Impacts of taxon-sampling schemes on Bayesian tip dating under the fossilized birth-death process

Evolutionary timescales can be inferred by molecular-clock analyses of
genetic data and fossil evidence. Bayesian phylogenetic methods such as
tip dating provide a powerful framework for inferring evolutionary
timescales, but the most widely used priors for tree topologies and node
times often assume that present-day taxa have been sampled randomly or
exhaustively. In practice, taxon sampling is often carried out so as to
include representatives of major lineages, such as orders or families. We
examined the impacts of different densities of diversified sampling on
Bayesian tip dating on unresolved fossilized birth-death (FBD) trees, in
which fossil taxa are topologically constrained but their exact placements
are averaged out. We used synthetic data generated by simulations of
nucleotide sequence evolution, fossil occurrences, and diversified taxon
sampling. Our analyses under the diversified-sampling FBD process show
that increasing taxon-sampling density does not necessarily improve
divergence-time estimates. However, when informative priors were specified
for the root age or when tree topologies were fixed to those used for
simulation, the performance of tip dating on unresolved FBD trees
maintains its accuracy and precision or improves with taxon-sampling
density. By exploring three situations in which models are mismatched, we
find that including all relevant fossils, without pruning off those that
are incompatible with the diversified-sampling FBD process, can lead to
underestimation of divergence times. Our reanalysis of a eutherian mammal
data set confirms some of the findings from our simulation study, and
reveals the complexity of diversified taxon sampling in phylogenomic data
sets. In highlighting the interplay of taxon-sampling density and other
factors, the results of our study have practical implications for using
Bayesian tip dating to infer evolutionary timescales across the Tree of
Life.