Time-stamped phylogenetic trees

Phylogeneticists are typically interested in obtaining time-stamped rooted phylogenetic trees. The assumption of a strict molecular clock throughout the tree was originally required to infer divergence dates, but subsequent development of relaxed clock models has allowed for the removal of such an assumption. Different relaxations of the molecular clock have been developed to accommodate a multitude of evolutionary scenarios. These models allow to estimate divergence times in two distinct scenarios: isochronous data sets, where some type of calibration needs to be provided, and heterochronous data sets, where the differences between sequences sampled at different times can be used to calibrate the molecular clock. Populations for which such studies are possible are known as measurably evolving populations and are characterized by sufficiently long or numerous sampled sequences and a fast mutation rate relative to the available range of sequence sampling times. While RNA viral evolution is the most well-known example of using such an approach, the definition of a measurably evolving population also applies to ancient DNA, and allows us to estimate divergence times without paleontological calibrations.status: publishe