Support for the deuterostome clade comes from systematic errors

There is a long-standing consensus that the animal phyla closest to our own phylum of Chordata are the Echinodermata and Hemichordata. These three phyla constitute the major clade of Deuterostomia. Recent analyses have questioned the support for the monophyly of Deuterostomia, however, showing that the branch leading to deuterostomes is very short and may be influenced by systematic error. Here we use a site-by-site approach to explore multiple sources of error. Under conditions that promote long-branch attraction (LBA) – especially branch-length heterogeneity and sites constrained in their amino acid composition – we find that deuterostome monophyly is strongly supported. When we make efforts to mitigate these sources of error, we cannot distinguish between monophyletic and paraphyletic Deuterostomia. Our findings have implications for the interpretation of putative deuterostome fossils, for the reconstruction of a bilaterian ancestor and, more generally, for how datasets for deep-time phylogenetic analyses are assembled and analyzed.