Over the past decade, a new set of methods for estimating dated trees has emerged.
Originally referred to as the fossilized birth–death (FBD) process, this single model has …

A lot of what we know about past speciation and extinction dynamics is based on statistically
fitting birth–death processes to phylogenies of extant species. Despite their wide use, the …

Viral phylogenies provide crucial information on the spread of infectious diseases, and many
studies fit mathematical models to phylogenetic data to estimate epidemiological parameters …

Species diversification—the balance between speciation and extinction—is fundamental to
our understanding of how species richness varies in space and time and throughout the …

Phylodynamic models generally aim at jointly inferring phylogenetic relationships, model
parameters, and more recently, the number of lineages through time, based on molecular …

Phylodynamic models use pathogen genome sequence data to infer epidemiological
dynamics. With the increasing genomic surveillance of pathogens, especially during the …

Genomic surveillance of SARS-CoV-2 has been instrumental in tracking the spread and
evolution of the virus during the pandemic. The availability of SARS-CoV-2 molecular …

Inferring the dynamics of pathogen transmission during an outbreak is an important problem
in infectious disease epidemiology. In mathematical epidemiology, estimates are often …

Accurately estimating the prevalence and transmissibility of an infectious disease is an
important task in genetic infectious disease epidemiology. However, generating accurate …

Phylodynamic models generally aim at jointly inferring phylogenetic relationships, model
parameters, and more recently, population size through time for clades of interest, based on …