Biological causes and impacts of rugged tree landscapes in phylodynamic inference.

ABSTRACT: Phylodynamic analysis has been instrumental in elucidating the epidemiological and evolutionary dynamics of pathogens. The Bayesian approach to phylodynamics integrates out phylogenetic uncertainty, which is typically substantial in phylodynamic datasets due to low genetic diversity. Bayesian phylodynamic analysis does not, however, scale with modern datasets, partly due to difficulties in traversing tree space. Here, we set out to characterize tree space of phylodynamic inference and assess its impacts on analysis difficulty and key biological estimates. By running extensive Bayesian analyses of 15 classic large phylodynamic datasets and carefully analyzing the posterior samples, we find that the posterior landscape in tree space ("tree landscape") is diffuse yet rugged, leading to widesp

SUBMITTER: Gao J 

PROVIDER: S-EPMC12259096 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature