Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation

Details Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation

2011-03-29

arxiv.org/abs/1103.5780v1

Biology

Quantitative Biology

Populations and Evolution

Scientific paper

The use of fossil evidence to calibrate divergence time estimation has a long history. More recently Bayesian MCMC has become the dominant method of divergence time estimation and fossil evidence has been re-interpreted as the specification of prior distributions on the divergence times of calibration nodes. These so-called "soft calibrations" have become widely used but the statistical properties of calibrated tree priors in a Bayesian setting has not been carefully investigated. Here we clarify that calibration densities, such as those defined in BEAST 1.5, do not represent the marginal prior distribution of the calibration node. We illustrate this with a number of analytical results on small trees. We also describe an alternative construction for a calibrated Yule prior on trees that allows direct specification of the marginal prior distribution of the calibrated divergence time, with or without the restriction of monophyly. This method requires the computation of the Yule prior conditional on the height of the divergence being calibrated. Unfortunately, a practical solution for multiple calibrations remains elusive. Our results suggest that direct estimation of the prior induced by specifying multiple calibration densities should be a prerequisite of any divergence time dating analysis.

Affiliated with

Also associated with

No associations

Rating

Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.

If you have personal experience with Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFWR-SCP-O-566587