Misspecification Strikes: ASTRAL can Mislead in the Presence of Hybridization, even for Nonanomalous Scenarios

Abstract

ASTRAL is a powerful and widely used tool for species tree inference, known for its computational speed and robustness under incomplete lineage sorting. The method has often been used as an initial step in species network inference to provide a backbone tree structure upon which hybridization events are later added to such a tree via other methods. However, we show empirically and theoretically, that this methodology can yield flawed results. Specifically, we demonstrate that under the network multispecies coalescent model—including nonanomalous scenarios—ASTRAL can produce a tree that does not correspond to any topology displayed by the true underlying network. This finding highlights the need for caution when using ASTRAL-based inferences in suspected hybridization cases.