Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation

TL;DR

This paper investigates the statistical properties of fossil-based calibration priors in Bayesian divergence time estimation, proposing an alternative method for more accurate prior specification and highlighting the need for direct prior estimation in analyses.

Contribution

It introduces a new calibrated Yule prior that directly specifies the marginal prior distribution of divergence times, improving divergence time estimation accuracy.

Findings

Calibration densities do not represent the marginal prior distribution.

A new construction for calibrated Yule priors allows direct prior specification.

Estimating the prior induced by multiple calibrations is essential for accurate divergence dating.

Abstract

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.