories. Grasses the Triticeae tribe provide particularly striking example incongruence among trees. Previous phylogenies, mostly inferred with one gene, in conflict several taxon positions. Therefore, obtaining resolved picture relationships genera species...
Ascidians belong to the tunicates, sister group of vertebrates and are recognized model organisms in field embryonic development, regeneration stem cells. ANISEED is main information system ascidian developmental biology. This article reports development since its initial publication 2010. Over past five years, we refactored from an custom schema extended version Chado redesigned all user back end interfaces. new architecture was used improve enrich description Ciona intestinalis based on...
Abstract Motivation: Traditionally, gene phylogenies have been reconstructed solely on the basis of molecular sequences; this, however, often does not provide enough information to distinguish between statistically equivalent relationships. To address this problem, several recent methods incorporated species phylogeny in tree reconstruction, leading dramatic improvements accuracy. Although probabilistic are able estimate all model parameters but computationally expensive, parsimony...
Phylogenetic networks can represent non-treelike evolutionary scenarios. Current, actively developed approaches for phylogenetic network inference jointly account evolution and incomplete lineage sorting (ILS). Unfortunately, this induces a very high computational complexity current tools only analyze small datasets.We present NetRAX, tool maximum likelihood (ML) of in the absence ILS. Our leverages state-of-the-art methods efficiently computing function on trees, extends them to via notion...