Abstract
Almost a decade ago, a new phylogeny of bilaterian animals was inferred from small-subunit ribosomal RNA (rRNA) that claimed the monophyly of two major groups of protostome animals: Ecdysozoa (e.g., arthropods, nematodes, onycho-phorans, and tardigrades) and Lophotrochozoa (e.g., annelids, molluscs, platyhelminths, brachiopods, and rotifers). How-ever, it received little additional support. In fact, several multigene analyses strongly argued against this new phylogeny.These latter studies were based on a large amount of sequence data and therefore showed an apparently strong statisticalsupport. Yet, they covered only a few taxa (those for which complete genomes were available), making systematic artifactsof tree reconstruction more probable. Here we expand this sparse taxonomic sampling and analyze a large data set (146genes, 35,371 positions) from a diverse sample of animals (35 species). Our study demonstrates that the incongruencesobserved between rRNA and multigene analyses were indeed due to long-branch attraction artifacts, illustrating the enormous impact of systematic biases on phylogenomic studies. A refined analysis of our data set excluding the most biasedgenes provides strong support in favor of the new animal phylogeny and in addition suggests that urochordates are moreclosely related to vertebrates than are cephalochordates. These findings have important implications for the interpretationof morphological and genomic data.