The bilaterally symmetric animals (Bilateria) are considered to comprise two monophyletic groups, Protostomia (Ecdysozoa and the Lophotrochozoa) and Deuterostomia (Chordata and the Xenambulacraria). Recent molecular phylogenetic studies have not consistently supported deuterostome monophyly. Here, we compare support for Protostomia and Deuterostomia using multiple, independent phylogenomic datasets. As expected, Protostomia is always strongly supported, especially by longer and higher-quality genes. Support for Deuterostomia, however, is always equivocal and barely higher than support for paraphyletic alternatives. Conditions that cause tree reconstruction errors—inadequate models, short internal branches, faster evolving genes, and unequal branch lengths—coincide with support for monophyletic deuterostomes. Simulation experiments show that support for Deuterostomia could be explained by systematic error. The branch between bilaterian and deuterostome common ancestors is, at best, very short, supporting the idea that the bilaterian ancestor may have been deuterostome-like. Our findings have important implications for the understanding of early animal evolution.

AbstractThe bilaterally symmetric animals (Bilateria) are considered to comprise two monophyletic groups, Protostomia and Deuterostomia. Protostomia contains the Ecdysozoa and the Lophotrochozoa; Deuterostomia contains the Chordata and the Xenambulacraria (Hemichordata, Echinodermata and Xenacoelomorpha). Their names refer to a supposed distinct origin of the mouth (stoma) in the two clades, but these groups have been differentiated by other embryological characters including embryonic cleavage patterns and different ways of forming their mesoderm and coeloms. Deuterostome monophyly is not consistently supported by recent studies. Here we compare support for Protostomia and Deuterostomia using five recently published, phylogenomic datasets. Protostomia is always strongly supported, especially by longer and higher quality genes. Support for Deuterostomia is always equivocal and barely higher than support for paraphyletic alternatives. Conditions that can cause tree reconstruction errors - inadequate models, short internal branch, faster evolving genes, and unequal branch lengths - correlate with statistical support for monophyletic deuterostomes. Simulation experiments show that support for Deuterostomia could be explained by systematic error. A survey of molecular characters supposedly diagnostic of deuterostomes shows many are not valid synapomorphies. The branch between bilaterian and deuterostome common ancestors, if real, is very short. This finding fits with growing evidence suggesting the common ancestor of all Bilateria had many deuterostome characteristics. This finding has important implications for our understanding of early animal evolution and for the interpretation of some enigmatic Cambrian fossils such as vetulicolians and banffiids.

The availability of complete sets of genes from many organisms makes it possible to identify genes unique to (or lost from) certain clades. This information is used to reconstruct phylogenetic trees; identify genes involved in the evolution of clade specific novelties; and for phylostratigraphy-identifying ages of genes in a given species. These investigations rely on accurately predicted orthologs. Here we use simulation to produce sets of orthologs that experience no gains or losses. We show that errors in identifying orthologs increase with higher rates of evolution. We use the predicted sets of orthologs, with errors, to reconstruct phylogenetic trees; to count gains and losses; and for phylostratigraphy. Our simulated data, containing information only from errors in orthology prediction, closely recapitulate findings from empirical data. We suggest published downstream analyses must be informed to a large extent by errors in orthology prediction that mimic expected patterns of gene evolution.