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Damien M \de Vienne

Damien M \de Vienne

About

44
Publications
9,222
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1,808
Citations
Citations since 2016
14 Research Items
1198 Citations
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2016201720182019202020212022050100150200
2016201720182019202020212022050100150200
2016201720182019202020212022050100150200
Introduction
Skills and Expertise
Additional affiliations
November 2013 - present
January 2011 - present
January 2011 - present
University Pompeu Fabra
Position
  • PostDoc Position

Publications

Publications (44)
Article
Full-text available
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 extant genomes. One of them is the effect of HGF on branch lengths of constructed phylogenies. This signature has...
Article
Full-text available
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, introgression and admixture, are therefore likely to involve "ghosts", i.e. extinct, unknown or unsampled lineages...
Preprint
Full-text available
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 extant genomes. One of them is the effect of HGF on branch lengths of constructed phylogenies. This signature has b...
Preprint
Full-text available
The data that is known and sampled in any evolutionary study is always a small part of what exists, known or not, or what has existed in the past and is extinct. Therefore it is likely that all detected past horizontal gene fluxes, hybridization, introgressions, admixtures or transfers, involve "ghosts", that is, extinct or unsampled lineages. The...
Article
Full-text available
Background The distinction between lineages of neotropical bats from the Pteronotus parnellii species complex has been previously made according to mitochondrial DNA, and especially morphology and acoustics, in order to separate them into two species. In these studies, either sample sizes were too low when genetic and acoustic or morphological data...
Article
Full-text available
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 Microbotryum anther‐smut fungi that are distantly related but infect the same host plants, the sister species Silene...
Article
Full-text available
Convergent adaptation provides unique insights into the predictability of evolution and ultimately into processes of biological diversification. Supergenes (beneficial gene linkage) are striking examples of adaptation, but little is known about their prevalence or evolution. A recent study on anther-smut fungi documented supergene formation by rear...
Preprint
Full-text available
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 reconstruction that use maximum likelihood optimization procedures on a small sample of concatenated genes. In this c...
Article
Full-text available
The Tree of Life (ToL) is meant to be a unique representation of the evolutionary relationships between all species on earth. Huge efforts are made to assemble such a large tree, helped by the decrease of sequencing costs and improved methods to reconstruct and combine phylogenies, but no tool exists today to explore the ToL in its entirety in a sa...
Chapter
Full-text available
The existence of sex represents a puzzle for evolutionists. Sex clearly allows increasing adaptability in the long term, but this advantage may occur too rarely to balance the costs of sex in the short term. Here, we fi rst outline the two main hypotheses proposed to explain the success of sex, based on short-term benefi ts: (i) the “red queen” hyp...
Article
Full-text available
Horizontal gene transfers (HGT), i.e., the transmission of genetic material between species not directly attributable to meiotic gene exchange, have long been acknowledged as a major driver of prokaryotic evolution and is increasingly recognized as an important source of adaptation in eukaryotes. In fungi in particular, many convincing examples of...
Article
Full-text available
Dimorphic mating-type chromosomes in fungi are excellent models for understanding the genomic consequences of recombination suppression. Their suppressed recombination and reduced effective population size are expected to limit the efficacy of natural selection, leading to genomic degeneration. Our aim was to identify the sequences of the mating-ty...
Article
Full-text available
Horizontal gene transfers (HGT), i.e., the transmission of genetic material between species not directly at- tributable to meiotic gene exchange, have long been acknowledged as a major driver of prokaryotic evolu- tion and is increasingly recognized as an important source of adaptation in eukaryotes. In fungi in particu- lar, many convincing exampl...
Article
Full-text available
From their origin as an early alpha proteobacterial endosymbiont to their current state as cellular organelles, large-scale genomic reorganization has taken place in the mitochondria of all main eukaryotic lineages. So far, most studies have focused on plant and animal mitochondrial genomes (mtDNA) but fungi provide new opportunities to study highl...
Article
Full-text available
Fungi are ideal model organisms for dissecting the genomic bases of adaptive divergence in eukaryotes. They have simple morphologies and small genomes, occupy contrasting, well identified ecological niches, tend to have short generation times and many are amenable to experimental approaches. Fungi also display diverse lifestyles, from saprotrophs t...
Article
Full-text available
Sex predominates in eukaryotes, despite its short-term disadvantage when compared to asexuality. Myriad models have suggested that short-term advantages of sex may be sufficient to counterbalance its twofold costs. However, despite decades of experimental work seeking such evidence, no evolutionary mechanism has yet achieved broad recognition as ex...
Article
Hosts and their symbionts are involved in intimate physiological and ecological interactions. The impact of these interactions on the evolution of each partner depends on the time-scale considered. Short-term dynamics - 'coevolution' in the narrow sense - has been reviewed elsewhere. We focus here on the long-term evolutionary dynamics of cospeciat...
Conference Paper
Full-text available
Résumé. Nous proposons une approche permettant de prédire des complexes impliquant trois protéines (appelés trimères) à partir de combinaison de classi-fieurs appris sur des complexes n'impliquant que deux protéines (dimères). La prédiction de ces trimères repose sur deux hypothèses biologiques : (i) deux protéines orthologues présentent des caract...
Article
Full-text available
The prediction of the network of protein-protein interactions (PPI) of an organism is crucial for the understanding of biological processes and for the development of new drugs. Machine learning methods have been successfully applied to the prediction of PPI in yeast by the integration of multiple direct and indirect biological data sources. Howeve...
Data
List of the 50 best ranked negative pairs detected in this study. (PDF)
Article
Parallels have been drawn between the evolution of nonrecombining regions in fungal mating-type chromosomes and animal and plant sex chromosomes, particularly regarding the stages of recombination cessation forming evolutionary strata of allelic divergence. Currently, evidence and explanations for recombination cessation in fungi are sparse, and th...
Article
Full-text available
Full genome data sets are currently being explored on a regular basis to infer phylogenetic trees, but there are often discordances among the trees produced by different genes. An important goal in phylogenomics is to identify which individual gene and species produce the same phylogenetic tree and are thus likely to share the same evolutionary his...
Article
Full-text available
Phylogenies are fundamental to comparative biology as they help to identify independent events on which statistical tests rely. Two groups of phylogenetic comparative methods (PCMs) can be distinguished: those that take phylogenies into account by introducing explicit models of evolution and those that only consider phylogenies as a statistical con...
Article
We studied the mode of reproduction and its evolution in the fungal subgenus Penicillium Biverticillium using phylogenetic and experimental approaches. We sequenced mating type (MAT) genes and nuclear DNA fragments in sexual and putatively asexual species. Examination of the concordance between individual trees supported the recognition of the morp...
Article
Hosts and their obligate pathogens exhibit intimate physiological interactions. How such interactions impact upon evolution of each partner varies depending on the timescale of interest. This chapter reviews theoretical advances and available data on host and pathogen evolution with regard to both short term (coevolution) and long term (cospeciatio...
Article
Understanding what determines the host range of pathogens and the potential for host shifts is of critical importance to controlling their introductions into new environments. The phylogeny of the hosts has been shown to be important: pathogens are more likely to be infectious on hosts closely related to their host-of-origin because of the similar...
Article
Microbotryum violaceum, the anther-smut fungus, forms a complex of sibling species which specialize on different plants. Previous studies have shown the presence of partial ecological isolation and F1 inviability, but did not detect assortative mating apart from a high selfing rate. We investigated other post-mating barriers and show that F1 hybrid...
Article
Full-text available
The R statistical analysis package has emerged as a popular platform for implementation of powerful comparative methods to understand the evolution of organismal traits and diversification. A hackathon was organized to bring together active R developers as well as end-users working on the integration of comparative phylogenetic methods within R to...
Article
Full-text available
In this review on fungal speciation, we first contrast the issues of species definition and species criteria and show that by distinguishing the two concepts the approaches to studying the speciation can be clarified. We then review recent developments in the understanding of modes of speciation in fungi. Allopatric speciation raises no theoretical...
Article
We report the development of 60 microsatellite markers on four species of the fungal complex Microbotryum, causing anther smut of the Caryophyllaceae. Microsatellites were found in four expressed sequence tag (EST) libraries, built from isolates of M. lychnis-dioicae, M. violaceum sensus stricto, M. lagerheimii and M. dianthorum, collected, respect...
Article
Full-text available
Phylogenetic trees are omnipresent in evolutionary biology and the comparison of trees plays a central role there. Tree congruence statistics are based on the null hypothesis that two given trees are not more congruent (topologically similar) than expected by chance. Usually, one searches for the most parsimonious evolutionary scenario relating two...
Article
Congruence between host and parasite phylogenies is often taken as evidence for cospeciation. However, 'pseudocospeciation', resulting from host-switches followed by parasite speciation, may also generate congruent trees. To investigate this process and the conditions favouring its appearance, we here simulated the adaptive radiation of a parasite...

Network

    • International St. Mary's Hospital and college of medicine, Catholic Kwandong University
    • French National Institute for Agriculture, Food, and Environment (INRAE)
    • French National Institute for Agriculture, Food, and Environment (INRAE)
    • IRB Barcelona Institute for Research in Biomedicine and Barcelona Supercomputing Centre (BSC)
    • University of Utah
Cited By