Phylogenetic estimation has largely come to rely on explicitly model-based methods. This
approach requires that a model be chosen and that that choice be justified. To date …

Most of the sophisticated methods to estimate evolutionary divergence between DNA
sequences assume that the two sequences have evolved with the same pattern of …

Background Understanding how biodiversity is shaped through time is a fundamental
question in biology. Even though tropical rain forests (TRF) represent the most diverse …

The authors consider Bayesian analysis for continuoustime Markov chain models based on
a conditional reference prior. For such models, inference of the elapsed time between chain …

Stochastic models of evolution play a prominent role in the field of molecular evolution; they
are used in applications as far-ranging as phylogeny estimation, uncovering the pattern of …

Plasmodium falciparum, the causative agent of malignant malaria, is among the most severe
human infectious diseases. The closest known relative of P. falciparum is a chimpanzee …

Background Hepatitis C virus (HCV) is estimated to affect 130–180 million people
worldwide. Although its origin is unknown, patterns of viral diversity suggest that HCV …

Time-scales of viral evolution and emergence have been studied widely, but are often poorly
understood. Molecular analyses of viral evolutionary time-scales generally rely on estimates …

Premise of the Study A key question in evolutionary biology is why some clades are more
successful by being widespread geographically, biome diverse, or speciesrich. To extend …

Viruses in the Ebolavirus and Marburgvirus genera (family Filoviridae) have been
associated with large outbreaks of hemorrhagic fever in human and nonhuman primates …