MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions.

ABSTRACT: The spread of infectious diseases is shaped by spatial and temporal aspects, such as host population structure or changes in the transmission rate or number of infected individuals over time. These spatiotemporal dynamics are imprinted in the genome of pathogens and can be recovered from those genomes using phylodynamics methods. However, phylodynamic methods typically quantify either the temporal or spatial transmission dynamics, which leads to unclear biases, as one can potentially not be inferred without the other. Here, we address this challenge by introducing a structured coalescent skyline approach, MASCOT-Skyline that allows us to jointly infer spatial and temporal transmission dynamics of infectious diseases using Markov chain Monte Carlo inference. To do so, we model the effective

SUBMITTER: Muller NF 

PROVIDER: S-EPMC10942421 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature