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Xenoturbellida and Acoelomorpha are marine worms with contentious ancestry. Both were originally associated with the flatworms (Platyhelminthes), butmolecular data have revised their phylogenetic positions, generally linking Xenoturbellida to the deuterostomes1,2 and positioning the Acoelomorpha as the most basally branching bilaterian group(s)3-6. Recent phylogenomic data suggested that Xenoturbellida and Acoelomorpha are sister taxa and together constitute an early branch of Bilateria7. Here we assemble three independent data sets-mitochondrial genes, a phylogenomic data set of 38,330 amino-acid positions and new microRNA (miRNA) complements- and show that the position of Acoelomorpha is strongly affected by a long-branch attraction (LBA) artefact. When we minimize LBA we find consistent support for a position of both acoelomorphs andXenoturbella within the deuterostomes. Themost likely phylogeny links Xenoturbella and Acoelomorpha in a clade we call Xenacoelomorpha. The Xenacoelomorpha is the sister group of the Ambulacraria (hemichordates and echinoderms). We show that analyses ofmiRNA complements8 have been affected by character loss in the acoels and that both groups possess one miRNA and the gene Rsb66 otherwise specific to deuterostomes. In addition,Xenoturbella shares one miRNA with the ambulacrarians, and two with the acoels. This phylogeny makes sense of the shared characteristics of Xenoturbellida andAcoelomorpha, such as ciliary ultrastructure and diffuse nervous system, and implies the loss of various deuterostome characters in the Xenacoelomorpha including coelomic cavities, through gut and gill slits.
In contrast to previous results1,2,4,9,10 (Fig. 1a), two recent phylogenomic studies have suggested a sister group relationship between Acoelomorpha and Xenoturbella. These studies disagree over where this clade might be placed, either at the base of Bilateria7 (Fig. 1b) or with the deuterostomes11 (Fig. 1c). The acoelomorph genes studied, however, show extremely high rates of sequence evolution. This bias could result in susceptibility to the LBA artefact: a systematic error that may be compounded by the short internal branches around the origin of the Bilateria12. Overcoming this potential artefact requires the analysis of large molecular data sets comprising many species and using a complex model of sequence evolution designed to reduce the impact of systematic errors12.
We assembled a largely complete set of mitochondrial protein sequences from four acoels using expressed sequence tag (EST) databases. Better-fitting models of molecular evolution are expected to be less sensitive to systematic errors, and cross validation13 shows...