Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data.

ABSTRACT:

Background

Early methods for estimating divergence times from gene sequence data relied on the assumption of a molecular clock. More sophisticated methods were created to model rate variation and used auto-correlation of rates, local clocks, or the so called "uncorrelated relaxed clock" where substitution rates are assumed to be drawn from a parametric distribution. In the case of Bayesian inference methods the impact of the prior on branching times is not clearly understood, and if the amount of data is limited the posterior could be strongly influenced by the prior.

Results

We develop a maximum likelihood method--Physher--that uses local or discrete clocks to estimate evolutionary rates and divergence times from heterochronous sequence data. Using two empirical data sets w

SUBMITTER: Fourment M 

PROVIDER: S-EPMC4222489 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature