Damien M. de Vienne
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View article: Age-Based Risk Estimates for <i>C9orf72</i> <sup>RE</sup>-related Diseases: Theoretical Developments and Added Value for Genetic Counselling
Age-Based Risk Estimates for <i>C9orf72</i> <sup>RE</sup>-related Diseases: Theoretical Developments and Added Value for Genetic Counselling Open
The C9orf72 hexanucleotide repeat expansion is the most common genetic cause of amyotrophic lateral sclerosis (ALS) or frontotemporal dementia (FTD). In genetic counselling, children of mutation carriers are often told that they have a 50%…
View article: HGTs are not SPRs: In the Presence of Ghost Lineages, Series of Horizontal Gene Transfers do not Result in Series of Subtree Pruning and Regrafting
HGTs are not SPRs: In the Presence of Ghost Lineages, Series of Horizontal Gene Transfers do not Result in Series of Subtree Pruning and Regrafting Open
When a gene is horizontally transferred (HGT), under the “replacement” model where the transferred gene replaces its homolog in the recipient genome, the corresponding gene phylogeny departs from the species phylogeny by a Subtree Prune an…
View article: multistrap: boosting phylogenetic analyses with structural information
multistrap: boosting phylogenetic analyses with structural information Open
In a phylogeny, trustworthy reliability branch support estimates are as important as the tree itself. We show that reliability support values based on bootstrapping can be improved by combining sequence and structural information from prot…
View article: Gene flow can reveal ghost lineages
Gene flow can reveal ghost lineages Open
Ghost species, encompassing extinct, unknown, and unsampled taxa, vastly outnumber those typically included in phylogenetic analyses. This hidden diversity has been shown to influence the study of horizontal gene flow (e.g. introgression a…
View article: Gene flow can reveal ghost lineages
Gene flow can reveal ghost lineages Open
Ghost species, encompassing extinct, unknown, and unsampled taxa, vastly outnumber those typically included in phylogenetic analyses. This hidden diversity has been shown to influence the study of horizontal gene flow (e.g., introgression …
View article: HGTs are not SPRs: In the presence of ghost lineages, series of Horizontal Gene Transfers do not result in series of Subtree Pruning and Regrafting
HGTs are not SPRs: In the presence of ghost lineages, series of Horizontal Gene Transfers do not result in series of Subtree Pruning and Regrafting Open
When a gene is horizontally transferred (HGT), under the “replacement” model where the transferred gene replaces its homolog in the recipient genome, the corresponding gene phylogeny departs from the species phylogeny by a Subtree Prune an…
View article: Response to “On the impact of incomplete taxon sampling on the relative timing of gene transfer events”
Response to “On the impact of incomplete taxon sampling on the relative timing of gene transfer events” Open
International audience
View article: PhylteR: Efficient Identification of Outlier Sequences in Phylogenomic Datasets
PhylteR: Efficient Identification of Outlier Sequences in Phylogenomic Datasets Open
In phylogenomics, incongruences between gene trees, resulting from both artifactual and biological reasons, can decrease the signal-to-noise ratio and complicate species tree inference. The amount of data handled today in classical phyloge…
View article: Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses
Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses Open
The accidental endogenization of viral elements within eukaryotic genomes can occasionally provide significant evolutionary benefits, giving rise to their long-term retention, that is, to viral domestication. For instance, in some endopara…
View article: Author response: Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses
Author response: Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses Open
View article: PhylteR: efficient identification of outlier sequences in phylogenomic datasets
PhylteR: efficient identification of outlier sequences in phylogenomic datasets Open
In phylogenomics, incongruences between gene trees, resulting from both artifactual and biological reasons, can decrease the signal-to-noise ratio and complicate species tree inference. The amount of data handled today in classical phyloge…
View article: Inferring phylogenetic trees from intramolecular distances with Phylo-IMD
Inferring phylogenetic trees from intramolecular distances with Phylo-IMD Open
Phylogenetic reconstruction is one of the most widely used modelling techniques in biology. While most available methods involve the use of sequence-based comparison it has long been discussed whether structural information could…
View article: Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses
Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses Open
The accidental endogenization of viral elements within eukaryotic genomes can occasionally provide significant evolutionary benefits, giving rise to their long-term retention, that is, to viral domestication. For instance, in some endopara…
View article: <i>tidy tree</i>: A New Layout for Phylogenetic Trees
<i>tidy tree</i>: A New Layout for Phylogenetic Trees Open
Many layouts exist for visualizing phylogenetic trees, allowing to display the same information (evolutionary relationships) in different ways. For large phylogenies, the choice of the layout is a key element, because the printable area is…
View article: Ghost lineages can invalidate or even reverse findings regarding gene flow
Ghost lineages can invalidate or even reverse findings regarding gene flow Open
Introgression, endosymbiosis, and gene transfer, i.e., horizontal gene flow (HGF), are primordial sources of innovation in all domains of life. Our knowledge on HGF relies on detection methods that exploit some of its signatures left on ex…
View article: Ghost Lineages Highly Influence the Interpretation of Introgression Tests
Ghost Lineages Highly Influence the Interpretation of Introgression Tests Open
Most species are extinct, those that are not are often unknown. Sequenced and sampled species are often a minority of known ones. Past evolutionary events involving horizontal gene flow, such as horizontal gene transfer, hybridization, int…
View article: Ghost lineages can invalidate or even reverse findings regarding gene flow
Ghost lineages can invalidate or even reverse findings regarding gene flow Open
Introgression, endosymbiosis and gene transfer, i . e . Horizontal Gene Flow (HGF), are primordial sources of innovation in all domains of life. Our knowledge on HGF relies on detection methods that exploit some of its signatures left on e…
View article: Ghost lineages highly influence the interpretation of introgression tests
Ghost lineages highly influence the interpretation of introgression tests Open
Most species are extinct; those that are not are often unknown. Sequenced and sampled species are often a minority of known ones. Past evolutionary events involving horizontal gene flow, such as horizontal gene transfer, hybridization, int…
View article: Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages
Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages Open
Summary Here we present Zombi, a tool to simulate the evolution of species, genomes and sequences in silico, that considers for the first time the evolution of genomes in extinct lineages. It also incorporates various features that have no…
View article: Tanglegrams Are Misleading for Visual Evaluation of Tree Congruence
Tanglegrams Are Misleading for Visual Evaluation of Tree Congruence Open
Evolutionary Biologists are often faced with the need to compare phylogenetic trees. One popular method consists in visualizing the trees face to face with links connecting matching taxa. These tanglegrams are optimized beforehand so that …
View article: Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot
Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot Open
More than any other genome components, Transposable Elements (TEs) have the capacity to move across species barriers through Horizontal Transfer (HT), with substantial evolutionary consequences. Previous large-scale surveys, based on full-…
View article: Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data
Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data Open
View article: Tanglegrams Are Misleading for Visual Evaluation of Tree Congruence
Tanglegrams Are Misleading for Visual Evaluation of Tree Congruence Open
Evolutionary Biologists are often faced with the need to compare phylogenetic trees. One popular method consists in visualizing the trees face to face with links connecting matching taxa. These tanglegrams are optimized beforehand so that …
View article: Co‐occurrence among three divergent plant‐castrating fungi in the same <i>Silene</i> host species
Co‐occurrence among three divergent plant‐castrating fungi in the same <i>Silene</i> host species Open
The competitive exclusion principle postulates that different species can only coexist in sympatry if they occupy distinct ecological niches. The goal of this study was to understand the geographical distribution of three species of Microb…
View article: Zombi: A phylogenetic simulator of trees, genomes and sequences that accounts for dead lineages
Zombi: A phylogenetic simulator of trees, genomes and sequences that accounts for dead lineages Open
Summary Here we present Zombi , a tool to simulate the evolution of species, genomes and sequences in silico , that considers for the first time the evolution of genomes in extinct lineages. It also incorporates various features that have …
View article: Multiple convergent supergene evolution events in mating-type chromosomes
Multiple convergent supergene evolution events in mating-type chromosomes Open
View article: Additional file 2: of Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data
Additional file 2: of Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data Open
Table S7. Data used in the study, including sex, forearm length, FME, genotype at 20 microsatellite markers for 748 Pteronotus sp. Data in bold are individuals identified as hybrids using microsatellite (N = 30) or mitochondrial data (N = …
View article: Overtraining often results in topologically incorrect species trees with maximum likelihood methods
Overtraining often results in topologically incorrect species trees with maximum likelihood methods Open
Background Overtraining occurs when an optimization process is applied for too many steps, leading to a model describing noise in addition to the signal present in the data. This effect may affect typical approaches for species tree recons…
View article: Pitfalls in supermatrix phylogenomics
Pitfalls in supermatrix phylogenomics Open
In the mid-2000s, molecular phylogenetics turned into phylogenomics, a development that improved the resolution of phylogenetic trees through a dramatic reduction in stochastic error. While some then predicted “the end of incongruence”, it…
View article: SONIFICATION OF PHYLOGENETIC TREES: LISTENING TO EVOLUTION
SONIFICATION OF PHYLOGENETIC TREES: LISTENING TO EVOLUTION Open
International audience