Is the deuterostome clade an artifact?

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 possible 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, support for Deuterostomia markedly decreases or even disappears. Our results call into question one of the longest-established major branches of the animal kingdom. A very short, or non-existent, deuterostome branch has implications for interpreting putative deuterostome fossils and for reconstructing the bilaterian ancestor.