Data from: Coalescent-based branch length estimation improves dating of species trees

Species trees need to be dated for many downstream applications. Typical
molecular dating methods take a phylogenetic tree with branch lengths in
substitution units, as well as a set of calibrations, as input and convert
the branch lengths of the species tree to the unit of time, while being
consistent with the pre-specified calibrations. When dating species trees
from multi-locus genome-scale datasets, the branch lengths and sometimes
the topology of the species tree are estimated using concatenation.
However, concatenation does not address gene tree heterogeneity across the
genome. While Bayesian dating methods can address some forms of gene tree
heterogeneity, such as incomplete lineage sorting, they are not scalable
to large datasets. In this paper, we introduce a new scalable pipeline for
dating species trees that addresses gene tree discordance for both
topology and branch length estimation. The pipeline uses discordance-aware
methods that account for incomplete lineage sorting for estimating the
topology and branch lengths, and maximum likelihood-based methods for the
dating step. Our simulation study on datasets with gene tree discordance
shows that this pipeline produces more accurate and less biased dates than
pipelines that use concatenation. Furthermore, it is substantially more
scalable and can handle datasets with thousands of species and genes. Our
results on two biological datasets demonstrate that this new pipeline
improves the inference of node ages and branch lengths for certain nodes,
particularly those closer to the tree tips, and improves the downstream
diversification analysis.