Clarifying Xenacoelomorpha phylogeny: A polarized quartet-based analysis with SeaLion

Recent phylogenomic work has renewed debate over internal relationships within Xenacoelomorpha, traditionally divided into the fast-evolving Acoelomorpha (Acoela + Nemertodermatida) and the more slowly evolving Xenoturbellida. A prominent alternative posits Xenacoela (Acoela + Xenoturbella), with the apparent monophyly of Acoelomorpha attributed to long-branch attraction (LBA). Here, we re-evaluate these internal relationships using SeaLion, a polarized-quartet framework, applied to (i) the original amino-acid supermatrices from three prior studies and (ii) the corresponding externally curated (filtered) datasets that have been reported to favor Xenacoela. For each dataset, we performed SeaLion-unfiltered analyses and analyses with SeaLion's internal quartet filters, RISK (convergence guard) and DIST (support-distance threshold), which remove quartets with high convergence risk or poor separation between competing topologies. Our analyses consistently support the monophyly of Acoelomorpha across a broad range of sequence data, with the three original datasets displaying particularly robust signals. Although a subset of SeaLion quartets in the externally curated datasets occasionally suggested alternative configurations, the application of RISK and DIST combined filtering strategies effectively minimized these conflicts. By optimizing the ratio of potentially convergent-to-apomorphic character states, our approach distinguishes phylogenetic signal from putative artifacts related to site-rate heterogeneity. Overall, our findings robustly affirm the Acoelomorpha clade and demonstrate the strength of the SeaLion method in resolving complex phylogenetic relationships, providing new insights into Xenacoelomorpha evolution.