Rehabilitating the benefits of gene tree correction in the presence of incomplete lineage sorting

Abstract Gene trees play an important role in various areas of phylogenomics. However, their reconstruction often relies on limited-length sequences and may not account for complex evolutionary events, such as gene duplications, losses, or incomplete lineage sorting (ILS), which are not modeled by standard phylogenetic methods. To address these challenges, it is common to first infer gene trees using fast algorithms for conventional models, then refine them through species tree-aware correction methods. Recently, it has been argued that such corrections can lead to overfitting and force gene trees to resemble the species tree, thereby obscuring genuine gene-level variation caused by ILS. In this paper, we challenge and refute this hypothesis, and we demonstrate that, when applied carefully, correction methods can offer significant benefits, even in the presence of ILS.