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Filtering artifactual signal increases support for Xenacoelomorpha and Ambulacraria sister relationship in the animal tree of life

Mulhair, Peter O.; McCarthy, Charley G.P.; Siu-Ting, Karen; Creevey, Christopher J.; O’Connell, Mary J.


Peter O. Mulhair

Charley G.P. McCarthy

Karen Siu-Ting

Christopher J. Creevey


Conflicting studies place a group of bilaterian invertebrates containing xenoturbellids and acoelomorphs, the Xenacoelomorpha, as either the primary emerging bilaterian phylum or within Deuterostomia, sister to Ambulacraria. Although their placement as sister to the rest of Bilateria supports relatively simple morphology in the ancestral bilaterian, their alternative placement within Deuterostomia suggests a morphologically complex ancestral bilaterian along with extensive loss of major phenotypic traits in the Xenacoelomorpha. Recent studies have questioned whether Deuterostomia should be considered monophyletic at all. Hidden paralogy and poor phylogenetic signal present a major challenge for reconstructing species phylogenies. Here, we assess whether these issues have contributed to the conflict over the placement of Xenacoelomorpha. We reanalyzed published datasets, enriching for orthogroups whose gene trees support well-resolved clans elsewhere in the animal tree.16 We find that most genes in previously published datasets violate incontestable clans, suggesting that hidden paralogy and low phylogenetic signal affect the ability to reconstruct branching patterns at deep nodes in the animal tree. We demonstrate that removing orthogroups that cannot recapitulate incontestable relationships alters the final topology that is inferred, while simultaneously improving the fit of the model to the data. We discover increased, but ultimately not conclusive, support for the existence of Xenambulacraria in our set of filtered orthogroups. At a time when we are progressing toward sequencing all life on the planet, we argue that long-standing contentious issues in the tree of life will be resolved using smaller amounts of better quality data that can be modeled adequately.


Mulhair, P. O., McCarthy, C. G., Siu-Ting, K., Creevey, C. J., & O’Connell, M. J. (2022). Filtering artifactual signal increases support for Xenacoelomorpha and Ambulacraria sister relationship in the animal tree of life. Current Biology, 32(23), 5180-5188.e3.

Journal Article Type Article
Acceptance Date Oct 18, 2022
Online Publication Date Nov 9, 2022
Publication Date Dec 5, 2022
Deposit Date Nov 28, 2022
Publicly Available Date Dec 1, 2022
Journal Current Biology
Print ISSN 0960-9822
Electronic ISSN 1879-0445
Publisher Cell Press
Peer Reviewed Peer Reviewed
Volume 32
Issue 23
Pages 5180-5188.e3
Keywords General Agricultural and Biological Sciences; General Biochemistry, Genetics and Molecular Biology
Public URL
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