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 fo..., , ## Coalescent-based dating datasets

This repository contains the datasets and scripts used in the following manuscript:

* Y. Tabatabaee, S. Claramunt, S. Mirarab (2026). Coalescent-based branch length estimation improves dating of species trees. Systematic Biology (in press). preprint available at [https://www.biorxiv.org/content/10.1101/2025.02.25.640207v1.abstract](https://www.biorxiv.org/content/10.1101/2025.02.25.640207v1.abstract)

For experiments in this study, we generated three sets of simulated datasets with gene tree discordance due to incomplete lineage sorting (ILS) and analyzed two avian biological datasets from [Harvey et. al. (2020)](https://www.science.org/doi/10.1126/science.aaz6970) and [Stiller et. al. (2024)](https://www.nature.com/articles/s41586-024-07323-1). The simulated datasets have model species trees with substitution-unit, generation-unit, and time-unit branch lengths.

### Simulated datasets

#### 30-taxon dataset (S30.tar.gz)

This dataset has six model ..., ,