Data from: An evaluation of different partitioning strategies for Bayesian estimation of species divergence times

The explosive growth of molecular sequence data has made it possible to
estimate species divergence times under relaxed-clock models using
genome-scale datasets with many gene loci. In order both to improve model
realism and to best extract information about relative divergence times in
the sequence data, it is important to account for the heterogeneity in the
evolutionary process across genes or genomic regions. Partitioning is a
commonly used approach to achieve those goals. We group sites that have
similar evolutionary characteristics into the same partition and those
with different characteristics into different partitions, and then use
different models or different values of model parameters for different
partitions to account for the among-partition heterogeneity. However, how
to partition data in practical phylogenetic analysis, and in particular in
relaxed-clock dating analysis, is more art than science. Here, we use
computer simulation and real data analysis to study the impact of the
partition scheme on divergence time estimation. The partition schemes had
relatively minor effects on the accuracy of posterior time estimates when
the prior assumptions were correct and the clock was not seriously
violated, but showed large differences when the clock was seriously
violated, when the fossil calibrations were in conflict or incorrect, or
when the rate prior was mis-specified. Concatenation produced the widest
posterior intervals with the least precision. Use of many partitions
increased the precision, as predicted by the infinite-sites theory, but
the posterior intervals might fail to include the true ages because of the
conflicting fossil calibrations or mis-specified rate priors. We analyzed
a dataset of 78 plastid genes from 15 plant species with serious clock
violation and showed that time estimates differed significantly among
partition schemes, irrespective of the rate drift model used. Multiple and
precise fossil calibrations reduced the differences among partition
schemes and were important to improving the precision of divergence time
estimates. While the use of many partitions is an important approach to
reducing the uncertainty in posterior time estimates, we do not recommend
its general use for the present, given the limitations of current models
of rate drift for partitioned data and the challenges of interpreting the
fossil evidence to construct accurate and informative calibrations.