wQFM-DISCO: DISCO-enabled wQFM improves phylogenomic analyses despite the presence of paralogs

Gene trees often differ from the species trees that contain them due to various factors, including incomplete lineage sorting (ILS), gene duplication and loss (GDL), and horizontal gene transfer (HGT). Several highly accurate species tree estimation methods have been introduced to explicitly address ILS, including AS-TRAL, a widely used statistically consistent method, and wQFM, a quartet amalgamation approach that is experimentally shown to be more accurate than ASTRAL. Two recent advancements, ASTRAL-Pro and DISCO, have emerged in the field of phylogenomics to consider gene duplication and loss (GDL) events. ASTRAL-Pro introduces a refined measure of quartet similarity, accounting for both orthology and paralogy. DISCO, on the other hand, offers a general strategy to decompose multicopy gene family trees into a collection of single-copy trees, allowing the utilization of methods previously designed for species tree inference in the context of single-copy gene trees. In this study, we first introduce some variants of DISCO to examine its underlying hypotheses and present analytical results on the statistical guarantees of DISCO. In particular, we introduce DISCO-R, a variant of DISCO with a refined and improved pruning strategy that provides more accurate and robust results. We then propose wQFM-DISCO (wQFM paired with DISCO) as an adaptation of wQFM to handle multicopy gene trees resulting from GDL events. Extensive evaluation studies on a collection of simulated and real data sets demonstrate that wQFM-DISCO is significantly more accurate than ASTRAL-Pro and other competing methods.