Impact of the tree prior on estimating clock rates during epidemic outbreaks.

ABSTRACT: Bayesian phylogenetics aims at estimating phylogenetic trees together with evolutionary and population dynamic parameters based on genetic sequences. It has been noted that the clock rate, one of the evolutionary parameters, decreases with an increase in the sampling period of sequences. In particular, clock rates of epidemic outbreaks are often estimated to be higher compared with the long-term clock rate. Purifying selection has been suggested as a biological factor that contributes to this phenomenon, since it purges slightly deleterious mutations from a population over time. However, other factors such as methodological biases may also play a role and make a biological interpretation of results difficult. In this paper, we identify methodological biases originating from the choice of t

SUBMITTER: Moller S 

PROVIDER: S-EPMC5910814 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature