P. Bastide

Modeling the velocity of evolving lineages and predicting dispersal patterns

This paper introduces PIV models to estimate dispersal velocity of evolving lineages and shows improved accuracy in predicting pathogen spread using West Nile virus data.

How fast are viruses spreading in the wild?

This study evaluates dispersal metrics for viruses using simulation and compares their spread in animal populations, finding robustness to sampling effort and human-mediated dispersal signatures.

The Cauchy Process on Phylogenies: a Tractable Model for Pulsed Evolution

This paper introduces the Cauchy Process as a tractable model for pulsed evolution on phylogenies, showing it can accurately reconstruct ancestral traits and capture complex evolutionary patterns.

Detection of orthologous genes with expression shifts linked to nickel hyperaccumulation across Eudicots

The paper identifies 31 orthologous gene groups with expression shifts linked to nickel hyperaccumulation across Eudicots using transcriptomic and phylogenetic analyses.

Accounting for within-species variation in continuous trait evolution on a phylogenetic network

This paper introduces a phylogenetic linear model for network-based comparative methods to account for within-species variation in continuous traits, showing its effectiveness through simulations and application to Polemonium data.

Phylogeographic and phylodynamic approaches to epidemiological hypothesis testing

This study uses phylogeographic and phylodynamic methods to test hypotheses about West Nile virus dispersal and genetic diversity, finding temperature influences on spread and no strong evidence for migratory bird flyway restriction.

nosoi: a stochastic agent-based transmission chain simulation framework in R

nosoi simulates transmission chains for infectious diseases using an agent-based framework, enabling validation of reconstruction methods and exploration of epidemic dynamics.

Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations

This paper extends Phylogenetic Comparative Methods to phylogenetic networks with reticulations, developing algorithms and statistical tests for trait evolution and transgressive evolution in Xiphophorus fishes.

Inference of Adaptive Shifts for Multivariate Correlated Traits

This paper introduces a method to detect adaptive shifts in multivariate correlated traits across phylogenetic trees, showing improved performance over existing methods.