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Clarifying Xenacoelomorpha phylogeny: A polarized quartet-based analysis with SeaLion.
Patrick Kück1, Mark Wilkinson2
1Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 160, Bonn, 53113, NRW, Germany.
Gene
|February 27, 2026
Summary
Phylogenetic analysis using the SeaLion method robustly supports the Acoelomorpha clade, challenging alternative hypotheses. This research clarifies internal relationships within Xenacoelomorpha, confirming monophyly despite potential evolutionary artifacts.
Area of Science:
- * Evolutionary Biology
- * Phylogenetics
- * Genomics
Background:
- * Internal relationships within Xenacoelomorpha are debated, with competing hypotheses of Acoelomorpha monophyly versus Xenacoela monophyly.
- * Previous studies have yielded conflicting results, potentially due to long-branch attraction (LBA) artifacts in rapidly evolving lineages.
- * The monophyly of Acoelomorpha (Acoela + Nemertodermatida) has been questioned, with an alternative proposing Xenacoela (Acoela + Xenoturbella).
Purpose of the Study:
- * To re-evaluate the internal phylogenetic relationships within Xenacoelomorpha.
- * To test the monophyly of Acoelomorpha against the Xenacoela hypothesis using a novel phylogenetic framework.
- * To assess the efficacy of the SeaLion method in resolving complex phylogenies and mitigating artifacts like LBA.
Main Methods:
- * Application of the SeaLion polarized-quartet framework to amino-acid supermatrices from three prior studies.
- * Analyses were conducted on both original and externally curated (filtered) datasets.
- * Utilized SeaLion's internal quartet filters, RISK (convergence guard) and DIST (support-distance threshold), to refine phylogenetic signal.
Main Results:
- * Analyses consistently supported the monophyly of Acoelomorpha across various datasets, particularly the original ones.
- * SeaLion's RISK and DIST filters effectively minimized conflicts arising from quartet configurations in curated datasets.
- * The method successfully distinguished genuine phylogenetic signal from artifacts related to site-rate heterogeneity.
Conclusions:
- * The findings robustly affirm the Acoelomorpha clade, providing strong evidence against the Xenacoela hypothesis.
- * The SeaLion method demonstrates significant power in resolving complex phylogenetic relationships within Xenacoelomorpha.
- * This study offers crucial insights into the evolutionary history of Xenacoelomorpha, highlighting the importance of artifact mitigation in phylogenomics.
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