Strategies for partitioning clockmodels in phylogenomic dating: Application to the angiosperm evolutionary timescale

Abstract

Evolutionary timescales can be inferred from molecular sequence data using a Bayesian phylogenetic approach. In these methods, themolecular clock is often calibrated using fossil data. The uncertainty in these fossil calibrations is important because it determines the limiting posterior distributionfordivergence-timeestimates as thesequence lengthtends toinfinity.Here,we investigatehowthe accuracy and precision of Bayesian divergence-time estimates improve with the increased clock-partitioning of genome-scale data into clock-subsets.We focus on a data set comprising plastome-scale sequences of 52 angiospermtaxa. There was little difference among the Bayesian date estimates whether we chose clock-subsets based on patterns of among-lineage rate heterogeneity or relative rates acrossgenes,orby randomassignment. Increasing thedegree of clock-partitioningusually ledtoanimprovement inthe precision of divergence-time estimates, but this increase was asymptotic to a limit presumably imposed by fossil calibrations. Our clock-partitioning approaches yielded highly precise age estimates for several key nodes in the angiospermphylogeny. For example, when partitioning the data into 20 clock-subsets based on patterns of among-lineage rate heterogeneity, we inferred crown angiosperms to have arisen 198-178Ma. This demonstrates that judicious clock-partitioning can improve the precision of molecular dating based on phylogenomic data, but the meaning of this increased precision should be considered critically.