Stéphane Guindon

Highly diverged non-vertebrate Ki-67 proteins with conserved biophysical and functional properties

Austin Haider, Aleksandra Zieminska, Geronimo Dubra, Kari Gaalswyk et autres

Abstract The Ki-67 protein is a widely used marker of mammalian cell proliferation that plays critical roles in heterochromatin organisation and mitotic perichromosomal layer formation. Thus, its apparent restriction to vertebrates is puzzling. However, sequences with limited homology to subdomains of Ki-67 …

us, fr (code pays fourni par la source)

Reconciling fast Hepatitis B evolutionary rates with ancient co-divergence

Philippe Lemey, Xiang Ji, Bram Vrancken, Magdalini Bletsa et autres

Estimating evolutionary rates and divergence times for hepatitis B virus (HBV) has long been complicated by conflicting calibration approaches and extensive rate variation. To unlock the full potential of ancient and modern HBV genomic data, we develop a Bayesian mixed-effects molecular clock …

be, us, fr, Afrique du Sud (code pays fourni par la source)

MutaPhy: A clade-based framework to detect genotype-phenotype associations on phylogenetic trees

Amélie Ngo, Stéphane Guindon, Vincent Pedergnana

Understanding how genetic variation in pathogens influences clinical phenotypes observed in infected hosts is a fundamental challenge in evolutionary genomics and public health. Phenotypic traits such as infection severity are often non-randomly distributed within the pathogen's phylogeny, suggesting the existence of evolutionary …

Grains, trade and war in the multimodal transmission of Rice yellow mottle virus: An historical and phylogeographical retrospective

Innocent Ndikumana, Geoffrey Onaga, Agnès Pinel‐Galzi, Pauline Rocu et autres

Rice yellow mottle virus (RYMV) is a major pathogen of rice in Africa. RYMV has a narrow host range limited to rice and a few related poaceae species. We explore the links between the spread of RYMV in East Africa and rice …

Rwanda, Côte d’Ivoire, fr, Tanzanie, Kenya, sg, be, us (code pays fourni par la source)

How fast are viruses spreading in the wild?

Simon Dellicour, Paul Bastide, Pauline Rocu, Denis Fargette et autres

Genomic data collected from viral outbreaks can be exploited to reconstruct the dispersal history of viral lineages in a two-dimensional space using continuous phylogeographic inference. These spatially explicit reconstructions can subsequently be used to estimate dispersal metrics that can be informative of …

be, fr, us (code pays fourni par la source)

Modeling the velocity of evolving lineages and predicting dispersal patterns

Paul Bastide, Pauline Rocu, Johannes Wirtz, Gabriel W. Hassler et autres

Accurate estimation of the dispersal velocity or speed of evolving organisms is no mean feat. In fact, existing probabilistic models in phylogeography or spatial population genetics generally do not provide an adequate framework to define velocity in a relevant manner. For instance, …

fr, us, be (code pays fourni par la source)

Grains, trade and war in the multimodal transmission of Rice yellow mottle virus: an historical and phylogeographical retrospective

Innocent Ndikumana, Geoffrey Onaga, Agnès Pinel‐Galzi, Pauline Rocu et autres

Abstract Rice yellow mottle virus (RYMV) is a major pathogen of rice in Africa. RYMV has a narrow host range limited to rice and a few related poaceae species. We explore the links between the spread of RYMV in East Africa and …

Rwanda, Côte d’Ivoire, fr, Tanzanie, Kenya, sg, be, us (code pays fourni par la source)

On the connections between the spatial Lambda–Fleming–Viot model and other processes for analysing geo-referenced genetic data

Johannes Wirtz, Stéphane Guindon

The introduction of the spatial Lambda-Fleming-Viot model (ΛV) in population genetics was mainly driven by the pioneering work of Alison Etheridge, in collaboration with Nick Barton and Amandine Véber about ten years ago (Barton et al., 2010; Barton et al., 2013). The …

fr (code pays fourni par la source)

Modeling the velocity of evolving lineages and predicting dispersal patterns

Paul Bastide, Pauline Rocu, Johannes Wirtz, Gabriel W. Hassler et autres

Accurate estimation of the dispersal velocity or speed of evolving organisms is no mean feat. In fact, existing probabilistic models in phylogeography or spatial population genetics generally do not provide an adequate framework to define velocity in a relevant manner. For instance, …

fr, us, be (code pays fourni par la source)

Trees

Gilles Didier, Stéphane Guindon

Trees describe evolutionary processes at different time scales. This chapter focuses on the two main probabilistic tree generating models, namely the birth-death process and the Kingman coalescent. It provides elements of combinatorics necessary to count these trees. The chapter determines the probabilities …

fr (code pays fourni par la source)

Models and Methods for Biological Evolution

Gilles Didier, Stéphane Guindon

Biological evolution is the phenomenon concerning how species are born, are transformed or disappear over time. Its study relies on sophisticated methods that involve both mathematical modeling of the biological processes at play and the design of efficient algorithms to fit these …

fr (code pays fourni par la source)

How fast are viruses spreading in the wild?

Simon Dellicour, Paul Bastide, Pauline Rocu, Denis Fargette et autres

Genomic data collected from viral outbreaks can be exploited to reconstruct the dispersal history of viral lineages in a two-dimensional space using continuous phylogeographic inference. These spatially explicit reconstructions can subsequently be used to estimate dispersal metrics allowing to unveil the dispersal …

be, fr, us (code pays fourni par la source)