Bertrand Yann

Bertrand Yann
Institute of Botany of the ASCR · Department of molecular biology

About

35
Publications
20,729
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
1,377
Citations

Publications

Publications (35)
Article
Full-text available
Premise: Although hybridization has played an important role in the evolution of many plant species, phylogenetic reconstructions that include hybridizing lineages have been historically constrained by the available models and data. Restriction-site-associated DNA sequencing (RADseq) has been a popular sequencing technique for the reconstruction o...
Article
Full-text available
Background: Whole genome duplication plays a central role in plant evolution. There are two main classes of polyploid formation: autopolyploids which arise within one species by doubling of similar homologous genomes; in contrast, allopolyploidy (hybrid polyploidy) arise via hybridization and subsequent doubling of nonhomologous (homoeologous) gen...
Preprint
Although hybridization has played an important role in the evolution of many species, phylogenetic reconstructions that include hybridizing lineages have been historically constrained by the available models and data. Recently, the combined development of high-throughput sequencing and evolutionary network models offer new opportunities for phyloge...
Article
Full-text available
Background Current evidence suggests that for more robust estimates of species tree and divergence times, several unlinked genes are required. However, most phylogenetic trees for non-model organisms are based on single sequences or just a few regions, using traditional sequencing methods. Techniques for massive parallel sequencing or next generati...
Data
DNA sequence alignment with loops down-weighted. The file contains the chloroplast sequence alignment and a Mr Bayes analysis block that excludes poorly aligned sites, as well as down-weighting the inverted loop regions by excluding all but one character in each inverted loop.
Data
DNA sequence alignment with loops. The file contains the chloroplast sequence alignment and a Mr Bayes analysis block that excludes poorly aligned sites, but includes the entire inverted loop regions.
Article
Several well-documented evolutionary processes are known to cause conflict between species level phylogenies and gene level phylogenies. Three of the most challenging processes for species tree inference are incomplete lineage sorting, hybridisation and gene duplication, which may result in unwarranted comparisons of paralogous genes. Several exist...
Article
Although hybridisation through genome duplication is well known, hybridisation without genome duplication (homoploid hybrid speciation, HHS) is not. Few well-documented cases have been reported. A possible instance of HHS in Medicago prostrata Jacq. was suggested previously, based on only two genes and one individual. We tested whether this species...
Article
Full-text available
The hypothesis of wide spread reticulate evolution in Tick-Borne Encephalitis virus (TBEV) has recently gained momentum with several publications describing past recombination events involving various TBEV clades. Despite a large body of work, no consensus has yet emerged on TBEV evolutionary dynamics. Understanding the occurrence and frequency of...
Data
Figs A-J and Tables A-J. Fig A, False positive rates in simulations without recombination for 100 replicates for the FE-, W- and S- subtypes. Fig B, True and false positive rates in simulations with recombination for 100 replicates for the recombination events 1–2 in the FE-subtype at four recombination fragment sizes (200, 1000, 2000 and 3000 bp)....
Article
Full-text available
The species phylogeny of Medicago L. (Leguminosae) remains unresolved, as there is significant incongruence between the published gene phylogenies. Here, we compare six of these gene phylogenies of Medicago, inferred from unlinked loci from the nuclear, chloroplast and mitochondrial genomes. Data from all loci were re-analysed, including gap-coding...
Article
Full-text available
There is a rising awareness that species trees are best inferred from multiple loci while taking into account processes affecting individual gene trees, such as substitution model error (failure of the model to account for the complexity of the data) and coalescent stochasticity (presence of incomplete lineage sorting). Although most studies have b...
Article
Full-text available
Next-generation sequencing technology has increased the capacity to generate molecular data for plant biological research, including phylogenetics, and can potentially contribute to resolving complex phylogenetic problems. The evolutionary history of Medicago L. (Leguminosae: Trifoliae) remains unresolved due to incongruence between published phylo...
Article
Full-text available
Erysimum includes 150–350 species distributed in the Northern Hemisphere, with Eurasia being the centre of greatest diversity. It is well known for its taxonomic complexity as a result of overlapping morphological characters. We present the first densely sampled phylogenetic analysis of Erysimum using internal transcribed spacer (ITS) DNA sequences...
Article
Full-text available
Despite being one of the larger genera of Caryophyllaceae with about 60 cushion-forming subshrubby species, Acanthophyllum is represented poorly in previous molecular phylogenetic studies. The genus is an important component of the subalpine steppe flora in Central to Southwest Asia. Although the placement of Acanthophyllum in the tribe Caryophylle...
Article
Full-text available
The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and blast searches, it is often advantageous to rely on either one of...
Article
Full-text available
The last twenty years have witnessed molecular data emerge as a primary research instrument in most branches of mycology. Fungal systematics, taxonomy, and ecology have all seen tremendous progress and have undergone rapid, far-reaching changes as disciplines in the wake of continual improvement in DNA sequencing technology. A taxonomic study that...
Article
Full-text available
The mammalian tick-borne flavivirus group (MTBFG) contains viruses associated with important human and animal diseases such as encephalitis and hemorrhagic fever. In contrast to mosquito-borne flaviviruses where recombination events are frequent, the evolutionary dynamic within the MTBFG was believed to be essentially clonal. This assumption was ch...
Data
Synoptic table of strains included in the alignments: ALN1, ALN2 and E_161. Information is provided on strain name, accession, geographical origin, year of isolation, sequence length and assigned clade. (DOC)
Data
a–b RDP3 analyses results. The x axis shows genome length in nucleotides, numbered form the start of ORFs after alignment with Neudoerfl (U27495) as reference. The y axis represents the metric used by each method for detecting recombination. Detected recombination signals appear as colored rectangles. (TIF)
Article
Full-text available
Reverse complementary DNA sequences––sequences that are inadvertently cast backward and in which all purines and pyrimidines are transposed––are not uncommon in sequence databases, where they may introduce noise into sequence-based research. We show that about 1% of the public fungal ITS sequences, the most commonly sequenced genetic marker in myco...
Article
Full-text available
Tick-borne encephalitis virus (TBEV) is a flavivirus with major impact on global health. The geographical TBEV distribution is expanding, thus making it pivotal to further characterize the natural virus populations. In this study, we completed the earlier partial sequencing of a TBEV pulled out of a pool of RNA extracted from 115 ticks collected on...
Article
Clade and monophyletic group on one hand and grade and paraphyletic group on the other hand are commonly used as pairs of interchangeable terms. I question this apparent synonymy and propose that “monophyly“ and “paraphyly“ should refer to a property of a set, whereas “clade“ and “grade“ should apply to individuals resulting from evolutionary proce...
Article
Full-text available
When scientists use a taxon name like Mammalia, it is important that they talk about the same thing. But, what does it mean to be the same thing in different phylogenetic hypotheses? And, how is taxonomic reference maintained across hypotheses? Here, we discuss the differences between real and hypothetical clades, and how such a distinction relates...
Article
Full-text available
The majority of biodiversity assessments use species as the base unit. Recently, a series of studies have suggested replacing numbers of species with higher ranked taxa (genera, families, etc.); a method known as taxonomic surrogacy that has an important potential to save time and resources in assesments of biological diversity. We examine the rela...