Abstract The development of High-Throughput Sequencing (HTS) technologies is having a
major impact on the genomic analysis of viral populations. Current HTS platforms can …

Phylodynamic methods have been essential to understand the interplay between the
evolution and epidemiology of infectious diseases. To date, the field has centered on …

Birth–death stochastic processes are the foundations of many phylogenetic models and are
widely used to make inferences about epidemiological and macroevolutionary dynamics …

INTRODUCTION Emerging infectious diseases pose one of the greatest threats to human
health and biodiversity. Phylodynamics is an effective tool for inferring epidemiological …

Genomic epidemiology plays an ever-increasing role in our understanding of and response
to the spread of infectious pathogens. Phylogeography, the reconstruction of the historical …

In the midst of an outbreak or sustained epidemic, reliable prediction of transmission risks
and patterns of spread is critical to inform public health programs. Projections of …

The fitness of a pathogen is a composite phenotype determined by many different factors
influencing growth rates both within and between hosts. Determining what factors shape …

Global linguistic diversity reflects the gradual gain and loss of languages over millennia, yet
half of the world's~ 6-7000 languages1 are threatened with extinction by the end of this …

Current phylogenetic clustering approaches for identifying pathogen transmission clusters
are limited by their dependency on arbitrarily defined genetic distance thresholds for within …

Beneficial and deleterious mutations cause the fitness of lineages to vary across a
phylogeny and thereby shape its branching structure. While standard phylogenetic models …