Performance of A Priori and A Posteriori Calibration Strategies in Divergence Time Estimation

Abstract

Relaxed molecular clock methods allow the use of genomic data to estimate divergence times across the tree of life. This is most commonly achieved in Bayesian analyses where the molecular clock is calibrated a priori through the integration of fossil information. Alternatively, fossil calibrations can be used a posteriori, to transform previously estimated relative divergence times that were inferred without considering fossil information, into absolute divergence times. However, as branch length is the product of the rate of evolution and the duration in time of the considered branch, the extent to which a posteriori-calibrated, relative divergence time methods can disambiguate time and rate, is unclear. Here, we use forward evolutionary simulations and compare a priori and a posteriori calibration strategies using different molecular clock methods and models. Specifically, we compare three Bayesian methods, the strict clock, uncorrelated clock and autocorrelated clock, and the non-Bayesian algorithm implemented in RelTime. We simulate phylogenies with multiple, independent substitution rate changes and show that correct timescales cannot be inferred without the use of calibrations. Under our simulation conditions, a posteriori calibration strategies almost invariably inferred incorrect rate changes and divergence times. The a priori integration of fossil calibrations is fundamental in these cases to improve the accuracy of the estimated divergence times. Relative divergence times and absolute timescales derived by calibrating relative timescales to geological time a posteriori, appear to be less reliable than a priori calibrated, timescales.

Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants

“…Some recent studies of the timing of land plant evolution have argued that fossil calibrations should not exert undue influence over divergence time estimates 23 , 40 . However, in the absence of fossil calibrations, relaxed molecular clocks fail to distinguish rate and time, and fossil calibrations are therefore important across the tree to inform rate variation and in turn increase the accuracy of age estimates 77 . Our approach thus sought to maximize the information in the fossil record and increase the sampling of fossil calibrations over previous studies 23 , 38 .…”

Assessing Rapid Relaxed-Clock Methods for Phylogenomic Dating

“…Many studies have tested the RelTime method and compared its accuracy with Bayesian methods. These studies applied RelTime in the analysis of empirical data sets as well as data sets simulated under a variety of evolutionary scenarios for large data sets ( Tamura et al 2012 , 2018 ; Mello et al 2017 ; Battistuzzi et al 2018 ; Barba-Montoya et al 2020 ; Beavan et al 2020 ; Tao, Tamura, and Kumar 2020 ). They report comparable performance of RelTime and Bayesian methods, with and without applying internal calibrations.…”

Introgression is widespread in the radiation of carnivorous Nepenthes pitcher plants

“…The crown age and ages within the EDG, however, should be unproblematic in this regards. On the other hand, divergence time estimates should generally be understood with caution, because molecular dating methods can show poor performance under some circumstances, and in particular the accuracy of a posteriori calibration methods such as RelTime is the matter of ongoing debate (Beavan et al, 2020).…”