2023/12/20 by Maxime Godfroid, Charles Coluzzi, Amaury Lambert +3 · 1 voice · 1 citation
Biochemistry, Genetics and Molecular Biology · #Evolution and Genetic Dynamics #Genetic diversity and population structure #Genomics and Phylogenetic Studies
paper · pdf · doi:10.1111/2041-210x.14190
openalex publication_date 2023/12/20 · openalex created_date 2023/12/22 · openalex updated_date 2026/07/30
Abstract Correlated evolution describes how multiple biological traits evolve together. Recently developed methods provide increasingly detailed results of correlated evolution, sometimes at elevated computational costs. Here, we present evo‐scope , a fast and fully automated pipeline with minimal input requirements to compute correlation between discrete traits evolving on a phylogenetic tree. Notably, we improve two of our previously developed tools that efficiently compute statistics of correlated evolution to characterize the nature, such as synergy or antagonism, and the strength of the interdependence between the traits. Furthermore, we improved the running time and implemented several additional features, such as genetic mapping, Bayesian Markov Chain Monte Carlo estimation, consideration of missing data and phylogenetic uncertainty. As an application, we scan a publicly available penicillin resistance data set of Streptococcus pneumoniae and characterize genetic mutations that correlate with antibiotic resistance. The pipeline is accessible both as a self‐contained Github repository ( https://github.com/Maxime5G/EvoScope ) and through a graphical galaxy interface ( https://galaxy.pasteur.fr/u/maximeg/w/evoscope ).